column_name	description
line_id	HipSci short cell line ID.
clone	HipSci iPSC clone number.
replicate	"Macrophage differentiation replicate number. Most iPSC lines were differentiated only once, but a handful of lines were differentiated multiple times."
ips_received	Date when iPSC line was received from HipSci.
ips_started	Date when iPSC culture was started.
passage_received	IPSC passage number at the time of receiving the cells.
received_as	Whether cells were received as alive or frozen.
media	Whether IPSCs were initially grown on feeder dependent (KSR) or feeder free (E8) medium.
EB_formation	Date of enbryoid body (EB) formation.
passage_diff	IPSC passage number at the time of EB formation.
diff_start	Date when EBs were transferred to myloid differentiation medium.
salmonella_date	Date of IFNg and Salmonella infection assay for RNA-seq
atac_date	Date of IFNg and Salmonella infection assay for ATAC-seq
flow_date	Date of flow cytometry assay.
medium_changes	Total number of medium changes performed during differentiation.
terminated	Date when macrophage differentiation culture was terminated.
status	QC status for the macrophage differentiation experiment. FC_QC_fail mean low macrophage purity; Diff_fail means failed differentiation; RNA_QC_fail means degraded RNA.
mean_purity	"Mean of flow cytometry CD14, CD16 and CD206 purity measurements."
max_purity	"Max of flow cytometry CD14, CD16 and CD206 purity measurements."
genotype_id	HipSci cell line id in the VCF file.
open_access	Whether the IPSC line (and sequencing data) is open access (1) or managed access (0).
sex	Biological sex of the iPSC line.
sample_id	Sample name.
condition_name	Name of the experimental condition.
atac_date	Date of the ATAC-seq experiment.
submission_date	Date ATAC-seq library was submitted for sequencing.
multiplex_pool	Pooled library batch.
bioanalyzer	Is bioanalyser data avaliable from Zenodo (https://doi.org/10.5281/zenodo.242383)? 
nextera_kit	Batch of the Nextera kit used for ATAC-seq.
assigned	Total number of paired-end fragments overlapping peaks.
assigned_frac	Fraction of non-mitochondrial reads assigned to consensus peaks.
mt_frac	Fraction of total reads aligned to the mitochondrial genome.
duplication	Fraction of fragments that were marked as duplicates by Picard MarkDuplicates.
peak_count	Number of peaks called by MACS2.
length_ratio	Ratio: # of short fragments (< 150 nt) / # long fragments (>= 150 nt). 
qtl_mapping	Was this sample used for caQTL mapping?
diff_access	Was this sample used in the differential accessibility analysis?