title: H1hESC_scRNAseq_A100B10_sustained

description:
single cell RNA
ING520A5

data_processing:
We used cell-ranger version 3.0.2 to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to human transcriptome GRCh38-3.0.0 (software and data available from 10x genomics).
Downstream analysis was performed using scanpy (V1.9)
Assembly: human GRCh38 (GRCh38-3.0.0 from 10x Genomics)
Supplementary files format and content: 10x counts matrix, features and barcode data

growth_protocol: WT hESCs were grown on growth factor-reduced Matrigel and maintained in mTeSR1 media.

extract_protocol:
Cells were washed with DPBS and dissociated with Gentle Cell Dissociation Buffer (Stem Cell Technologies) for a maximum of 20 minutes at 37 degrees, then triturated in mTeSR1. Cells were pelleted and resupended in 1% BSA in DPBS, and filtered using a 35 um cell strainer.
The quality and concentration of each single cell suspension was measured using Trypan blue and the Eve automatic cell counter. Where necessary samples were diluted to a concentration of ~1000 cells/ul and approximately 10 000 cells were loaded for each sample into a separate channel of a Chromium Chip B for use in the 10X Chromium Controller. The cells were partitioned into nanoliter scale Gel Beads in emulsions (GEMs) and lysed using the Chromium Single cell 3’ v3 GEM, Library and Gel Bead Kit (cat: 1000075). The RNA was reversed transcribed and amplified using 11 cycles of PCR. Libraries were prepared from the cDNA using a further 12 cycles of amplification and QC’d using the Agilent TapeStation. The libraries were pooled and sequenced on the HiSeq 4000
10x Chromium Single Cell 3' Capture v3

treatment_protocol: H1 hESCs were differentiated with different regiments of Activin A (Cambridge Bio: GFH6) and BMP4 (LifeTechnologies: PHC9534) in TeSR-E6 (STEMCELL Technologies) based basal media containing FGF2 (20 µg/mL; LifeTechnologies: PHG0026), Insulin (3.2µM; Merck: I1882) and LY29004 (1µM; Cambridge Bio: CAY70920-25) for up to 72 hours with media changes every 24 hours. Samples included treatments switched between A100B10 to B50 at 24 and 48 hours, or B50 to A100B10 at 24 and 48 hours, as well as B50 and A10010 sustained conditions treated with cues for 72 hours.

value: WT

value: 72 hours


title: H1hESC_scRNAseq_A100B10toB50_48hrs

status: Public on Oct 01 2025

type: SRA

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
single cell RNA
ING520A3

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: genotype

tag: treatment

tag: treatment duration


title: H1hESC_scRNAseq_B50toA100B10_24hrs

description:
single cell RNA
ING520A2


title: H1hESC_scRNAseq_A100B10toB50_24hrs

description:
single cell RNA
ING520A1


title: 96hrs, scRNASEQ

first: Naomi

last: Moris

address: 1 Midland Way

institute: Francis Crick Institute

description:
10x Genomics SingleCell 3' v4
TIL6475A2

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.6.0.1 pipeline, aligning to the GRCh38 transcriptome (2020) using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.4.1.0  using  Seurat (v4.4.0) package
Assembly: GRCh38
Supplementary files format and content: Tab-separated cellranger 6.0.1 output files : barcodes ID's, features files and count files
Supplementary files format and content: .loupe file viewable in LoupeBrowser 7.0.1

source_name: human induced pluripotent stem cells

growth_protocol: Cells were cultured in incubators at 37 °C and 5% CO2, and cultured routinely in mTeSRTM 1 (STEMCELL Technologies, 85850) on 0.25 ug/cm2 recombinant laminin iMatrix-511 silk E8- coated plates (Amsbio, AMS892 021). Cultures of 80-90% confluency were passaged using AccutaseTM (STEMCELL Technologies, 07922) and single cells were seeded with medium supplemented with 10 µM Y-27632 (ROCK inhibitor; Tocris Biosciences, 1254). Fresh medium was exchanged daily.

extract_protocol:
hTLSs were collected from 96WPs and pooled together. TypLE was added to the samples and incubated at 37°C for 15-20 minutes. Samples were then gently pipetted up and down in TrypLE until dissociated into single cells. Cells were then spun in the centrifuge at 170g for 4 minutes, resuspended in PBS-/- + 0.04% BSA, and kept on ice until further processing.
SingleCell 3' v3

treatment_protocol: See accompanying manuscript for full details of the experimental protocol to generate hTLS models.

tag: tissue

value: human induced pluripotent stem cells

value: laminB1-RFP AICS-0034 cl.62

value: Human induced pluripotent stem cell (iPSC)

tag: time point


title: 120hrs, scRNASEQ

description:
10x Genomics SingleCell 3' v5
TIL6475A3


title: Untreated_0hr_R1

description: H1 hESCs cultured in mTeSR Rep1

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.5
Reads were aligned to the human genome GRCh38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.3.0 against human annotation release 86 from Ensembl
Assembly: Ensembl GRCh38 release-86
Supplementary files format and content: raw count matrix of sequencing reads

growth_protocol: The hESC line H1 was grown on growth factor-reduced Matrigel (Corning) and maintained in mTeSR1 (STEMCELL Technologies)

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit as per manufacturer's instructions
Libraries were prepared from 400 ng of RNA according to manufacturer’s instructions using the KAPA RNA HyperPrep Kit (Roche, Kit Code: KK8580)

treatment_protocol: For differentiation experiments cells were cultured in TeSR E5 (STEMCELL Technologies) with Insulin 3.2µM (Sigma I1882),   human FGF2 20 ng/mL (Invitrogen PHG0026) and LY29004 1µM (Cambridge Biosciences CAY70920) with BMP4 (Invitrogen PHC9534) and/or Activin A (Cambridge Biosciences GFH6-10) at specified concentrations.

value: mTeSR

tag: repeat


title: Activin100BMP410_1hr_R2

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 1 hour Rep2


title: High-1000x_seq3

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

country: USA

institute: Gladstone-UCSF Institute of Genomic Immunology

library_source: genomic

data_processing:
A table of individual guide abundance in each sample was generated using the count command in MAGeCK version 0.5.8
Assembly: None
Supplementary files format and content: Count of guide RNAs, raw counts
Library strategy: CRISPR sequencing

molecule: genomic DNA

source_name: CD4+CD25- T cells

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
After sorting, cells were washed with PBS, counted, pelleted, and resuspending at up to 5E6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl of sample. 16µl of NaCl (5M) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8µl of RNAse A (10mg/ml, resuspended in ddH2O) (Zymo, Cat #E1008) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, 8µl of Proteinase K (20mg/ml) (Zymo, Cat #D3001) was added, the sample was vortexed briefly, and incubated at 55°C for 1 hour. A phase lock tube (Quantabio, Cat #2302820) was prepared for each sample by spinning down the gel to the bottom of the tube at 20,000g for 1 minute and then 400µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1) was added to each tube. 400µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40µl of Sodium Acetate (3M), 1µl GlycoBlue (Invitrogen, Cat # AM9515), and 600µl of room temperature isopropanol was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo, Cat No: D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
sgRNA was amplified and barcoded from the genomic DNA according to the protocol by Joung et al. (Joung et al. 2017). Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Samples were then cleaned and concentrated in Zymo Spin-V columns (Zymo, Cat #C1016-50) following Joung et al., and eluted in 150 uL of Zymo DNA elution buffer. Up to 2 µg of each library were loaded on a 2% agarose gel, and the band at ~250 base pairs was extracted using the Zymoclean Gel DNA recovery kit (Zymo, Cat #D4008). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854). Samples were then sequenced on an Illumina HiSeq 4000 using 10-30% PhiX (Illumina, Cat #15017872), and a custom sequencing primer.

treatment_protocol: CD4+CD25- T cells were infected with lentivirus containing a 6000 guide RNA CRISPR library. Cas9 ribonucleoprotein complex was electroporated. 6 days after electroporation, FACS was performed to isolate CD25 high and low expressing cells.

value: CD4+CD25- T cells


title: 72hrs, scRNASEQ

description:
10x Genomics SingleCell 3' v3
TIL6475A1


title: Low_Coverage_Low_MOI_D3_Q4

description: high_low_MOI_screens_D1_D2_D3_2022-04-23.count.txt

data_processing:
A table of individual guide abundance in each sample was generated using the count command in MAGeCK version 0.5.8
Assembly: None
Supplementary files format and content: Count of guide RNAs, raw counts

extract_protocol:
After sorting, cells were washed with PBS, counted, pelleted, and resuspending at up to 5E6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl of sample. 16µl of NaCl (5M) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8µl of RNAse A (10mg/ml, resuspended in ddH2O) (Zymo, Cat #E1008) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, 8µl of Proteinase K (20mg/ml) (Zymo, Cat #D3001) was added, the sample was vortexed briefly, and incubated at 55°C for 1 hour. A phase lock tube (Quantabio, Cat #2302820) was prepared for each sample by spinning down the gel to the bottom of the tube at 20,000g for 1 minute and then 400µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1) was added to each tube. 400µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40µl of Sodium Acetate (3M), 1µl GlycoBlue (Invitrogen, Cat # AM9515), and 600µl of room temperature isopropanol was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo, Cat No: D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
sgRNA was amplified and barcoded from the genomic DNA according to the protocol by Joung et al. (Joung et al. 2017). Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Samples were then cleaned and concentrated in Zymo Spin-V columns (Zymo, Cat #C1016-50) following Joung et al., and eluted in 150 uL of Zymo DNA elution buffer. Up to 2 µg of each library were loaded on a 2% agarose gel, and the band at ~250 base pairs was extracted using the Zymoclean Gel DNA recovery kit (Zymo, Cat #D4008). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854). Samples were then sequenced on an Illumina HiSeq 4000 using 10-30% PhiX (Illumina, Cat #15017872), and a custom sequencing primer.
CRISPR sequencing

tag: expressing


title: Low-1000x_seq3


title: Low_Coverage_Low_MOI_D3_Q3


title: Low_Coverage_Low_MOI_D3_Q2


title: H1hESC_scRNAseq_B50toA100B10_48hrs

description:
single cell RNA
ING520A4


title: Activin100BMP410_12hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 12 hours Rep1


title: Low_Coverage_Low_MOI_D2_Q2


title: Low_Coverage_Low_MOI_D2_Q4


title: Low_Coverage_Low_MOI_D2_Q1


title: Low_Coverage_Low_MOI_D1_Q4


title: Activin100BMP410_6hr_R1

description: H1 hESCs cultured in Activin 100 ng/mL and BMP4 10 ng/mL for 6 hours Rep1


title: Low_Coverage_Low_MOI_D1_Q3


title: H1hESC_scRNAseq_B50_sustained

description:
single cell RNA
ING520A6


title: Low_Coverage_Low_MOI_D1_Q2


title: Low_Coverage_High_MOI_D3_Q2


title: Low_Coverage_High_MOI_D3_Q4


title: Low_Coverage_High_MOI_D2_Q4


title: Low_Coverage_High_MOI_D3_Q1


title: Low_Coverage_High_MOI_D1_Q4


title: Low_Coverage_High_MOI_D1_Q3


title: Low_Coverage_High_MOI_D2_Q2


title: Low_Coverage_High_MOI_D2_Q1


title: Low_Coverage_Low_MOI_D3_Q1


title: High_Coverage_Low_MOI_D3_Q3


title: High_Coverage_Low_MOI_D3_Q1


title: Low_Coverage_High_MOI_D1_Q1


title: High_Coverage_Low_MOI_D3_Q4


title: High_Coverage_Low_MOI_D3_Q2


title: Low_Coverage_Low_MOI_D2_Q3


title: High_Coverage_Low_MOI_D2_Q4


title: High_Coverage_Low_MOI_D2_Q1


title: High_Coverage_Low_MOI_D1_Q3


title: High_Coverage_Low_MOI_D2_Q3


title: High_Coverage_Low_MOI_D1_Q4


title: High_Coverage_Low_MOI_D1_Q2


title: Low_Coverage_High_MOI_D2_Q3


title: High_Coverage_High_MOI_D3_Q4


title: Low_Coverage_High_MOI_D3_Q3


title: High_Coverage_High_MOI_D3_Q2


title: High_Coverage_Low_MOI_D1_GFP


title: High_Coverage_High_MOI_D3_Q1


title: Low_Coverage_High_MOI_D1_Q2


title: High_Coverage_High_MOI_D2_Q4


title: High_Coverage_High_MOI_D3_GFP


title: High_Coverage_High_MOI_D2_Q2


title: High_Coverage_High_MOI_D2_Q3


title: High_Coverage_Low_MOI_D3_GFP


title: High_Coverage_High_MOI_D2_GFP


title: High_Coverage_High_MOI_D1_Q4


title: High_Coverage_High_MOI_D1_Q3


title: High_Coverage_High_MOI_D2_Q1


title: High_Coverage_Low_MOI_D2_Q2


title: High_Coverage_High_MOI_D1_Q2


title: Low_Coverage_Low_MOI_D1_Q1


title: High_Coverage_High_MOI_D1_Q1


title: High_Coverage_High_MOI_D1_GFP


title: L1EGH1101360--sh2.R

city: shanghai

first: Xiucheng

last: Liu

address: zhengmin road 557

country: China

institute: Shanghai pulmonary hospital

data_processing:
The ribosomal RNA (rRNA) was removed from the total RNA using the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.
Then, HTSeq software (v0.9.1) was used to obtain the transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization, and differentially expressed mRNAs were identified by p-value and fold change.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HPMVECs

extract_protocol:
HPMVECs were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Smartor118-three gas incubator (China Innovation Instrument, Ningbo, China) was used to mimic protocols of supplemental oxygen delivery in vitro. HPMVECs were treated with hyperoxia (80% O2 / 5%CO2 / 15% N2) for 24.

value: Lung capillaries


title: High_Coverage_Low_MOI_D2_GFP


title: L1EGH1101358--hyp3.R


title: L1EGH1101359--sh1.R


title: L1EGH1101357--hyp2.R


title: L1EGH1101356--hyp1.R


title: High_Coverage_High_MOI_D3_Q3


title: L1EGH1101355--con3.R


title: L1EGH1101353--con1.R


title: NOA2_3_9_6

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was seperated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
For Cut Tag data, the total reads were trimmed using bbduk and trimmomatic, with the length cut-off 35 bp and aligned to hg19 using bowtie with the options (--very-sensitive --end-to-end). Then low-quality reads were removed using samtools with the option (-q 35). Biological replicates were merged. MACS2 was used to call narrow peaks with options (-g hs -f BAMPE -B --call-summits -q 0.001). Bigwigs were generated using bedtools and bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles. For Cut Tag part, we used NovoNGS ® CUT&Tag 2.0 High-Sensitivity Kit (N259-YH01, Novoprotein) to capture PRDM9 binding sites.

tag: tag

value: male

tag: age

value: NOA


title: NOA2_3_9_7


title: NOA2_3_9_3


title: NOA2_3_9_4


title: L1EGH1101354--con2.R


title: NOA2_3_8_6


title: NOA2_3_9_2


title: NOA2_3_9_8


title: NOA2_3_7_7


title: NOA2_3_8_4


title: NOA2_3_7_4


title: NOA2_3_8_2


title: NOA2_3_7_8


title: NOA2_3_7_6


title: NOA2_3_6_8


title: NOA2_3_7_5


title: NOA2_3_8_1


title: High_Coverage_Low_MOI_D1_Q1


title: L1EGH1101361--sh3.R


title: NOA2_3_5_8


title: NOA2_3_6_1


title: NOA2_3_6_5


title: NOA2_3_5_7


title: NOA2_3_5_6


title: NOA2_3_6_6


title: NOA2_3_5_5


title: NOA2_3_5_2


title: NOA2_3_4_8


title: NOA2_3_4_5


title: NOA2_3_4_1


title: ZHX2 KO3

city: Jinan

first: Yuan

last: Xia

address: Wenhua road 44#

institute: Qilu hospital of Shandong University

description: Library name: Sample6

data_processing:
The raw reads were quality filtered and trimmed. The cleaned reads were then mapped to mm10. Only proper pairs with both reads mapped to the genome were used for further analysis. Differentially expressed genes (DEGs) were obtained from raw read counts via the R package limma (version 3.40.6). DEGs were screened using the thresholds |log2FC| > 1 and p- value < 0.05. Heatmap and volcano plots were used to visualize the DEGs. Gene network analysis was performed with the NetworkAnalyst 3.0 online tool (https://www.networkanalyst.ca). Gene set enrichment analysis (GSEA) was used to identify enriched biological pathways associated with the KO of Zhx2.
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

organism: Mus musculus

source_name: SVZ

extract_protocol:
Total RNA was extracted from the SVZ of Zhx2+/+ and Zhx2Δ/Δ mice using a Direct-zol RNA MicroPrep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocols.
Libraries were generated via polymerase chain reaction amplification and quantified on a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were pooled and sequenced (paired-end 50 bp) on an Illumina HiSeq 3000 platform to an average depth of 60 million reads per sample.

value: SVZ

value: ZHX4 KO


title: NOA2_3_3_6


title: NOA2_3_3_5


title: NOA2_3_3_8


title: ZHX2 KO1

description: Library name: Sample4

value: ZHX2 KO


title: ZHX2 KO2

description: Library name: Sample5

value: ZHX3 KO


title: ZHX2 WT2

description: Library name: Sample2


title: NOA2_3_3_2


title: ZHX2 WT3

description: Library name: Sample3


title: ZHX2 WT1

description: Library name: Sample1


title: scRNA-seq, WT bone marrow cells

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

description:
Library name: CWT
scRNA-seq using whole WT BM cells after hemolysis

data_processing:
Reads alignment on mouse mm10 genome and aggregation of the datasets were performed with CellRanger 7.2.0 (10x Genomics) with default parameters.For all analyses, we employed standard pre-processing and UMAP dimensionality reduction was performed using the Scanpy 1.10.2
Assembly: mm10
Supplementary files format and content: h5ad expression matrix files with cluster annotations

source_name: bone marrow cells

extract_protocol:
Primary BM cells were isolated from the femurs and tibias of 8-12-week-old mice. Briefly, bones were dissected, cleaned of muscle and connective tissue, and flushed with ice-cold α-MEM (Gibco) using a 25G needle into a 50mL falcon tube. The resulting cell suspension was passed through a 70 μm cell strainer (Corning) to remove debris and clumps, followed by centrifugation at 300 × g for 5 minutes at 4°C. To eliminate erythrocytes, the cell pellet was resuspended in pre-warmed RBC lysis buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH7.4) and incubated for 2 minutes at room temperature. The reaction was quenched by adding cold α-MEM, followed by two washes with 1× PBS and centrifugation at 500 × g for 5 minutes at 4°C. Cells were then resuspended in PBS + 0.04% bovine serum albumin (BSA), filtered through a 35 μm strainer, and stained with 7-AAD viability dye (BioLegend, #420403) to exclude dead cells. Live, single cells were sorted using a Cytek Aurora 4 flow cytometer.
Libraries were constructed with a Chromium Single Cell 3′ Library kit, according to the manufacturer's protocol.

value: 8-12 weeks old

value: bone marrow cells


title: NOA2_3_1_6


title: scATAC-seq, Irf8cKO bone marrow cells

description:
Library name: CKO
10x scATAC-seq using whole Irf8cKO BM cells after hemolysis

library_source: genomic single cell

data_processing:
The fastq files were processed with Cellranger-atac v1.0.1 with mm10 assembly, and the following analyses were performed with Signac v1.14.0.
Assembly: mm10

extract_protocol:
Primary BM cells were isolated from the femurs and tibias of 8-12-week-old mice. Briefly, bones were dissected, cleaned of muscle and connective tissue, and flushed with ice-cold α-MEM (Gibco) using a 25G needle into a 50mL falcon tube. The resulting cell suspension was passed through a 70 μm cell strainer (Corning) to remove debris and clumps, followed by centrifugation at 300 × g for 5 minutes at 4°C. To eliminate erythrocytes, the cell pellet was resuspended in pre-warmed RBC lysis buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH7.4) and incubated for 2 minutes at room temperature. The reaction was quenched by adding cold α-MEM, followed by two washes with 1× PBS and centrifugation at 500 × g for 5 minutes at 4°C. Cells were then resuspended in PBS + 0.04% bovine serum albumin (BSA), filtered through a 35 μm strainer, and stained with 7-AAD viability dye (BioLegend, #420403) to exclude dead cells. Live, single cells were sorted using a Cytek Aurora 4 flow cytometer.
Libraries were constructed with a Chromium Next GEM Single Cell ATAC Library kit, according to the manufacturer's protocol.


title: NOA2_3_1_8


title: NOA2_3_2_1


title: scATAC-seq, WT bone marrow cells

description:
Library name: WT
10x scATAC-seq using whole WT BM cells after hemolysis

value: WT


title: NOA2_3_2_7


title: Tg, sIL10ra-2

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

description: Library name: DR3-8

data_processing:
STAR was used to align FASTQ files to genome.
BAM files were used to generate gene counts using Rsamtools and the summarize overlaps function with the Genomic Alignments package.
Differential gene expression analysis was performed with the DESeq2 package.
Assembly: GRCm39.107
Supplementary files format and content: comma-separated files include count values for each sample

molecule: polyA RNA

source_name: brain

extract_protocol:
RNA was extracted from frozen, pulverized forebrains using TRIzol reagent (Invitrogen) followed by an RNeasy mini column (Qiagen) with an on-column DNase treatment.
RNA sequencing libraries were contructed using Illumina's TruSeq RNA Library Prep kit version 2; libraries were sequenced on paired-end, 100-bp runs on a NextSeq 2000 using a pooled strategy to minimize batch effects.

treatment_protocol: Neonatal mice were injected intracerebralventricularly with rAAV encoding Collagen Domain constructs or PBS (control) were aged 3 months and euthanized,brains were harvested. One hemibrain was snap-frozen in isopentane on dry ice and then stored at -80 degrees C until pulverized and  homogenized for RNA extractions.

value: brain

value: Tg

tag: Sex

value: M

tag: batch


title: scRNA-seq, Irf8cKO bone marrow cells

description:
Library name: CKO
scRNA-seq using whole Irf8cKO BM cells after hemolysis


title: NOA2_3_1_5


title: NOA2_3_2_4


title: NOA2_3_1_3


title: Tg, sIL10ra-3

description: Library name: DR3-1

value: F


title: Tg, sIL10ra-4

description: Library name: DR5-1


title: Tg, sIL10ra-1

description: Library name: DR1-12


title: Tg, Non-inj-6

description: Library name: C70

value: Non-inj


title: NOA2_3_12_6


title: NOA2_3_12_1


title: NOA2_3_1_1


title: NOA2_3_2_8


title: Tg, Non-inj-3

description: Library name: C64


title: Tg, Non-inj-5

description: Library name: C65


title: NOA2_3_11_1


title: Tg, Non-inj-4

description: Library name: C62


title: NOA2_3_11_2


title: NTg, Non-inj-6

description: Library name: C61

value: NTg


title: NOA2_3_10_5


title: NOA2_3_10_4


title: NTg, Non-inj-5

description: Library name: C56


title: NTg, Non-inj-4

description: Library name: C60


title: NOA2_2_9_1


title: NOA2_3_10_7


title: NOA2_2_8_8


title: NOA2_2_8_7


title: Tg, Non-inj-2

description: Library name: C58


title: NTg, Non-inj-2

description: Library name: C59


title: Tg, Non-inj-1

description: Library name: C52


title: NOA2_3_10_3


title: Tg, sIL4r-5

description: Library name: C44


title: NTg, Non-inj-3

description: Library name: C54


title: Tg, sIL4r-4

description: Library name: C36


title: Tg, sIL4r-2

description: Library name: C35


title: NTg, Non-inj-1

description: Library name: C53


title: NOA2_3_10_2


title: NOA2_3_1_2


title: NOA2_2_8_1


title: NOA2_2_7_8


title: Tg, sIL4r-3

description: Library name: C22


title: Tg, sIL4r-1

description: Library name: C20


title: NOA2_2_7_7


title: Tg, sIL10ra-6

description: Library name: C19


title: NOA2_2_7_5


title: Tg, sIL10ra-5

description: Library name: C15


title: NOA2_2_7_3


title: NOA2_2_7_2


title: NOA2_2_8_5


title: Eomes+IL10+ (P3) rep 3

city: Brisbane

first: Kate

last: Gartlan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer

description:
Library name: Sample 11 RNA
ZP4015G3P2

data_processing:
Sequence reads in each fastq file were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly with the gene, transcript, and exon features of Ensembl (release 75) gene model. Expression was estimated using RSEM (version 1.2.30) and was used as input to assess differential gene expression between groups using the edgeR R package.
Assembly: mm9
Supplementary files format and content: raw_counts.csv

source_name: spleen

extract_protocol:
Spleens (n = 16) were taken on day +14 and pooled from every 4 mice leading to 4 pooled samples. CD4+ T cells were enriched with MACS selection, stained with CD90.2 Pacific Blue, CD4 APC/Cy7, H2Dd AF647 and FACS sorted to P1 (Eomes- IL10-), P2 (Eomes+ IL10-) and P3 (Eomes+ IL10+) based on the expression of mCherry and GFP.
Sort-purified CD4+ T cell subsets (350 – 500 x10^3 cells per sample) were stored in TRIzol reagent and sent to Macrogen (Seoul, South Korea) for bulk RNAseq.

treatment_protocol: B6D2F1 recipients were transplanted with TCD BM (5x106) and naive CD4+ T cells (CD44loCD62Lhi 0.5x106) from EomesmCherry/IL-10GFP donors.

value: spleen

value: CD4+ T cells

value: Mice transplanted with TCD BM and CD4+ T cells from allogeneic donors and analyzed on day 14


title: NOA2_2_6_4

value: male

value: NOA


title: NOA2_2_6_3


title: NOA2_2_6_1


title: NOA2_2_5_7


title: NOA2_2_5_8


title: Eomes+IL10+ (P3) rep 1

description:
Library name: Sample 9 RNA
ZP4015G1P2


title: Eomes+IL10- (P2) rep 4

description:
Library name: Sample 8 RNA
ZP4015G4P3


title: NOA2_2_5_6


title: Eomes+IL10+ (P3) rep 2

description:
Library name: Sample 10 RNA
ZP4015G2P2


title: Eomes-IL10- (P1) rep 3

description:
Library name: Sample 3 RNA
ZP4015G3P4


title: NOA2_2_5_4


title: Eomes+IL10- (P2) rep 3

description:
Library name: Sample 7 RNA
ZP4015G3P3


title: NOA2_2_5_3


title: Eomes-IL10- (P1) rep 2

description:
Library name: Sample 2 RNA
ZP4015G2P4


title: NOA2_2_5_2


title: NOA2_2_7_6


title: NOA2_2_5_1


title: Eomes-IL10- (P1) rep 1

description:
Library name: Sample 1 RNA
ZP4015G1P4


title: NOA2_2_6_7


title: Eomes+IL10+ (P3) rep 4

description:
Library name: Sample 12 RNA
ZP4015G4P2


title: kidney_sick, BCR

city: Berlin

first: Andreia

middle: C.

last: Lino

address: Charitéplatz 1

country: Germany

institute: Charité – Universitätsmedizin Berlin

description:
10x Genomics
vanDuc_mBCR_filtered_contig.fasta.gz
vanDuc_mBCR_filtered_contig_annotations.csv

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content: *.fasta files containing the DNA information for the samples Supplementary files format and content: *.csv files contain the BCR sequencing information for each sample Supplementary files format and content: *.h5 files contain matrix, and feature information for each sample as well as the Cite-seq reads for each sample

source_name: Kidney

extract_protocol:
PCs from those tissues were enriched using anti-CD138 magnetic beads followed by cell sorting. Single cell suspension were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (v1.1, single index) following the manufacturer’s instructions.
The purified cDNA was amplified and then used for 5’ gene expression (GEX), CITE-Seq and BCR library preparation using the Single Cell 5’ Library & Gel Bead Kit (v1.1, 10x Genomics). BCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit. Through fragmentation, adapter ligation and index PCR the final GEX and BCR libraries were obtained. The CITE-Seq libraries were obtained only by index PCR. The quality of single cell 5’ GEX, CITE-Seq and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent). The sequencing was performed on a NextSeq2000 device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: 0) and NextSeq 1000/2000 P3 reagent kits (300 Cycles, Illumina) for BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: 0, 20% PhiX spike-in).

value: Kidney

tag: disease state

value: sick

tag: strain

value: CD138 + Plasma Cells

value: female

tag: library type

value: BCR


title: kidney_sick, GEX

description:
10x Genomics
Kidney_filtered_feature_bc_matrix.h5

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content: *.fasta files containing the DNA information for the samples Supplementary files format and content: *.csv files contain the BCR sequencing information for each sample Supplementary files format and content: *.h5 files contain matrix, and feature information for each sample as well as the Cite-seq reads for each sample
Library strategy: CITE-seq

value: mRNA


title: NOA2_2_4_6


title: NOA2_2_4_8


title: spleen_sick, BCR

description:
10x Genomics
Spleen_sick_moBCR_filtered_contig.fasta.gz
Spleen_sick_moBCR_filtered_contig_annotations.csv

source_name: Spleen

value: Spleen


title: NOA2_2_3_5


title: Eomes+IL10- (P2) rep 2

description:
Library name: Sample 6 RNA
ZP4015G2P3


title: spleen_sick, GEX

description:
10x Genomics
Spleen_sick_filtered_feature_bc_matrix.h5


title: Eomes+IL10- (P2) rep 1

description:
Library name: Sample 5 RNA
ZP4015G1P3


title: spleen_sick, ADT

library_source: other

molecule: protein

value: ADT


title: spleen_healthy, ADT

description:
10x Genomics
Spleen_healthy_filtered_feature_bc_matrix.h5

value: healthy


title: NOA2_2_3_6


title: NOA2_2_4_4


title: kidney_sick, ADT


title: NOA2_2_3_4


title: BM_sick, BCR

description:
10x Genomics
BM_sick_moBCR_filtered_contig.fasta.gz
BM_sick_moBCR_filtered_contig_annotations.csv

source_name: Bone Marrow

value: Bone Marrow


title: spleen_healthy, BCR

description:
10x Genomics
Spleen_healthy_moBCR_filtered_contig.fasta.gz
Spleen_healthy_moBCR_filtered_contig_annotations.csv


title: NOA2_2_3_3


title: NOA2_2_3_1


title: Eomes-IL10- (P1) rep 4

description:
Library name: Sample 4 RNA
ZP4015G4P4


title: spleen_healthy, GEX


title: NOA2_2_4_2


title: BM_sick, ADT

description:
10x Genomics
BM_sick_filtered_feature_bc_matrix.h5


title: NOA2_2_2_7


title: NOA2_2_4_7


title: NOA2_2_2_5


title: BM_healthy, BCR

description:
10x Genomics
BM_healthy_moBCR_filtered_contig.fasta.gz
BM_healthy_moBCR_filtered_contig_annotations.csv


title: BM_sick, GEX


title: NOA2_2_2_4


title: BM_healthy, ADT

description:
10x Genomics
BM_healthy_filtered_feature_bc_matrix.h5


title: NOA2_2_2_1


title: GAC B-cell a103A BCR

city: Birmingham

first: Rodney

middle: Glenn

last: King

state: AL

address: 411 Shelby Interdisciplinary Biomedical Research Building 1825 University Boulevard

department: Microbiology

institute: University of Alabama at Birmingham

description: 10x Genomics

data_processing:
FASTQ sequencing files were processed with Cellranger v3.0.2 (https://www.10xgenomics.com/support/software/cell-ranger/downloads)
Assembly: hg38
Supplementary files format and content: Comma separated files and count matrix output from Cellranger

source_name: Tonsil

extract_protocol:
Tonsil tissue was mechanically processed by passage through a 100um cell strainer to achieve a single cell suspension. Resulting cells were washed in ice cold PBS and stained with antibodies to idenify CAG reactive B cells and B cell subsets. Stained cell populations were sorted on an BD FACS Aria II into FACS buffer (PBS, 1% FBS) and subjected to 10x.
Libraries where generated using 10x chromium GEX and BCRseq recommended protocols

value: Tonsil

value: B cell


title: NOA2_2_1_8


title: NOA2_2_1_7


title: GAC B-cell a103A GEX

description: 10x Genomics


title: CD19 B-cell a103A GEX

description: 10x Genomics


title: GAC B-cell a051A BCR

description: 10x Genomics


title: NOA2_2_1_6


title: GAC B-cell a051A GEX

description: 10x Genomics


title: CD19 B-cell a103A BCR

description: 10x Genomics


title: NOA2_2_1_5


title: NOA2_2_1_4


title: BM_healthy, GEX


title: NOA2_2_12_5


title: LentiMPRA CRS-barcode association library

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
For mapping inserted fragments to MPRA barcodes, the paired-end reads were first merged using pear=0.9.6, and aligned to the fragment library using bowtie2=2.3.5. Then barcodes uniquely assigned to fragments were selected and a dataset mapping barcodes to inserted fragments was created.
For counting unique reads for each fragment in the assay, first the UMI read (R2) was appended to the read names (R1 and R3). Sequences were then merged using pear=0.9.6, and counted for both the RNA and DNA fractions.
A logistic regression model was then used to test the ratio of ratio differences between referernce, mutated, and scrambled sequences.
Assembly: hg38
Supplementary files format and content: TSV file containing the MPRA enrichment scores
Library strategy: lentiMPRA

growth_protocol: C4-2B cells were continually cultured in RPMI-1640 + 10% FBS + 1X Amphotericin B + 1X Pen-Strep in 5% C02 at 37C.

extract_protocol:
Cells were transduced with lentiMPRA library and 48 hours post-transduction, gDNA and RNA extracted via AllPrep DNA/RNA Mini Kit (Qiagen Cat. #80204).
LentiMPRA library was constructed according to previous publication (rf Gordon et. al 2020).

value: Prostate cancer epithelial


title: NOA2_2_12_3


title: CD19 B-cell a051A GEX

description: 10x Genomics


title: NOA2_2_12_4


title: CD19 B-cell a051A BCR

description: 10x Genomics


title: NOA2_2_12_2


title: NOA2_2_12_1


title: BIHi004-B_Not_Classifiable_4

type: genomic

first: Eilis

last: Perez

institute: Charité Universitätsmedizin Berlin

hyb_protocol: standard Illumina Protocols

scan_protocol: standard Illumina Protocols

data_processing: Raw DNA methylation data were pre-processed using R (v 4.3.3). Signal intensities were obtained from IDAT files using the Bioconductor package minfi (v 1.40.0) (Aryee et al., 2014). Dye bias correction was performed using the Noob (normal-exponential out-of-band) method with the preprocessNoob function without “between-array normalisation” (Triche et al., 2013). Data filtering steps included the removal of probes with detection p-values greater than 0.05 in more than 10% of samples, probes containing single nucleotide polymorphisms (SNPs) at the CpG site, probes located on sex chromosomes, and cross-reactive probes as previously described (Capper et al., 2018; Chen et al., 2013).  Beta values for DNA methylation were calculated from normalised data using the minfi getBeta function.

label: Cy3 and Cy5

label_protocol: standard Illumina Protocols

extract_protocol: DNA extraction was performed on harvested cell pellets using the Maxwell® RSC Instrument (Promega) with either the Maxwell® RSC Cultured Cells DNA Kit (Cat# AS1620) or the  Maxwell® RSC Blood DNA Kit (Cat# AS1400) for fresh and frozen cell samples, and the Maxwell® RSC FFPE Plus DNA Purification Kit (Cat# AS1720) for paraformaldehyde (PFA)-fixed cell samples, with no difference in DNA methylation analysis quality observed. Extracted DNA quantities were measured using the Quantus system together with the “QuantiFluor® ONE dsDNA” kit (Promega).

value: Astrocyte Day 7

value: Female

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.

tag: cohort

value: Surplus


title: NOA2_2_12_6

value: male

value: NOA


title: BIHi004-B_Not_Classifiable_3

tag: cell line

value: Astrocyte Day 21


title: BIHi005-A_Not_Classifiable_3

tag: cell type

value: Astrocyte Day 12

value: Male


title: NOA2_2_11_5


title: BIHi005-A_Not_Classifiable_4


title: NOA2_2_11_7


title: BIHi005-A_Not_Classifiable_2


title: NOA2_2_11_2


title: NOA2_2_12_8


title: BIHi001-B_Not_Classifiable_12

value: Astrocyte Day 19


title: NOA2_2_10_8


title: BIHi001-B_Not_Classifiable_11


title: BIHi001-B_Not_Classifiable_9


title: NOA2_2_10_5


title: BIHi004-B_Not_Classifiable_1


title: BIHi001-B_Not_Classifiable_8


title: NOA2_2_10_4


title: BIHi001-B_Not_Classifiable_10


title: NOA2_2_10_2


title: NOA2_1_9_8


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_14

value: Neural Stem Cells Day 21

value: iPSCs were seeded on Geltrex in Essential 8 with 10 µM Y-27632, then switched after 2 days to neural induction medium (DMEM/F12, B27, N2, L-glutamine, HEPES, 10 µM dorsomorphin, 10 µM SB431542) for 7 days with daily medium changes. Differentiation efficiency was assessed by FACS for PAX6, Nestin, SOX1, and SOX2, and samples with >85% expression were stored at -80 °C. Neural stem cells were subsequently derived from ectoderm by maintaining in the induction medium for 18 days with daily medium changes, and harvested at -80 °C.

value: Validation


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_13

value: Training


title: NOA2_2_10_3


title: NOA2_1_9_6


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_12


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_11


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_10


title: NOA2_1_9_2


title: NOA2_1_8_5


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_9


title: NOA2_1_8_3


title: NOA2_1_8_8


title: NOA2_2_11_4


title: NOA2_2_11_1


title: BIHi004-B_Not_Classifiable_2


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_7


title: NOA2_1_8_2


title: NOA2_1_7_3


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_1


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_2


title: NOA2_1_5_6


title: NOA2_1_7_2


title: BIHi001-A_iPSC_derived_Mesoderm_1

value: Pericyte mesoderm Day 5

value: iPSCs were differentiated to mesoderm and endothelial progenitors as in Patsch et al. (https://doi.org/10.1038/ncb3205). At day 0, cells were cultured in Endo Priming medium (DMEM/F12 + Neurobasal, B27–VitA, N2, β-mercaptoethanol, GlutaMAX, 6 µM CHIR, 25 ng/ml BMP4) for 72 h, followed by Endo Induction medium (StemPro-34, GlutaMAX, 200 ng/ml VEGF, 2 µM Forskolin) for 48 h. CD144+ cells were isolated as endothelial progenitors, and CD144– cells retained as pericyte progenitors.


title: UCSFi001-A_iPSC_derived_Mesoderm_2

value: Endothelial mesoderm Day 5


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_5


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_4


title: BIHi005-A_iPSC_derived_Mesoderm_5


title: NOA2_1_6_2


title: NOA2_1_2_7


title: BIHi250-A_iPSC_derived_Mesoderm_2


title: NOA2_1_2_2


title: NOA2_1_3_2


title: NOA2_1_8_4


title: NOA2_1_1_2


title: NOA2_1_10_7


title: BIHi045-A-2_iPSC_derived_Mesoderm_1

value: Trilineage Mesoderm

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.


title: BIHi005-A-93_iPSC_derived_Mesoderm_1


title: NOA2_1_11_1


title: BIHi005-A_iPSC_derived_Mesoderm_4


title: BIHi001-B_iPSC_derived_Mesoderm_2


title: NOA2_1_10_5


title: BIHi005-A-92_iPSC_derived_Mesoderm_1


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_8


title: BIHi001-B_iPSC_derived_Neural_Stem_Cells_3


title: RNA_NOA2_3


title: BIHi005-A_iPSC_derived_Mesoderm_3


title: NOA2_1_10_3


title: RNA_NOA2_1


title: RNA_NOA2_2


title: BIHi001-B-10_iPSC_derived_Mesoderm_1


title: BIHi001-B-6_iPSC_derived_Mesoderm_1


title: BIHi001-B-2_iPSC_derived_Mesoderm_1


title: NOA2_1_7_6


title: BIHi001-B-1_iPSC_derived_Mesoderm_1


title: NOA2_1_11_4


title: BIHi005-A_iPSC_derived_Mesoderm_2


title: BIHi001-B-10_iPSC_derived_Mesoderm_2


title: Normal_4_7_9_1

description: Sample 1299

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

tag: condition

value: Normal

tag: testis

value: testis


title: Normal_4_7_9_5

description: Sample 1300

value: male


title: UCSFi001-A23_iPSC_derived_Mesoderm_3


title: Normal_4_7_9_7

description: Sample 1301


title: UCSFi001-A23_iPSC_derived_Mesoderm_2


title: BIHi250-A_iPSC_derived_Mesoderm_1

value: Female


title: BIHi005-A_iPSC_derived_Mesoderm_1


title: Normal_4_7_8_6

description: Sample 1298


title: Normal_4_7_8_4

description: Sample 1297


title: Normal_4_7_6_5

description: Sample 1294


title: Normal_4_7_7_2

description: Sample 1296


title: Normal_4_7_6_8

description: Sample 1295


title: Normal_4_7_6_3

description: Sample 1293


title: UCSFi001-A_iPSC_derived_Lung_2

value: Lung Progenitors Day 15

value: iPSCs were adapted to mTeSR1 on Geltrex, seeded at 3×10⁶ cells/well in 6WP with 10 µM Y-27632, and differentiated using the STEMdiff Definitive Endoderm Kit (StemCell Technologies). At day 3, cells were assessed by FACS for CXCR4 (CD184) and SOX17, with cultures >90% efficiency stored at -80 °C or used for lung differentiation. For lung progenitors, day 3 endoderm cells were replated in cSFDM medium with 10 µM SB431542, 2 µM dorsomorphin, and 10 µM Y-27632, followed by anterior foregut induction (day 4–6) and subsequent lung induction medium (cSFDM + 3 µM CHIR, 10 ng/ml BMP4, 100 nM retinoic acid) until day 15. Lung progenitors were isolated by CPM expression using magnetic separation and stored as pellets at -80 °C.


title: BIHi001-B_iPSC_derived_Mesoderm_1

value: Male


title: BIHi250-A_iPSC_derived_Lung_3


title: Normal_4_7_9_8

description: Sample 1302


title: Normal_4_7_5_8

description: Sample 1291


title: BIHi005-A_iPSC_derived_Lung_2


title: Normal_4_7_5_7

description: Sample 1290


title: Normal_4_7_6_2

description: Sample 1292


title: BCRTi005-A_iPSC_derived_Lung_2


title: BIHi001-B_iPSC_derived_Lung_5


title: Normal_4_7_5_4

description: Sample 1288


title: BIHi001-B_iPSC_derived_Lung_4


title: Normal_4_7_4_8

description: Sample 1287


title: BIHi001-B_iPSC_derived_Lung_1


title: UCSFi001-A23_iPSC_derived_Mesoderm_1


title: BIHi250-A_iPSC_derived_Endothelial_cells_3

value: Endothelial cells Day 15

value: iPSCs were differentiated to mesoderm and endothelial progenitors as in Patsch et al. (https://doi.org/10.1038/ncb3205). At day 0, cells were cultured in Endo Priming medium (DMEM/F12 + Neurobasal, B27–VitA, N2, β-mercaptoethanol, GlutaMAX, 6 µM CHIR, 25 ng/ml BMP4) for 72 h, followed by Endo Induction medium (StemPro-34, GlutaMAX, 200 ng/ml VEGF, 2 µM Forskolin) for 48 h. CD144+ cells were isolated as endothelial progenitors, and CD144– cells retained as pericyte progenitors. Endothelial progenitors were matured in EGM-2 (Lonza), with CD31/CD144 expression confirming endothelial identity (>90% CD31+), and all fractions were stored as pellets at -80 °C.


title: Normal_4_7_4_2

description: Sample 1285


title: UCSFi001-A23_iPSC_derived_Endothelial_cells_1

value: Endothelial cells Day 14


title: BIHi001-B_iPSC_derived_Endothelial_cells_1


title: Normal_4_7_2_8

description: Sample 1282


title: Normal_4_7_11_5

description: Sample 1280


title: BIHi250-A_iPSC_derived_Endothelial_cells_2

value: Endothelial cells Day 10

value: Validation


title: Normal_4_7_2_1

description: Sample 1281


title: BIHi005-A_iPSC_derived_Endothelial_cells_5

value: Training


title: Normal_4_7_3_1

description: Sample 1283


title: Normal_4_7_10_8

description: Sample 1279


title: UCSFi001-A_iPSC_derived_Endothelial_cells_4

value: Endothelial cells Day 11


title: BIHi250-A_iPSC_derived_Endothelial_cells_1


title: Normal_4_7_1_2

description: Sample 1276


title: Normal_4_7_5_5

description: Sample 1289


title: Normal_4_7_10_2

description: Sample 1277


title: Normal_4_6_8_4

description: Sample 1275


title: BIHi001-B_iPSC_derived_Lung_3


title: BIHi001-B_iPSC_derived_Lung_2


title: Normal_4_7_4_3

description: Sample 1286


title: UCSFi001-A_iPSC_derived_Endothelial_cells_2


title: Normal_4_6_7_6

description: Sample 1273


title: Normal_4_7_3_3

description: Sample 1284


title: BIHi005-A_iPSC_derived_Endothelial_cells_2


title: BIHi005-A_iPSC_derived_Endothelial_cells_1


title: Normal_4_6_7_7

description: Sample 1274


title: BIHi250-A_iPSC_derived_Endoderm_1

value: Trilineage Endoderm


title: UCSFi001-A_iPSC_derived_Endothelial_cells_1


title: BIHi005-A-93_iPSC_derived_Endoderm_1

value: Surplus


title: Normal_4_6_5_6

description: Sample 1270


title: Normal_4_6_4_2

description: Sample 1269


title: BIHi045-A-2_iPSC_derived_Endoderm_1

value: 70-80% confluent iPSCs were seeded and differentiated into Ectoderm, Endoderm and Mesoderm using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec), following manufacturer´s instructions. At day 7 of differentiation cells were harvested using Accutase or TrypLE (both Gibco). FACS analysis was performed to characterise ectodermal (SOX2, PAX6), endodermal (CXCR4, SOX17) and mesodermal (CD144, CD140b -Miltenyi Biotec, 130-121-052-) cells. The remaining cells were collected as pellet and stored at -80°C.


title: Normal_4_6_2_7

description: Sample 1268

value: Normal


title: Normal_4_6_6_5

description: Sample 1272

value: testis


title: BIHi005-A_iPSC_derived_Endothelial_cells_3


title: BIHi005-A_iPSC_derived_Endothelial_cells_4


title: BIHi001-B-8_iPSC_derived_Endoderm_1


title: BIHi001-B-7_iPSC_derived_Endoderm_1


title: Normal_4_6_2_5

description: Sample 1267

value: male


title: Normal_4_6_2_3

description: Sample 1265


title: UCSFi001-A_iPSC_derived_Endothelial_cells_3


title: Normal_4_6_12_4

description: Sample 1264


title: Normal_4_7_10_4

description: Sample 1278


title: BIHi001-B-4_iPSC_derived_Endoderm_1


title: BIHi001-B-3_iPSC_derived_Endoderm_1


title: Normal_4_6_2_4

description: Sample 1266


title: BIHi001-B-2_iPSC_derived_Endoderm_1


title: Normal_4_6_12_3

description: Sample 1263


title: BIHi001-B-1_iPSC_derived_Endoderm_1


title: BIHi005-A_iPSC_derived_Endoderm_1

value: Lung Endoderm Day 3


title: Normal_4_6_11_7

description: Sample 1262


title: Normal_4_6_11_2

description: Sample 1260


title: Normal_4_6_11_6

description: Sample 1261


title: Normal_4_6_6_1

description: Sample 1271


title: BIHi001-B_iPSC_derived_Endoderm_4


title: BIHi001-B_iPSC_derived_Endoderm_2


title: BIHi001-B_iPSC_derived_Endoderm_3


title: BIHi001-B_iPSC_derived_Endoderm_1


title: Normal_4_6_10_5

description: Sample 1257


title: Normal_4_6_10_1

description: Sample 1256


title: BIHi001-B_iPSC_derived_Ectoderm_7

value: Neural Stem Cells Ectoderm Day 7

value: iPSCs were seeded on Geltrex in Essential 8 with 10 µM Y-27632, then switched after 2 days to neural induction medium (DMEM/F12, B27, N2, L-glutamine, HEPES, 10 µM dorsomorphin, 10 µM SB431542) for 7 days with daily medium changes. Differentiation efficiency was assessed by FACS for PAX6, Nestin, SOX1, and SOX2, and samples with >85% expression were stored at -80 °C. Neural stem cells were subsequently derived from ectoderm by maintaining in the induction medium for 18 days with daily medium changes, and harvested at -80 °C.


title: Normal_4_5_9_1

description: Sample 1254


title: Normal_4_6_10_8

description: Sample 1258


title: Normal_4_6_1_1

description: Sample 1255


title: BIHi001-B_iPSC_derived_Ectoderm_5

value: Male


title: BIHi005-A-24_iPSC_derived_Ectoderm_2


title: Normal_4_5_7_4

description: Sample 1252


title: BIHi005-A-1_iPSC_derived_Ectoderm_1


title: BIHi005-A-24_iPSC_derived_Ectoderm_1


title: Normal_4_5_6_5

description: Sample 1250


title: BIHi250-A_iPSC_derived_Ectoderm_1

value: Female


title: Normal_4_5_6_8

description: Sample 1251


title: Normal_4_5_8_6

description: Sample 1253


title: BIHi005-A_iPSC_derived_Ectoderm_1


title: Normal_4_5_6_4

description: Sample 1249


title: BIHi004-A_iPSC_derived_Ectoderm_1


title: BIHi004-B_iPSC_derived_Ectoderm_1


title: Normal_4_5_6_3

description: Sample 1248


title: BIHi001-B_iPSC_derived_Ectoderm_4


title: Normal_4_5_6_2

description: Sample 1247


title: BIHi001-B_iPSC_derived_Ectoderm_3


title: Normal_4_5_5_7

description: Sample 1245


title: Normal_4_5_6_1

description: Sample 1246


title: Normal_4_6_11_1

description: Sample 1259


title: Normal_4_5_5_3

description: Sample 1243


title: BIHi001-B_iPSC_derived_Ectoderm_1


title: Normal_4_5_5_4

description: Sample 1244


title: BIHi001-B-6_iPSC_derived_Ectoderm_1

value: Trilineage Ectoderm


title: BIHi001-B-5_iPSC_derived_Ectoderm_1


title: BIHi001-B-4_iPSC_derived_Ectoderm_1


title: Normal_4_5_5_1

description: Sample 1241


title: Normal_4_5_5_2

description: Sample 1242


title: Normal_4_5_4_6

description: Sample 1240


title: BIHi001-B-1_iPSC_derived_Ectoderm_1


title: Normal_4_5_3_8

description: Sample 1238


title: BIHi001-B-10_iPSC_derived_Ectoderm_1


title: Normal_4_5_4_2

description: Sample 1239


title: Normal_4_5_2_6

description: Sample 1235


title: BIHi001-B_Not_Classifiable_6

value: Astrocyte day 37 (MACS sorted)

value: iPSCs were differentiated into ectoderm for 7 days, dissociated, and seeded (15,000 cells/cm²) onto Geltrex/Matrigel or vitronectin in neural induction medium with 10 µM Y-27632. After 48 h, cells were cultured in Astrocyte Medium (ScienCell) with medium changes every 48 h and passaged at ~90% confluency. After 30 days, GLAST-positive cells were isolated using the Anti-GLAST MicroBead Kit (Miltenyi Biotec) and stored at -80 °C.


title: BIHi001-B-3_iPSC_derived_Ectoderm_1


title: Normal_4_5_3_6

description: Sample 1237


title: Normal_4_5_3_1

description: Sample 1236


title: BIHi001-B-2_iPSC_derived_Ectoderm_1


title: BIHi001-B_Not_Classifiable_3

value: Astrocyte Day 19


title: BIHi001-B_Not_Classifiable_2


title: BIHi001-B_iPSC_derived_Ectoderm_2

value: Training


title: Normal_4_5_2_2

description: Sample 1233


title: BIHi001-B_Not_Classifiable_1


title: Normal_4_5_2_3

description: Sample 1234


title: Normal_4_5_12_8

description: Sample 1231


title: Normal_4_5_2_1

description: Sample 1232


title: Normal_4_5_11_6

description: Sample 1230


title: BIHi001-A_iPSC_derived_Ectoderm_1


title: BIHi250-A_iPSC_4

value: iPSC

value: iPSCs) were cultured on growth factor–reduced Geltrex (Gibco) in E8 or mTeSR (Stem Cell Technologies) medium with daily exchange. Cells were passaged as clumps with 0.5 mM EDTA (Thermo Fisher) every 2–4 days once >70% confluent. All lines were obtained from the BIH Core Unit Pluripotent Stem Cells and Organoids (BIH-CUSCO) with ethical approval. Full protocols are available at https://www.protocols.io/view/good-practices-in-hpsc-handling-gdqmbs5u7.


title: Normal_4_5_10_7

description: Sample 1229


title: Normal_4_5_10_6

description: Sample 1228


title: BIHi250-A_iPSC_3


title: Normal_4_5_1_2

description: Sample 1227


title: BIHi005-A_iPSC_5

value: Validation


title: BIHi001-B_iPSC_5


title: Normal_4_4_9_8

description: Sample 1226


title: BIHi045-A_iPSC_1


title: Normal_4_4_8_3

description: Sample 1223


title: Normal_4_4_9_3

description: Sample 1224


title: BIHi250-A_iPSC_2


title: Normal_4_4_9_4

description: Sample 1225


title: BIHi001-B-6_iPSC_1


title: UCSFi001-A23_iPSC_1


title: Normal_4_4_7_8

description: Sample 1221


title: Normal_4_4_8_2

description: Sample 1222


title: BIHi001-B_iPSC_4


title: BIHi001-B-5_iPSC_1


title: Normal_4_4_7_4

description: Sample 1219


title: BIHi005-A-92_iPSC_1


title: Normal_4_4_7_7

description: Sample 1220


title: BIHi001-B-3_iPSC_1


title: Normal_4_4_6_5

description: Sample 1217


title: BIHi001-B-1_iPSC_1


title: Normal_4_4_7_1

description: Sample 1218


title: BIHi001-B-10_iPSC_1


title: BIHi001-B_iPSC_3


title: Normal_4_4_5_5

description: Sample 1215


title: Normal_4_4_6_1

description: Sample 1216


title: Normal_4_4_5_4

description: Sample 1214


title: BIHi250-A_iPSC_1


title: BU3 NG_iPSC_1

source_name: BU3 NG

value: BU3 NG


title: Normal_4_4_5_2

description: Sample 1213

value: Normal


title: BIHi005-A-93_iPSC_1


title: BIHi005-A_iPSC_4


title: Normal_4_4_4_5

description: Sample 1211

value: testis


title: Normal_4_4_4_8

description: Sample 1212

value: male


title: BIHi005-A_iPSC_2


title: BIHi005-A_iPSC_1


title: Normal_4_4_4_4

description: Sample 1210


title: CAMi014-A_iPSC_1


title: Normal_4_4_4_3

description: Sample 1209


title: Normal_4_4_3_5

description: Sample 1205


title: Normal_4_4_3_6

description: Sample 1206


title: Normal_4_4_4_2

description: Sample 1208


title: KT21-MG1 cells treated with negative control miRNA, replicate 3

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

description: Library name: KT_neg_4

data_processing:
Reads were aligned to hg38.p11 genome with STAR software, they are provided as is from the output with --quantMode.
Assembly: GRCh38
Supplementary files format and content: .csv file with counts

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% (KT21-MG1) or 20% (Ben-Men-1) FBS and 1% Pen Strep (15140122, Gibco).

extract_protocol:
Total RNA from cultured cells was isolated with High Pure RNA Isolation Kit (Roche).
One μg of total RNA from each tissue sample was used for mRNA library preparation using poly A enrichment kit Novogene NGS RNA Library Prep Set (Novogene). The quality of libraries was assessed using the Agilent Bioanalyzer 2100 system (Agilent). The procedure was performed by Novogen sequencing servoce provider; for the cell lines.

treatment_protocol: The cells were seeded per well of 24-well plate in culture medium and transfected with 50 nM miRNA mimics (hsa-miR-1265 (YM00470622-ADB , Qiagen), hsa-miR-21-5p (YM00470856-ADB, Qiagen) and negative control mimic (YM00479902-AGB; Qiagen) with 1% (v/v) HiPerFect Transfection Reagent (Qiagen), according to the manufacturer’s instructions. The next day, culture medium was changed to fresh basic medium. The cells were harvested or subjected to in vitro tests at 48 h after transfection.

value: human-derive cancer cell line

tag: treatment

value: negative control miRNA


title: KT21-MG1 cells treated with negative control miRNA, replicate 2

description: Library name: KT_neg_3


title: Normal_4_4_3_3

description: Sample 1203


title: KT21-MG1 cells treated with hsa-miR-21-5p, replicate 3

description: Library name: KT_21_5_4

value: hsa-miR-21-5p mimic


title: KT21-MG1 cells treated with negative control miRNA, replicate 1

description: Library name: KT_neg_2


title: KT21-MG1 cells treated with hsa-miR-21-5p, replicate 2

description: Library name: KT_21_5_3


title: BIHi001-B_iPSC_2

value: Male


title: Normal_4_4_3_4

description: Sample 1204


title: KT21-MG1 cells treated with hsa-miR-21-5p, replicate 1

description: Library name: KT_21_5_2


title: Normal_4_4_12_7

description: Sample 1200


title: BIHi005-A_iPSC_3


title: KT21-MG1 cells treated with hsa-miR-1256, replicate 2

description: Library name: KT_1265_3

value: hsa-miR-1265 mimic


title: KT21-MG1 cells treated with hsa-miR-1256, replicate 3

description: Library name: KT_1265_4


title: BIHi001-B_iPSC_1


title: Normal_4_4_12_3

description: Sample 1199


title: Normal_4_4_12_1

description: Sample 1198


title: Normal_4_4_11_5

description: Sample 1197


title: Normal_4_4_4_1

description: Sample 1207


title: KT21-MG1 cells treated with hsa-miR-1256, replicate 1

description: Library name: KT_1265_1


title: Normal_4_4_11_4

description: Sample 1196


title: Normal_4_4_11_1

description: Sample 1195


title: Ben-Men1 cells treated with negative control miRNA, replicate 3

description: Library name: BM_neg_3


title: Ben-Men1 cells treated with negative control miRNA, replicate 1

description: Library name: BM_neg_1


title: Ben-Men1 cells treated with hsa-miR-1256, replicate 3

description: Library name: BM_1265_3


title: Normal_4_4_10_6

description: Sample 1194


title: Ben-Men1 cells treated with negative control miRNA, replicate 2

description: Library name: BM_neg_2


title: Normal_4_4_1_6

description: Sample 1192


title: Ben-Men1 cells treated with hsa-miR-1256, replicate 2

description: Library name: BM_1265_2


title: Ben-Men1 cells treated with hsa-miR-1256, replicate 1

description: Library name: BM_1265_1


title: Normal_4_4_10_4

description: Sample 1193


title: Normal_4_4_1_5

description: Sample 1191


title: Normal_4_4_2_4

description: Sample 1202


title: Normal_4_3_9_2

description: Sample 1189


title: Normal_4_4_2_1

description: Sample 1201


title: Normal_4_3_9_1

description: Sample 1188


title: Normal_4_3_9_5

description: Sample 1190


title: MCF7 Rep1 cfChromatin, cfMNase-Seq, 30 min MNase digestion

city: Toronto

first: Scott

middle: Victor

last: Bratman

state: ON

address: 101 College Ave.

department: Medical Biophysics

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: MCF7_cfMNase_Rep1

data_processing:
UMIs were extracted using UMI-tools (v1.1.1) with a regular expression pattern to identify and append UMIs to the read headers.
Processed reads were aligned to the hg38 human genome using Bowtie2 (v2.4.1).
Duplicates were removed based on UMIs and alignment coordinates using UMI-tools. Low-quality mapped reads were filtered with Samtools view (v1.9) using a mapping quality threshold of 30. Quality metrics, including alignment statistics, were assessed at each step using Samtools flagstat.
Counts per 10,000 bp bin were calculated from BAM files (in bigWig format), using DeepTools. bigWig files were generated with Reads Per Kilobase per Million mapped reads (RPKM) normalization, centered and extended read options.
Assembly: hg38
Supplementary files format and content: bigWig, for all samples
Library strategy: cfMNase-Seq

molecule: other

source_name: Breast; Mammary gland

growth_protocol: All cell lines were grown in their respective media (CAMA-1, MCF7, and A549 in Dulbecco's Modified Eagle Medium; HCT116 and SUD-HL-6 in Roswell Park Memorial Institute 1640) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution (Wisent Bioproducts). Cell lines were grown in adherent/suspension dishes and in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Conditioned media was collected in exponential growth phase. The media was spun at 2500g for 10 min at 4 °C, transferred to a new tube, and spun again at 16100g for 10 min at 4 °C. The supernatant was transferred to a new tube and kept at 4 °C until MNase digestion.
MNase master mix was prepared at 20,000 Units/mL (U/mL) by combining 440 μL of ddH20, 50 μL of MNase buffer, 5 μL of BSA, and 5 μL of 2,000,000 U/mL MNase (New England Biolabs, CAT #M0247S). MNase was added to cell line conditioned media supernatant at a final concentration of 133 U/mL and incubated in a 37 ºC water bath for 30 min. The reaction was stopped by adding 5 mM EDTA (Invitrogen, CAT #15575020).
After MNase digestion, purification of DNA from cell-free chromatin was performed using the Qiagen Circulating Nucleic Acid kit (CAT #55114). The DNA was quantified using the Qubit High Sensitivity dsDNA kit (Life Technologies, CAT #Q33231) and analyzed with a Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit (CAT #5067-4626).
Libraries were prepared from 20 ng of purified DNA using the KAPA Hyperprep Kit with Library Amplification Primer Mix (Roche, CAT #07962363001) and adapters containing unique molecular identifiers from Integrated DNA Technologies. The libraries were cleaned-up using Beckman Coulter AMPure XP beads (CAT #A63882) with a 0.8× cleanup before library amplification and a 0.9X cleanup afterward. The libraries were amplified with six PCR cycles. Quality control was performed with a Qubit High Sensitivity dsDNA kit and  Agilent 2100 Bioanalyzer.

tag: tissue

value: Breast; Mammary gland

value: Epithelial


title: MCF7 RNA-Seq

description: Library name: MCF7_RNAseq

data_processing:
Expression matrices were constructed using Nextflow (v24.10.1) nf-core RNA-seq pipelines (v3.14.0)
FASTQ files were aligned to hg38 using STARv2 aligner (v2.7.10a).
Gene expression levels were quantified using RSEM (v1.3.0).
Assembly: hg38
Supplementary files format and content: transcripts counts (FPKM and TPM) matrix for each sample

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution.

extract_protocol:
RNA was extracted from cells with NucleoSpin RNA kit (Machery Nagel).
The RNA library was prepared by polyA capture and reverse transcription of cDNA (conducted by Novogene Corporation).


title: Normal_4_3_8_8

description: Sample 1187


title: MCF7 Rep2 cfChromatin, cfMNase-Seq, 30 min MNase digestion

description: Library name: MCF7_cfMNase_Rep2


title: Moderate benzene exposure13

city: Chongqing

first: Lei

address: No. 301, Dashi Road, Nanping, Nan’an District

institute: The First Affiliated Hospital of Chongqing Medical and Pharmaceutical College

description:
Library name: Patient13
10x Genomics

data_processing:
Raw sequencing reads were aligned to the human genome (hg38) using Cell Ranger Count (v7.1.0). Low-quality cells, defined as those with fewer than 200 detected features, more than 2500 features, or a mitochondrial gene contamination rate exceeding 10%, were excluded from further analysis.
Assembly: hg38
Supplementary files format and content: matrix files

source_name: PBMC

extract_protocol:
Peripheral blood samples were collected in EDTA or heparin-anticoagulated tubes. A total of 4 mL of blood was transferred to a 15 mL centrifuge tube and diluted 1:1 with Dulbecco’s Phosphate-Buffered Saline (DPBS). Two fresh 15 mL centrifuge tubes were prepared with 4 mL of Ficoll-Paque™ PLUS (Cytiva) in each. The diluted blood was carefully layered over the Ficoll, maintaining a clear interface between the layers. Samples were centrifuged at 750 × g for 25 minutes at room temperature, with acceleration and deceleration rates set to 9 and 1, respectively. After centrifugation, the PBMCs appeared as a distinct white interface between the plasma and Ficoll layers. This layer was carefully aspirated into a new 15 mL tube and brought up to 10 mL with DPBS. The cells were washed by centrifugation at 250 × g for 10 minutes at 4°C. If red blood cells (RBCs) were present in the pellet, 1 mL of RBC lysis buffer was added, mixed gently, and incubated for 1 minute. Subsequently, 5 mL of DPBS was added, followed by centrifugation at 350 × g for 5 minutes at 4°C. The supernatant was discarded, and the pellet was resuspended in 5 mL of DPBS and centrifuged again under the same conditions. This washing step was repeated once. PBMC concentration, viability, and clumping rate were assessed using a CountStar cell counter. The final cell suspension was adjusted to 1 × 10⁶ cells/mL in DPBS. Prior to scRNA-seq, cell number and viability were re-evaluated, ensuring a viability rate exceeding 85%.
scRNA-seq libraries were prepared according to the manufacturer's instructions for the 10× Genomics Single Cell 3′ Gel Bead and Library Kit (v3 Chemistry) (Pleasanton, CA). The final libraries were pooled and sequenced on the Illumina NovaSeq X Plus system with 100G paired-end sequencing in PE150 mode.

value: PBMC


title: Normal_4_3_7_1

description: Sample 1184


title: Moderate benzene exposure15

description:
Library name: Patient15
10x Genomics


title: Normal_4_3_8_1

description: Sample 1186


title: Moderate benzene exposure16

description:
Library name: Patient16
10x Genomics


title: Moderate benzene exposure14

description:
Library name: Patient14
10x Genomics


title: Normal_4_3_7_7

description: Sample 1185


title: Moderate benzene exposure12

description:
Library name: Patient12
10x Genomics


title: Normal_4_3_6_3

description: Sample 1182


title: Normal_4_3_6_8

description: Sample 1183


title: Moderate benzene exposure11

description:
Library name: Patient11
10x Genomics


title: Normal_4_3_6_2

description: Sample 1181


title: Mild benzene exposure10

description:
Library name: Patient10
10x Genomics


title: Normal_4_3_5_8

description: Sample 1180


title: Mild benzene exposure9

description:
Library name: Patient9
10x Genomics


title: Normal_4_3_5_7

description: Sample 1179


title: Normal_4_3_5_5

description: Sample 1178


title: Normal_4_3_5_3

description: Sample 1177


title: Mild benzene exposure6

description:
Library name: Patient6
10x Genomics


title: Mild benzene exposure7

description:
Library name: Patient7
10x Genomics


title: Normal_4_3_5_1

description: Sample 1176


title: Mild benzene exposure5

description:
Library name: Patient5
10x Genomics


title: Mild benzene exposure4

description:
Library name: Patient4
10x Genomics


title: Normal_4_3_4_7

description: Sample 1174


title: Normal_4_3_4_8

description: Sample 1175


title: Normal_4_3_2_7

description: Sample 1172


title: Mild benzene exposure3

description:
Library name: Patient3
10x Genomics


title: Mild benzene exposure1

description:
Library name: Patient1
10x Genomics


title: Mild benzene exposure2

description:
Library name: Patient2
10x Genomics


title: Normal_4_3_2_4

description: Sample 1171


title: CD45+cells, PBMC, CD8 T cell-depleted PBMC-transferred

city: Yokohama-shi

first: Yuzo

last: Koda

address: 1000 Kamoshida, Aoba-ku, Yokohama-shi, Kanagawa

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

description:
Library name: Sample 4
10x Genomics

data_processing:
Sequence reads from all samples were processed using a Cell Ranger (10x Genomics). Seurat version 5.1.0 was used to aggregate and analyze the processed data by following the official vignettes (https://satijalab.org/seurat/articles/seurat5_integration). Quality control was first performed, filtering out cells with >20% mitochondrial reads and with <200 or >6,000 reads. Cells that passed the quality control were normalized.
Assembly: GRCh38
Supplementary files format and content: tsv file, mtx file

source_name: Peripheral blood of humanized mice

extract_protocol:
The peripheral blood and salivary gland tissues were collected from immunodeficient mice transplanted with either human PBMCs or PBMCs depleted of CD8 T cells. Peripheral blood was lysed using HLB solution to remove red blood cells and obtain cell suspensions of PBMC. The salivary gland tissues were transferred to GentleMACS™ C tube (Miltenyi Biotec) containing 2 mL digestion buffer supplemented with 10% fetal bovine serum (FBS), 0.5–1 mg/mL Collagenase, and 0.1 mg/mL DNase I. Tissues were mechanically dissociated into small fragments using the GentleMACS™ Octo dissociator (Miltenyi Biotec). Samples were then incubated at 37°C for 45 min with continuous rotation to enhance enzymatic digestion. After incubation, tissue suspensions were allowed to further dissociate using the GentleMACS™ Octo dissociator. The resulting suspensions were diluted with RPMI, transferred to 15 mL conical tubes, and centrifuged. After discarding the supernatant, cell pellets were resuspended in 5 mL 40% Percoll. A density gradient was created with 2 mL 75% Percoll gently layered beneath the 40% Percoll solution. The gradient was centrifuged at 700–800 × g for 20 min at 20°C. The mononuclear cells in the middle layer were carefully collected. Finally, the cells were resuspended in fluorescence-activated cell sorting (FACS) buffer and used cell sorting.
Human CD45+ cells were sorted from the pooled cells of four mice and approximately 13,500 cells with >95% survival rate were loaded into a Chromium Chip K to generate single cell emulsion using Chromium Next GEM Single Cell 5' Kit v2 and a Chromium Controller (10x Genomics). RNA-seq libraries were then prepared using Chromium Next GEM Single Cell 5' Kit v2 following the manufacturer’s instructions (10x Genomics). The generated single-cell RNA sequencing libraries were sequenced using a NovaSeq 6000 platform (Illumina).

value: Peripheral blood of humanized mice

value: Infiltrated human cells in humanized mice


title: CD45+cells, SG, CD8 T cell-depleted PBMC-transferred

description:
Library name: Sample 3
10x Genomics

source_name: Salivary grand of humanized mice

value: Salivary grand of humanized mice


title: PBMC (pre-transfer)

description:
Library name: Sample 1
10x Genomics

source_name: Human peripheral blood

value: Human peripheral blood

value: Source PBMC


title: HCMV-72hpi HELF cells RNA-seq 2

city: Shenyang

first: Yang

address: No. 36. Sanhao street, Heping District

description:
Library name: HELF_72h_2
HCMV infected HELF cells were collected at 72 hours post-infection (hpi).

data_processing:
Quality control and adapter/low-quality trimming were performed.
Trimmed reads were aligned to the human reference genome GRCh38/hg38; primary alignments were retained for quantification.
Gene-level counts were summarized against a GRCh38 gene annotation (Ensembl/GENCODE). A cross-sample matrix of raw counts and FPKM values was generated for HELF_1, HELF_2, HCMV_HELF_1, and HCMV_HELF_2.
Differential expression between HCMV-infected and mock conditions was computed using replicate-aware statistics, reporting log₂ fold-change and multiple-testing-adjusted P values (FDR).
Assembly: GRCh38/hg38
Supplementary files format and content: Gene-by-sample expression matrix (file: all.genes.expression.xls).
Supplementary files format and content: Differential-expression workbook (file: mRNA_HELF-vs-HCMV_HELF.all.annot.xlsx) summarizing infected vs. mock comparisons.

source_name: embryonic lung

growth_protocol: HELF (human embryonic lung fibroblast) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified 5%CO₂ atmosphere at 37°C.

extract_protocol:
Total RNA was isolated from each sample using a column-based purification with on-column DNase treatment. High-quality RNA was used for library preparation.
Strand-specific mRNA-seq libraries were prepared from poly(A)-selected RNA. RNA was fragmented and converted to cDNA, followed by end repair, A-tailing, adaptor ligation, and PCR amplification. Libraries were sequenced on an Illumina platform with paired-end 150-bp reads.

treatment_protocol: Cells were infected with human cytomegalovirus (HCMV) HANTwo conditions were used: mock-infected HELF cells and HELF cells infected with human cytomegalovirus (HCMV) HAN strain (MOI = 3), harvested at 72 hours post-infection (hpi). strain(moi=3) and harvested at 72 hours post-infection (hpi).

value: embryonic lung

value: human embryonic lung fibroblasts

value: HELF cells were infected with HCMV clinical strain HAN, which was isolated from a urine sample of a 5-month-old infant hospitalized in Shengjing Hospital of China Medical University, at a multiplicity of infection (MOI) of 3.


title: HCMV-72hpi HELF cells RNA-seq 1

institute: Shengjing Hospital of China Medical University

description:
Library name: HELF_72h_1
HCMV infected HELF cells were collected at 72 hours post-infection (hpi).


title: mock-infected HELF cells RNA-seq 2

description:
Library name: HELF_U_2
Mock-infected cells were harvested as control.

value: HELF cells were mock-infected.


title: Mild benzene exposure8

description:
Library name: Patient8
10x Genomics


title: CD45+cells, SG, PBMC-transferred

description:
Library name: Sample 2
10x Genomics


title: Normal_4_3_12_4

description: Sample 1168

value: male

value: Normal

value: testis


title: Normal_4_3_11_8

description: Sample 1166


title: mock-infected HELF cells RNA-seq 1

description:
Library name: HELF_U_1
Mock-infected cells were harvested as control.


title: Normal_4_3_10_7

description: Sample 1164


title: Normal_4_3_10_8

description: Sample 1165


title: monocytes_invitro_RNA_rep4

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: human_monocytesrep4_RNA_rep4

data_processing:
All epigenetic libraries were mapped to hg38 genome using STAR (v2.7.9a) with default parameters and converted into HOMER tag directories. The findPeaks command from HOMER was used to call peaks. For ATAC-seq and MEF2C ChIP-seq, only peaks with an Irreproducible Discovery Rate (IDR) < 0.05 was used for downstream analysis. ATAC peak lists from MEF2C CTRL, HET and KO iMG ATAC were merged with HOMER’s mergePeaks and annotated for H3K27ac reads with HOMER’s annotatePeaks. DESeq2 was used to identify ATAC peaks that are differentially acetylated between MEF2C CTRL and KO iMG groups. Overlapping differentially acetylated ATAC peaks with MEF2C IDR peaks from CTRL samples were determined using the package GenomicRanges (v.1.54.1).
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR. Raw RNA-sequencing files were evaluated for quality control using FastQC. Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’. Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts. Quantified read counts were normalized and analyzed using DESeq2 to determine differential expression between groups, within the R statistical computing environment.
Assembly: hg38
Supplementary files format and content: tab-delimited text tpm file
Supplementary files format and content: tab-delimited text peak file

source_name: umbilical cord blood

extract_protocol:
To perform the RNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries. RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions
For ATAC-seq, live cells were rinsed with 1X PBS and lysed with cold 50 mL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 x g for 10 min at 4°C, the resulting nuclei pellet was re-suspended in 50 mL tranposase reaction mix (Illumnia #20034197) and incubated at 37°C for 30 min.
For ATAC-seq, Zymo ChIP DNA Clean and Concentrator-5 kit (Zymo Research D5205) was used to purify the DNA, which was then amplified with Nextera primers (1.25 M) using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final libraries were purified by gel excision of 155-250 bp fragments and single-end sequenced.
For RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: umbilical cord blood

value: monocytes


title: monocytes_invitro_RNA_rep3

description: Library name: human_monocytesrep3_RNA_rep3


title: Normal_4_3_10_5

description: Sample 1163

source_name: testis


title: monocytes_invitro_RNA_rep2

description: Library name: human_monocytesrep2_RNA_rep2


title: Normal_4_3_10_2

description: Sample 1161


title: Normal_4_3_10_3

description: Sample 1162


title: Normal_4_3_2_1

description: Sample 1170


title: Normal_4_3_10_1

description: Sample 1160


title: Normal_4_3_1_2

description: Sample 1159


title: monocytes_invitro_ATAC_rep2

description: Library name: human_Monocytesinvitro2_ATAC_rep2


title: Normal_4_3_12_7

description: Sample 1169


title: monocytes_invitro_RNA_rep1

description: Library name: human_monocytesrep1_RNA_rep1


title: monocytes_invitro_ATAC_rep3

description: Library name: human_Monocytesinvitro3_ATAC_rep3


title: Normal_4_3_12_1

description: Sample 1167


title: Normal_4_2_9_4

description: Sample 1158


title: Normal_4_2_9_3

description: Sample 1157


title: monocytes_invitro_ATAC_rep1

description: Library name: human_Monocytesinvitro1_ATAC_rep1


title: Control_71N_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_71N_Control_rep2
H3K27ac ChIP input

data_processing:
All epigenetic libraries were mapped to hg38 genome using STAR (v2.7.9a) with default parameters and converted into HOMER tag directories. The findPeaks command from HOMER was used to call peaks. For ATAC-seq and MEF2C ChIP-seq, only peaks with an Irreproducible Discovery Rate (IDR) < 0.05 was used for downstream analysis. ATAC peak lists from MEF2C CTRL, HET and KO iMG ATAC were merged with HOMER’s mergePeaks and annotated for H3K27ac reads with HOMER’s annotatePeaks. DESeq2 was used to identify ATAC peaks that are differentially acetylated between MEF2C CTRL and KO iMG groups. Overlapping differentially acetylated ATAC peaks with MEF2C IDR peaks from CTRL samples were determined using the package GenomicRanges (v.1.54.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text peak file
Supplementary files format and content: Bedgraph.gz

source_name: IPSC-derived microglia

extract_protocol:
Chromatin ImmunoPreciptation-seq library preparation was performed as previously described on 1,000,000 cells per cell line per replicate. For H3K27ac ChIP, the cells were fixed in 1% PFA, pelleted at 1000 x g for 5 min at 4°C, and flash frozen. Frozen cell pellets were lysed on ice in ice-cold LB3 (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylarcisine, 1X protease inhibitor cocktail).
For ChIP-seq, library preparation was performed using the NebNext Ultra II DNA Library Prep Kit (New England Biolabs E7645). Crosslinking was reversed with overnight proteinase K treatment. The DNA was purified using SpeedBeads (Thermo Scientific Fisher 651520505025) in 20% PEG8000, 1.5 M NaCl to final 12% PEG concentration and then amplified using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final library was purified by gel excision of 200-500 bp fragments and single-end sequenced

value: IPSC-derived microglia

value: iPSC-derived microglia

tag: genotype

tag: chip antibody

value: H3K27ac (Active Motif 39685, 1 ug per sample)


title: Normal_4_2_9_2

description: Sample 1156


title: Normal_4_2_8_8

description: Sample 1155


title: Normal_4_2_8_7

description: Sample 1154


title: KO_IG4_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_IG4_KO_rep2
H3K27ac ChIP input


title: Normal_4_2_8_4

description: Sample 1152


title: Normal_4_3_3_1

description: Sample 1173


title: Control_42N_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_42N_Control_rep2
H3K27ac ChIP input


title: Control_42N_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_42N_Control_rep1
H3K27ac ChIP input


title: Normal_4_2_8_3

description: Sample 1151


title: HET_2H11_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_2H11_Het_rep2
H3K27ac ChIP input


title: Normal_4_2_8_2

description: Sample 1150


title: HET_2H11_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_2H11_Het_rep1
H3K27ac ChIP input


title: Control_71N_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_71N_Control_rep1
H3K27ac ChIP input


title: KO_2H10_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_2H10_KO_rep2
H3K27ac ChIP input


title: Normal_4_2_8_1

description: Sample 1149


title: Normal_4_2_7_8

description: Sample 1148


title: KO_2H10_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_2H10_KO_rep1
H3K27ac ChIP input


title: Normal_4_2_7_7

description: Sample 1147


title: HET_237_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_237_Het_rep1
H3K27ac ChIP input


title: Normal_4_2_7_3

description: Sample 1145


title: HET_237_H3K27ac_input_rep2

description:
Library name: human_iMG_ChIP_input_237_Het_rep2
H3K27ac ChIP input


title: Normal_4_2_7_1

description: Sample 1144


title: KO_IG4_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_IG4_KO_rep2
H3K27ac ChIP


title: Normal_4_2_6_8

description: Sample 1143


title: KO_IG4_H3K27ac_input_rep1

description:
Library name: human_iMG_ChIP_input_IG4_KO_rep1
H3K27ac ChIP input


title: Normal_4_2_5_8

description: Sample 1141


title: Control_71N_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_71N_Control_rep2
H3K27ac ChIP


title: Normal_4_2_8_5

description: Sample 1153


title: Normal_4_2_5_7

description: Sample 1140


title: KO_IG4_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_IG4_KO_rep1
H3K27ac ChIP


title: Normal_4_2_5_6

description: Sample 1139


title: Normal_4_2_5_2

description: Sample 1138


title: HET_2H11_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_2H11_Het_rep2
H3K27ac ChIP


title: Control_42N_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_42N_Control_rep2
H3K27ac ChIP


title: Normal_4_2_4_5

description: Sample 1136


title: Control_71N_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_71N_Control_rep1
H3K27ac ChIP


title: KO_2H10_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_2H10_KO_rep2
H3K27ac ChIP


title: Normal_4_2_4_2

description: Sample 1135


title: KO_2H10_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_2H10_KO_rep1
H3K27ac ChIP


title: HET_237_H3K27ac_rep2

description:
Library name: human_iMG_ChIP_H3K27ac_237_Het_rep2
H3K27ac ChIP


title: Control_42N_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_42N_Control_rep1
H3K27ac ChIP


title: Normal_4_2_3_5

description: Sample 1134


title: HET_237_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_237_Het_rep1
H3K27ac ChIP


title: Normal_4_2_3_3

description: Sample 1133


title: Normal_4_2_5_1

description: Sample 1137


title: Normal_4_2_3_1

description: Sample 1132


title: KO_2H10_MEF2C_input_rep1

description:
Library name: human_KO2H10_iMGs_ChIP_input_rep4_CTN_rep1
MEF2C ChIP input

value: MEF2C (Cell Signaling Technology #5030, 1 ug per sample)


title: KO_IF37_MEF2C_ChIP_rep1

description:
Library name: human_KO1F37_iMGs_ChIP_MEF2C_CTN_rep1
MEF2C ChIP


title: KO_2H10_MEF2C_input_rep2

description:
Library name: human_KO2H10_iMGs_ChIP_MEF2C_rep4_CTN_rep1
MEF2C ChIP


title: Normal_4_2_2_8

description: Sample 1131


title: Normal_4_2_2_7

description: Sample 1130


title: HET_2H11_MEF2C_ChIP_rep1

description:
Library name: human_HET2H11_iMGs_ChIP_MEF2C_CTN_rep1
MEF2C ChIP


title: KO_1F37_MEF2C_input_rep1

description:
Library name: human_KO1F37_iMGs_ChIP_input_CTN_rep1
MEF2C ChIP input


title: HET_2H11_MEF2C_input_rep1

description:
Library name: human_HET2H11_iMGs_ChIP_input_CTN_rep1
MEF2C ChIP input


title: HET_2H11_H3K27ac_rep1

description:
Library name: human_iMG_ChIP_H3K27ac_2H11_Het_rep1
H3K27ac ChIP


title: Normal_4_2_6_2

description: Sample 1142


title: Normal_4_2_2_5

description: Sample 1128


title: Normal_4_2_7_5

description: Sample 1146


title: HET_237_MEF2C_ChIP_rep1

description:
Library name: human_HET237_iMGs_ChIP_MEF2C_CTN_rep1
MEF2C ChIP


title: Control_D4N_MEF2C_input_rep1

description:
Library name: human_CTRLD4N_iMGs_ChIP_input_CTN_rep1
MEF2C ChIP input


title: Normal_4_2_12_8

description: Sample 1125


title: Normal_4_2_12_3

description: Sample 1123


title: Normal_4_2_12_5

description: Sample 1124


title: Control_42N_MEF2C_ChIP_rep1

description:
Library name: human_CTRL42N_iMGs_ChIP_MEF2C_CTN_rep1
MEF2C ChIP


title: Normal_4_2_2_6

description: Sample 1129


title: Normal_4_2_12_2

description: Sample 1122


title: Control_42N_MEF2C_input_rep1

description:
Library name: human_CTRL42N_iMGs_ChIP_input_CTN_rep1
MEF2C ChIP input


title: Normal_4_2_11_2

description: Sample 1121


title: Normal_4_2_2_3

description: Sample 1127


title: Normal_4_2_11_1

description: Sample 1120


title: KO_IG4_ATAC_rep2

description: Library name: human_iMG_ATAC_IG4_MEF2CKO_rep2

data_processing:
All epigenetic libraries were mapped to hg38 genome using STAR (v2.7.9a) with default parameters and converted into HOMER tag directories. The findPeaks command from HOMER was used to call peaks. For ATAC-seq and MEF2C ChIP-seq, only peaks with an Irreproducible Discovery Rate (IDR) < 0.05 was used for downstream analysis. ATAC peak lists from MEF2C CTRL, HET and KO iMG ATAC were merged with HOMER’s mergePeaks and annotated for H3K27ac reads with HOMER’s annotatePeaks. DESeq2 was used to identify ATAC peaks that are differentially acetylated between MEF2C CTRL and KO iMG groups. Overlapping differentially acetylated ATAC peaks with MEF2C IDR peaks from CTRL samples were determined using the package GenomicRanges (v.1.54.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text peak file

extract_protocol:
For ATAC-seq, live cells were rinsed with 1X PBS and lysed with cold 50 mL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 x g for 10 min at 4°C, the resulting nuclei pellet was re-suspended in 50 mL tranposase reaction mix (Illumnia #20034197) and incubated at 37°C for 30 min.
For ATAC-seq, Zymo ChIP DNA Clean and Concentrator-5 kit (Zymo Research D5205) was used to purify the DNA, which was then amplified with Nextera primers (1.25 M) using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final libraries were purified by gel excision of 155-250 bp fragments and single-end sequenced.


title: Normal_4_2_10_7

description: Sample 1119


title: Normal_4_2_10_4

description: Sample 1118


title: Control_71N_ATAC_rep1

description: Library name: human_iMG_ATAC_71N_MEF2CCtrl_rep1


title: Control_71N_ATAC_rep2

description: Library name: human_iMG_ATAC_71N_MEF2CCtrl_rep2


title: Normal_4_2_10_2

description: Sample 1117


title: Control_42N_ATAC_rep1

description: Library name: human_iMG_ATAC_42N_MEF2CCtrl_rep1


title: Normal_4_2_2_1

description: Sample 1126


title: HET_237_MEF2C_input_rep1

description:
Library name: human_HET237_iMGs_ChIP_input_CTN_rep1
MEF2C ChIP input


title: Control_D4N_MEF2C_ChIP_rep1

description:
Library name: human_CTRLD4N_iMGs_ChIP_MEF2C_CTN_rep1
MEF2C ChIP


title: KO_2H10_ATAC_rep2

description: Library name: human_iMG_ATAC_2H10_MEF2CKO_rep2


title: HET_2H11_ATAC_rep1

description: Library name: human_iMG_ATAC_2H11_MEF2CHet_rep1


title: KO_2H10_ATAC_rep1

description: Library name: human_iMG_ATAC_2H10_MEF2CKO_rep1


title: Normal_4_1_8_4

description: Sample 1114


title: HET_237_ATAC_rep2

description: Library name: human_iMG_ATAC_237_MEF2CHet_rep2


title: Normal_4_1_7_2

description: Sample 1112


title: Normal_4_1_7_3

description: Sample 1113


title: Normal_4_1_4_1

description: Sample 1109


title: Normal_4_1_3_4

description: Sample 1108


title: Normal_4_1_5_1

description: Sample 1110


title: Normal_4_1_5_3

description: Sample 1111


title: 264-A_CDDP_SP600125_16h_rep3

first: Lois

last: Hew

description:
Library name: Cisplatin_SP600125_Sample3
12-CDDP-SP10uM
contrasts_full.CDDP_vs_CDDP_SP_ID16.csv
contrasts_full.NaCl_vs_CDDP_SP_ID15.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
12-CDDP-SP10uM

data_processing:
RNAseq reads were aligned to human genome (GRCh38.p7) with STAR-version 2.7.3a using default parameters.
Raw counts were obtained with featureCounts and normalized counts from DESeq2 as follows.
Reads were assigned to genes with featureCounts version 2.0.0 with the following parameters: -t exon -g gene_id -s 0 -p. gene annotation - Gencode GRCh38/v25.
Differential expression analysis carried out with DESeq2-version 1.32.0 using default parameters.
Gene set enrichment analysis was carried out with R package tmod version 0.50.07 with MSigDB gene sets.
Assembly: GRCh38.p7 (Gencode GRCh38/v25)
Supplementary files format and content: csv file for raw count matrix of all samples
Supplementary files format and content: csv file for normalized count matrix of all samples
Supplementary files format and content: csv files of differential expression results between comparison groups

growth_protocol: iPSC-DSN were cultured in neurobasal media supplemented with 1x N2, 1x B27 without vitamin A, 1x GlutaMAX, 0.01mM beta-mercaptoethanol, 25ng/ml beta-NGF, 25ng/ml BDNF, 25ng/ml NT3, 25ng/ml GDNF, and 100U/ml of Penicillin-Streptomycin or 1x Antibiotic-Antimycotic

extract_protocol:
RNA was extracted using Aurum Total RNA Mini Kit from Bio-Rad according to manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB, Ipswich). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies), and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and basecalling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was tolerated for index sequence identification.

treatment_protocol: iPSC-DSN were treated with chemotherapy drug (100nM PTX / 50nM VCR / 10nM BTZ / 10µM CDDP) in combination with/without 10µM SP600125. Vehicle counterparts for PTX, BTZ and SP600125 are DMSO. Vehicle counterpart for VCR is water. Vehicle counterpart for CDDP is NaCl. PTX-treated cells were incubated for 48h while the rest were incubated for 16h before RNA extraction.

value: iPSC-DSN


title: Normal_4_1_12_7

description: Sample 1107


title: 264-A_CDDP_SP600125_16h_rep1

description:
Library name: Cisplatin_SP600125_Sample1
10-CDDP-SP10uM
contrasts_full.CDDP_vs_CDDP_SP_ID16.csv
contrasts_full.NaCl_vs_CDDP_SP_ID15.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
10-CDDP-SP10uM


title: KO_IG4_ATAC_rep1

description: Library name: human_iMG_ATAC_IG4_MEF2CKO_rep1


title: Normal_4_2_1_4

description: Sample 1116


title: Normal_4_1_8_6

description: Sample 1115


title: Normal_4_1_11_8

description: Sample 1106


title: Control_42N_ATAC_rep2

description: Library name: human_iMG_ATAC_42N_MEF2CCtrl_rep2