title: Normal_4_1_1_5

description: Sample 1104


title: Normal_4_1_10_4

status: Public on Oct 01 2025

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: Sample 1105

library_source: genomic

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".

molecule: genomic DNA

organism: Homo sapiens

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.

tag: gender

value: male

tag: age

tag: condition

value: Normal

tag: testis

value: testis


title: 264-A_CDDP-vehicle_16h_rep3

city: Berlin

first: Lois

last: Hew

address: Charitéplatz 1

country: Germany

institute: Charité – Universitätsmedizin Berlin

description:
Library name: Cisplatin_vehicle_Sample3
6-NaCl-DMSO
contrasts_full.NaCl_vs_CDDP_ID14.csv
contrasts_full.NaCl_vs_CDDP_SP_ID15.csv
6-NaCl-DMSO

library_source: transcriptomic

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

molecule: polyA RNA

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.

tag: cell line

tag: cell type

value: iPSC-DSN

tag: treatment


title: Normal_3_8_9_8

description: Sample 1103


title: 264-A_CDDP_16h_rep1

description:
Library name: Cisplatin_Sample1
7-CDDP-10uM
contrasts_full.CDDP_vs_CDDP_SP_ID16.csv
contrasts_full.NaCl_vs_CDDP_ID14.csv
7-CDDP-10uM


title: HET_2H11_ATAC_rep2

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

country: USA

institute: University of Texas at Austin

description: Library name: human_iMG_ATAC_2H11_MEF2CHet_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

source_name: IPSC-derived microglia

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.

tag: tissue

value: IPSC-derived microglia

value: iPSC-derived microglia

tag: genotype


title: Normal_3_8_9_7

description: Sample 1102


title: HET_237_ATAC_rep1

description: Library name: human_iMG_ATAC_237_MEF2CHet_rep1


title: 264-A_CDDP-vehicle_16h_rep1

description:
Library name: Cisplatin_vehicle_Sample1
4-NaCl-DMSO
contrasts_full.NaCl_vs_CDDP_ID14.csv
contrasts_full.NaCl_vs_CDDP_SP_ID15.csv
4-NaCl-DMSO


title: 264-A_BTZ_SP600125_16h_rep3

description:
Library name: Bortezomib_SP600125_Sample3
9-264a-BTZ-SP
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
9-264a-BTZ-SP


title: 264-A_CDDP-vehicle_16h_rep2

description:
Library name: Cisplatin_vehicle_Sample2
5-NaCl-DMSO
contrasts_full.NaCl_vs_CDDP_ID14.csv
contrasts_full.NaCl_vs_CDDP_SP_ID15.csv
5-NaCl-DMSO


title: Normal_3_8_9_1

description: Sample 1099


title: 264-A_CDDP_SP600125_16h_rep2

description:
Library name: Cisplatin_SP600125_Sample2
11-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
11-CDDP-SP10uM


title: Normal_3_8_9_5

description: Sample 1101


title: Normal_3_8_9_2

description: Sample 1100


title: 264-A_BTZ_SP600125_16h_rep2

description:
Library name: Bortezomib_SP600125_Sample2
8-264a-BTZ-SP
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
8-264a-BTZ-SP


title: 264-A_CDDP_16h_rep3

description:
Library name: Cisplatin_Sample3
9-CDDP-10uM
contrasts_full.CDDP_vs_CDDP_SP_ID16.csv
contrasts_full.NaCl_vs_CDDP_ID14.csv
9-CDDP-10uM


title: 264-A_BTZ_SP600125_16h_rep1

description:
Library name: Bortezomib_SP600125_Sample1
7-264a-BTZ-SP
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
7-264a-BTZ-SP


title: Normal_3_8_8_8

description: Sample 1098


title: Normal_3_8_8_4

description: Sample 1096


title: 264-A_BTZ_16h_rep3

description:
Library name: Bortezomib_Sample3
6-264a-BTZ
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_ID6.csv
6-264a-BTZ


title: Normal_3_8_8_6

description: Sample 1097


title: Normal_3_8_8_3

description: Sample 1095


title: 264-A_BTZ_16h_rep1

description:
Library name: Bortezomib_Sample1
4-264a-BTZ
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_ID6.csv
4-264a-BTZ


title: 264-A_CDDP_16h_rep2

description:
Library name: Cisplatin_Sample2
8-CDDP-10uM
contrasts_full.CDDP_vs_CDDP_SP_ID16.csv
contrasts_full.NaCl_vs_CDDP_ID14.csv
8-CDDP-10uM


title: Normal_3_8_7_6

description: Sample 1093


title: Normal_3_8_7_7

description: Sample 1094


title: 264-A_BTZ-vehicle_16h_rep3

description:
Library name: Bortezomib_vehicle_Sample3
3-264a-DMSO
contrasts_full.DMSO3_vs_BTZ_ID6.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
3-264a-DMSO


title: 264-A_BTZ-vehicle_16h_rep2

description:
Library name: Bortezomib_vehicle_Sample2
2-264a-DMSO
contrasts_full.DMSO3_vs_BTZ_ID6.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
2-264a-DMSO


title: Normal_3_8_7_4

description: Sample 1091


title: Normal_3_8_7_5

description: Sample 1092


title: Normal_3_8_6_8

description: Sample 1090


title: 264-A_VCR_SP600125_16h_rep2

description:
Library name: Vincristine_SP600125_Sample2
9-264A-Vinc50nm-SP60012510uM-16h-290722
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
9-264A-Vinc50nm-SP60012510uM-16h-290722


title: Normal_3_8_6_5

description: Sample 1089


title: 264-A_VCR_SP600125_16h_rep3

description:
Library name: Vincristine_SP600125_Sample3
10-264A-Vinc50nm-SP60012510uM-16h-290722
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
10-264A-Vinc50nm-SP60012510uM-16h-290722


title: 264-A_BTZ-vehicle_16h_rep1

description:
Library name: Bortezomib_vehicle_Sample1
1-264a-DMSO
contrasts_full.DMSO3_vs_BTZ_ID6.csv
contrasts_full.DMSO3_vs_BTZ_SP_ID7.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
1-264a-DMSO


title: 264-A_VCR_SP600125_16h_rep1

description:
Library name: Vincristine_SP600125_Sample1
8-264A-Vinc50nm-SP60012510uM-16h-290722
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
8-264A-Vinc50nm-SP60012510uM-16h-290722


title: 264-A_VCR_16h_rep1

description:
Library name: Vincristine_Sample1
1-VCR-50nM
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_ID10.csv
1-VCR-50nM


title: 264-A_VCR_16h_rep3

description:
Library name: Vincristine_Sample3
3-VCR-50nM
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_ID10.csv
3-VCR-50nM


title: Normal_3_8_5_2

description: Sample 1086


title: Normal_3_8_5_8

description: Sample 1087


title: 264-A_VCR_16h_rep2

description:
Library name: Vincristine_Sample2
2-VCR-50nM
contrasts_full.VCR_vs_VCR_SP_ID12.csv
contrasts_full.Water_vs_VCR_ID10.csv
2-VCR-50nM


title: Normal_3_8_5_1

description: Sample 1085


title: 264-A_VCR-vehicle_16h_rep3

description:
Library name: Vincristine_vehicle_Sample3
7-264A-H2O-DMSO-16h-290722
contrasts_full.Water_vs_VCR_ID10.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
7-264A-H2O-DMSO-16h-290722


title: Normal_3_8_6_3

description: Sample 1088


title: Normal_3_8_4_2

description: Sample 1084


title: 264-A_BTZ_16h_rep2

description:
Library name: Bortezomib_Sample2
5-264a-BTZ
contrasts_full.BTZ_vs_BTZ_SP_ID8.csv
contrasts_full.DMSO3_vs_BTZ_ID6.csv
5-264a-BTZ


title: 264-A_VCR-vehicle_16h_rep2

description:
Library name: Vincristine_vehicle_Sample2
6-264A-H2O-DMSO-16h-290722
contrasts_full.Water_vs_VCR_ID10.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
6-264A-H2O-DMSO-16h-290722


title: Normal_3_8_3_8

description: Sample 1083


title: Normal_3_8_3_3

description: Sample 1081


title: Normal_3_8_3_7

description: Sample 1082


title: 264-A_PTX_SP600125_48h_rep4

description:
Library name: Paclitaxel_SP600125_Sample4
4-264A-PTX100nm-SP60012510uM-48h-290722
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
4-264A-PTX100nm-SP60012510uM-48h-290722


title: 264-A_PTX_SP600125_48h_rep3

description:
Library name: Paclitaxel_SP600125_Sample3
12-264A-PTX100nm-SP60012510uM-48h-220722
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
12-264A-PTX100nm-SP60012510uM-48h-220722


title: Normal_3_8_3_1

description: Sample 1079


title: 264-A_PTX_SP600125_48h_rep1

description:
Library name: Paclitaxel_SP600125_Sample1
10-264A-PTX100nm-SP60012510uM-48h-220722
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
10-264A-PTX100nm-SP60012510uM-48h-220722


title: Normal_3_8_3_2

description: Sample 1080


title: Normal_3_8_2_7

description: Sample 1078


title: 264-A_PTX_48h_rep3

description:
Library name: Paclitaxel_Sample3
CS03_23-264-PTX
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
23-264-PTX


title: Normal_3_8_2_3

description: Sample 1077


title: 264-A_PTX_48h_rep2

description:
Library name: Paclitaxel_Sample2
CS03_21-264-PTX
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
21-264-PTX


title: Normal_3_8_2_2

description: Sample 1076


title: Normal_3_8_12_8

description: Sample 1075


title: 264-A_PTX_48h_rep1

description:
Library name: Paclitaxel_Sample1
CS03_19-264-PTX
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO3_vs_PTX_ID2.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
19-264-PTX


title: Normal_3_8_12_4

description: Sample 1073


title: 264-A_PTX-vehicle_48h_rep5

description:
Library name: Paclitaxel_vehicle_Sample5
CS03_22-264-DMSO
contrasts_full.DMSO3_vs_PTX_ID2.csv
22-264-DMSO


title: Normal_3_8_12_5

description: Sample 1074


title: Normal_3_8_11_2

description: Sample 1071


title: Normal_3_8_11_3

description: Sample 1072


title: 264-A_PTX-vehicle_48h_rep6

description:
Library name: Paclitaxel_vehicle_Sample6
CS03_24-264-DMSO
contrasts_full.DMSO3_vs_PTX_ID2.csv
26-264-DMSO


title: 264-A_PTX-vehicle_48h_rep4

description:
Library name: Paclitaxel_vehicle_Sample4
CS03_20-264-DMSO
contrasts_full.DMSO3_vs_PTX_ID2.csv
20-264-DMSO


title: 264-A_PTX-vehicle_48h_rep2

description:
Library name: Paclitaxel_vehicle_Sample2
9-264A-DMSO-DMSO-48h-220722
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
9-264A-DMSO-DMSO-48h-220722


title: Normal_3_8_10_4

description: Sample 1069


title: 264-A_PTX-vehicle_48h_rep1

description:
Library name: Paclitaxel_vehicle_Sample1
7-264A-DMSO-DMSO-48h-220722
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
7-264A-DMSO-DMSO-48h-220722


title: 264-A_SP600125_48h_rep4

description:
Library name: SP600125_Sample4
2-264A-SP600125-10uM-48h-290722
contrasts_full.DMSO1_vs_SP_ID0.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
2-264A-SP600125-10uM-48h-290722


title: 264-A_SP600125_48h_rep3

description:
Library name: SP600125_Sample3
6-264A-SP600125-10uM-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
6-264A-SP600125-10uM-48h-220722


title: Normal_3_8_1_8

description: Sample 1068


title: Normal_3_8_1_5

description: Sample 1067


title: 264-A_SP600125_48h_rep2

description:
Library name: SP600125_Sample2
5-264A-SP600125-10uM-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
5-264A-SP600125-10uM-48h-220722


title: Normal_3_8_10_7

description: Sample 1070


title: Normal_3_8_1_1

description: Sample 1066


title: 264-A_VCR-vehicle_16h_rep1

description:
Library name: Vincristine_vehicle_Sample1
5-264A-H2O-DMSO-16h-290722
contrasts_full.Water_vs_VCR_ID10.csv
contrasts_full.Water_vs_VCR_SP_ID11.csv
5-264A-H2O-DMSO-16h-290722


title: 264-A_PTX_SP600125_48h_rep2

description:
Library name: Paclitaxel_SP600125_Sample2
11-264A-PTX100nm-SP60012510uM-48h-220722
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
contrasts_full.PTX_vs_PTX_SP_ID3.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
11-264A-PTX100nm-SP60012510uM-48h-220722


title: 264-A_SP600125_48h_rep1

description:
Library name: SP600125_Sample1
4-264A-SP600125-10uM-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
contrasts_full.SP_vs_BTZ_SP_ID9.csv
contrasts_full.SP_vs_CDDP_SP_ID17.csv
contrasts_full.SP_vs_PTX_SP_ID5.csv
contrasts_full.SP_vs_VCR_SP_ID13.csv
4-264A-SP600125-10uM-48h-220722


title: Normal_3_7_9_1

description: Sample 1065


title: 264-A_SP600125-vehicle_48h_rep4

description:
Library name: SP600125_vehicle_Sample4
1-264A-DMSO-1-4800-48h-290722
contrasts_full.DMSO1_vs_SP_ID0.csv
1-264A-DMSO-1-4800-48h-290722


title: 264-A_SP600125-vehicle_48h_rep2

description:
Library name: SP600125_vehicle_Sample2
2-264A-DMSO-1-4800-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
2-264A-DMSO-1-4800-48h-220722


title: 264-A_SP600125-vehicle_48h_rep3

description:
Library name: SP600125_vehicle_Sample3
3-264A-DMSO-1-4800-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
3-264A-DMSO-1-4800-48h-220722


title: Normal_3_7_7_2

description: Sample 1062


title: 264-A_SP600125-vehicle_48h_rep1

description:
Library name: SP600125_vehicle_Sample1
1-264A-DMSO-1-4800-48h-220722
contrasts_full.DMSO1_vs_SP_ID0.csv
1-264A-DMSO-1-4800-48h-220722


title: Normal_3_7_6_6

description: Sample 1061


title: Normal_3_7_7_4

description: Sample 1063


title: Normal_3_7_6_5

description: Sample 1060


title: Normal_3_7_8_5

description: Sample 1064


title: Normal_3_7_6_4

description: Sample 1059


title: Normal_3_7_6_3

description: Sample 1058


title: 8709-TO-2 / Normal CO alone

city: Nashville

first: Ege

middle: T

last: Kavalali

state: TN

address: 465 21st Avenue South, 7130A MRBIII

department: Pharmacology

institute: Vanderbilt University

description:
Library name: 8709-TO-0002
Pip-seq (Normal CO alone)

library_source: transcriptomic single cell

data_processing:
The raw data was aligned with PIPseeker 1.0.0 with human hg38 reference. For gene preprocessing and filtering, all genes expressed in less than three cells were removed. Cells expressing less than 200 genes, or had more than 20% mitochondrial gene expression, were also removed.  For the remaining preprocessing analysis, Seurat was used: total counts were normalized by cell, then data were log transformed. Highly variable genes were determined with Seurat selection.method = "vst", and nfeatures = 3000. A PCA, and UMAP clustering were then calculated using FindNeighbors and FindClusters with resolution = 0.5.
Assembly: hg38
Supplementary files format and content: tab separated value files and matrix files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: hESC-derived brain

growth_protocol: H1 human ES cells (WiCell, WA01) were maintained in mTeSR media on Matrigel coated 6-well plates. H69 SCLC cells (NCI-H69, human lung carcinoma) were maintained in RPMI media with 5% FBS and 1% P/S.  Cerebral organoids were maintained in Differentiation Type II medium.

extract_protocol:
Cells used for single-cell RNA seq were prepared according to PIPseq Single Cell Capture and Lysis User Guide. A cell suspension was prepared in the Cell Suspension Buffer provided from the PIPseqTM T2 3’ Single Cell Capture and Lysis Kit v2.0. Cells were added into Pre-templated Instant Partitions (PIPs) and vortexed.
Stable emulsions containing captured mRNA were subsequently washed and cDNA synthesis was conducted according to the manufacturer’s instructions. cDNA products were submitted to the Vanderbilt University VANTAGE core where whole genome sequencing (WGS) library generation was performed.  cDNA libraries were _x000B_sequenced on an Illumina NovaSeq 6000 instrument at a read depth of 100 million.

treatment_protocol: Cerebral organoids (4-6 weeks old) were co-cultured together with mKate2-labelled H69 SCLC cells in one well of a 24-well plate at a concentration of 100,000 H69 cells per organoid. For the first 24 hours, co-cultured samples were maintained in RPMI media with 5% FBS and 1% P/S at 37°C without agitation. Following this initial 24 hours, organoids were gently washed in PBS and transferred to a single well of a 6-well plate containing 3 mL of organoid differentiation medium type II and placed on an orbital shaker for an additional 24 hrs.  After 48 hrs of incubation, cerebral organoids alone, two-dimensional H69 cultures, and tumor-bearing cerebral organoids were dissociated into single-cell suspensions with collagenase type II. Cells were filtered through a 40 um strainer and resuspended in ice cold PBS/2%BSA. Cell viability was checked at every step of the process by Trypan Blue Exclusion. Samples were processed through the particle-templated instant partition sequencing (PIP-seq) platform using Fluent BioSciences’ PIPseqTM T2 3’ Single Cell Capture and Lysis Kit v2.0.

value: hESC-derived brain

value: H1 hESC

value: Brain


title: 8709-TO-9 / 2D H69 cells

description:
Library name: 8709-TO-0009
Pip-seq (2D H69 cells)

value: SCLC tumor cell line


title: Normal_3_7_6_2

description: Sample 1057


title: 8709-TO-6 / CO+H69 co-culture

description:
Library name: 8709-TO-0006
Pip-seq (CO+H69 co-culture)

source_name: hESC-derived brain + SCLC tumor cells

value: hESC-derived brain + SCLC tumor cells

value: H1 hESC + NCI-H69

value: Brain and SCLC Tumor


title: 264-A_PTX-vehicle_48h_rep3

description:
Library name: Paclitaxel_vehicle_Sample3
3-264A-DMSO-DMSO-48h-290722
contrasts_full.DMSO2_vs_PTX_ID1.csv
contrasts_full.DMSO2_vs_PTX_SP_ID4.csv
3-264A-DMSO-DMSO-48h-290722


title: Normal_3_7_5_4

description: Sample 1055


title: Normal_3_7_5_3

description: Sample 1054


title: CD34+ cells, Day45 timepoint, XPO1, Donor JK21

city: Memphis

first: Jeffery

last: Klco

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Library name: 3081313_SJNORM085481_C6-JK21_D45-XPO1-AB1

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: hg38+ custom rDNA build from  DOI:  https://doi.org/10.1101/2022.11.10.514243
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: Human cord-blood CD34+ cells

growth_protocol: cbCD34+ cells were growin in SFEM II supplemented with pen-strep, I-glutamine, and recombinant human SCF, FLT-3, TPO and IL-6 (all 50ng/mL PeproTech),  500nM (#72332, STEMCELL Technologies) for UM729, and 500nM SR-1 (1µmol/L, #72344, STEMCELL Technologies), PDX cells were grown in AML media which is StemSpan™ SFEM II (StemCell Technologies 09655) supplemented with human cytokines IL-6 (10ng/mL, PeproTech, 200-06), FLT-3 ligand (50ng/mL, PeproTech, 300-19), IL-3 (10ng/mL, PeproTech, 200-03), and human SCF (50ng/mL, PeproTech, 300-07)

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

value: Human cord-blood CD34+ cells

tag: chip antibody

value: XPO1 (Cell Signaling Technologies, 46249)


title: CD34+ cells, Day45 timepoint, H3K27a, Donor JK23

description: Library name: 3081319_SJNORM085482_C6-JK23_D45-H3K27Ac-AB5

value: H3K27ac (Cell Signaling Technologies,  8173)


title: CD34+ cells, Day45 timepoint, H3K27a, Donor JK21

description: Library name: 3081318_SJNORM085481_C6-JK21_D45-H3K27Ac-AB5


title: CD34+ cells, Day45 timepoint, XPO1, Donor JK23

description: Library name: 3081314_SJNORM085482_C6-JK23_D45-XPO1-AB1


title: CD34+ cells, Day45 timepoint, XPO1, Donor JK17

description: Library name: 3081312_SJNORM085480_C6-JK17_D45-XPO1-AB1


title: Normal_3_7_5_2

description: Sample 1053


title: CD34+ cells, Day45 timepoint, UBTF, Donor JK21

description: Library name: 3081310_SJNORM085481_C6-JK21_D45-UBTF-AB2

value: UBTF (Abcam, ab244287)


title: CD34+ cells, Day45 timepoint, UBTF, Donor JK23

description: Library name: 3081311_SJNORM085482_C6-JK23_D45-UBTF-AB2


title: Normal_3_7_3_3

description: Sample 1051

value: male


title: Normal_3_7_3_2

description: Sample 1050

value: Normal


title: Normal_3_7_5_1

description: Sample 1052

value: testis


title: Normal_3_7_3_1

description: Sample 1049


title: CD34+ cells, Day45 timepoint, UBTF, Donor JK17

description: Library name: 3081309_SJNORM085480_C6-JK17_D45-UBTF-AB2


title: Normal_3_7_2_3

description: Sample 1048


title: CD34+ cells, Day20 timepoint, H3K27a, Donor JK23

description: Library name: 3081308_SJNORM085482_C5-JK23_D20-H3K27Ac-AB5


title: CD34+ cells, Day20 timepoint, H3K27a, Donor JK21

description: Library name: 3081307_SJNORM085481_C5-JK21_D20-H3K27Ac-AB5


title: Normal_3_7_12_8

description: Sample 1047


title: Normal_3_7_5_5

description: Sample 1056


title: CD34+ cells, Day20 timepoint, H3K27ac, Donor JK17

description: Library name: 3081306_SJNORM085480_C5-JK17_D20-H3K27Ac-AB5


title: CD34+ cells, Day45 timepoint, H3K27ac, Donor JK17

description: Library name: 3081317_SJNORM085480_C6-JK17_D45-H3K27Ac-AB5


title: Normal_3_7_12_6

description: Sample 1046


title: Normal_3_7_12_1

description: Sample 1045


title: CD34+ cells, Day20 timepoint, XPO1, Donor JK23

description: Library name: 3081302_SJNORM085482_C5-JK23_D20-XPO1-AB1


title: CD34+ cells, Day20 timepoint, XPO1, Donor JK21

description: Library name: 3081301_SJNORM085481_C5-JK21_D20-XPO1-AB1


title: Normal_3_7_11_3

description: Sample 1043


title: CD34+ cells, Day20 timepoint, XPO1, Donor JK17

description: Library name: 3081300_SJNORM085480_C5-JK17_D20-XPO1-AB1


title: CD34+ cells, Day20 timepoint, UBTF, Donor JK23

description: Library name: 3081299_SJNORM085482_C5-JK23_D20-UBTF-AB2


title: Normal_3_7_11_2

description: Sample 1042


title: CD34+ cells, Day20 timepoint, UBTF, Donor JK17

description: Library name: 3081297_SJNORM085480_C5-JK17_D20-UBTF-AB2


title: Normal_3_7_10_4

description: Sample 1040


title: Normal_3_7_10_3

description: Sample 1039


title: CD34+ cells, Day3 timepoint, H3K27a, Donor JK21

description: Library name: 3081295_SJNORM085481_C4-JK21_D3-H3K27Ac-AB5


title: CD34+ cells, Day3 timepoint, H3K27ac, Donor JK17

description: Library name: 3081294_SJNORM085480_C4-JK17_D3-H3K27Ac-AB5


title: Normal_3_7_10_1

description: Sample 1038


title: Normal_3_7_1_4

description: Sample 1037


title: Normal_3_7_1_3

description: Sample 1036


title: CD34+ cells, Day3 timepoint, XPO1, Donor JK21

description: Library name: 3081289_SJNORM085481_C4-JK21_D3-XPO1-AB1


title: Normal_3_7_1_2

description: Sample 1035


title: CD34+ cells, Day3 timepoint, XPO1, Donor JK17

description: Library name: 3081288_SJNORM085480_C4-JK17_D3-XPO1-AB1


title: CD34+ cells, Day3 timepoint, UBTF, Donor JK23

description: Library name: 3081287_SJNORM085482_C4-JK23_D3-UBTF-AB2


title: CD34+ cells, Day3 timepoint, XPO1, Donor JK23

description: Library name: 3081290_SJNORM085482_C4-JK23_D3-XPO1-AB1


title: Normal_3_6_8_8

description: Sample 1033


title: Normal_3_7_11_4

description: Sample 1044


title: Normal_3_6_9_5

description: Sample 1034


title: Normal_3_6_8_7

description: Sample 1032


title: CD34+ cells, Day3 timepoint, UBTF, Donor JK21

description: Library name: 3081286_SJNORM085481_C4-JK21_D3-UBTF-AB2


title: CD34+ cells, Day3 timepoint, UBTF, Donor JK17

description: Library name: 3081285_SJNORM085480_C4-JK17_D3-UBTF-AB2


title: Normal_3_6_8_6

description: Sample 1031


title: CD34+ cells, Day20 timepoint, UBTF, Donor JK21

description: Library name: 3081298_SJNORM085481_C5-JK21_D20-UBTF-AB2


title: Normal_3_6_8_5

description: Sample 1030


title: Normal_3_6_7_7

description: Sample 1029


title: Normal_3_7_10_8

description: Sample 1041


title: Control

description: Library name: 3081284_SJNORM085489_C1-Pool_JK17_JK21_JK23-H3K4me3-AB12

value: H3K4me3 (EpiCypher, 13-0041)


title: Normal_3_6_7_4

description: Sample 1028


title: CD34+ cells, Day3 timepoint, H3K27a, Donor JK23

description: Library name: 3081296_SJNORM085482_C4-JK23_D3-H3K27Ac-AB5


title: Elta_rep2

description:
Library name: SJNORM077216_C20-JMB93_FKBP12-UBTF-TD54-5E_Eltanexor_rep2
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.

molecule: total RNA

source_name: Cord-blood CD34+ cells

extract_protocol:
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055)). RNA was then quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the Illumina Stranded Total RNA Prep kit according to the manufacturer’s instructions (Illumina, PN 20072063). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).

value: Cord-blood CD34+ cells

value: Eltanexor


title: Elta_rep3

description:
Library name: SJNORM077216_C21-JMB93_FKBP12-UBTF-TD54-5E_Eltanexor_rep3
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv


title: Normal_3_6_7_2

description: Sample 1027


title: Elta_rep1

description:
Library name: SJNORM077216_C19-JMB93_FKBP12-UBTF-TD54-5E_Eltanexor_rep1
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv


title: dTAG-13_rep3

description:
Library name: SJNORM077216_C18-JMB93_FKBP12-UBTF-TD54-5E_dTAG-13_rep3
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv


title: Normal_3_6_7_1

description: Sample 1026


title: Normal_3_6_6_5

description: Sample 1025


title: dTAG-13_rep2

description:
Library name: SJNORM077216_C17-JMB93_FKBP12-UBTF-TD54-5E_dTAG-13_rep2
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv


title: Normal_3_6_6_1

description: Sample 1024


title: dTAG-13_rep1

description:
Library name: SJNORM077216_C16-JMB93_FKBP12-UBTF-TD54-5E_dTAG-13_rep1
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv


title: Normal_3_6_5_7

description: Sample 1023


title: Normal_3_6_5_6

description: Sample 1022


title: Normal_3_6_4_1

description: Sample 1021


title: DMSO_rep1

description:
Library name: SJNORM077216_C13-JMB93_FKBP12-UBTF-TD54-5E_DMSO_rep1
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv

value: DMSO


title: DMSO_rep2

description:
Library name: SJNORM077216_C14-JMB93_FKBP12-UBTF-TD54-5E_DMSO_rep2
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv


title: Control_IgG

description: Library name: 3081283_SJNORM085489_C1-Pool_JK17_JK21_JK23-IGG-AB14

value: IgG (EpiCypher, 13-0042)


title: Normal_3_6_3_5

description: Sample 1018


title: Normal_3_6_3_8

description: Sample 1020


title: Normal_3_6_3_6

description: Sample 1019


title: Patient 3, normal tissue

city: Fuzhou

first: Wu

last: Jiayue

state: Fujian

address: No. 134, Dongjie Street, Gulou District, Fuzhou City

institute: Fujian province hospital

description:
Library name: Sample ccRCC006
SeekOne

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: normal tissue

extract_protocol:
First, the samples were washed three times with PBS. The tissues were completely minced with scissors, and tissue digestion solution was added, followed by digestion on a shaker at 37ºC for 60 minutes. The resulting cell suspension was filtered through 100μm and 40μm strainers. After low-speed centrifugation to pellet the cells, red blood cell lysis buffer was used to remove red blood cells. Subsequently, the cell concentration was adjusted to the optimal level for the subsequent library construction steps.
Single-cell RNA-Seq libraries were prepared using the SeekOne® DD kit. Cells were mixed with reverse transcription reagent and added to Chip S3. Barcoded Hydrogel Beads and partitioning oil were dispensed into Chip S3 wells. Reverse transcription was performed at 42°C for 90 min and inactivated at 85°C for 5 min. cDNA was purified, amplified in polymerase chain reaction (PCR), cleaned, fragmented, repaired, A-tailed, and ligated to a sequencing adaptor. Indexed PCR was then performed to amplify the DNA representing the 3’ polyA part of expressing genes, containing cell barcode and unique molecular index. Libraries were cleaned with solid phase reversible immobilization beads, quantified by qPCR, and sequenced on DNBSEQ-T7 with PE150 read length.

value: normal tissue

tag: individual


title: Normal_3_6_2_7

description: Sample 1017


title: Patient 2, tumor tissue

description:
Library name: Sample ccRCC003
SeekOne

source_name: tumor tissue

value: tumor tissue


title: Patient 2, normal tissue

description:
Library name: Sample ccRCC004
SeekOne


title: Normal_3_6_2_6

description: Sample 1016


title: Patient 3, tumor tissue

description:
Library name: Sample ccRCC005
SeekOne


title: Normal_3_6_2_2

description: Sample 1015


title: Patient 1, normal tissue

description:
Library name: Sample ccRCC002
SeekOne


title: Normal_3_6_2_1

description: Sample 1014


title: Normal_3_6_12_8

description: Sample 1013


title: Patient 1, tumor tissue

description:
Library name: Sample ccRCC001
SeekOne


title: Normal_3_6_12_6

description: Sample 1012


title: Normal_3_6_12_5

description: Sample 1011


title: Normal_3_6_12_4

description: Sample 1010


title: Normal_3_6_12_1

description: Sample 1009


title: Normal_3_6_11_8

description: Sample 1008


title: Patient 2, bone marrow-derived mesenchymal stem cells, JMJD3, H3K4me3 (Input)

city: Caen

first: Catherine

last: Baugé

address: Esplanade de la paix

country: France

institute: Université de Caen Normandie

description: Library name: Patient2_JMJD3, IN

data_processing:
Quality control of sequencing reads was performed using FastQC. Reads were aligned to the reference genome (GRCh38/hg38) obtained from the UCSC genome browser using BWA software v.0.7.5a. Samples were filtered for regions blacklisted by the ENCODE project. PCR duplicates and multimapping reads were removed using samtools. Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using SICER with optimized parameters for each histone mark.
Assembly: hg38
Supplementary files format and content: peaks bed files

source_name: bone marrow

growth_protocol: For bone marrow-derived mesenchymal stem cells: alpha-MEM supplemented with 10% fetal bovine serum (Lonza, Levallois-Perret, France), 2 mM L-glutamine, 1 ng/ml FGF-2 (Merck, Loiret, France), and antibiotics (penicillin-streptomycin, Lonza) at 37°C in 5% CO₂; For chondrogenesis: DMEM supplemented with antibiotics (penicillin-streptomycin, Lonza), 100 nM dexamethasone (Merck), 50 mg/ml ascorbic acid-2-phosphate (Merck), 40 µg/ml proline (Merck), 1 mM sodium pyruvate (Merck), a 1:100 dilution of Insulin-Transferrin-Selenium (ITS) +1 supplement (Merck), and 10 ng/ml TGF-β3 (Merck)

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico sonication device (Diagenode)
Libraries were prepared using IP-Star® Compact Automated System (Diagenode) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).

treatment_protocol: pCMV-HA-UTX (#24168, Addgene) or pCMV-HA-JMJD3 (#24167, Addgene) or pmax-GFP (Amaxa)

value: bone marrow


title: Patient 2, bone marrow-derived mesenchymal stem cells, UTX, H3K4me3 (Input)

description: Library name: Patient2_UTX, IN

value: UTX


title: Patient 2, bone marrow-derived mesenchymal stem cells, JMJD3, H3K27me3 (ChIP)

description: Library name: Patient2_JMJD3_H3K27me3, ChIP


title: Patient 2, bone marrow-derived mesenchymal stem cells, JMJD3, H3K4me3 (ChIP)

description: Library name: Patient2_JMJD3_H3K4me3, ChIP


title: Patient 2, bone marrow-derived mesenchymal stem cells, GFP, H3K27me3 (ChIP)

description: Library name: Patient2_GFP_H3K27me3, ChIP

value: GFP


title: Patient 2, bone marrow-derived mesenchymal stem cells, GFP, H3K4me3 (Input)

description: Library name: Patient2_GFP, IN


title: Patient 2, bone marrow-derived mesenchymal stem cells, GFP, H3K4me3 (ChIP)

description: Library name: Patient2_GFP_H3K4me3, ChIP


title: Normal_3_6_11_4

description: Sample 1006


title: Normal_3_6_11_1

description: Sample 1005


title: Patient 2, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K27me3 (ChIP)

description: Library name: Patient2_GSK-J4_H3K27me3, ChIP


title: Patient 2, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K4me3 (ChIP)

description: Library name: Patient2_GSK-J4_H3K4me3, ChIP


title: Normal_3_6_1_8

description: Sample 1002


title: Patient 2, bone marrow-derived mesenchymal stem cells, UTX, H3K27me3 (ChIP)

description: Library name: Patient2_UTX_H3K27me3, ChIP


title: Normal_3_6_10_1

description: Sample 1003


title: Patient 2, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K4me3 (Input)

description: Library name: Patient2_GSK-J4, IN


title: Patient 2, bone marrow-derived mesenchymal stem cells, Control, H3K27me3 (ChIP)

description: Library name: Patient2_control_H3K27me3, ChIP

value: chondrogenic medium


title: Patient 2, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K27me3 (ChIP)

description: Library name: Patient2_undiff_H3K27me3, ChIP

value: MSC medium


title: DMSO_rep3

description:
Library name: SJNORM077216_C15-JMB93_FKBP12-UBTF-TD54-5E_DMSO_rep3
RNAseq_elta_vs_DMSO_log2CPM_diff.tsv
RNAseq_dTAG_vs_DMSO_log2CPM_diff.tsv


title: Normal_3_6_10_8

description: Sample 1004


title: Normal_3_6_1_1

description: Sample 1000


title: Patient 2, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K4me3 (Input)

description: Library name: Patient2_undiff, IN


title: Normal_3_5_9_5

description: Sample 999


title: Patient 2, bone marrow-derived mesenchymal stem cells, UTX, H3K4me3 (ChIP)

description: Library name: Patient2_UTX_H3K4me3, ChIP


title: Patient 2, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K4me3 (ChIP)

description: Library name: Patient2_undiff_H3K4me3, ChIP


title: Patient 2, bone marrow-derived mesenchymal stem cells, Control, H3K4me3 (Input)

description: Library name: Patient2_control, IN


title: Normal_3_5_8_8

description: Sample 997


title: Normal_3_6_11_6

description: Sample 1007


title: Normal_3_5_9_2

description: Sample 998


title: Patient 2, bone marrow-derived mesenchymal stem cells, Control, H3K4me3 (ChIP)

description: Library name: Patient2_control_H3K4me3, ChIP


title: Normal_3_5_8_4

description: Sample 996


title: Normal_3_5_8_3

description: Sample 995


title: Patient 1, bone marrow-derived mesenchymal stem cells, UTX, H3K4me3 (Input)

description: Library name: Patient1_UTX, IN


title: Normal_3_5_8_2

description: Sample 994


title: Patient 1, bone marrow-derived mesenchymal stem cells, UTX, H3K4me3 (ChIP)

description: Library name: Patient1_UTX_H3K4me3, ChIP


title: Patient 1, bone marrow-derived mesenchymal stem cells, UTX, H3K27me3 (ChIP)

description: Library name: Patient1_UTX_H3K27me3, ChIP


title: Normal_3_5_7_7

description: Sample 993


title: Patient 1, bone marrow-derived mesenchymal stem cells, JMJD3, H3K4me3 (ChIP)

description: Library name: Patient1_JMJD3_H3K4me3, ChIP


title: Patient 1, bone marrow-derived mesenchymal stem cells, JMJD3, H3K27me3 (ChIP)

description: Library name: Patient1_JMJD3_H3K27me3, ChIP


title: Normal_3_5_7_4

description: Sample 991


title: Normal_3_5_7_3

description: Sample 990


title: Normal_3_5_7_6

description: Sample 992


title: Patient 1, bone marrow-derived mesenchymal stem cells, GFP, H3K27me3 (ChIP)

description: Library name: Patient1_GFP_H3K27me3, ChIP


title: Normal_3_5_7_2

description: Sample 989


title: Patient 1, bone marrow-derived mesenchymal stem cells, GFP, H3K4me3 (Input)

description: Library name: Patient1_GFP, IN


title: Normal_3_5_6_8

description: Sample 987


title: Patient 1, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K27me3 (ChIP)

description: Library name: Patient1_GSK-J4_H3K27me3, ChIP


title: Patient 1, bone marrow-derived mesenchymal stem cells, GFP, H3K4me3 (ChIP)

description: Library name: Patient1_GFP_H3K4me3, ChIP


title: Patient 1, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K4me3 (Input)

description: Library name: Patient1_GSK-J4, IN


title: Normal_3_5_6_4

description: Sample 985


title: Patient 1, bone marrow-derived mesenchymal stem cells, GSK-J4, H3K4me3 (ChIP)

description: Library name: Patient1_GSK-J4_H3K4me3, ChIP


title: Normal_3_5_6_6

description: Sample 986


title: Normal_3_5_7_1

description: Sample 988


title: Normal_3_5_6_1

description: Sample 984


title: Normal_3_5_5_6

description: Sample 983


title: Patient 1, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K27me3 (ChIP)

description: Library name: Patient1_undiff_H3K27me3, ChIP


title: Normal_3_6_1_2

description: Sample 1001


title: Patient 1, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K4me3 (ChIP)

description: Library name: Patient1_undiff_H3K4me3, ChIP


title: Normal_3_5_4_5

description: Sample 979


title: Patient 1, bone marrow-derived mesenchymal stem cells, Control, H3K4me3 (ChIP)

description: Library name: Patient1_control_H3K4me3, ChIP


title: Normal_3_5_3_8

description: Sample 977


title: Patient 1, bone marrow-derived mesenchymal stem cells, undifferentiated, H3K4me3 (Input)

description: Library name: Patient1_undiff, IN


title: AH66

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

department: School of Medicine

country: Australia

institute: Western Sydney University

description: Library name: Sample 30

data_processing:
Sequencing of libraries was performed with Novaseq SP flowcell for 100bp paired end reads.
Data processing was performed using the Strand Next Generation Sequencing software (version 4- Build 242089, Strand Life Sciences), by aligning the Fastq files to the human reference genome (hg38) with Ensembl annotation. Raw reads with an average base quality below 20 and reads which have failed quality control (QC) were removed.
EdgeR (v3.12.1) analysis was performed to identify differentially expressed (DE) genes using normalized reads for T1D (without and with albuminuria) versus controls with log2Fold Change (FC), p-values, and q-values after Bonferroni correction.
Confounder correction algorithm (RUVseq: Remove Unwanted Variation Sequencing) with k=10 was applied for T1D with albuminuria versus T1D without albuminuria (i.e. normoalbuminuria) comparison (as recommended for RNA-seq datasets with small sample size).
Assembly: hg38
Supplementary files format and content: csv files include TMM values for all sample.

source_name: Treg

growth_protocol: Sorted Treg cell samples were isolated for RNA. The RNA of each sample was used for RNA-seq.

extract_protocol:
RNA was isolated from sorted Treg cells using  TRIzol®-based manual RNA extraction method with the addition of glycogen.
RNA-sequencing involved quality check, library preparations with the Illumina® Stranded Total RNA Prep kit, ligation with Ribo-Zero Plus including DNase treatment.

value: Treg

tag: characteristic

tag: other id_for_file_name

tag: other id_for_sample


title: Patient 1, bone marrow-derived mesenchymal stem cells, Control, H3K4me3 (Input)

description: Library name: Patient1_control, IN


title: Normal_3_5_2_6

description: Sample 974


title: Normal_3_5_3_1

description: Sample 975


title: Normal_3_5_4_1

description: Sample 978


title: Patient 1, bone marrow-derived mesenchymal stem cells, Control, H3K27me3 (ChIP)

description: Library name: Patient1_control_H3K27me3, ChIP


title: AH25

description: Library name: Sample 25


title: Normal_3_5_5_5

description: Sample 982


title: AH63

description: Library name: Sample 27


title: Normal_3_5_4_7

description: Sample 980


title: Patient 1, bone marrow-derived mesenchymal stem cells, JMJD3, H3K4me3 (Input)

description: Library name: Patient1_JMJD3, IN


title: Normal_3_5_3_3

description: Sample 976


title: AH65

description: Library name: Sample 29


title: AH24

description: Library name: Sample 24


title: AH26

description: Library name: Sample 26


title: Normal_3_5_5_3

description: Sample 981


title: AH23

description: Library name: Sample 23


title: AH64

description: Library name: Sample 28


title: Normal_3_5_11_7

description: Sample 970


title: Normal_3_5_2_5

description: Sample 973


title: AH21

description: Library name: Sample 21


title: Normal_3_5_11_6

description: Sample 969


title: AH20

description: Library name: Sample 20


title: AH22

description: Library name: Sample 22


title: AH19

description: Library name: Sample 19


title: Normal_3_5_11_3

description: Sample 966


title: Normal_3_5_11_4

description: Sample 967


title: AH18

description: Library name: Sample 18


title: Normal_3_5_10_2

description: Sample 963


title: AH17

description: Library name: Sample 17


title: AH14

description: Library name: Sample 15


title: Normal_3_5_1_4

description: Sample 961


title: AH15

description: Library name: Sample 16


title: Normal_3_5_10_7

description: Sample 964


title: AH11

description: Library name: Sample 12


title: AH13

description: Library name: Sample 14


title: Normal_3_5_1_3

description: Sample 960


title: AH12

description: Library name: Sample 13


title: Normal_3_5_11_8

description: Sample 971


title: Normal_3_4_9_5

description: Sample 959


title: AH11R

description:
Library name: Sample 11
AH11_S3 is a replicate of sample J12 i.e. AH11_S9 replicate


title: Normal_3_4_9_2

description: Sample 958


title: AH09

description: Library name: Sample 10


title: Normal_3_4_9_1

description: Sample 957


title: Normal_3_5_11_5

description: Sample 968


title: Normal_3_5_11_1

description: Sample 965


title: AH08R

description:
Library name: Sample 8
AH08_S2 is a replicate of sample J09 i.e. AH08_S7 replicate


title: Normal_3_5_12_5

description: Sample 972


title: AH07

description: Library name: Sample 7


title: Normal_3_4_8_8

description: Sample 956


title: Normal_3_4_8_5

description: Sample 954


title: Normal_3_4_8_7

description: Sample 955


title: Normal_3_5_1_8

description: Sample 962


title: AH04

description: Library name: Sample 5


title: Normal_3_4_8_2

description: Sample 952


title: AH01

description: Library name: Sample 1


title: AH02

description: Library name: Sample 3


title: Normal_3_4_7_6

description: Sample 949


title: Normal_3_4_7_8

description: Sample 950


title: iPSC Patient 5, induction 3

city: London

first: Nuria

last: Seto-Salvia

address: 1 Wakefield St

department: Clinical and Movement Neuroscience

country: United Kingdom

institute: UCL Queen Sq Institute of Neurology

description:
Library name: iPSC32
Column name in_all_samples.txt: iPSC32

data_processing:
Quality control : Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts, and Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. The index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. ClusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways
Assembly: Human (GRCh38/hg38)
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample

growth_protocol: Cells were maintened with Essential 8 media with Essential 8 supplement, without antibiotics in a 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol™ (Life Technologies) according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Original fibroblasts were reprogrammed into iPSCs by episomal plasmids (OCT4/p53, SOX2/KLF4, and L-MYC/LIN28A) as described by Bang et a, 2018. doi: 10.1080/19768354.2018.1451367

value: induced pluripotent stem cell


title: Normal_3_4_7_1

description: Sample 946

value: male


title: iPSC Patient 5, induction 1

description:
Library name: iPSC30
Column name in_all_samples.txt: iPSC30


title: Normal_3_4_7_2

description: Sample 947

value: Normal


title: Normal_3_4_6_7

description: Sample 945

value: testis


title: iPSC Patient 5, induction 2

description:
Library name: iPSC31
Column name in_all_samples.txt: iPSC31


title: Normal_3_4_6_5

description: Sample 944


title: iPSC Patient 4, induction 3

description:
Library name: iPSC29
Column name in_all_samples.txt: iPSC29


title: AH08

description: Library name: Sample 9


title: Normal_3_4_6_4

description: Sample 943


title: iPSC Patient 4, induction 1

description:
Library name: iPSC27
Column name in_all_samples.txt: iPSC27


title: iPSC Patient 4, induction 2

description:
Library name: iPSC28
Column name in_all_samples.txt: iPSC28


title: iPSC Patient 3, induction 2

description:
Library name: iPSC25
Column name in_all_samples.txt: iPSC25


title: AH05

description: Library name: Sample 6


title: Normal_3_4_8_3

description: Sample 953


title: AH03

description: Library name: Sample 4


title: iPSC Patient 3, induction 1

description:
Library name: iPSC24
Column name in_all_samples.txt: iPSC24


title: Normal_3_4_8_1

description: Sample 951


title: Normal_3_4_5_2

description: Sample 939


title: AH02R

description:
Library name: Sample 2
AH02_S1 is replicate of sample J03 i.e. AH02_S2 replicate


title: Normal_3_4_5_6

description: Sample 940


title: Normal_3_4_5_8

description: Sample 941


title: Normal_3_4_6_2

description: Sample 942


title: iPSC Patient 2, induction 3

description:
Library name: iPSC23
Column name in_all_samples.txt: iPSC23


title: Normal_3_4_5_1

description: Sample 938


title: iPSC Patient 2, induction 2

description:
Library name: iPSC22
Column name in_all_samples.txt: iPSC22


title: Normal_3_4_4_3

description: Sample 935


title: Normal_3_4_4_4

description: Sample 936


title: iPSC Patient 1, induction 2

description:
Library name: iPSC18
Column name in_all_samples.txt: iPSC18


title: Normal_3_4_4_1

description: Sample 934


title: Normal_3_4_4_6

description: Sample 937


title: Normal_3_4_3_8

description: Sample 933


title: iPSC Control 5, induction 3

description:
Library name: iPSC16
Column name in_all_samples.txt: iPSC16

value: WT


title: iPSC Patient 3, induction 3

description:
Library name: iPSC26
Column name in_all_samples.txt: iPSC26


title: iPSC Control 5, induction 2

description:
Library name: iPSC14
Column name in_all_samples.txt: iPSC14


title: iPSC Patient 1, induction 1

description:
Library name: iPSC17
Column name in_all_samples.txt: iPSC17


title: Normal_3_4_3_5

description: Sample 932


title: Normal_3_4_3_1

description: Sample 931


title: iPSC Control 4, induction 3

description:
Library name: iPSC12
Column name in_all_samples.txt: iPSC12


title: iPSC Control 4, induction 2

description:
Library name: iPSC11
Column name in_all_samples.txt: iPSC11


title: Normal_3_4_7_3

description: Sample 948


title: Normal_3_4_2_5

description: Sample 928


title: iPSC Control 3, induction 3

description:
Library name: iPSC9
Column name in_all_samples.txt: iPSC9

source_name: C3 - UKK

value: C3 - UKK


title: iPSC Control 3, induction 2

description:
Library name: iPSC8
Column name in_all_samples.txt: iPSC8


title: Normal_3_4_11_5

description: Sample 925


title: Normal_3_4_2_8

description: Sample 930


title: iPSC Control 3, induction 1

description:
Library name: iPSC7
Column name in_all_samples.txt: iPSC7


title: Normal_3_4_2_7

description: Sample 929


title: iPSC Control 4, induction 1

description:
Library name: iPSC10
Column name in_all_samples.txt: iPSC10


title: iPSC Control 2, induction 3

description:
Library name: iPSC6
Column name in_all_samples.txt: iPSC6

source_name: C2 - Bio0N

value: C2 - Bio0N


title: iPSC Patient 1, induction 3

description:
Library name: iPSC19
Column name in_all_samples.txt: iPSC19


title: iPSC Control 2, induction 2

description:
Library name: iPSC5
Column name in_all_samples.txt: iPSC5


title: Normal_3_4_11_2

description: Sample 923


title: Normal_3_4_10_7

description: Sample 922


title: Normal_3_4_11_8

description: Sample 926


title: Normal_3_3_9_8

description: Sample 920


title: Normal_3_4_2_4

description: Sample 927


title: iPSC Control 2, induction 1

description:
Library name: iPSC4
Column name in_all_samples.txt: iPSC4


title: iPSC Control 1, induction 2

description:
Library name: iPSC2
Column name in_all_samples.txt: iPSC2


title: iPSC Control 5, induction 1

description:
Library name: iPSC13
Column name in_all_samples.txt: iPSC13


title: iPSC Control 1, induction 3

description:
Library name: iPSC3
Column name in_all_samples.txt: iPSC3


title: iPSC Control 1, induction 1

description:
Library name: iPSC1
Column name in_all_samples.txt: iPSC1


title: Normal_3_3_9_4

description: Sample 919


title: Normal_3_3_8_5

description: Sample 917


title: Patient2, normal tissue

description:
Library name: Sample RC006
10×Genomics

data_processing:
To assess metabolic activity across the samples, we employed the scMetabolism package with the “VISION” method, We analyzed the scRNA-seq data with the Seurat”  package. we generated Seurat objects using “CreateSeuratObject” package, filtering cells based on criteria (nFeature_RNA < 10,000, nCount_RNA < 50,000, percent.mt < 50). We then normalized the data using “NormalizeData” package and identified highly variable genes using “FindVariableFeatures” package. Employing default parameters, we clustered cells into 16 groups with “FindClusters” package and visualized these clusters using UMAP. We identified differentially expressed genes (DEGs) per cluster using “FindAllMarkers” package. Finally, we manually annotated cell subsets based on the expression of classical marker genes curated from prior studies and analyzing the data against the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic gene sets.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
To prepare the clinical samples, we initially washed them in PBS. Unwanted tissues were trimmed away with scissors. The remaining tissue was cut into small fragments of 1-2 mm and incubated in a tissue digestion solution for 45 min. The resulting cell suspension was filtered through 70 μm and 40 μm strainers. After centrifugation at a low speed to pellet the cells, a red blood cell lysis buffer was applied to eliminate red blood cells. The cell concentration was subsequently adjusted to an optimal level for the subsequent steps of scRNA-seq and library construction.
Guided by the manufacturer’s directions for the 10×Genomics Chromium Single Cell 30 Reagent Kit (V3 chemistry), our scRNA-seq approach was designed to isolate 10,000 single cells per sample. The cDNA libraries were amplified through 12 cycles of PCR and then subjected to 150 bp paired-end sequencing on the Illumina NovaSeq 6000 platform, yielding around 100G of raw reads per sample.

value: kidney


title: Normal_3_3_8_8

description: Sample 918


title: Normal_3_4_1_3

description: Sample 921


title: Normal_3_3_7_2

description: Sample 913


title: Normal_3_3_8_4

description: Sample 916


title: Normal_3_3_7_5

description: Sample 914


title: Patient1, normal tissue

description:
Library name: Sample RC004
10×Genomics


title: Patient2, tumor tissue

description:
Library name: Sample RC005
10×Genomics


title: Normal_3_3_6_6

description: Sample 912


title: Normal_3_3_6_2

description: Sample 911


title: Patient1, tumor tissue

description:
Library name: Sample RC003
10×Genomics


title: Normal_3_3_8_1

description: Sample 915


title: hRMEC, PGE2, sample 3

first: Amy

middle: Kathryn

last: Stark

description: Library name: 13228-GM-0012

data_processing:
Illumina Real Time Analysis NovaSeq Control Software (1.8.0) was used for base calling. Data were filtered and analyzed using Microsoft Excel.
Assembly: hg38
Supplementary files format and content: .csv files for each cell type including gene names matched to Ensembl transcript IDs, computed differential expression, and statistics

source_name: retina

growth_protocol: hRMEC were grown on culture dishes coated with Attachment Factor (Cell Systems, #4Z0-201) in Endothelial Basal Media (EBM; Cell Systems, #4Z3-500-R) supplemented with 10% fetal bovine serum (FBS; R&D Systems; Minneapolis, MN; Catalog #S11550; Lot #M22319) and EGM SingleQuots (Lonza; Basel, Switzerland; #CC-4133). Passage 8 cells were used for experiments. ARPE-19 were grown in DMEM/F-12 supplemented with 10% FBS and 1% penicillin/streptomycin on uncoated culture dishes. Passage 24 cells were used for experiments. Cells were maintained in incubators held at 37C, 5% CO2, and 95% humidity.

extract_protocol:
Cells were washed with cold PBS, lysed, and total RNA was extracted using the RNeasy Mini Kit (Qiagen; Germantown, MD; #74106) according to the manufacturer's protocol. RNA samples were submitted to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core laboratory (Nashville, TN) for RNA sequencing (RNA-Seq). Total RNA was quantified using a BioTek Synergy Multimode Plate reader and BioTek Gen5 2.09 software before being processed for RNA sequencing. RNA quality was determined using the Agilent Bioanalyzer 2100 Instrument (Agilent; Santa Clara, CA).
RNA-Seq libraries were prepared using 200 ng of total RNA and the NEBNext rRNA Depletion Kit (New England Biolabs; Ipswich, MA; #E6310X) according to manufacturer's instructions. This kit employs an RNaseH-based method to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA, and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. The mRNA was enriched via poly-A-selection using oligoDT beads (New England Biolabs) and then the RNA was thermally fragmented and converted to cDNA. The cDNA was adenylated for adaptor ligation and PCR amplified. The libraries were sequenced using the NovaSeq 6000 (Illumina; San Diego, CA) with 150 bp paired end reads targeting 50 M reads per sample.

treatment_protocol: hRMEC or ARPE-19 were stimulated for 6 hours with 100 nM PGE2 or DMSO vehicle

value: retina

value: retinal microvascular endothelial

value: 100 nM PGE2


title: hRMEC, PGE2, sample 2

description: Library name: 13228-GM-0011


title: hRMEC, vehicle, sample 2

description: Library name: 13228-GM-0008

value: DMSO


title: Normal_3_3_5_7

description: Sample 910


title: hRMEC, vehicle, sample 1

description: Library name: 13228-GM-0007


title: hRMEC, vehicle, sample 3

description: Library name: 13228-GM-0009


title: Normal_3_3_4_8

description: Sample 908


title: Normal_3_3_4_6

description: Sample 906


title: ARPE-19, PGE2, sample 1

description: Library name: 13228-GM-0004

value: retinal pigment epithelial


title: Normal_3_3_4_3

description: Sample 905


title: Normal_3_3_4_7

description: Sample 907


title: iPSC Patient 2, induction 1

description:
Library name: iPSC21
Column name in_all_samples.txt: iPSC21


title: Normal_3_3_3_3

description: Sample 903


title: hRMEC, PGE2, sample 1

description: Library name: 13228-GM-0010


title: ARPE-19, vehicle, sample 3

description: Library name: 13228-GM-0003


title: ARPE-19, vehicle, sample 2

description: Library name: 13228-GM-0002


title: Normal_3_4_11_4

description: Sample 924


title: Normal_3_3_4_2

description: Sample 904


title: hct116_wt_chip_input_rep3

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description: Library name: hct116_wt_chip_input_rep3

data_processing:
ChIP-seq datasets were processed to remove the Illumina adapters using Cutadapt (v4.4) with the parameters “--poly-a -q 25 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”121. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1).
For visualization, filtered BAM files from above were converted into normalized bigWig signal tracks using bamCoverage module of the deepTools package (v3.5.5). Parameters used were “--effectiveGenomeSize 2913022398 --binSize 1 --normalizeUsing RPGC --extendReads 150 --outFileFormat bigwig”. For each condition, signal mean was calculated using bigwigAverage module.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: bigWig
Supplementary files format and content: hct116_exon_counts_si11_vs_ctrl_144h.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
1% formaldehyde in DMEM was added to HCCT116 WT, DKO or TKO cells for 10 min, and quenched with 0.1 M glycine. Isolated nuclei were lysed and sonicated using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed sepharose beads for 2 h at 4°C. Pre-cleared chromatin was incubated with ChIP-grade antibodies against H3K9me3 or H3K27me3 overnight. 20 ng of D. melanogaster S2 chromatin and 0.5 μg of H2Av antibody were added as spike-in to each sample. Dynabeads™ Protein A (Invitrogen, 10002D) or G (Invitrogen, 10004D) were added. After 4 h at 4°C, beads were pelleted, washed, and bound chromatin eluted with 1% SDS, 100 mM NaHCO3. After digestion with Proteinase K (Thermo Scientific) at 50°C for 3 h and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified by qPCR. To prepare samples for RNA-seq, 2 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
For ChIP-seq analyses, the quantity of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L), following the manufacturer’s protocol. Briefly, ChIP and input samples (15 ng) were end-repaired and polyadenylated. The adapters containing the index for multiplexing were then ligated. The quality and quantity of the enriched libraries were validated using 4200 TapeStation System (Agilent).

value: Human colon cancer cell line


title: Normal_3_3_2_8

description: Sample 901


title: Normal_3_3_3_1

description: Sample 902


title: ARPE-19, vehicle, sample 1

description: Library name: 13228-GM-0001


title: hct116_wt_chip_input_rep1

description: Library name: hct116_wt_chip_input_rep1


title: Normal_3_3_12_8

description: Sample 900


title: hct116_wt_chip_h3k9me3_rep2

description: Library name: hct116_wt_chip_h3k9me3_rep2


title: Normal_3_3_12_4

description: Sample 899


title: Normal_3_3_12_3

description: Sample 898


title: hct116_wt_chip_h3k9me3_rep1

description: Library name: hct116_wt_chip_h3k9me3_rep1


title: hct116_wt_chip_h3k9me3_rep3

description: Library name: hct116_wt_chip_h3k9me3_rep3


title: Normal_3_3_12_2

description: Sample 897


title: ARPE-19, PGE2, sample 3

description: Library name: 13228-GM-0006


title: hct116_wt_chip_input_rep2

description: Library name: hct116_wt_chip_input_rep2


title: Normal_3_3_5_4

description: Sample 909


title: hct116_wt_chip_h3k27me3_rep3

description: Library name: hct116_wt_chip_h3k27me3_rep3


title: hct116_wt_chip_h3k27me3_rep1

description: Library name: hct116_wt_chip_h3k27me3_rep1


title: Normal_3_3_11_1

description: Sample 893


title: hct116_wt_chip_h3k27me3_rep2

description: Library name: hct116_wt_chip_h3k27me3_rep2


title: hct116_lbr_tmpo_lmna_ko_chip_input_rep3

description: Library name: hct116_lbr_tmpo_lmna_ko_chip_input_rep3


title: Normal_3_3_11_4

description: Sample 894


title: hct116_lbr_tmpo_lmna_ko_chip_input_rep1

description: Library name: hct116_lbr_tmpo_lmna_ko_chip_input_rep1


title: Normal_3_3_1_7

description: Sample 890


title: Normal_3_3_10_5

description: Sample 891


title: Normal_3_3_1_4

description: Sample 889


title: hct116_lbr_tmpo_lmna_ko_chip_input_rep2

description: Library name: hct116_lbr_tmpo_lmna_ko_chip_input_rep2


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k9me3_rep2


title: ARPE-19, PGE2, sample 2

description: Library name: 13228-GM-0005


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k9me3_rep1


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k27me3_rep3


title: Normal_3_3_1_1

description: Sample 888


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k9me3_rep3


title: Normal_3_2_9_6

description: Sample 886


title: Normal_3_2_9_7

description: Sample 887


title: Normal_3_3_12_1

description: Sample 896


title: Normal_3_2_8_7

description: Sample 884


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k27me3_rep2


title: hct116_lbr_tmpo_ko_chip_input_rep3

description: Library name: hct116_lbr_tmpo_ko_chip_input_rep3


title: Normal_3_2_8_6

description: Sample 883


title: Normal_3_3_11_6

description: Sample 895


title: hct116_lbr_tmpo_ko_chip_input_rep2

description: Library name: hct116_lbr_tmpo_ko_chip_input_rep2


title: Normal_3_2_8_4

description: Sample 882


title: Normal_3_2_9_3

description: Sample 885


title: Normal_3_2_7_7

description: Sample 881


title: Normal_3_2_7_5

description: Sample 880


title: hct116_lbr_tmpo_ko_chip_h3k9me3_rep2

description: Library name: hct116_lbr_tmpo_ko_chip_h3k9me3_rep2


title: Normal_3_2_7_4

description: Sample 879


title: Normal_3_3_10_7

description: Sample 892


title: hct116_lbr_tmpo_ko_chip_h3k9me3_rep3

description: Library name: hct116_lbr_tmpo_ko_chip_h3k9me3_rep3


title: Normal_3_2_6_6

description: Sample 878


title: hct116_lbr_tmpo_ko_chip_h3k9me3_rep1

description: Library name: hct116_lbr_tmpo_ko_chip_h3k9me3_rep1


title: hct116_lbr_tmpo_ko_chip_h3k27me3_rep3

description: Library name: hct116_lbr_tmpo_ko_chip_h3k27me3_rep3


title: hct116_lbr_tmpo_ko_chip_h3k27me3_rep1

description: Library name: hct116_lbr_tmpo_ko_chip_h3k27me3_rep1


title: Normal_3_2_6_2

description: Sample 876


title: hct116_lbr_tmpo_ko_chip_h3k27me3_rep2

description: Library name: hct116_lbr_tmpo_ko_chip_h3k27me3_rep2


description: Library name: hct116_lbr_tmpo_lmna_ko_chip_h3k27me3_rep1


title: Normal_3_2_5_4

description: Sample 874


title: Normal_3_2_6_4

description: Sample 877


title: scATAC_GATA2SETBP1ASXL1_repetition_3

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

description: Library name: GSArep3_ATAC

library_source: genomic single cell

data_processing:
After demultiplexing, raw sequencing reads were trimmed using Cutadapt (DOI: https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences and low-quality bases. Trimmed reads were then aligned to the reference genome (GRCh38) using Bowtie2 (PMC332238) with parameters -X 2000 --no-discordant --no-mixed --very-sensitive. Following alignment, BAM files were sorted and indexed using SAMtools (https://doi.org/10.1093/gigascience/giab008). Alignments in the mitochondrial chromosome, with quality lower than 30 or overlapping blacklisted regions were removed. Filtered BAM files were turned to BED files using BEDTools (https://doi.org/10.1093/bioinformatics/btq033 ) and PCR duplicates were removed for those reads sharing the same cell barcode, chromosome and start and end position of the alignment. Fragment files were generated from the deduplicated BED file, including Tn5 shifting. Deeptools (doi:10.1093/nar/gkw257.) was used to generate Bigwig files and to check for Transcription Start Site (TSS) enrichment. R (v 4.4.2) was used to plot the fragment size distribution, count and plot the number of fragments per barcode and perform an initial filtering of barcodes with less than 100 fragments.
Fragment files were processed with Signac (v. 1.14.0) and Seurat (v. 5.2.1) packages. Fragment objects were created, and peak calling was performed separately for each condition using MACS2 (https://doi.org/10.1186/gb-2008-9-9-r137). Peaks were filtered based on empirical thresholds to retain high-confidence regions. A consensus peak list was generated by merging peaks across all conditions and fragment counts were quantified within these regions to build a chromatin accessibility assay and create a Seurat object.
Quality control (QC) metrics were computed for each cell, including TSS enrichment, nucleosome signal scores, and fraction of reads in peaks (FRiP). Cells were filtered based on these metrics, as well as thresholds for minimum and maximum numbers of accessible peaks, determined through iterative QC visualization and empirical adjustment.
Normalization of the accessibility matrix was performed using term-frequency inverse document frequency (TF-IDF) transformation, followed by linear dimensionality reduction via singular value decomposition (SVD). Low-dimensional embedding was achieved using Uniform Manifold Approximation and Projection (UMAP), and cell clustering was performed using a shared nearest neighbor (SNN) graph-based method.
Assembly: GRCh38
Supplementary files format and content: merged_metadata_all_samples.tsv is a tab-separated file containing per-cell metadata for all samples.
Supplementary files format and content: peak_count_matrix.mtx is a sparse matrix in Matrix Market format representing fragment counts per peak per cell. Each row corresponds to a genomic peak, and each column corresponds to a cell barcode.

source_name: HSPC-derived iPSCs

extract_protocol:
The single cell ATAC-sequencing extraction protocol were produced using the  SHARE-seq protocol (Ma et al., 2020),
The single cell ATAC-sequencing libraries were produced using the  SHARE-seq protocol (Ma et al., 2020),

value: HSPC-derived iPSCs

tag: sample group


title: Normal_3_2_5_1

description: Sample 872


title: Normal_3_2_5_3

description: Sample 873


title: scATAC_GATA2ASXL1_repetition_3

description: Library name: GArep3_ATAC


title: Normal_3_2_4_8

description: Sample 871


title: hct116_lbr_tmpo_ko_chip_input_rep1

description: Library name: hct116_lbr_tmpo_ko_chip_input_rep1


title: scATAC_GATA2ASXL1_repetition_2

description: Library name: GArep2_ATAC


title: Normal_3_2_4_1

description: Sample 869


title: scATAC_GATA2ASXL1_repetition_1

description: Library name: GArep1_ATAC


title: Normal_3_2_4_6

description: Sample 870


title: scATAC_GATA2SETBP1ASXL1_repetition_2

description: Library name: GSArep2_ATAC


title: scATAC_GATA2SETBP1_repetition_3

description: Library name: GSrep3_ATAC


title: scATAC_GATA2SETBP1_repetition_2

description: Library name: GSrep2_ATAC


title: Normal_3_2_3_4

description: Sample 868


title: scATAC_GATA2SETBP1ASXL1_repetition_1

description: Library name: GSArep1_ATAC


title: scATAC_GATA2SETBP1_repetition_1

description: Library name: GSrep1_ATAC


title: Normal_3_2_2_8

description: Sample 866


title: Normal_3_2_2_5

description: Sample 865


title: scATAC_GATA2_repetition_2

description: Library name: Grep2_ATAC


title: Normal_3_2_2_4

description: Sample 864


title: scATAC_GATA2_repetition_1

description: Library name: Grep1_ATAC


title: Normal_3_2_3_2

description: Sample 867


title: Normal_3_2_5_5

description: Sample 875


title: scATAC_Parental_repetition_3

description: Library name: Prep3_ATAC

value: Parental


title: Normal_3_2_2_3

description: Sample 863


title: scATAC_Parental_repetition_2

description: Library name: Prep2_ATAC


title: scATAC_Parental_repetition_1

description: Library name: Prep1_ATAC


title: Normal_3_2_2_2

description: Sample 862


title: Normal_3_2_12_8

description: Sample 860


title: Normal_3_2_12_3

description: Sample 858


title: RNA-seq K562 TPL Rep2

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Instituto de Biotecnología - UNAM

description: Library name: Sample 5

data_processing:
Alignment: STAR, using default parameters
Raw counts: htseq-count
Differential expression analysis: DESeq2
Assembly: hg19
Supplementary files format and content: bigwig file corresponding to each RNA-seq sample

growth_protocol: K562 cells were maintained at 37°C in a humidified 5% CO2 and cultured with RPMI medium supplemented with 10% FBS

extract_protocol:
RNA was harvested using the reagent TRIzol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.

treatment_protocol: K562 cells were counted and seeded at a confluency of 500,000 cells per ml. DMSO or 250 nM of triptolide (TPL) were added to the media and incubated for 4 hours

value: 4h 250 nM Triptolide


title: Normal_3_2_12_4

description: Sample 859


title: Normal_3_2_11_1

description: Sample 857


title: Normal_3_2_10_8

description: Sample 856


title: RNA-seq K562 DMSO Rep3

description: Library name: Sample 3


title: RNA-seq K562 DMSO Rep1

description: Library name: Sample 1


title: RNA-seq K562 TPL Rep3

description: Library name: Sample 6


title: Normal_3_2_10_2

description: Sample 854


title: RNA-seq K562 TPL Rep1

description: Library name: Sample 4


title: CUT&Tag H3K27ac K562 TPL Rep3

description: Library name: Sample 5

data_processing:
Alignment: Bowtie2, using default parameters
Peak calling: SEACR
Differential enrichment analysis: DESeq2
Assembly: hg19
Supplementary files format and content: bigwig file corresponding to each CUT&Tag H3K27ac sample
Library strategy: CUT&Tag

extract_protocol:
Cells were processed following the instructions on the CUTANA EpiCypher CUT&Tag Kit
Libraries were prepared using the EpiCypher CUT&Tag Kit instructions


title: RNA-seq K562 DMSO Rep2

description: Library name: Sample 2


title: CUT&Tag H3K27ac K562 TPL Rep2

description: Library name: Sample 4


title: Normal_3_2_1_5

description: Sample 852


title: scATAC_GATA2_repetition_3

description: Library name: Grep3_ATAC


title: Normal_3_2_1_7

description: Sample 853


title: Normal_3_2_10_6

description: Sample 855


title: Normal_3_2_1_4

description: Sample 851


title: CUT&Tag H3K27ac K562 DMSO Rep2

description: Library name: Sample 2


title: Normal_3_1_9_4

description: Sample 849


title: Normal_3_2_2_1

description: Sample 861


title: CUT&Tag H3K27ac K562 TPL Rep1

description: Library name: Sample 3


title: CUT&Tag H3K27ac K562 DMSO Rep1

description: Library name: Sample 1


title: Normal_3_1_9_2

description: Sample 848


title: Normal_3_2_1_3

description: Sample 850


title: ERCC3 ChIP-exo K562 TPL

description: Library name: Sample 3

data_processing:
Alignment: Bowtie2, using default parameters
Bigwig files: generated with bamcompare
Assembly: hg19
Supplementary files format and content: bigwig file corresponding to each ChIP-exo sample

extract_protocol:
Cells were processed at the Epigenomics Facility at the Cornell Institute of Biotechnology
Libraries were prepared at the Epigenomics Facility at the Cornell Institute of Biotechnology

treatment_protocol: K562 cells were counted and seeded at a confluency of 500,000 cells per ml. DMSO or 1 micromolar of triptolide (TPL) were added to the media and incubated for 1 hour

value: 1h 1 micromolar Triptolide


title: IgG ChIP-exo K562 TPL

description: Library name: Sample 4


title: IgG ChIP-exo K562 DMSO

description: Library name: Sample 2


title: ERCC3 ChIP-exo K562 DMSO

description: Library name: Sample 1


title: Normal_3_1_7_8

description: Sample 846

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.

value: male


title: Normal_3_1_8_2

description: Sample 847

value: Normal


title: Normal_3_1_7_6

description: Sample 844

value: testis


title: PRO-seq K562 1h 1 uM  Rep2

description:
Library name: Sample 8
PROseq_1h1uM_TPL_fwd.bw
PROseq_1h1uM_TPL_rv.bw

data_processing:
Alignment: bowtie2, using default parameters
Differential expression analysis: DESeq2
Assembly: hg19
Supplementary files format and content: bigwig file corresponding to each PRO-Seq sample
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
PRO-seq was performed following the protocol published in Mahat, DB., et al., 2016, Nature Protocols
Libraries were prepared using the TruSeq Small RNA kit

treatment_protocol: K562 cells were counted and seeded at a confluency of 500,000 cells per ml. DMSO or Triptolide were added to the media according to the concentration indicated in the sample name

value: WT


title: PRO-seq K562 4h 250 nM  Rep2

description:
Library name: Sample 6
PROseq_4h250nM_TPL_fwd.bw
PROseq_4h250nM_TPL_rv.bw


title: PRO-seq K562 4h 250 nM  Rep1

description:
Library name: Sample 5
PROseq_4h250nM_TPL_fwd.bw
PROseq_4h250nM_TPL_rv.bw


title: Normal_3_1_6_4

description: Sample 843


title: Normal_3_1_5_6

description: Sample 841


title: Normal_3_1_7_7

description: Sample 845


title: PRO-seq K562 1h 250 nM  Rep1

description:
Library name: Sample 3
PROseq_1h250nM_TPL_fwd.bw
PROseq_1h250nM_TPL_rv.bw

value: 1h 250 nM Triptolide


title: PRO-seq K562 DMSO Rep2

description:
Library name: Sample 2
PROseq_DMSO_fwd.bw
PROseq_DMSO_rv.bw


title: Normal_3_1_6_2

description: Sample 842


title: PRO-seq K562 DMSO Rep1

description:
Library name: Sample 1
PROseq_DMSO_fwd.bw
PROseq_DMSO_rv.bw


title: Normal_3_1_3_3

description: Sample 838


title: Normal_3_1_4_6

description: Sample 839


title: HCT116_RAD21_AID_auxins (Input)

city: Moscow

first: Vladimir

middle: S

last: Viushkov

address: 1-12 Leninskie Gory

department: Faculty of Biology, Department of Molecular Biology

country: Russia

institute: Lomonosov Moscow State University

description: Library name: HCT116_RAD21_AID_auxins, Input

data_processing:
Sequencing data were processed on the Galaxy portal (https://usegalaxy.eu/). During processing, reads were first trimmed using Trimmomatic (version 0.39). Illumina adapters clipping was performed using build-in TrueSeq3-PE adapter sequences with the following parameters: seed mismatches = 2, palindrome clip threshold = 30, simple clip threshold = 10, minAdapterLength = 4, keepBothReads = True. Leading low quality or N bases were removed (below quality 3). Sliding window quality trimming was performed with averaging acros 4 bases and average required quality of 15. Finally, only reads with a minimum length of 20 bases were preserved.
The reads remaining paired after trimming were aligned to the human reference genome, assembly GCA_000001405.15_GRCh38_no_alt_analysis_set, downloaded from NCBI ftp server (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/). Bowtie2 (version 2.5.3) was used for alignment. The alignment was performed with the --maxins=1000 parameter, as well as with the --no-mixed, --no-discordant and --very-sensitive (end-to-end) parameters active. The other parameters had their default values.
Duplicate reads were removed with MarkDuplicates tool (version 3.1.1.0) from Picard toolset with default parameters.
To construct coverage profiles normalized to Input, the bamCompare tool from deepTools (version 3.5.4) was used. Profiles were built with bin size = 10 bp. Minimum mapping quality for reads was set to 5. Only the first read in each read pair was used to plot profiles (SAM flag of 64). Paired reads were extended to the corresponding fragment lengths with a paired-end extension option (--extendReads). SkipNAs option was used to skip non-covered regions. Each sample was normalized to fragments per kilobase per million mapped reads (RPKM). Normalization on Input control was carried out by calculating the ratio of the number of reads.
MACS2 (version 2.2.9.1) with Input control was used to search for RAD21 binding peaks in HCT116 cells. The value of effective genome size was 2805636231. Peak definition was based on q-value with a minimum of 0.05.
Assembly: GRCh38
Supplementary files format and content: Input normalized RAD21 binding profiles are in bigWig format
Supplementary files format and content: RAD21 binding peaks in HCT116 WT cells are in narrowPeak file format

growth_protocol: DMEM with 10% FBS and antibiotic-antimycotic, 5% CO2 atmosphere, at 37C

extract_protocol:
Cells (2 million) were seeded in 2 ml of DMEM medium into the wells of a six-well plate one day before the experiment. The next day, IAA and alpha-NAA (500 μM each) were added to indicated cells for 6 hours, after which the medium was removed and the cells were fixed in 1 ml of 1% formaldehyde solution in serum-free DMEM for 10 minutes. To neutralize formaldehyde, glycine was added to a concentration of 125 mM for 2 minutes. Then the cells were detached with a cell scraper. The cells were washed with DPBS and then lysed in 500 μl of cold RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.5% SDC (sodium deoxycholate), 0.1% SDS, 1% NP-40) with the addition of PMSF to 1 mM and 5 μl of Protease Inhibitor Cocktail (P8340, Sigma-Aldrich). Lysates were sonicated on a Branson Digital Sonifier 450 in four series of 10 pulses in the mode of 7 sec ON / 30 sec OFF at a power of 10%. Breaks between series were 4 minutes. The cells were kept on ice, pre-cooled to -20C, during the entire sonication period. Then the cell debris was sedimented by centrifugation for 5 min at 20,000 g at 4C. Supernatants (chromatin fraction) were transferred to Amicon Ultra 0.5 ml 30K filter units (Merck Millipore) and centrifuged for 5 min at 14,000 g at 4C. The solution remaining in the filter was transferred to a new tube and its volume was brought to 1 ml with IP buffer (15 mM Tris-HCl 8.0, 0.01% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM PMSF, Protease Inhibitor Cocktail (P8340, Sigma-Aldrich) 10 μl per 1 ml buffer volume). 100 μl were taken as Input and frozen at -20. The volume of samples was adjusted to 1 ml with IP buffer, and 2 μl of anti-RAD21 antibodies (ab992, Abcam) were added to the samples for overnight incubation under constant rotation at +4C. The next day, 25 μl of Protein A/G ChIP grade magnetic beads (Thermo Fisher Scientific) were added to the samples, after being pre-washed in 1 ml of RIPA buffer with 0.5% BSA overnight under constant rotation at +4C. The samples were bound to the beads for 6 hours under constant rotation at +4C. The beads were then washed sequentially in WBA (20 mM Tris-HCl 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), WBB (same as WBA, except 500 mM NaCl was used), and WBC (10 mM Tris-HCl 8.0, 1% SDC, 1% NP-40, 1 mM EDTA, 250 mM LiCl) buffers for 10 min under constant rotation at +4C. Formaldehyde cross-links and proteins were then destroyed by incubating the beads in TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) supplemented with proteinase K to 0.5 μg/μl and SDS to 0.5% overnight at 65C on a shaker at 1400 rpm. Input was de-crosslinked in the same way. DNA was further purified from samples by phenol-chloroform extraction, precipitated with ethanol and sodium acetate with the addition of yeast tRNA and glycogen as co-precipitants. The DNA pellets were dissolved in 50 μl of 10 mM Tris-HCl buffer pH 8.0. RNase A (R1253, Thermo Fisher Scientific) was added to the samples to a concentration of 0.2 mg/ml for 30 min at 37C. DNA was then further purified using MagPure A4 XP Beads (Magen) and eluted in 50 μl of 10 mM Tris-HCl buffer pH 8.0.
DNA ends were then repaired in a 100 μl reactions containing 50 μl sample, 0.5 mM each dNTP, 5 μl T4 polynucleotide kinase (M0201L, NEB), 4 μl T4 DNA polymerase (M0203L, NEB), 1 μl Klenow fragment (M0210L, NEB), in 1x T4 DNA ligase buffer (Thermo Fisher Scientific). Reactions were incubated for 30 min at RT, after which DNA was purified from the reactions using MagPure A4 XP Beads (Magen) and eluted in 50 μl 10 mM Tris-HCl pH 8.0. 100 ng of Input DNA was treated similarly. Samples were then A-tailed. For this, 100 μl reactions containing 50 μl of sample, 0.5 mM dATP, and 5 μl of exo(-) Klenow fragment (M0212S, NEB) in 1x NEBuffer 2 (NEB) were mixed. The reactions were incubated for 30 min at 37C, after which DNA was purified from the reactions using MagPure A4 XP Beads and eluted in 30 μl of 10 mM Tris-HCl pH 8.0. Adapters were then ligated to the samples in 50 μl reactions containing 30 μl of sample, 0.5 μl of Illumina TrueSeq adapters, and 10U of T4 DNA ligase (EL0011, Thermo Fisher Scientific) in 1x buffer supplied with T4 DNA ligase. Reactions were incubated overnight at room temperature, after which DNA was purified from the reactions using MagPure A4 XP Beads and eluted in 30 µl of 10 mM Tris-HCl pH 8.0. Libraries were then amplified to achieve sufficient DNA for sequencing. Six 25 µl reactions were performed with each sample. Each reaction contained 4 µl of the appropriate sample DNA, 0.2 mM of each dNTP, Illumina PE1.0 and PE2.0 primers to 0.5 µM, and 0.5 U Q5 HotStart High-Fidelity DNA Polymerase (NEB) in the enzyme buffer supplied. Amplification was performed using the following program: 98C for 30 s, then the required number of cycles (98C 10 s - 67C 15 s - 72C 30 s), and then a final extension by 1 min at 72C. The number of PCR cycles was 9 for Input and 14 cycles for samples after immunoprecipitation. The required number of cycles was determined in a preliminary PCR carried out under the same conditions, but with sampling after certain cycles and monitoring the degree of DNA amplification by electrophoresis in agarose gel. After preparative amplification, reactions with one type of template were combined, and DNA from the reactions was purified using MagPure A4 XP Beads and eluted in 40 μl of 10 mM Tris-HCl pH 8.0. Quality control of the samples was performed by electrophoresis in agarose gel. In case of detection of adapter dimer bands, the DNA libraries were additionally purified from the gel (the smear region between the 200-1000 bp markers) using the Cleanup Mini kit (Evrogen). DNA was then further purified using MagPure A4 XP Beads and eluted in 30 µl 10 mM Tris-HCl pH 8.0. The resulting libraries were sequenced on an Illumina Novaseq 6000 instrument to generate 100-bp paired-end reads.

treatment_protocol: If indicated, cells wre treated with a combination of indole-3-acetic acid and alpha-naphthaleneacetic acid (500 uM each) for 6 hours

value: mAID degron integration into RAD21 gene, OsTIR1 ubiqutin ligase expression

value: 6 hours with a combination of indole-3-acetic acid and alpha-naphthaleneacetic acid (500 uM each)

value: RAD21 (ab992, Abcam)


title: Normal_3_1_5_3

description: Sample 840


title: Normal_3_1_12_2

description: Sample 835


title: HCT116_RAD21_AID_auxins (ChIP)

description: Library name: HCT116_RAD21_AID_auxins, ChIP


title: HCT116_RAD21_AID_untreated (ChIP)

description: Library name: HCT116_RAD21_AID_untreated, ChIP

value: untreated


title: Normal_3_1_11_3

description: Sample 834


title: HCT116_WT_untreated (ChIP)

description: Library name: HCT116_WT, ChIP


title: Normal_3_1_12_3

description: Sample 836


title: Normal_3_1_10_1

description: Sample 832


title: Normal_3_1_10_2

description: Sample 833


title: Normal_3_1_1_4

description: Sample 831