title: sham_H3

city: chongqing

first: Fating

last: Zhou

state: chongqing

address: No. 1 Jiankang Road, Yuzhong District

department: Department of Emergency Medicine, Chongqing Emergency Medical Center

institute: Chongqing University Central Hospital

description: Library name: sample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes transcript counts for each sample

source_name: control group, replicate biosample 3

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: heart

tag: Sex

value: male


title: HS_H1

status: Public on Jul 26 2025

type: SRA

country: China

description: Library name: sample 4

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: HS group, replicate biosample 1

tag: tissue

tag: strain


title: HS_H3

description: Library name: sample 6

source_name: HS group, replicate biosample 3


title: sham_H1

description: Library name: sample 1

source_name: control group, replicate biosample 1


title: GPR68-/- right 4

city: New Orleans

first: XIANGMING

last: ZHA

state: LA

address: 1324 Tulane Ave

department: Neurosurgery

country: USA

institute: Tulane University

description:
Library name: F4
F4

data_processing:
Library construction, RNA sequencing (Illumina platforms), and generation of FPKM and initial set of differential genes were performed by Novogene. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome were built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix (MMP), which can generate a precise mapping result for junction reads. Alignments were parsed using TopHat program and differential expressions were determined through DESeq2/edgeR.
Assembly: GRCm39
Supplementary files format and content: .xls format

source_name: brain

extract_protocol:
Trizol
mRNA

value: brain

tag: genotype


title: HS_H2

description: Library name: sample 5

source_name: HS group, replicate biosample 2


title: sham_H2

description: Library name: sample 2

source_name: control group, replicate biosample 2


title: RL95-2 cells, Control Biol. Repl 3

city: Ljubljana

first: Marija

last: Gjorgoska

state: Outside North America

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana

description:
Library name: Sample 12
Column name in FPKM_All_Samples.txt: RL95-2_Control_C

data_processing:
Raw reads were processed with fastp software to remove adapter sequences, poly-N reads, and low-quality reads. Clean reads were aligned to the reference genome (Homo Sapiens [GRCh38/hg38]) using HISAT2 v2.0.5.
Gene-level counts were generated using featureCounts v1.5.0-p3, and gene expression was quantified as FPKM.
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Assembly: GRCh38

organism: Homo sapiens

growth_protocol: Ishikawa cells were maintained in Eagle’s Minimum Essential Medium (#M5650, Gibco) with 5% FBS. RL95-2 cells were maintained in DMEM/F12 (#D6421, Sigma Aldrich GmbH) with 10% FBS, 2.5 mM L-glutamine. Cells were maintained in humidified athmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Macherey Nagel RNA extraction kit ((#740933.5, Macherey-Nagel GmbH&Co, Germany).
mRNA sequencing was performed at Novogene Inc. mRNA was enriched using poly-T oligo-attached magnetic beads and fragmented. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand synthesis using dTTP for non-directional libraries. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library quality was assessed by Qubit, real-time PCR, and Bioanalyzer to determine concentration and fragment size distribution. Libraries were pooled and sequenced on an Illumina platform using paired-end 150 bp (PE150) reads, generating approximately 12 Gb of raw data per sample.

treatment_protocol: Ishikawa cells were seeded at cell density 3.5 x 10^5/well in 6-well plates in complete culture medium. RL95-2 cells were seeded at cell density 3.5 millions/well in 6-well plates in complete culture media. After 24h, the culture media was replaced with phenol-red free, steroid-free culture media with L-glutamine as a supplement. 5 uL of steroid in ethanol/well was added. Cells were incubated for 72h in humidified athmosphere with 5% CO2 at 37C.

tag: cell line

tag: cell type

value: Endometrial cancer cell line

value: Wild type

tag: treatment

value: Control (ethanol)

tag: batch


title: GPR68-/- right 3

description:
Library name: F3
F3


title: RL95-2 cells, Control Biol. Repl 2

description:
Library name: Sample 11
Column name in FPKM_All_Samples.txt: RL95-2_Control_B


title: GPR68-/- right 2

description:
Library name: F2
F2


title: GPR68-/- right 1

description:
Library name: F1
F1


title: RL95-2 cells, Control Biol. Repl 1

description:
Library name: Sample 10
Column name in FPKM_All_Samples.txt: RL95-2_Control_A


title: GPR68-/- left 4

description:
Library name: E4
E4


title: Ishikawa cells, 10 nM 11KDH Biol. Repl. 3

description:
Library name: Sample 9
Column name in FPKM_All_Samples.txt: Ish_11KDHT_10nM_C

source_name: Ishikawa

value: Ishikawa

value: 10 nM 11-keto-dihydrotestosterone (11KDHT)


title: Ishikawa cells, 10 nM 11KDH Biol. Repl. 2

description:
Library name: Sample 8
Column name in FPKM_All_Samples.txt: Ish_11KDHT_10nM_B


title: Ishikawa cells, 10 nM 11KDH Biol. Repl. 1

description:
Library name: Sample 7
Column name in FPKM_All_Samples.txt: Ish_11KDHT_10nM_A


title: GPR68-/- left 2

description:
Library name: E2
E2


title: GPR68-/- sham 3

description:
Library name: D3
D3


title: Ishikawa cells, 10 nM DHT Biol. Repl. 2

description:
Library name: Sample 5
Column name in FPKM_All_Samples.txt: Ish_DHT_10nM_B

value: 10 nM dihydrotestosterone (DHT)


title: Ishikawa cells, 10 nM DHT Biol. Repl. 1

description:
Library name: Sample 4
Column name in FPKM_All_Samples.txt: Ish_DHT_10nM_A


title: GPR68-/- sham 2

description:
Library name: D2
D2


title: Ishikawa cells, Control Biol. Repl 3

description:
Library name: Sample 3
Column name in FPKM_All_Samples.txt: Ish_Control_C


title: WT mcao right 4

description:
Library name: C4
C4

value: wild type


title: WT mcao right 3

description:
Library name: C3
C3


title: Ishikawa cells, Control Biol. Repl 2

description:
Library name: Sample 2
Column name in FPKM_All_Samples.txt: Ish_Control_B


title: Ishikawa cells, Control Biol. Repl 1

description:
Library name: Sample 1
Column name in FPKM_All_Samples.txt: Ish_Control_A


title: GPR68-/- left 3

description:
Library name: E3
E3


title: GPR68-/- sham 1

description:
Library name: D1
D1


title: Patient3, Hemin#3

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

description: Library name: 3H75A_3

data_processing:
For RNA-seq, library was prepared concentration was quantified using a Qubit 2.0 fluorometer, and fragment size distribution was assessed using an Agilent Bioanalyzer.
Sequencing was performed on the Illumina NextSeq 500 platform. FASTQ files were processed using the RNA Express module (Illumina).
Raw reads were aligned to human genome (GRCh38/hg38) using STAR aligner. Downstream analysis, including normalization and differential gene expression, was performed in R (v4.0.3) using the edgeR package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: erythroid progenitors

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Invitrogen). 0.5 µg of total RNA was used for the constrcution of sequencing libraries.
For RNA-seq, libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following the manufacturer’s protocol.

value: Peripheral blood

value: erythroid

value: Hemin


title: Patient3, Hemin#1

description: Library name: 3H75A_1


title: WT mcao left 4

description:
Library name: B4
B4


title: GPR68-/- left 1

description:
Library name: E1
E1


title: WT G2 + rapa HiC

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

country: France

institute: CNRS

description: Library name: LCH2

library_source: genomic

data_processing:
HiCstuff (www.github.com/koszullab/hicstuff) version 3.0.1; Chromosight (www.github.com/koszullab/chromosight) v1.3.1 36; Bowtie2 (version 2.3.4.1 available online at http://bowtie-bio.sourceforge.net/bowtie2/); Samtools (version 1.9 available online at http://www.htslib.org/download/); Bedtools (version 2.29.1 available online at https://bedtools.readthedocs.io/en/latest/content/installation.html); Cooler (version 0.8.7- 0.8.11 available online at https://cooler.readthedocs.io/en/latest/); bamCoverage (version 3.4.1 https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html)
Processing of the reads, computation of contact matrices, and generation of contact maps: Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012). PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
Computation of the contact probability as a function of genomic distance: Computation of the contact probability as a function of genomic distance P(s) and its derivative have been determined using the “distance law” function of Hicstuff with default parameters, averaging the contact data of entire chromosome arms. P(s) from two independent replicates were determined and plotted.
For ChIP-seq analysis: Bowtie2 was used for two rounds of alignments, first on C.glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively mapped on S. cerevisiae (an vice-versa for C.glabrata). The obtained SAM file was converted into a BAM file, sorted and indexed using Samtools. ChIP-seq profiles were then normalised by the number of million sequences and converted into BigWig using bamCoverage. Profiles were multiplied by the ORi factor (WCEglabrataIPcerevisiae / WCEcerevisiaeIPglabrata, in which WCE glabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads) using Integrated Genome Browser
Loop detection and scoring with Chromosight: Chromosight 1.3.1 36 was used to call loops de novo from contact maps binned at 1 kb and balanced with Cooler. Matrices were subsampled to contain the same total number of contacts.  De novo loop calling was computed using the “ detect ”  mode of Chromosight, with minimum loop length set at 2kb, percentage undetected set at 25 and pearson correlation threshold set at 0.315. Loop strength was quantified for each loop using the quantify mode of Chromosight and the mean loop score was calculated for each condition. Loop pile-up of averaged 17kb windows were generated with Chromosight. De novo loop calling and scoring were performed on independent HiC replicates, where indicated, which were subsampled independently for each experiment, using the number of contacts of the least covered map or subsampling to 20M reads. Loop score is shown as mean ± standard deviation.
Assembly: S.  cerevisiae W303: Telomere to telomere assembly, Gift from O’Donnell et al., BioRxiv 2022 ; C. glabrata: http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/current/
Supplementary files format and content: bigWig
Supplementary files format and content: cool

molecule: genomic DNA

organism: Saccharomyces cerevisiae W303

source_name: Unicellular eukaryote

growth_protocol: cells were grown overnight in YPD

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Samples were sonicated using Covaris (DNA 300bp). For ChIP seq data: The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transfer in tubes 2mL containing glass beads before mechanical cells lysis.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

value: Unicellular eukaryote


title: Patient3, PBS#1

description: Library name: 3H0A_1

value: PBS


title: Patient3, PBS#3

description: Library name: 3H0A_3


title: Rpb1/3 AA G2 HiC

description: Library name: LCH4


title: Rpb1/3 AA +45min rapa G2 HiC

description: Library name: LCH5


title: WT mcao left 3

description:
Library name: B3
B3


title: Patient2, Hemin+DMKG#2

description: Library name: 2HDMKG_2

value: Hemin+DMKG


title: Patient2, Hemin+DMKG#3

description: Library name: 2HDMKG_3


title: Patient2, Hemin+DMKG#1

description: Library name: 2HDMKG_1


title: WT mcao right 2

description:
Library name: C2
C2


title: WT mcao left 2

description:
Library name: B2
B2


title: WT mcao right 1

description:
Library name: C1
C1


title: Patient3, Hemin#2

description: Library name: 3H75A_2


title: Patient2, Hemin+DMF#3

description: Library name: 2HDMF_3

value: Hemin+DMF


title: Patient2, Hemin+DMF#2

description: Library name: 2HDMF_2


title: WT mcao left 1

description:
Library name: B1
B1


title: Patient2, Hemin#3

description: Library name: 2H75B_3


title: Patient2, Hemin+DMF#1

description: Library name: 2HDMF_1


title: WT sham 3

description:
Library name: A3
A3


title: Patient3, PBS#2

description: Library name: 3H0A_2


title: Patient2, Hemin#2

description: Library name: 2H75B_2


title: Ishikawa cells, 10 nM DHT Biol. Repl. 3

description:
Library name: Sample 6
Column name in FPKM_All_Samples.txt:Ish_DHT_10nM_C


title: Patient2, PBS#3

description: Library name: 2H0B_3


title: Patient2, PBS#2

description: Library name: 2H0B_2


title: Patient2, DMKG#3

description: Library name: 2DMKG_3

value: DMKG


title: WT sham 1

description:
Library name: A1
A1


title: p52ki/ki5

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description:
Library name: p52ki/ki5
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: p52Ki5

data_processing:
In-house Fastq files were mapped to the mouse reference genome GRCm38 using Hisat2 v2.1.0. Bam files are sorted and indexed using samtools v1.8. The number of reads aligned to each mouse gene was calculated using featureCounts (a subfunction of the software subread-v1.6.2). log2(CPM+1) values are calculated using raw counts.
Assembly: GRCm38
Supplementary files format and content: RNA_Seq_preGCB_counts.tsv includes raw counts for each Sample
Supplementary files format and content: logCPM_withGeneNames.tsv, includes log2(CPM+1) normalized values for each Sample

source_name: spleen Pre-GC B cells

extract_protocol:
The total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA was assessed using either RiboGreen (Thermo Fisher Scientific) or Agilent Bioanalyser.
cDNA libraries were prepared using 0.5 ng of total RNA, or half of the RNA sample where concentration was too low to be accurately quantified. The SMARTSeq v2 protocol was used with 17 PCR cycles and the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina Novaseq 6000 targeting at least 13 million read-pairs/sample.

value: spleen Pre-GC B cells


title: Patient2, DMKG#2

description: Library name: 2DMKG_2


title: Patient2, DMKG#1

description: Library name: 2DMKG_1


title: Patient2, DMF#3

description: Library name: 2DMF_3

value: DMF


title: Patient2, DMF#2

description: Library name: 2DMF_2


title: p52ki/ki4

description:
Library name: p52ki/ki4
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: p52Ki4


title: p52ki/ki3

description:
Library name: p52ki/ki3
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: p52Ki3


title: Patient2, Hemin#1

description: Library name: 2H75B_1


title: Patient1, Hemin#3

description: Library name: 1H75_3


title: Patient2, PBS#1

description: Library name: 2H0B_1


title: Patient1, Hemin#2

description: Library name: 1H75_2


title: p52ki/ki2

description:
Library name: p52ki/ki2
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: p52Ki2


title: HiC 3386 Scc1-aid

description: Library name: FB8


title: HiC 3527 Smc5-aid Smc6-aid

description: Library name: FB7


title: HiC 3373 WT

description: Library name: FB5


title: FB134-16c +IAA from G1 HiC

description: Library name: CH78-285


title: WT G2 HiC

description: Library name: LCH1


title: HiC 3813 Smc2-aid

description: Library name: FB6


title: G2 arrested cells 25°C + 1h no rapa 25°C + 1h shift 35,5°C ChIP IP

description: Library name: LCH25


title: G2 arrested cells 25°C + 1h no rapa 25°C + 1h shift 35,5°C ChIP Input

description: Library name: LCH24


title: Patient1, Hemin#1

description: Library name: 1H75_1


title: p52ki/ki1

description:
Library name: p52ki/ki1
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: p52Ki1


title: Patient1, PBS#3

description: Library name: 1H0_3


title: WT4

description:
Library name: WT4
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: WT4

value: WT


title: Patient1, PBS#1

description: Library name: 1H0_1


title: Patient2, DMF#1

description: Library name: 2DMF_1


title: G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C + 1h shift 35,5°C ChIP IP

description: Library name: LCH23


title: WT3

description:
Library name: WT3
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: WT3


title: WT sham 2

description:
Library name: A2
A2

value: brain


title: WT2

description:
Library name: WT2
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv:  WT2


title: Patient1, PBS#2

description: Library name: 1H0_2


title: G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C + 1h shift 35,5°C ChIP Input

description: Library name: LCH22


title: G2 arrested cells 25°C + 1h no rapa 25°C Rpb1 ChIP Input

description: Library name: LCH20


title: G2 arrested cells 25°C + 1h no rapa 25°C Rpb1 ChIP IP

description: Library name: LCH21


title: p52ki5Act_29

description:
Library name: p52ki5Act_29
Column name in counts.tsv: p52ki5Act_29

data_processing:
In-house Fastq files were mapped to the mouse reference genome GRCm38 using Hisat2 v2.1.0. Bam files are sorted and indexed using samtools v1.8. The number of reads aligned to each mouse gene was calculated using featureCounts (a subfunction of the software subread-v1.6.2).
Assembly: GRCm38
Supplementary files format and content: counts.tsv includes raw counts for each Sample

source_name: spleen activated B cells

extract_protocol:
RNA was extracted from FACS-sorted naïve, activated,  pre-GC and GC B cells and stored at -80°C. The total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA was assessed using either RiboGreen (Thermo Fisher Scientific) or Agilent Bioanalyser.
cDNA libraries were prepared using 0.5 ng of total RNA, or half of the RNA sample where concentration was too low to be accurately quantified. The SMARTSeq v2 protocol was used with 17 PCR cycles and the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina Novaseq 6000 targeting at least 13 million read-pairs/sample.

value: spleen activated B cells


title: G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C Rpb1 ChIP Input

description: Library name: LCH18


title: p52ki5GCB_30

description:
Library name: p52ki5GCB_30
Column name in counts.tsv: p52ki5GCB_30

source_name: spleen  GC B cells

value: spleen  GC B cells


title: G2 arrested cells 25°C Rpb1 ChIP Input

description: Library name: LCH16


title: G2 arrested cells 25°C Rpb1 ChIP IP

description: Library name: LCH17


title: HiC G2 arrested cells 25°C + 1h no rapa 25°C + 1h shift 35,5°C  Bis

description: Library name: LCH15


title: G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C Rpb1 ChIP IP

description: Library name: LCH19


title: p52ki5Nai_28

description:
Library name: p52ki5Nai_28
Column name in counts.tsv: p52ki5Nai_28

source_name: spleen naive B cells

value: spleen naive B cells


title: HiC G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C + 1h shift 35,5°C  Bis

description: Library name: LCH14


title: p52ki3Act_23

description:
Library name: p52ki3Act_23
Column name in counts.tsv: p52ki3Act_23


title: HiC G2 arrested cells 25°C Bis

description: Library name: LCH13


title: WT1

description:
Library name: WT1
Column name in RNA_Seq_preGCB_counts.tsv and logCPM_withGeneNames.tsv: WT1


title: p52ki3Nai_22

description:
Library name: p52ki3Nai_22
Column name in counts.tsv: p52ki3Nai_22


title: HiC G2 arrested cells 25°C + 1h no rapa 25°C + 1h shift 35,5°C

description: Library name: LCH12


title: p52ki2GCB_21

description:
Library name: p52ki2GCB_21
Column name in counts.tsv: p52ki2GCB_21


title: HiC G2 arrested cells 25°C + 1h rapamycin 1µg/ml 25°C + 1h shift 35,5°C

description: Library name: LCH11


title: p52ki2Act_20

description:
Library name: p52ki2Act_20
Column name in counts.tsv: p52ki2Act_20


title: HiC G2 arrested cells 25°C

description: Library name: LCH10


title: WT4GCB_12

description:
Library name: WT4GCB_12
Column name in counts.tsv: WT4GCB_12


title: p52ki2Nai_19

description:
Library name: p52ki2Nai_19
Column name in counts.tsv: p52ki2Nai_19


title: WT4Act_11

description:
Library name: WT4Act_11
Column name in counts.tsv: WT4Act_11


title: WT4NAIVE_10

description:
Library name: WT4NAIVE_10
Column name in counts.tsv: WT4NAIVE_10


title: WT3GCB_9

description:
Library name: WT3GCB_9
Column name in counts.tsv: WT3GCB_9


title: WT3Act_8

description:
Library name: WT3Act_8
Column name in counts.tsv: WT3Act_8


title: WT3NAIVE_7

description:
Library name: WT3NAIVE_7
Column name in counts.tsv: WT3NAIVE_7


title: Ly3_Relb rep2

description: Library name: L_Relb

data_processing:
In-house Fastq ChIP-seq files were aligned to mouse reference genome GRCm38 using bowtie27 v2.5.4. Generated alignment bam files then used as input for Homer8 v5.1 software to create Tag directories using makeTagDirectory. Downstream analysis is performed using created tag directories. bedGraph files are generated with makeUCSCfile.
Assembly: GRCh38
Supplementary files format and content: bedgraph

growth_protocol: Cultured OCI-LY3 human DLBCL cells were used in ChIP experiments. OCI-Ly3 cells stored in the -80°C freezer in the lab, originally obtained from ATCC, were thawed and cultured in IMDM media (Gibco) supplemented with 10% of FBS and 1% of penicillin/streptomycin in T75 flasks.

extract_protocol:
Firstly, harvested cells were washed in PBS. For the first crosslinking step, each cell pellet was resuspended in 1 ml of PBS containing 4µl of disuccinimidyl glutarate (DSG, Thermo Fisher Scientific: 20593) and incubated for 45 minutes on a rotator. Samples were then washed twice with PBS before second cross-linking with 1080µl of 37% formaldehyde in 40 ml of PBS and left on the rotator at room temperature for 10 minutes. The reaction was stopped using 2.5 ml of 2M glycine. Samples were washed twice with PBS and resuspended in 2 ml of SDS lysis buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 10% SDS) with protease inhibitors and centrifuged at 1500 rpm for 5 minutes at 4°C. Subsequently, 2 ml of ChIP buffer (2 parts of SDS-lysis and 1 part of Triton-dilution buffer: 100 mM Tris-HCl pH 8.6, 100 mM NaCl, 5 mM EDTA, 5% Triton X-100) was added, and samples were split equally into two different 15 ml tubes for sonication. Cells were sonicated for 25 minutes at high output intensity at 4°C until they became clear and then centrifuged at 14,000 rpm for 30 minutes. The supernatant was pre-cleared with 60µl of protein A/G sepharose beads (Sigma Aldrich: 11719408001 and 11719406001) or 20ul of ChIP-grade magnetic beads (Thermo Scientific: 26162) at 4°C on a rotator for 2 hours. For input, 10% of the supernatant volume was set aside from the centrifuged samples. The remaining sample volume was divided equally into different tubes for incubation with 10 ug of primary antibody overnight on a rotator at 4°C. The antibodies for different proteins of interest and IgG control were added in equal amounts (Supp. Table 2). The next day, 60 μl of protein A/G sepharose beads or 20ul of ChIP-grade magnetic beads were added to the samples and incubated for 4 hours at 4°C. After discarding the supernatant upon centrifugation or a magnetic stand, the beads in the tubes were sequentially washed in 4 different buffers before the elution step.
Purified DNA samples were sent to NovogeneAIT Genomics facility for ChIP-seq. Briefly, the DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries are pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: B cell lymphoma


title: WT1GCB_3

description:
Library name: WT1GCB_3
Column name in counts.tsv: WT1GCB_3


title: Ly3_PolII_IP rep1

description: Library name: L_PolII_IP


title: WT1Act_2

description:
Library name: WT1Act_2
Column name in counts.tsv: WT1Act_2


title: Ly3_p52 rep2

description: Library name: L_p52


title: WT1NAIVE_1

description:
Library name: WT1NAIVE_1
Column name in counts.tsv: WT1NAIVE_1


title: Ly3_IgG_IP rep2

description: Library name: L_IgG_IP


title: Ly3_H3K27Me_IP rep1

description: Library name: L_H3K27Me_IP


title: Tsc1f/fAlbCre+ mice, 10-month old, mouse #3

description:
Library name: 10m_B3
Column name in raw_counts_all_samples.txt: 10m_B3

data_processing:
Library concentration was quantified using a Qubit 2.0 fluorometer, and fragment size distribution was assessed using an Agilent Bioanalyzer.
Sequencing was performed on the Illumina NextSeq 500 platform. FASTQ files were processed using the RNA Express module (Illumina).
Raw reads were aligned to mouse genome (GRCm38/mm10) using STAR aligner. Downstream analysis, including normalization and differential gene expression, was performed in R (v4.0.3) using the edgeR package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver tumor

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Invitrogen). 0.5 µg of total RNA was used for the constrcution of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following the manufacturer’s protocol.

value: liver

value: hepatocyte


title: Ly3_H3K27Ac_IP rep2

description: Library name: L_H3K27Ac_IP


title: Tsc1f/fAlbCre+ mice, 10-month old, mouse #2

description:
Library name: 10m_B2
Column name in raw_counts_all_samples.txt: 10m_B2


title: Ly3_Input_DNA rep2

description: Library name: L_Input_DNA


title: Ly3_H3K4Me3_IP rep1

description: Library name: L_H3K4Me3_IP


title: Tsc1f/fAlbCre+ mice, 10-month old, mouse #1

description:
Library name: 10m_B1
Column name in raw_counts_all_samples.txt: 10m_B1


title: Tsc1f/f mice, 10-month old, mouse #3

description:
Library name: 10m_A3
Column name in raw_counts_all_samples.txt: 10m_A3

source_name: liver tissue


title: Ly3_ETS1 rep2

description: Library name: L_ETS1


title: Ly3_RelB rep1

description: Library name: Ly3_RelB


title: Tsc1f/f mice, 10-month old, mouse #2

description:
Library name: 10m_A2
Column name in raw_counts_all_samples.txt: 10m_A2


title: Ly3_P52 rep1

description: Library name: Ly3_P52


title: Tsc1f/f mice, 10-month old, mouse #1

description:
Library name: 10m_A1
Column name in raw_counts_all_samples.txt: 10m_A1


title: Tsc1f/fAlbCre+/Nrf2-/- mice, 10-month old, mouse #2

description:
Library name: 10m_C2
Column name in raw_counts_all_samples.txt: 10m_C2


title: Tsc1f/fAlbCre+/Nrf2-/- mice, 10-month old, mouse #3

description:
Library name: 10m_C3
Column name in raw_counts_all_samples.txt: 10m_C3


title: Tsc1f/fAlbCre+/Nrf2-/- mice, 10-month old, mouse #1

description:
Library name: 10m_C1
Column name in raw_counts_all_samples.txt: 10m_C1


title: PBMC, healthy, 84H, BCR

city: Baltimore

first: Andy Kwan Pui

last: Chan

state: MD

address: 615 N Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University

description: Library name: 84H-D0-BCR

library_source: transcriptomic single cell

data_processing:
The multi pipeline of 10× Genomics Cell Ranger v9.0.1 was used to perform demultiplexing and gene alignment per sample. Genome assembly of Mmul10 (accession: GCA_003339765; version: 114) was processed via the mkref pipeline of 10× Genomics Cell Ranger v9.0.1 to generate the reference genome for sequence alignment of the GEX library. The BCR VDJC reference genome was curated from two sources: 1) the international ImMunoGeneTics (IMGT) information system with the most recent VDJ genes (accessed in May 2025) and 2) published literature.
Cell Ranger output file filtered_feature_bc_matrix.h5 was loaded into RStudio (R version 4.3.1) via the command Read10x from Seurat v5.0.1. Only single cells with <10% of mitochondrial genes (percent.mt) and 200-4000 unique gene counts (nFeature_RNA) were included.
Doublets were predicted using DoubletFinder v2.0.3, which assigned doublet scores to each cell in the dataset. Those that were marked doublets, ~7.5% per sample, were later removed from subsequent analysis.
In the Cell Ranger output directory vdj_b , the file filtered_contig_annotations.csv from each sample was loaded into R via the command combineBCR of the package scRepertoire v1.12.0, in order to process and combine all files into one object
Using the command VDJ_GEX_matrix from the package platypus v3.4.1, the BCR-VDJ library of each sample was processed and combined with GEX Seurat object as an integrated object.
Assembly: Mmul10 (accession: GCA_003339765; version: 114), also bespoke RM BCR VDJC immunogenetic reference
Supplementary files format and content: cell_metadata.txt.gz, feature.tsv, matrix.mtx, barcodes.tsv - all from the integrated B cell only Seurat object (subsetted from the original PBMC object), with 13,849 single cells to analyze for B cell subsets

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
For each sample, macaques were first sedated with 10-15 mg/kg ketamine or ketamine/dexmedetomidine(0.025mg/kg) intramuscularly. Heparinized blood was collected from the femoral vein. Plasma and peripheral blood mononuclear cells were isolated by whole blood gradient centrifugation on Lympholyte-Mammal (Cedarlane Lab). Plasma was frozen at -20C for subsequent analysis.
Single-cell capture and library creation were performed using Chromium single cell 5' reagent kits user guide (v2 chemistry dual index) with feature barcoding technology for cell surface protein and immune receptor mapping according to 10× Genomics specifications. Specifically, PBMCs were first loaded with Single Cell VDJ 5’ Gel Beads and partitioning oil onto a Chromium Next GEM Chip K to produce single-cell gel bead-in-emulsions (GEMs). It was followed by gel bead dissolution and cell lysis, allowing for poly-adenylated mRNA transcripts to be reverse-transcribed into 10x-barcoded full-length cDNA. Later, cDNAs were amplified via polymerase chain reaction (PCR) and subsequently sequenced on Illumina Novaseq 6000.One library was first generated to elucidate the mRNA transcript expression (RNA); from which another library was generated to describe specifically B cell receptor (BCR) repertoire (VDJ) for each single B cell.

value: PBMC

value: F

value: Unmanipulated, healthy

tag: library type

value: mRNA - VDJ/BCR


title: PBMC, healthy, 47G, GEX

description:
Library name: 47G-D0-GEX
5'GEX

value: mRNA


title: PBMC, healthy, 83H, BCR

description: Library name: 83H-D0-BCR


title: PBMC, healthy, 69G, GEX

description:
Library name: 69G-D0-GEX
5'GEX


title: PBMC, healthy, 84H, GEX

description:
Library name: 84H-D0-GEX
5'GEX


title: PBMC, healthy, 69G, BCR

description: Library name: 69G-D0-BCR


title: PBMC, healthy, 47G, BCR

description: Library name: 47G-D0-BCR


title: PBMC, healthy, 83H, GEX

description:
Library name: 83H-D0-GEX
5'GEX


title: Hep3B, L2HG #2

description: Library name: B3HG1_2

data_processing:
For RNA-seq, library was prepared concentration was quantified using a Qubit 2.0 fluorometer, and fragment size distribution was assessed using an Agilent Bioanalyzer. For metabolic library screen, genomic DNA were PCR amplified with forward primer actgacGATATTAGTACAAAATACGTGAC and reverse primer agtctgAAAGCACCGACTCGGTGCCAC (lowercase letters indicate sample-specific barcodes). PCR products were purified and sequenced using an Illumina HiSeq 2500 platform. Sequencing reads were aligned to the reference sgRNA library, and sgRNA abundance was quantified.Results were reported as: percent total sgRNA reads, calculated by summing all reads mapped to sgRNAs targeting a specific gene and expressing this as a percentage of the total sgRNA reads reads for both the initial and final populations. For ATAC-seq, the quality of purified DNA libraries was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies), and libraries were sequenced on an Illumina NextSeq 500 platform to generate paired-end 2 × 42 bp reads. Raw sequencing reads were aligned to the human genome (GRCh37/hg19) using Bowtie2. Uniquely mapped reads were retained for downstream analysis. Peaks of chromatin accessibility were identified using HOMER to generate bigWig files and call significant peaks by using Genrich v0.5 (https://github.com/jsh58/Genrich). The BAM and bigwig files were visualized using UCSC Genome Browser (http://genome.ucsc.edu/index.html), Integrated Genome Browser (http://bioviz.org) and Integrative Genomics Viewer (http://www.broadinstitute.org/igv/).
Sequencing was performed on the Illumina NextSeq 500 platform. FASTQ files were processed using the RNA Express module (Illumina).
Raw reads were aligned to human genome (GRCh38/hg38) using STAR aligner. Downstream analysis, including normalization and differential gene expression, was performed in R (v4.0.3) using the edgeR package.
Assembly: hg19 (ATAC-seq) hg38 (RNA-seq)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Invitrogen). 0.5 µg of total RNA was used for the constrcution of sequencing libraries. For metabolic screen, genomic DNA from HuH7 cells were extracted by using the phenol-chloroform method. For ATAC-seq, a total of 50,000 cells per condition were harvested, washed with ice-cold PBS, and lysed in ATAC lysis buffer (provided by the assay kit). Nuclei were collected by centrifugation at 500xg for 10 minutes at 4°C.
For RNA-seq, libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following the manufacturer’s protocol. For metabolic library screen,  sgRNA inserts were PCR-amplified using Q5 High-Fidelity DNA Polymerase (New England Biolabs, Cat# M0491) with 100 ug of gDNA per sample  following the manufacturer’s protocol. For ATAC-seq, library preparation was performed using the ATAC-seq kit (Active Motif, Cat# 53150) according to the manufacturer’s instructions.

value: hepatocellular carcinoma


title: Hep3B, No_L2HG #1

description: Library name: B3HG0_1

value: no treatment


title: Hep3B, No_L2HG #2

description: Library name: B3HG0_2


title: SNU398, L2HG #3

description: Library name: S398HG1_3


title: SNU398, L2HG #2

description: Library name: S398HG1_2


title: SNU398, No_L2HG #1

description: Library name: S398HG0_1


title: Hep3B, No_L2HG #3

description: Library name: B3HG0_3


title: Hep3B, L2HG

description: Library name: 3B_HG1_1


title: Hep3B, L2HG #1

description: Library name: B3HG1_1


title: SW1573 wildtype

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam University Medical Center

description: Library name: Sample 6

data_processing:
STAR alignment tool (version 2.5.3a) was used for data processing
Assembly: Sequences were mapped to the human reference genome assembly GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for eah Sample
Supplementary files format and content: csv file include FPKM values for each Sample

extract_protocol:
A total of 0.5 µg of RNA was reverse transcribed into complementary DNA (cDNA) using the First Strand cDNA Synthesis Kit (Thermo Scientific) for the constructions of sequencing libraries.
RNA libraries for RNA-seq were preparewd using Illumina TruSeq Stranded total RNA Library Prep gold Kit following manufacturer's instructions.


title: Hep3B, No-L2HG

description: Library name: 3B_HG0_1


title: SNU398, L2HG #1

description: Library name: S398HG1_1


title: SNU398, No_L2HG #2

description: Library name: S398HG0_2


title: Hep3B, L2HG #3

description: Library name: B3HG1_3


title: SNU398, No_L2HG #3

description: Library name: S398HG0_3


title: SW1573 drug-resistant

description: Library name: Sample 5


title: HuH7, initial

description: Library name: H7_0

data_processing:
For RNA-seq, library was prepared concentration was quantified using a Qubit 2.0 fluorometer, and fragment size distribution was assessed using an Agilent Bioanalyzer. For metabolic library screen, genomic DNA were PCR amplified with forward primer actgacGATATTAGTACAAAATACGTGAC and reverse primer agtctgAAAGCACCGACTCGGTGCCAC (lowercase letters indicate sample-specific barcodes). PCR products were purified and sequenced using an Illumina HiSeq 2500 platform. Sequencing reads were aligned to the reference sgRNA library, and sgRNA abundance was quantified.Results were reported as: percent total sgRNA reads, calculated by summing all reads mapped to sgRNAs targeting a specific gene and expressing this as a percentage of the total sgRNA reads reads for both the initial and final populations. For ATAC-seq, the quality of purified DNA libraries was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies), and libraries were sequenced on an Illumina NextSeq 500 platform to generate paired-end 2 × 42 bp reads. Raw sequencing reads were aligned to the human genome (GRCh37/hg19) using Bowtie2. Uniquely mapped reads were retained for downstream analysis. Peaks of chromatin accessibility were identified using HOMER to generate bigWig files and call significant peaks by using Genrich v0.5 (https://github.com/jsh58/Genrich). The BAM and bigwig files were visualized using UCSC Genome Browser (http://genome.ucsc.edu/index.html), Integrated Genome Browser (http://bioviz.org) and Integrative Genomics Viewer (http://www.broadinstitute.org/igv/).
Sequencing was performed on the Illumina NextSeq 500 platform. FASTQ files were processed using the RNA Express module (Illumina).
Raw reads were aligned to human genome (GRCh38/hg38) using STAR aligner. Downstream analysis, including normalization and differential gene expression, was performed in R (v4.0.3) using the edgeR package.
Assembly: hg19 (ATAC-seq) hg38 (RNA-seq)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: CRISPR Screen


title: HuH7, final

description: Library name: H7_1

value: Imidazole ketone erastin


title: PBMC, healthy, 43F, BCR

description: Library name: 43F-D0-BCR

value: M


title: Ly3_Input rep1

description: Library name: Ly3_Input


title: H460 wildtype

description: Library name: Smaple 4


title: Ly3_IgG rep1

description: Library name: Ly3_IgG


title: PBMC, healthy, 43F, GEX

description:
Library name: 43F-D0-GEX
5'GEX


title: H460 drug-resistant

description: Library name: Sample 3


title: PBMC, healthy, 13F, BCR

description: Library name: 13F-D0-BCR


title: PC9_Veh

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: PC9_Veh

data_processing:
Sequenced reads were aligned to GRCh38 reference genome and quantified using CellRanger (v 7.1) (47). Potential ‘doublet’ cells in each sample were predicted and removed with the software package “scrublet” (v 0.2.3). Cells that were either in the bottom 10% of UMI counts or in the bottom 10% of feature count (genes) were filtered out from each sample. Also, cells with more than 25% mitochondrial read content were removed. After filtering, 5,210 cells in the lymph node sample and 5,325 cells in the tumor sample were retained for further analysis.
Assembly: GRCh38
Supplementary files format and content: h5 files of cellranger output

extract_protocol: We interrogated the availability of surgical specimens of patients who had received neo-adjuvant EGFR-TKIs at Dana-Farber Cancer Institute (Boston, MA, US), at Policlinico Universitario A. Gemelli IRCCS (Rome, Italy) and at Cochin Hospital AP-HP (Paris, France). All patients had signed an informed consent to participate to molecular studies and the studies were approved by the local institutional review boards.

value: All cells

value: Vehicle


title: DFCI282_Vehicle

description: Library name: DFCI282_Vehicle


title: PC9_Osi

description: Library name: PC9_Osi

value: Osimertinib


title: Ly3_H3K27 rep1

description: Library name: Ly3_H3K27


title: WT, FUDR, rep2

status: Public on Jul 25 2025

city: Riverside

first: Anusha

last: Iyengar

state: CA

address: 900 University Ave

department: Biochemistry

institute: University of California, Riverside

description: RNA-seq

data_processing:
Genome alignment (STAR), HTSeq
Assembly: Caenorhabditis_elegans.WBcel235.112
Supplementary files format and content: HTSeq count table containing number of counts for each gene for each library

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
Zymo research direct-zol RNA mini prep kit
NEBNext poly(A) mRNA magnetic isolation, and NEBNext ultra RNA library prep kit for Illumina

value: Whole worm

tag: age

value: WT

value: FUDR 50uM


title: DFCI282_Ositreated

description: Library name: DFCI282_Ositreated


title: WT, OP50, rep3

description: RNA-seq

value: Untreated


title: WT, FUDR, rep1

description: RNA-seq


title: WT, OP50, rep1

description: RNA-seq


title: PBMC, healthy, 13F, GEX

description:
Library name: 13F-D0-GEX
5'GEX


title: WT, FUDR, rep3

description: RNA-seq


title: A549 wildtype

description: Library name: Sample 2


title: A549 drug-resistant

description: Library name: Sample 1


title: Ly3_ETS1 rep1

description: Library name: Ly3_ETS1

value: B cell lymphoma


title: Subject_C17_Blood (BRC-seq)

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample_Fq_18
BCR

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 (10x Genomics)
Assembly: GRCH38
Supplementary files format and content: Compressed tab-separated values files, unfiltered single cell barcode gene expression matrix

source_name: Blood

extract_protocol:
Nasal tissue samples were minced, digested in a DNAse/Liberase solution for 30 minutes, strained and washed to create a single cell suspension. Paired whole blood was centrifuged layered on Histopaque 1077, with PBMC layer extracted and washed. Nasal and PBMC samples were loaded as single cell suspensions without sorting
ScRNAseq gene expression libraries were contructed in accordance with the manufacturer protocol,  with TCR enrichment using the Chromium Single Cell Human BCR Amplification Kit (Single cell 5' v2 protocol, 10x Genomics)

value: Blood

value: Healthy control


title: Subject_C21_Blood (BRC-seq)

description:
Library name: Sample_Fq_14
BCR


title: Subject_C24_Blood (BRC-seq)

description:
Library name: Sample_Fq_10
BCR


title: Subject_C26_Nasal (BRC-seq)

description:
Library name: Sample_Fq_38
BCR

source_name: Nasal

value: Nasal


title: Subject_C19_Nasal (BRC-seq)

description:
Library name: Sample_Fq_9
BCR


title: WT, OP50, rep2

description: RNA-seq


title: Subject_C24_Nasal (BRC-seq)

description:
Library name: Sample_Fq_11
BCR


title: Subject_C21_Nasal (BRC-seq)

description:
Library name: Sample_Fq_15
BCR


title: Subject_C20_Blood (BRC-seq)

description:
Library name: Sample_Fq_4
BCR


title: Subject_C19_Blood (BRC-seq)

description:
Library name: Sample_Fq_8
BCR


title: Subject_12_Nasal (BRC-seq)

description:
Library name: MC9785408
BCR

value: Conval COVID


title: Subject_12_Blood (BRC-seq)

description:
Library name: MC9785390
BCR


title: Subject_C20_Nasal (BRC-seq)

description:
Library name: Sample_Fq_5
BCR


title: Subject_11_Blood (BRC-seq)

description:
Library name: MC9785389
BCR


title: Subject_C17_Nasal (BRC-seq)

description:
Library name: Sample_Fq_19
BCR


title: Subject_10_Nasal (BRC-seq)

description:
Library name: MC9785388
BCR


title: Subject_9_Blood (BRC-seq)

description:
Library name: MC9785385
BCR


title: Subject_10_Blood (BRC-seq)

description:
Library name: MC9785387
BCR


title: Subject_9_Nasal (BRC-seq)

description:
Library name: MC9785386
BCR


title: Subject_7_Nasal (BRC-seq)

description:
Library name: MC9785382
BCR

value: Active COVID


title: Subject_8_Blood (BRC-seq)

description:
Library name: MC9785383
BCR


title: Subject_7_Blood (BRC-seq)

description:
Library name: MC9785381
BCR


title: Subject_6_Nasal (BRC-seq)

description:
Library name: MC9785380
BCR


title: Subject_5_Nasal (BRC-seq)

description:
Library name: MC9785378
BCR


title: Subject_4_Nasal (BRC-seq)

description:
Library name: MC9785376
BCR


title: Subject_8_Nasal (BRC-seq)

description:
Library name: MC9785384
BCR


title: Subject_6_Blood (BRC-seq)

description:
Library name: MC9785379
BCR


title: Subject_5_Blood (BRC-seq)

description:
Library name: MC9785377
BCR


title: Subject_2_Nasal (BRC-seq)

description:
Library name: Sample_Fq4_COVID
BCR


title: Subject_3_Blood (BRC-seq)

description:
Library name: Sample_Fq6_COVID
BCR


title: Subject_1_Blood (BRC-seq)

description:
Library name: Sample_Fq1_COVID
BCR


title: Subject_4_Blood (BRC-seq)

description:
Library name: MC9785375
BCR


title: Subject_3_Nasal (BRC-seq)

description:
Library name: Sample_Fq5_COVID
BCR


title: RA02_B

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
Library name: RA02_B
10x Genomics

data_processing:
BCL files were demultiplexed into FASTQ files using cellranger mkfastq (v6.1.2). FASTQ files were processed using cellranger count to align reads and generate gene-barcode matrices. Ambient RNA contamination was removed using SoupX. Doublets were identified and excluded prior to normalization.
Quality control was performed in Seurat (v5) by filtering out cells with low UMI or gene counts and high mitochondrial RNA content. RNA counts for each sample were normalized using SCTransform individually  with cell cycle regression. ADT data were normalized using centered log-ratio (CLR) transformation across cells (margin = 2).
Samples were integrated using Harmony. Dimensionality reduction was performed using principal component analysis (PCA) and visualized with UMAP using the top 10 principal components. Clustering was performed using the Louvain algorithm at resolution 0.2. T cells clusters were identified using canonical markers.
Raw counts were extracted for cells annotated as T cells and converted to H5 matrices
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 matrix files

source_name: T cells, CD45⁺-sorted

extract_protocol:
Ultrasound-guided synovial biopsy samples were collected from rheumatoid arthritis (RA) patients at baseline and after 12 weeks of treatment under IRB-approved protocols with informed consent. Synovial tissue was perfused to remove peripheral blood, followed by mechanical and enzymatic dissociation to obtain single-cell suspensions. Cells were stained with fluorophore-conjugated antibodies targeting immune markers, and fluorescence-activated cell sorting (FACS) was used to enrich for live CD45⁺ immune cells.
Sorted cells were processed using the 10x Genomics Chromium platform for single-cell RNA sequencing.  Libraries were prepared using the Chromium Single Cell 3′ v2 chemistry according to the manufacturer’s protocol.

value: Synovial tissue

value: T cells

value: baseline

value: Female


title: RA17_B

description:
Library name: RA17_B
10x Genomics

data_processing:
BCL files were demultiplexed into FASTQ files using cellranger mkfastq (v6.1.2). FASTQ files were processed using cellranger count to align reads and generate gene-barcode matrices. Ambient RNA contamination was removed using SoupX. Doublets were identified and excluded prior to normalization.
Quality control was performed in Seurat (v5) by filtering out cells with low UMI or gene counts and high mitochondrial RNA content. RNA counts for each sample were normalized using SCTransform individually  with cell cycle regression. ADT data were normalized using centered log-ratio (CLR) transformation across cells (margin = 2).
Samples were integrated using Harmony. Dimensionality reduction was performed using principal component analysis (PCA) and visualized with UMAP using the top 10 principal components. Clustering was performed using the Louvain algorithm at resolution 0.2. T cells clusters were identified using canonical markers.
Raw counts were extracted for cells annotated as T cells and converted to H5 matrices
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 matrix files
Library strategy: CITE-seq


title: v1_J2_RIP_scramble_3

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

description: Library name: v1_J2_RIP_scramble_3

data_processing:
Reads were trimmed using fastp (v.0.20.0), then aligned to the hg38 genome using STAR (v2.7.3a). Transposable elements were identified using the human RepeatMasker and Tetranscripts. Differentially expressed genes and TEs were analyzed with DESeq2 (v1.30.1) using a likelihood ratio test with a reduced model.
Assembly: hg38
Supplementary files format and content: v1_normalized_counts.csv
Supplementary files format and content: v2_normalized_counts.csv
Supplementary files format and content: v3_normalized_counts.csv

source_name: primary human astrocytes

extract_protocol:
J2-immunoprecipiated RNAs were isolated using the Magna RIP Kit (Sigma) and a phenol-chloroform extraction. Input RNA were isolated using a phenol-chloroform extraction.
RNA libraries were prepared using an abundance-based rRNA-depleted total RNA kit (Zymo), a polyadenylated RNA kit (Universal Plus), and a probed-based ribosomal RNA depleted total RNA kit (NEBNext/Zymo). All protocols were followed according to the manufacturers' protocols.

value: primary human astrocytes

value: scramble siRNA

value: version 1


title: RA03_B

description:
Library name: RA03_B
10x Genomics

value: Male


title: Subject_2_Blood (BRC-seq)

description:
Library name: Sample_Fq3_COVID
BCR


title: RA13_B

description:
Library name: RA13_B
10x Genomics


title: RA08_B

description:
Library name: RA08_B
10x Genomics


title: RA04_B

description:
Library name: RA04_B
10x Genomics


title: RA07_F

description:
Library name: RA07_F
10x Genomics

value: followup


title: RA01_B

description:
Library name: RA01_B
10x Genomics


title: RA11_B

description:
Library name: RA11_B
10x Genomics


title: RA14_B

description:
Library name: RA14_B
10x Genomics


title: RA12_F

description:
Library name: RA12_F
10x Genomics


title: RA07_B

description:
Library name: RA07_B
10x Genomics


title: RA14_F

description:
Library name: RA14_F
10x Genomics


title: RA10_B

description:
Library name: RA10_B
10x Genomics


title: RA15_F

description:
Library name: RA15_F
10x Genomics


title: RA10_F

description:
Library name: RA10_F
10x Genomics


title: RA16_F

description:
Library name: RA16_F
10x Genomics


title: RA12_B

description:
Library name: RA12_B
10x Genomics


title: RA06_B

description:
Library name: RA06_B
10x Genomics


title: RA05_B

description:
Library name: RA05_B
10x Genomics


title: Subject_1_Nasal (BRC-seq)

description:
Library name: Sample_Fq2_COVID
BCR


title: RA09_B

description:
Library name: RA09_B
10x Genomics


title: v1_J2_RIP_scramble_2

description: Library name: v1_J2_RIP_scramble_2


title: v1_J2_RIP_ADAR1_KD_3

description: Library name: v1_J2_RIP_ADAR1_KD_3

value: ADAR1 siRNA


title: v1_J2_RIP_ADAR1_KD_2

description: Library name: v1_J2_RIP_ADAR1_KD_2


title: v1_J2_RIP_ADAR1_KD_1

description: Library name: v1_J2_RIP_ADAR1_KD_1


title: v1_J2_input_scramble_2

description: Library name: v1_J2_input_scramble_2


title: v1_J2_input_ADAR1_KD_1

description: Library name: v1_J2_input_ADAR1_KD_1


title: v1_J2_input_scramble_3

description: Library name: v1_J2_input_scramble_3


title: v2_J2_RIP_scramble_2

description: Library name: v2_J2_RIP_scramble_2

value: version 2


title: v2_J2_RIP_ADAR1_KD_2

description: Library name: v2_J2_RIP_ADAR1_KD_2


title: v2_J2_RIP_ADAR1_KD_3

description: Library name: v2_J2_RIP_ADAR1_KD_3


title: v2_J2_RIP_ADAR1_KD_1

description: Library name: v2_J2_RIP_ADAR1_KD_1


title: v1_J2_input_ADAR1_KD_3

description: Library name: v1_J2_input_ADAR1_KD_3


title: v1_J2_input_ADAR1_KD_2

description: Library name: v1_J2_input_ADAR1_KD_2


title: v2_J2_input_ADAR1_KD_2

description: Library name: v2_J2_input_ADAR1_KD_2


title: v2_J2_RIP_scramble_1

description: Library name: v2_J2_RIP_scramble_1


title: v3_J2_RIP_scramble_3

description: Library name: v3_J2_RIP_scramble_3

value: version 3


title: v3_J2_RIP_ADAR1_KD_2

description: Library name: v3_J2_RIP_ADAR1_KD_2


title: v3_J2_RIP_ADAR1_KD_3

description: Library name: v3_J2_RIP_ADAR1_KD_3


title: v2_J2_input_scramble_1

description: Library name: v2_J2_input_scramble_1


title: v2_J2_input_scramble_2

description: Library name: v2_J2_input_scramble_2


title: v3_J2_RIP_ADAR1_KD_1

description: Library name: v3_J2_RIP_ADAR1_KD_1


title: v3_J2_RIP_scramble_1

description: Library name: v3_J2_RIP_scramble_1


title: v3_J2_RIP_scramble_2

description: Library name: v3_J2_RIP_scramble_2


title: v1_J2_input_scramble_1

description: Library name: v1_J2_input_scramble_1


title: v1_J2_RIP_scramble_1

description: Library name: v1_J2_RIP_scramble_1


title: v2_J2_input_scramble_3

description: Library name: v2_J2_input_scramble_3


title: v3_J2_input_scramble_3

description: Library name: v3_J2_input_scramble_3


title: v3_J2_input_scramble_2

description: Library name: v3_J2_input_scramble_2


title: v3_J2_input_scramble_1

description: Library name: v3_J2_input_scramble_1


title: v2_J2_RIP_scramble_3

description: Library name: v2_J2_RIP_scramble_3


title: v2_J2_input_ADAR1_KD_3

description: Library name: v2_J2_input_ADAR1_KD_3


title: v2_J2_input_ADAR1_KD_1

description: Library name: v2_J2_input_ADAR1_KD_1


title: AGS, sgEmpty, H3K36me3, Dox D4, ChIP

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: Library name: AGS_sgEmpty_H3K36me3_D4

data_processing:
Basecalls were performed using bcl2fastq.
Data were mapped to the University of California Santa Cruz human genome assembly (hg19) using Bowtie2 and duplicated reads were removed using Picard tools.
bigwig files were generated using HOMER software.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: AGS

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptmycin, 1% non-essential amino acid. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. For SETD1A, RNAP2, Ser2P and H3K36me3 ChIP, we fixed cells with 2 mM DSG for 30 min before formaldehyde fixation. After washing and cell lysis, nuclei pellets were sonicated by using Picoruptor (Diagenode)
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems).

treatment_protocol: Doxycycline was prepared to a stock solution at a concentration of 1 mg/mL in PBS and used as 1:1000 dilution.

value: AGS

value: Human gastric cancer cell line

value: SETD1A knockout D4

value: Doxycycline 4 days


title: AGS, sgEmpty, H3K36me3, Dox D6, ChIP

description: Library name: AGS_sgEmpty_H3K36me3_D6

value: SETD1A knockout D6

value: Doxycycline 6 days


title: v3_J2_input_ADAR1_KD_2

description: Library name: v3_J2_input_ADAR1_KD_2


title: AGS, sgEmpty, H3K36me3, Dox D2, ChIP

description: Library name: AGS_sgEmpty_H3K36me3_D2

value: SETD1A knockout D2

value: Doxycycline 2 days


title: v3_J2_input_ADAR1_KD_1

description: Library name: v3_J2_input_ADAR1_KD_1


title: AGS, sgSETD1A, H3K36me3, Dox D6, ChIP

description: Library name: AGS_sgSETD1A_H3K36me3_D6


title: B-cells VDJ-B donor H8

city: Paris

first: Sebastien

last: Mella

address: 28 rue du Dr Roux

department: Immunology

institute: Institut Pasteur

description:
Library name: H8_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript

data_processing:
Cellranger multi (v.7.1.0 samples H7/H8; v.6.0.1 other) to generate 5' gene expression library and VDJ library
Assembly: 10X human reference refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: cellranger multi output mRNA count matrix, and VDJ information

source_name: filtered B-cells

extract_protocol:
The cryopreserved cells were thawed into warm RPMI (Sigma-Aldrich) added with 10% FBS and counted for flow cytometry analysis. At least 500,000 cells viable cells were used per panel and samples with <75% viability were discarded. Cells were stained with Zombie Aqua fixable viability kit on ice for 20 min (Biolegend) to discriminate live and dead cells. After washing, cells were stained with surface markers on ice for 30 min. After washing, cells were fixed and permeabilized with True-Nuclear Transcription Factor Buffer set (Biolegend) per manufacturer’s instructions, followed by intracellular staining with anti-Ki-67, Granzyme B and Granzyme K antibodies. Cells were resuspended in FACS buffer and analyzed on a BD FACSAria Fusion (BD Biosciences). Data were analyzed with FlowJo software v.10.10.0. Cells were counted and assessed for viability. From the PBMC, we performed a positive selection of B cells with magnetic beads (human CD19 MicroBeads, Miltenyi Biotec). The flow-through was used for the subsequent negative selection of T cells (Human Pan T Cell Isolation Kit, Miltenyi Biotec).
Chromium Next GEM Single Cell V(D)J Reagent Kit, applying the protocol 10x CG000207RevE Lib VDJ Tet B+ LibGEX was used to integrate transcriptional profile with the immune repertoire of individual cells, full-length paired T-cell receptor (TCR) and B-cell immunoglobulin (Ig) transcripts. Samples were thawed following the 10x Genomics demonstrated protocol (Dropwise Media Addition & Sequential Dilution, document CG000447). 5000-20000 cells (depending on donor) were loaded on the 10X Chromium Controller to target capturing half of the loaded cells. The barcoded cDNA was processed to prepare cDNA library and VDJ library. Quality control quantification of cDNA and libraries were performed on the 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent) and the Qubit with dsDNA HS Assay Kit (ThermoFisher). Libraries were sequenced on Illumina NovaSeq, at a sequencing depth of 20.000 read pairs per cell for gene expression libraries and 5.000 read pairs per cell for V(D)J enriched libraries.

value: filtered B-cells

value: B-cells

value: VDJ-B


title: AGS, sgSETD1A, H3K36me3, Dox D2, ChIP

description: Library name: AGS_sgSETD1A_H3K36me3_D2


title: AGS, sgEmpty, H3K36me3, Dox D0, ChIP

description: Library name: AGS_sgEmpty_H3K36me3_D0

value: SETD1A wt

value: Doxycycline 0 days


title: AGS, sgSETD1A, H3K36me3, Dox D0, ChIP

description: Library name: AGS_sgSETD1A_H3K36me3_D0


title: B-cells GEX donor H8

description:
Library name: H8_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: GEX


title: Pooled samples (Input)

city: Vancouver

first: Gerben

last: Duns

state: BC

address: 675 West 10th Ave

department: Lymphoid Cancer Research

country: Canada

institute: BC Cancer

description: Library name: pooled_input

data_processing:
ChIP-seq  libraries were aligned to the genome build GRCh37 using BWA MEM.
Deeptools v.3.5.1 was used to generate BigWig files for plotting and visualization, normalizing using reads per kilobases per million mapped reads (rpkm), with parameters of “ --ignoreDuplicates --samFlagExclude 1028 --minMappingQuality 5 --binSize 20 –extendReads”.
Genome browser snapshots were visualized on the UCSC Genome Browser.
MACS v.2.2.7.1 was used to call narrow peaks using the parameters “-f BAMPE --seed 1234 -B --extsize 120” and high confidence peak regions were selected using a q-value threshold of 0.1.
Assembly: GRCh37
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

source_name: cell line

growth_protocol: Karpas-1106p cells were cultured in RPMI-1640 supplemented with 20% FBS. All cell lines were maintained at 37°C in a 5% CO₂ incubator.

extract_protocol:
samples were processed by Active Motif, which performed chromatin preparation, ChIP reactions, library construction, and sequencing. Chromatin was extracted by adding lysis buffer and disrupted using a Dounce homogenizer. The lysates were sonicated to shear DNA into fragments averaging 300–500 bp using the PIXUL® Multi-Sample Sonicator (Active Motif, catalog no. 53130). Genomic DNA (Input) was prepared by treating chromatin aliquots with RNase, proteinase K, and heat for de-crosslinking, followed by SPRI bead purification (Beckman Coulter, catalog no. B23318) and quantification using a Qubit fluorometer (Thermo Fisher Scientific).
Illumina sequencing libraries were constructed from ChIP and Input DNAs through a series of enzymatic steps, including end repair, dA-tailing, and adaptor ligation. These steps were automated using the Apollo 342 system and the Takara PrepX DNA Library Kit. After a final PCR amplification, the libraries were quantified and sequenced using Illumina’s NovaSeq 6000 platform (75 nt single-end reads).

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells

tag: chip antibody


title: AGS, sgSETD1A, H3K36me3, Dox D4, ChIP

description: Library name: AGS_sgSETD1A_H3K36me3_D4


title: B-cells VDJ-B donor H7

description:
Library name: H7_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor S2

description:
Library name: S2_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript

source_name: filtered T-cells

value: filtered T-cells

value: T-cells

value: VDJ-T


title: B-cells VDJ-B donor S2

description:
Library name: S2_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: v3_J2_input_ADAR1_KD_3

description: Library name: v3_J2_input_ADAR1_KD_3

value: primary human astrocytes

value: ADAR1 siRNA

value: version 3


title: Karpas1106p, IRF4-WT replicate 2 (ChIP)

description: Library name: karpas1106_con26-2_IRF4

value: anti-IRF4 (P173) antibody (Cell Signaling Technology, catalog no. 4948)


title: Karpas1106p, IRF4-WT replicate 1 (ChIP)

description: Library name: karpas1106_con26-1_IRF4


title: Karpas1106p, IRF4-C99R replicate 1 (ChIP)

description: Library name: karpas1106_C99R-1_IRF4


title: Karpas1106p, IRF4-C99R replicate 2 (ChIP)

description: Library name: karpas1106_C99R-2_IRF4


title: B-cells GEX donor S2

description:
Library name: S2_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor S2

description:
Library name: S2_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor S1

description:
Library name: S1_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells GEX donor H7

description:
Library name: H7_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor S1

description:
Library name: S1_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells VDJ-B donor S1

description:
Library name: S1_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: IgG, repeat2, CUT&Tag_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: IgG_repeat2

data_processing:
The raw reads were further filtered by Cutadapt (version: cutadapt-4.7).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using Bowtie2 (Version 2.5.1).
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 (version 2.2.9.1) to detect genomic regions enriched for multiple overlapping DNA fragments (peaks).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

source_name: colon

extract_protocol:
Cultured-ILC2s were sorted by FACSMelody.
CUT&Tag libraries was generated and indexed using Hyperactive Universal CUT&Tag Assay Kit for Illumina and then TurePrep Index Kit for Illumina.

value: colon

value: immune cell


title: B-cells GEX donor S1

description:
Library name: S1_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: filtered B-cells


title: T-cells VDJ-T donor H6

description:
Library name: H6_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor H6

description:
Library name: H6_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor H5

description:
Library name: H5_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: IgG, repeat1, CUT&Tag_seq

description: Library name: IgG_repeat1


title: B-cells GEX donor H6

description:
Library name: H6_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: B-cells


title: S20C_16S

city: xuzhou

first: Jianteng

last: zhou

state: JiangSu

address: Tongshan road 209, Xuzhou Medical University, Xuzhou, China

department: College of Life Sciences

institute: Xuzhou Medical University

description:
Library name: S20C_16S
Testicular microbiota INVADE-Seq in 20-month-old mice

library_source: other

data_processing:
scRNA-seq data processing Raw FASTQ files were processed using Cell Ranger (v9.0.0, 10x Genomics) to align reads to the mm10 genome and generate unique molecular identifier (UMI) count matrices. Subsequent analysis was performed using Seurat32 (v4.0.0) in R. Low-quality cells and multiplets were filtered based on: (1) detected genes (<200), (2) total UMIs (<1,000), (3) log10GenesPerUMI (<0.7), (4) mitochondrial UMI percentage (>10%), and (5) hemoglobin UMI percentage (>5%). DoubletFinder 33 (v2.0.3) was applied to identify potential doublets. Normalized data were subjected to principal component analysis (PCA), and the first 50 principal components were used for uniform manifold approximation and projection (UMAP) visualization and clustering via the Louvain algorithm in Seurat. Cell types were allocated to each cluster using the abundance of known marker genes as described previously.
Generation of Bacteria UMI Matrixes from the INVADEseq bacterial 16S rRNA library The bacterial 16S rRNA gene enrichment library was processed to generate UMI matrices according to previous reports23 using a workflow integrating CellRanger, BEDTools34, Trimmomatic35, Picard and GATK PathSeq36. Raw FASTQ files were first processed with CellRanger count to align reads to the reference genome. The resulting BAM file was converted to FASTQ format using BEDTools, and adapter sequences were trimmed from Read 1 using Trimmomatic with parameters to remove low-quality bases and clip the first 15 nucleotides. The trimmed FASTQ was converted back to BAM format with Picard FastqToSam and processed using GATK PathSeq to filter host reads and identify bacterial sequences, using specified reference databases for host and microbial genomes. The output BAM file containing bacterial annotations and summary CSV were then integrated with the corresponding CellRanger output from the gene expression (GEX) library using a custom Python script. This script associated bacterial 16S sequences with valid cell barcodes identified in the GEX library, generating files including genus-level assignments per cell, raw read mappings, and validated bacterial-cell associations.
Integration of Bacteria UMI Matrix with Single-Cell Data The bacterial UMI CSV table was imported as a dataframe with row names set to cell barcodes. The total bacterial UMIs per cell were calculated and added as a new column. This matrix was then merged with the Seurat object containing the single-cell transcriptomic data using AddMetaData, ensuring all cells without detected bacteria were assigned zero values. Cells were classified as bacterial-positive if they harbored ≥1 bacterial UMIs.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: other

source_name: testis

growth_protocol: housed under specific pathogen-free conditions and ad libitum access to food and water.

extract_protocol:
Tissue dissociation was performed under sterile conditions. Freshly collected testes were washed twice with ice-cold RPMI 1640 medium containing 0.04% BSA, minced into ~0.5 mm³ pieces with surgical scissors, and transferred to an enzymatic digestion solution containing RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). Samples were incubated at 37°C for 30–60 min with gentle inversion every 5–10 min. The resulting cell suspension was filtered through a 40-μm cell strainer, centrifuged at 300 × g for 5 min at 4°C, and the pellet was resuspended in medium. Red blood cells were lysed using Miltenyi buffer for 10 min at 4°C. After centrifugation, the pellet was washed once and resuspended in 1 ml RPMI 1640 with 0.04% BSA. Cell concentration and viability were assessed using a Luna-FL counter or Trypan Blue staining.
Single-cell transcriptome sequencing Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, PN-1000263) were used for scRNA-seq and INVADEseq according to the User Guide (CG000331). Single cell suspension was adjusted to 700-1200 cells/μL. 20,000 cells were mixed with reverse transcription Master Mix, 16S primer (5′-GGGTTGCGCTCGTTG-3′, final concentration 16 μmol/L) and loaded into a Chromium chip K with gel beads and partitioning oil to generate GEMs on a 10x Chromium Controller，following with reverse transcription PCR and preamplification of the full-length cDNA. The cDNA QC was performed using Agilent 4150 TapeStation (Agilent Technologies). The cDNA was used to construct the transcriptome sequencing library using a 10x Genomics Library Construction Kit (PN-1000190). High-throughput sequencing was performed on the Illumina NovaSeq X Plus sequencer with PE-150 mode.  INVADEseq Library sequencing The INVADEseq bacterial 16S rRNA library was constructed according to reference25  with minor modification.16S rRNA primers for amplification were Forward Primer (FP): 5′-GATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ and Reverse Primer (RP):5′-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCACGRCA CGAGCTGACGAC-3′. The 16S rRNA gene was enriched from 2 μL of cDNA using 1 μmol/L each of FP and RP, and 50 μL of Amp Mix (10x Genomics, PN-2000047) with the following PCR program: initial denaturation at 98°C for 45 sec; 35 cycles of 98°C for 20 sec, 67°C for 30 sec (with a 2°C/sec gradient warming), and 72°C for 1 min; and a final extension at 72°C for 1 min. The amplified products were purified using 0.8x SPRI beads (Beckman) and size-selected on an agarose gel to recover fragments between 955-1215 bp. A second round of amplification was performed on the recovered products under the same conditions but with 20 cycles. After purification with 0.8x SPRI beads, the product size was confirmed using an Agilent 4150 TapeStation. Following the Chromium Next GEM Single Cell 5' Kit v2 (Dual Index) User Guide, 50 ng of the purified product was adjusted to 30 μL and mixed with 50 μL of Amp Mix (PN-2000047) and 20 μL of Dual Index TT Set A (PN-1000215) for PCR amplification: 98°C for 45 sec; 15 cycles of 98°C for 20 sec, 54°C for 30 sec, and 72°C for 20 sec; and a final extension at 72°C for 1 min. The amplified products were purified with 0.8x SPRI beads, size-selected for 955-1215 bp fragments on an agarose gel, and qualified using an Agilent 4150 TapeStation. High-throughput sequencing was performed on an Illumina NovaSeq X Plus sequencer in PE-150 mode.

value: testis

value: 16s RNA


title: B-cells VDJ-B donor H4

description:
Library name: H4_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript

value: VDJ-B


title: T-cells VDJ-T donor H4

description:
Library name: H4_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells VDJ-B donor H5

description:
Library name: H5_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: S20B_GEX

description:
Library name: S20B_GEX
Single-cell sequencing of testicles in 20-month-old mice

value: mRNA


title: S20B_16S

description:
Library name: S20B_16S
Testicular microbiota INVADE-Seq in 20-month-old mice


title: T-cells VDJ-T donor H3

description:
Library name: H3_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor H5

description:
Library name: H5_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: S20A_GEX

description:
Library name: S20A_GEX
Single-cell sequencing of testicles in 20-month-old mice


title: S5C_GEX

description:
Library name: S5C_GEX
Single-cell sequencing of testicles in 5-month-old mice


title: S20A_16S

description:
Library name: S20A_16S
Testicular microbiota INVADE-Seq in 20-month-old mice


title: S5B_16S

description:
Library name: S5B_16S
Testicular microbiota INVADE-Seq in 5-month-old mice


title: S20C_GEX

description:
Library name: S20C_GEX
Single-cell sequencing of testicles in 20-month-old mice


title: S5A_GEX

description:
Library name: S5A_GEX
Single-cell sequencing of testicles in 5-month-old mice


title: A1

status: Public on Jul 27 2025

first: Chen

last: He

address: Wenhua Road

data_processing:
llumina Casava1.7 sotware used for bascealing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000182965.3 whole genome using hisat2
Fragment Per Kilobase per Million bases of library size (FPKM) were calculated using cufflinks v2.2.1
The differentially expressed genes were detected as previously described based on the parameters of DeSeq2: Fold change > = 2.00 and Probability > = 0.8 with a significant false discovery rate-adjusted P value (FDR) <0.05
Assembly: GCF_000182965.3
Supplementary files format and content: tab delimited text files include FPKM values for each Sample.

organism: Candida albicans

growth_protocol: Overnight grown C. albicans SC5314  was diluted to E6 cells per mL in RPMI1640 medium, and treated with 0.5μg/mL Amb alone or plus 8μg/mL rimonabant at 30℃ for 6 h.  The same volume of dimethyl sulfoxide-treated cells were set as control group.

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 0.5μg/mL Amb


title: S5B_GEX

description:
Library name: S5B_GEX
Single-cell sequencing of testicles in 5-month-old mice


title: T-cells GEX donor H4

description:
Library name: H4_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: GEX


title: B-cells GEX donor H5

description:
Library name: H5_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: S5C_16S

description:
Library name: S5C_16S
Testicular microbiota INVADE-Seq in 5-month-old mice


title: T-cells GEX donor H3

description:
Library name: H3_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: filtered T-cells


title: B-cells VDJ-B donor H6

description:
Library name: H6_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells GEX donor H4

description:
Library name: H4_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: NoTx_3

city: Tucson

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

description: Library name: SAMPLE 12

data_processing:
Raw data of fastq format were  processed through in-house perl scripts. The clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Assembly: Mus Musculus (mm39)
Supplementary files format and content: DESeq2 pvalue<=0.05 |log2FoldChange|>=0.0 DEG tables

source_name: Tumor

extract_protocol:
Animal / Human Tissue
This protocol involves an automated homogenization method that uses liquid nitrogen and a tissue homogenizer to homogenize the tissue sample. After homogenization, TRIzolTM is added to the tube containing the powdered sample, and the mixture is vortexed and incubated to lyse the cells. The supernatant is then transferred to a new tube and mixed with chloroform. The mixture is centrifuged, and the aqueous phase containing RNA is transferred to a new tube. The RNA is then precipitated with isopropanol and washed with ethanol. The result is RNA that can be used for downstream applications.

treatment_protocol: Mice received mono or combo therapies twice weekly ,intraperitoneally (i.p.)

value: Tumor


title: T-cells VDJ-T donor H2

description:
Library name: H2_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript

value: T-cells

value: VDJ-T


title: S5A_16S

description:
Library name: S5A_16S
Testicular microbiota INVADE-Seq in 5-month-old mice


title: T-cells GEX donor H2

description:
Library name: H2_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor S6

description:
Library name: S6_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: No Tx_2

description: Library name: SAMPLE 11


title: No Tx_1

description: Library name: SAMPLE 10


title: Combo_3

description: Library name: SAMPLE 9


title: T-cells VDJ-T donor S6

description:
Library name: S6_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: Combo_2

description: Library name: SAMPLE 8


title: AgoCD40_3

description: Library name: SAMPLE 6


title: AgoCD40_2

description: Library name: SAMPLE 5


title: passage1, mouse #1-5

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Raw RNA-Seq reads were first trimmed for quality and adapter removal using Trim Galore. The cleaned reads were then aligned to the reference genome using HISAT2. Subsequently, read counts were quantified using featureCounts with the Gencode vM33 GTF annotation file.
Assembly: GRCm39
Supplementary files format and content: tab-delimeted raw count matrix

source_name: spleen

extract_protocol:
RNA was extracted using Rneasy mini kit(Qiagen), all samples normalized to 50ng total concentration in 11ul for input to library preparation
Samples were then prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#  E7420) according to manufactures protocol, barcoded using NEBNext® Multiplex Oligos for Illumina (NEB #E6440S/L)

value: spleen


title: B-cells GEX donor S6

description:
Library name: S6_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells GEX donor S5

description:
Library name: S5_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: passage 1, mouse #1-3


title: Combo_1

description: Library name: SAMPLE 7


title: B-cells GEX donor S4

description:
Library name: S4_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: AgoCD40_1

description: Library name: SAMPLE 4


title: T-cells GEX donor S4

description:
Library name: S4_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor S5

description:
Library name: S5_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor S5

description:
Library name: S5_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells VDJ-B donor S6

description:
Library name: S6_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: aIL1R1_3

description: Library name: SAMPLE 3


title: aIL1R1_1

description: Library name: SAMPLE 1


title: aIL1R1_2

description: Library name: SAMPLE 2


title: WT B cells,  mouse #3

source_name: spleen-B cell selected

value: spleen-B cell selected


title: T-cells VDJ-T donor S4

description:
Library name: S4_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: passage 1, mouse #1-4


title: B-cells VDJ-B donor S5

description:
Library name: S5_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells VDJ-B donor S4

description:
Library name: S4_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor S3

description:
Library name: S3_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells GEX donor S3

description:
Library name: S3_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: T-cells VDJ-T donor H1

description:
Library name: H1_VDJ-T
10X genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains transcript


title: WT B cells,  mouse #2


title: T-cells GEX donor H1

description:
Library name: H1_GEX-T
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: WT B cells,  mouse #1


title: B-cells VDJ-B donor H1

description:
Library name: H1_VDJ-B
10X genomics
polyA RNA
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript


title: B-cells GEX donor H1

description:
Library name: H1_GEX-B
10X genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript


title: 150548_C7

city: Zurich

first: Mitchell

last: Levesque

address: Wagistrasse 18

country: Switzerland

institute: University of Zurich

description: 10X Chromium Single Cell 3' v3.1 Chemistry Dual Index

data_processing:
The sequenced reads were processed using the Cell Ranger analysis pipeline v.7.0.1 to generate FASTQ files and align sequencing reads to a pre-built human reference transcriptome version GRCh38-3.0.0 by 10x genomics. The raw binary format output with cell barcodes and unique molecular identifier count results were used for the downstream analysis.
Using the Scanpy tookit, the binary data in hierarchical data format (H5) from each sample were combined into an AnnData object. The basic filtering was performed on the number of genes expressed in the count matrix, total counts per cell and the percentage of counts in mitochondrial genes to reduce the number of poor-quality cells present in the data. The highly variable genes were identified using the built-in function from Scanpy. The doublets were identified using Scrublet and to make each cell comparable, the data is normalized to 10,000 reads per cell and corrected by regressing out using total counts, percentage of the mitochondrial genes expressed and the cell cycle scores. Lastly, the cells expressing high levels of immune cells and CD45+ were excluded from the downstream analysis. For embeddings analysis, the data is corrected using Harmony algorithm to reduce the effects of the sample specific effects, and then the mesenchymal and melanocytic marker expressions data is projected in UMAP.
Assembly: cellranger reference GRCh38-3.0.0
Supplementary files format and content: 10x-Genomics-formatted hdf5 file with observations/cells named by their barcode

extract_protocol:
Describe the protocols used to extract and prepare the material to be sequenced:  The 10x Genomics Chromium system was used for single-cell RNA sequencing. Cells were loaded onto a 10x Chromium Controller according to the manufacturer’s specifications to achieve a target of approximately 1000 - 3000 cells per sample. First-strand cDNA synthesis was performed in droplets using 10x Genomics reagents, then cDNA was amplified using a 15 cycle PCR to generate sufficient material for library construction.
Describe the library construction protocol: cDNA was fragmented, end-repaired, and A-tailed following the 10x Genomics protocol.  Adapters containing sequencing primers and sample indices were ligated to the prepared fragments. Size selection was performed using SPRIselect reagent (Beckman Coulter) to select fragments of approximately 400 bp. The quality and size distribution of the final library were assessed using an Agilent Tapestation using D5000 High Sensitivity reagents.
Single-cell RNA-seq (scRNA-seq) library prepared using 10x Genomics Chromium Single Cell 3' Solution. The libraries were sequenced on an Illumina NextSeq 2000 system, aiming for a depth of approximately 20,000 reads per cell, using paired-end sequencing.

value: melanoma


title: DTC72020

source_name: dissociated tumor cells

value: dissociated tumor cells


title: DTC01220MM


title: 140307_C8


title: COLO320-DM cells YY1-CUT&Tag

city: Tianjin

first: Luning

last: Qin

address: No.38 Tongyan Road, Haihe Education Park, Tianjin, China

institute: Nankai university

description:
Library name: sample4
CUT&Tag for YY1 in 200000 COLO320-DM cells

data_processing:
For the original image data of sequencing results, the software Bcl2fastq (v2.20.0.422) was used for base calling, preliminary quality analysis, and the original sequencing data were obtained. The results were stored in the FASTQ file format. The quality assessment of the sequencing data was analyzed using the software FastQC (v0.11.4). The software Cutadapt (version 1.9.1) was utilized to preprocess the original data, filter out low-quality data, and remove contaminating and adapter sequences. The filtered clean sequencing data were aligned and statistically analyzed with the reference genome hg38 using the alignment software bowtie2 (Version: 2.2.6).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Using the Hieff NGS® Multi-Cut &Tag Library Prep Kit for Illumina® (YEASEN), approximately 200,000 cells were collected, counted, and resuspended in 1× Wash Buffer, followed by the addition of ConA Beads. The mixture was incubated at room temperature for 10 minutes. Next, the cell-magnetic bead complex was resuspended in pre-cooled Primary Antibody Buffer containing lig3 (1:50), YY1 (1:50), H3K4me3 (1:50), and H3K27ac (1:50), and incubated at room temperature for 2 hours. After the incubation, a 1× Dig-300 Buffer containing Anti-mouse Tn5 and Anti-rabbit Tn5 was added to facilitate DNA transposition, which was performed at room temperature for 1 hour. Subsequently, transposase was activated, and the reaction was incubated at 37 °C for 60 minutes. Following transposition, a termination solution containing Proteinase K and a DNA spike-in mix was added, and the reaction was incubated at 55 °C for 30 minutes to digest proteins. Genomic DNA was then purified using DNA Extract Beads.
The library was amplified using HiFi Amplification Mix in a PCR program consisting of an initial 3-minute extension at 72 °C, followed by 3 minutes of denaturation at 95 °C. The amplification cycle included 10 seconds of denaturation at 98 °C, 15 seconds of annealing at 60 °C, and a 1-minute extension at 72 °C. After amplification, the library was purified using DNA Selection Beads, and any residual impurities were removed by magnetic bead recovery and ethanol washing. The beads were air-dried and resuspended in ddH₂O to produce a library suitable for sequencing on the Illumina platform. Library quality was assessed using the Agilent 2100 Bioanalyzer.

value: colorectal cancer

tag: antibody

value: Mouse monoclonal anti-YY1 (H-10), Santa Cruz, Cat# sc-7341;


title: COLO320-HSR cells YY1-CUT&Tag

description:
Library name: sample5
CUT&Tag for YY1 in 200000 COLO320-HSR cells


title: 140307_C2


title: HiC data for COLO320-HSR cells

description:
Library name: sample02
HiCUT in COLO320-DM cells.

data_processing:
The raw image data files obtained from the Illumina sequencing platform are converted into Sequenced Reads through Base Calling analysis, and the results are stored in the FASTQ file format. Referring to the Distiller - nf pipeline, for the clean data obtained from quality control, the bwa software is used to align the data, and the method parameters are selected as bwa mem -SP. Subsequently, pairtools is used to classify the alignment results. The hichipper package is used for correction and then loops are identified, and reads within the range of 5K - 2M are selected for analysis. Subsequently, the diffloop package is used to perform differential analysis on the loop intensities of different samples. The identified loops are filtered for significant loops using FDR < 0.01 and counts > 2.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were first cross-linked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 5 minutes. The cells were then subjected to a secondary cross-linking with 3 mM EGS for 40 minutes, and the cross-linking was quenched with 0.4M glycine for 10 minutes. The doubly cross-linked cells were washed with PBS containing 0.05% bovine serum albumin and permeabilized with 0.05% digitonin at room temperature for 15 minutes. They were subsequently treated with 0.1% SDS at 65 °C for 10 minutes, and SDS was neutralized at 37 °C with 1.8% Triton X-100 for 15 minutes. Chromatin DNA was then digested at 37 °C for 2 hours using 50 U each of MboI and DdeI (NEB), followed by DNA end filling with 15 U Klenow (NEB) and dNTPs at 37 °C for 1 hour. DNA ligation was performed at 16 °C for 4 hours using 50 U T4 DNA Ligase (NEB) to ligate adjacent DNA regions. After washing the cells twice in wash buffer, they were incubated overnight with diluted primary antibody in a Dig-wash buffer containing 2 mM EDTA. The next day, the secondary antibody was added and incubated at room temperature for 1 hour. The cells were washed twice in Dig-Wash buffer to remove unbound antibodies. The pG-Tn5 adapter complex was prepared in Dig-300 buffer and incubated with the cells at room temperature for 1 hour, followed by two washes to remove unbound pG-Tn5. The cells were then resuspended in Tagmentation buffer and incubated at 37 °C for 1 hour. Tagmentation was terminated by incubation at 55 °C for 1 hour in a solution containing 16 mM EDTA, 0.1% SDS, and 0.16 mg/mL protease K. DNA was extracted using phenol-chloroform-isoamyl alcohol and ethanol precipitation.
Library amplification was performed by PCR: 3 minutes at 72 °C, 30 seconds at 98 °C, followed by 16 cycles of 15 seconds at 98 °C, 30 seconds at 60 °C, and 30 seconds at 72 °C, with a final 3-minute extension at 72 °C. The amplified DNA was purified using Ampure XP beads, and the libraries were sequenced on the Illumina NovaSeq platform.


title: WCM1078_veh_rep2

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: ne1078_veh2

data_processing:
STAR RSEM
Assembly: hg38
Supplementary files format and content: tsv

source_name: prostate

extract_protocol:
RNA was extracted using Qiagen column purification kit
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: prostate

value: patient-derived organoids

value: WT

value: vehicle


title: COLO320-DM cells H3K27ac-CUT&Tag

description:
Library name: sample1
CUT&Tag for H3K27ac in 200000 COLO320-DM cells

value: H3K27ac, CST, Cat#8173T


title: 150548_C8


title: COLO320-DM cells H3K4me3-CUT&Tag

description:
Library name: sample2
CUT&Tag for H3K4me3 in 200000 COLO320-DM cells

value: H3K4me3, CST, Cat#9751T