This DATSETNAMEreadme.txt file was generated on 2022-05-17 by YUJI SANO
<help text is included in angle brackets, and can be deleted before saving>


GENERAL INFORMATION

1. Title of Dataset: 

2. Author Information
	A. Principal Investigator Contact Information
		Name: YUJI SANO
		Institution: Chugai Pharmaceutical Co.,Ltd.
		Address: 200 Kajiwara Kamakura Kanagawa JAPAN 247-8530
		Email: sanoyui@chugai-pharm.co.jp

	B. Associate or Co-investigator Contact Information
		Name: 
		Institution: 
		Address: 
		Email: 

	C. Alternate Contact Information
		Name: 
		Institution: 
		Address: 
		Email: 

3. Date of data collection (single date, range, approximate date) : 2015-2021

4. Geographic location of data collection: Kanagawa JAPAN

5. Information about funding sources that supported the collection of the data: Chugai Pharmaceutical Co.,Ltd.


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: All data is obtained using human samples, so please contact to sanoyui@chugai-pharm.co.jp if anyone wants to use our data.

2. Links to publications that cite or use the data: Nature communications (URL not available at this moment)

3. Links to other publicly accessible locations of the data: NA

4. Links/relationships to ancillary data sets: NA

5. Was data derived from another source? no
	A. If yes, list source(s): 

6. Recommended citation for this dataset: All data is obtained using human samples, so please contact to sanoyui@chugai-pharm.co.jp if anyone wants to use our data.



DATA & FILE OVERVIEW

1. File List: 
<list all files (or folders, as appropriate for dataset organization) contained in the dataset, with a brief description>
・nCounter_DFUR_IFNg_TNFa_MKN45_in vitro
・nCounter_EGFR-TRAB_paclitaxel_MKN45/huNOG
・nCounter_ERY974_capecitabine_MKN45/huNOG_day3,7,14
・RNAseq_ERY974_capecitabine_MKN45/huNOG
・RNAseq_ERY974_cisplatin_NCI-H446/huNOG
・RNAseq_ERY974_paclitaxel_NCI-H446/huNOG
・RNAseq_ERY974_PC10_NCI-H446_MKN45_MKN74_huNOG


2. Relationship between files, if important: NA

3. Additional related data collected that was not included in the current data package: NA

4. Are there multiple versions of the dataset? yes/no:No
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>
For the RNAseq_ERY974_PC10_NCI-H446_MKN45_MKN74_huNOG, Tumour RNA data of baseline and ERY974-treated tumour samples was collected using
PC10, NCI-H446, MKN74, or MKN45 tumors inoculated into huNOG mice. After the tumour was established, 
vehicle or 1 mg/kg ERY974 was intravenously administered once.After three days, the mice were sacrificed (n = 3), 
and the tumours were collected for RNAseq. 

For the RNAseq_ERY974_paclitaxel_NCI-H446/huNOG, and RNAseq_ERY974_cisplatin_NCI-H446/huNOG, These data are analysis for the mechanism of combination therapy 
utilizing the huNOG/NCI-H446 model.The huNOG mice inoculated with NCI-H446 tumours were intravenously injected with 20 mg/kg paclitaxel,
or 7.5 mg/kg cisplatin one day before the administration of 5 mg/kg ERY974 in the combination group. 
In the monotherapy group, each agent was administered as described above. 
Then, tumours were collected on day 6 after ERY974 administration and used for RNAseq. 

For the nCounter_ERY974_capecitabine_MKN45/huNOG_day3,7,14, huNOG mice inoculated with MKN45 tumours were orally administered 359 mg/kg capecitabine 
for four (day 3 samples) or five (day 7 and 14 samples) consecutive days,  
starting one day before the administration of 5 mg/kg ERY974. In the monotherapy group, each agent was administered as described above. 
Then, the tumours were collected on days 3, 7, and 14 after ERY974 administration and used for RNAseq analyses to determine the most sitable timing for combination effect 

For the RNAseq_ERY974_capecitabine_MKN45/huNOG,and the nCounter_EGFR-TRAB_paclitaxel_MKN45/huNOG,
huNOG mice inoculated with MKN45 tumours were orally administered 359 mg/kg capecitabine for four five consecutive days, 
starting one day before the administration of 5 mg/kg ERY974. In the monotherapy group, each agent was administered as described above. 
Then, the tumours were collected on days 14 after ERY974 administration and used for RNAseq analyses. 
For the mechanism analysis of the combination of EGFR-TRAB with paclitaxel, 
huNOG mice inoculated with MKN45 tumours were administered with 20 mg/kg paclitaxel one day before the administration of 5 mg/kg EGFR-TRAB in the combination group. 
In the monotherapy group, each agent was administered as described above. 
Then,tumours were collected on day 6 after EGFR-TRAB administration and extracted RNA was used for nCounter analysis.

For the nCounter_DFUR_IFNg_TNFa_MKN45_in vitro, MKN45 cells (1 × 104) were plated in a 6-well plate, followed by the addition of 1 nM 5ʹ-DFUR and/or 1 ng/mL IFNg. 
After 24 h, RNA was extracted,and analyzed with nCounter using the PanCancer Pathway Panel (NanoString). 
Data analysis was performed using nSolver v4.0. 


2. Methods for processing the data: 
<describe how the submitted data were generated from the raw or collected data>
The RNAseq reads were mapped to human (GRCh38) and mouse (GRCm38) transcripts simultaneously using RefSeq (Release 62; http://www.ncbi.nlm.nih.gov/refseq/) 
using bowtie 1.1.2 (maintained by Johns Hopkins University). Reads mapped to the transcripts of both organisms were excluded, 
followed by the calculation of fragments per kilobase of transcript per million reads mapped (FPKM) 
using RSEM v1.2.31(The GNU General Public License) parameters as -n 2 -e 99999999 -l 25 -I 1 -S -X 1000 -a -m 200.
The nCounter data was analysed with nSolver v4.0.

3. Instrument- or software-specific information needed to interpret the data: For nCounter data analysis, nSolver4 software was used.
<include full name and version of software, and any necessary packages or libraries needed to run scripts>

4. Standards and calibration information, if appropriate: NA

5. Environmental/experimental conditions: Descibed above.

6. Describe any quality-assurance procedures performed on the data: QC was conducted in TAKARA where RNAseq data is obtained.
For nCounter analysis, QC was conducted with nSolver v4.0.

7. People involved with sample collection, processing, analysis and/or submission: Yumiko Azuma, Toshiaki Tsunenari, Yoko Kayukawa, 
Yukari Nishito, Toru Maruyama, Yasuko Kinoshita 


DATA-SPECIFIC INFORMATION FOR: nCounter_DFUR_IFNg_TNFa_MKN45_in vitro
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 7

2. Number of cases/rows: 790

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Sample ID
NA3 (gene name)
NA4 (gene ID)
MKN45 control
MKN45 DFUR
MKN45 IFNg
MKN45 DFUR+IFNg

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA


DATA-SPECIFIC INFORMATION FOR: nCounter_EGFR-TRAB_paclitaxel_MKN45/huNOG
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 31

2. Number of cases/rows: 795

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
File name
NA1 (gene name)
NA16 (gene ID)
MKN45huNOG  day6 vehicle-1
MKN45huNOG  day6 vehicle-2
MKN45huNOG  day6 vehicle-3
MKN45huNOG  day6 vehicle-4
MKN45huNOG  day6 vehicle-5
MKN45huNOG  day6 vehicle-6
MKN45huNOG  day6 vehicle-7
MKN45huNOG day6 EGFR-TRAB-1
MKN45huNOG day6 EGFR-TRAB-2
MKN45huNOG day6 EGFR-TRAB-3
MKN45huNOG day6 EGFR-TRAB-4
MKN45huNOG day6 EGFR-TRAB-5
MKN45huNOG day6 EGFR-TRAB-6
MKN45huNOG day6 EGFR-TRAB-7
MKN45huNOG day6 pcalitaxel-1
MKN45huNOG day6 pcalitaxel-2
MKN45huNOG day6 pcalitaxel-3
MKN45huNOG day6 pcalitaxel-4
MKN45huNOG day6 pcalitaxel-5
MKN45huNOG day6 pcalitaxel-6
MKN45huNOG day6 pcalitaxel-7
MKN45huNOG day6 combo-1
MKN45huNOG day6 combo-2
MKN45huNOG day6 combo-3
MKN45huNOG day6 combo-4
MKN45huNOG day6 combo-5
MKN45huNOG day6 combo-6
MKN45huNOG day6 combo-7

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:huNOG as humamized NOG mice, TRAB as T cell-refirecting antibody


DATA-SPECIFIC INFORMATION FOR: nCounter_ERY974_capecitabine_MKN45/huNOG_day3,7,14
<repeat this section for each dataset, folder or file, as appropriate>
nCounter_ERY974_capecitabine_MKN45/huNOG_day3,7,14

1. Number of variables: 39

2. Number of cases/rows: 791

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Sample ID
NA2 (gene name)
NA3 (gene ID)
vehicle day3_1
vehicle day3_2
vehicle day3_3
ERY974 day3_1
ERY974 day3_2
ERY974 day3_3
xeloda day3_1
xeloda day3_2
xeloda day3_3
combo day7_1
combo day7_2
combo day7_3
vehicle day7_1
vehicle day7_2
vehicle day7_3
ERY974 day7_1
ERY974 day7_2
ERY974 day7_3
xeloda day7_1
xeloda day7_2
xeloda day7_3
combo day7_1
combo day7_2
combo day7_3
vehicle day14_1
vehicle da14_2
vehicle day14_3
ERY974 day14_1
ERY974 day14_2
ERY974 day14_3
xeloda day14_1
xeloda day14_2
xeloda day14_3
combo day14_1
combo day14_2
combo day14_3


4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA


DATA-SPECIFIC INFORMATION FOR: RNAseq_ERY974_capecitabine_MKN45/huNOG
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 25

2. Number of cases/rows: 27105

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Sample ID
MKN45/huNOG vehicle_1
MKN45/huNOG vehicle_2
MKN45/huNOG vehicle-3
MKN45/huNOG vehicle-4
MKN45/huNOG vehicle-5
MKN45/huNOG vehicle-6
MKN45/huNOG ERY974_1
MKN45/huNOG ERY974_2
MKN45/huNOG ERY974_3
MKN45/huNOG ERY974_4
MKN45/huNOG ERY974_5
MKN45/huNOG ERY974_6
MKN45/huNOG Capecitabine_1
MKN45/huNOG Capecitabine_2
MKN45/huNOG Capecitabine_3
MKN45/huNOG Capecitabine_4
MKN45/huNOG Capecitabine_5
MKN45/huNOG Capecitabine_6
MKN45/huNOG ERY974+capecitabine_1
MKN45/huNOG ERY974+capecitabine_2
MKN45/huNOG ERY974+capecitabine_3
MKN45/huNOG ERY974+capecitabine_4
MKN45/huNOG ERY974+capecitabine_5
MKN45/huNOG ERY974+capecitabine_6

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA


DATA-SPECIFIC INFORMATION FOR: RNAseq_ERY974_cisplatin_NCI-H446/huNOG
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 37

2. Number of cases/rows: 27106

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Sample ID
NCI-H446/huNOG Vehicle_1
NCI-H446/huNOG Vehicle_2
NCI-H446/huNOG Vehicle_3
NCI-H446/huNOG Vehicle_4
NCI-H446/huNOG Vehicle_5
NCI-H446/huNOG Vehicle_6
NCI-H446/huNOG Vehicle_7
NCI-H446/huNOG Vehicle_8
NCI-H446/huNOG Vehicle_9
NCI-H446/huNOG ERY974_1
NCI-H446/huNOG ERY974_2
NCI-H446/huNOG ERY974_3
NCI-H446/huNOG ERY974_4
NCI-H446/huNOG ERY974_5
NCI-H446/huNOG ERY974_6
NCI-H446/huNOG ERY974_7
NCI-H446/huNOG ERY974_8
NCI-H446/huNOG ERY974_9
NCI-H446/huNOG Cisplatin_1
NCI-H446/huNOG Cisplatin_2
NCI-H446/huNOG Cisplatin_3
NCI-H446/huNOG Cisplatin_4
NCI-H446/huNOG Cisplatin_5
NCI-H446/huNOG Cisplatin_6
NCI-H446/huNOG Cisplatin_7
NCI-H446/huNOG Cisplatin_8
NCI-H446/huNOG Cisplatin_9
NCI-H446/huNOG ERY974 + cisplatin_1
NCI-H446/huNOG ERY974 + cisplatin_2
NCI-H446/huNOG ERY974 + cisplatin_3
NCI-H446/huNOG ERY974 + cisplatin_4
NCI-H446/huNOG ERY974 + cisplatin_5
NCI-H446/huNOG ERY974 + cisplatin_6
NCI-H446/huNOG ERY974 + cisplatin_7
NCI-H446/huNOG ERY974 + cisplatin_8
NCI-H446/huNOG ERY974 + cisplatin_9

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA


DATA-SPECIFIC INFORMATION FOR: RNAseq_ERY974_paclitaxel_NCI-H446/huNOG
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 39

2. Number of cases/rows: 27106

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
NCI-H446/huNOG Vehicle_1
NCI-H446/huNOG Vehicle_2
NCI-H446/huNOG Vehicle_3
NCI-H446/huNOG Vehicle_4
NCI-H446/huNOG Vehicle_5
NCI-H446/huNOG Vehicle_6
NCI-H446/huNOG Vehicle_7
NCI-H446/huNOG Vehicle_8
NCI-H446/huNOG Vehicle_9
NCI-H446/huNOG Vehicle_10
NCI-H446/huNOG ERY974_1
NCI-H446/huNOG ERY974_2
NCI-H446/huNOG ERY974_3
NCI-H446/huNOG ERY974_4
NCI-H446/huNOG ERY974_5
NCI-H446/huNOG ERY974_6
NCI-H446/huNOG ERY974_7
NCI-H446/huNOG ERY974_8
NCI-H446/huNOG ERY974_9
NCI-H446/huNOG ERY974_10
NCI-H446/huNOG Paclitaxel_1
NCI-H446/huNOG Paclitaxel_2
NCI-H446/huNOG Paclitaxel_3
NCI-H446/huNOG Paclitaxel_4
NCI-H446/huNOG Paclitaxel_5
NCI-H446/huNOG Paclitaxel_6
NCI-H446/huNOG Paclitaxel_7
NCI-H446/huNOG Paclitaxel_8
NCI-H446/huNOG Paclitaxel_9
NCI-H446/huNOG ERY974 + paclitaxel_1
NCI-H446/huNOG ERY974 + paclitaxel_2
NCI-H446/huNOG ERY974 + paclitaxel_3
NCI-H446/huNOG ERY974 + paclitaxel_4
NCI-H446/huNOG ERY974 + paclitaxel_5
NCI-H446/huNOG ERY974 + paclitaxel_6
NCI-H446/huNOG ERY974 + paclitaxel_7
NCI-H446/huNOG ERY974 + paclitaxel_8
NCI-H446/huNOG ERY974 + paclitaxel_9

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA


DATA-SPECIFIC INFORMATION FOR: RNAseq_ERY974_PC10_NCI-H446_MKN45_MKN74_huNOG
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 27

2. Number of cases/rows: 24141

3. Variable List: descibed below
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Gene ID
Gene symbol
Transcript ID
PC10/huNOG Vehicle-1
PC10/huNOG Vehicle-2
PC10/huNOG Vehicle-3
PC10/huNOG ERY974-1
PC10/huNOG ERY974-2
PC10/huNOG ERY974-3
NCI-H446/huNOG Vehicle-1
NCI-H446/huNOG Vehicle-2
NCI-H446/huNOG Vehicle-3
NCI-H446/huNOG ERY974-1
NCI-H446/huNOG ERY974-2
NCI-H446/huNOG ERY974-3
MKN74/huNOG Vehicle-1
MKN74/huNOG Vehicle-2
MKN74/huNOG Vehicle-3
MKN74/huNOG ERY974-1
MKN74/huNOG ERY974-2
MKN74/huNOG ERY974-3
MKN45/huNOG Vehicle-1
MKN45/huNOG Vehicle-2
MKN45/huNOG Vehicle-3
MKN45/huNOG ERY974-1
MKN45/huNOG ERY974-2
MKN45/huNOG ERY974-3

4. Missing data codes: NA
<list code/symbol and definition>

5. Specialized formats or other abbreviations used:NA