title: L26298_TNFa+IL4_treated_3

city: New York

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

data_processing:
The FastQ files from sequencing were aligned to human genome (GRCh38) using gsnap (2017-11-15) with default options. The read counts for each gene were calculated using featureCounts (version 1.6.0) and GTF file from ensemble genome browser (Homo_sapiens.GRCh38.91.gtf.
Assembly: GRCh38
Supplementary files format and content: lab1456_featureCounts_table_s2.tab

source_name: Primary astroglia

growth_protocol: Hydrogels were prepared using a StarPEG-heparin backbone. Human astrocytes were encapsulated in 3D hydrogels using 6.00 mM heparin and 2.24 mM StarPEG. The polymers were dissolved in DPBS (Dulbecco's Phosphate-Buffered Saline without magnesium or calcium) and mixed in a 1:1 volume ratio under sterile conditions to achieve a final volume of 50 µl per hydrogel. The hydrogel polymerization occurred at room temperature for 30 minutes before cell encapsulation.

extract_protocol:
RNA was isolated from hydrogels using the RNA was isolated using Norgen Total RNA Purification Kit.
Complete cDNA was synthesized from the obtained mRNA with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase. After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75bp single-end sequencing on the Illumina HiSeq2000 platform providing on average 31 million reads per sample.

treatment_protocol: Human astrocytes encapsulated in hydrogels were treated with TNFα (Peprotech, catalog no. 300-01A, 0.1 μg/ml, 5.7471 nM), IL4 (Peprotech, catalog no. 200-04, 0.1 μg/ml, 6.6225 nM), or a combination of both. These treatments were prepared by diluting stock solutions in complete astrocyte medium (Astrocyte medium, ScienCell Res. Lab., catalog no. 1801, supplemented with 2% FBS, 1X Astrocyte Growth Supplement, and 1X Pen/Strep) and were applied continuously over 21 days.

value: Primary astroglia

value: wild type


title: 33219_HepG2_FOXA1_rep2-1

status: Public on Jul 02 2026

type: SRA

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

country: USA

institute: Cornell University

library_source: genomic

data_processing:
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg38
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome
Library strategy: Benzonase ChIP-exo (6.1)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 cells were grown in suspension at ~0.5-1.0 x 106 cell/mL in complete IMDM with ~10% FBS and ~1% PenStrep at 5% CO2 and 37oC.

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C.  Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA), The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected.
Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.

tag: cell line

tag: growthmedia

value: DMEM

tag: pegr id

tag: method

value: Benzonase ChIP-exo (6.1)

tag: target

tag: antibody

tag: biological replicate

tag: resequencing replicate


title: Mix-IV-Replicate-4

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

description: Library name: X16

library_source: transcriptomic

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Mus_musculus.GRCm39) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values. We started with 35,534 genes and removed 15,077 sparse genes, leaving us with 20,457 genes. We normalized each sample’s reads to 1M reads.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text file includes both ENSMUSG and gene name identifiers, and normalized expression levels per gene.

molecule: total RNA

organism: Mus musculus

source_name: Whole colon

growth_protocol: C57BL6/J mice were bred and maintained under a 12-hour light/dark cycle and fed standard chow in SPF conditions at the Azrieli Faculty of Medicine of the Bar-Ilan University. 8- to 12-week-old mice were used for all experiments.

extract_protocol:
RNA from flash frozen colonic tissues was extracted using RNeasy Plus Universal mini kit (Qiagen). The integrity of the isolated RNA was analyzed using the Agilent TS HS RNA Kit and TapeStation 4200 at the Genome Technology Center at the Azrieli Faculty of Medicine, Bar-Ilan University. 1000 ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L).
RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L).  Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via either oral gavage, intraperitoneal or intravenous injection. Mice received 2.5mg of either ampicillin, metronidazole, neomycin, vancomycin or a mix of all four antibiotics, in 100µl of PBS. Control mice received 100µl of PBS. Four hours after the last treatment mice were euthanized and tissues extracted.

tag: tissue

value: Whole colon

tag: genotype

value: WT

tag: treatment

value: Mix-IV


title: Player 3 pre-soccer match

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

description: Library name: player_3_socpre

data_processing:
RNA-seq reads were demultiplexed using bcl2fastq/2.20.0 and preprocessed with fastp/0.23.4. Gene abundance was quantified with Salmon/1.5.2.
Assembly: GENCODE Release 39 based on GRCh38
Supplementary files format and content: csv text file includes the counts for each sample

molecule: polyA RNA

source_name: muscle

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientiﬁc)
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, #E7490 and #E7760)

value: muscle


title: L26297_TNFa+IL4_treated_2

tag: cell type


title: ChIPseq_SynTEF1_RGFP109_Input_for_S5P_rep2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description:
Library name: 2511474_S5P_SynTEF1_109_Input
Drosophila melanogaster spike-in

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000. Samples with Drosophila melanogaster spike-in were mapped the the human-fly hybrid genome instead, and reads mapping to human reference were further extracted.
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Assembly: hg38 (GRCh38.p12), dm6
Supplementary files format and content: bigwig, narrowPeak (narrow peaks signals) and BED files (broad peak signals)

source_name: B-Lymphocyte

growth_protocol: RPMI + 15% FBS + anti/anti. BRD4 samples were grown -anti/anti

extract_protocol:
Chromatin was immunoprecipitated using the standard Covaris protocol and purified on silica columns. Samples with Drosophila melanogaster spike-in were processed using a common ChIP protocol and purified using phenol-chloroform extraction
Libraries were constructed using standard Illumina protocols

treatment_protocol: Samples were treated for 24 hours using indicated compounds

value: B-Lymphocyte

value: Patient Derived B-Lymphocytes

tag: chip antibody

tag: batch


title: ChIPseq_SynTEF1_RGFP109_S5P_rep2

description:
Library name: 2511473_S5P_SynTEF1_109_IP
Drosophila melanogaster spike-in

value: S5P, Active Motif 61085


title: Mix-IV-Replicate-3

description: Library name: X15


title: Player 3 post-soccer match

description: Library name: player_3_socpost


title: ChIPseq_RGFP109_Input_for_S5P_rep2

description:
Library name: 2511472_S5P_109_Input
Drosophila melanogaster spike-in


title: L26295_TNFa+IL4_treated_1


title: Mix-IV-Replicate-2

description: Library name: X14


title: ChIPseq_RGFP109_S5P_rep2

description:
Library name: 2511471_S5P_109_IP
Drosophila melanogaster spike-in


title: L26291_IL4_treated_3


title: ChIPseq_SynTEF1_Input_for_S5P_rep2

description:
Library name: 2511470_S5P_SynTEF1_Input
Drosophila melanogaster spike-in


title: Mix-IV-Replicate-1

description: Library name: X13


title: ChIPseq_SynTEF1_S5P_rep2

description:
Library name: 2511469_S5P_SynTEF1_IP
Drosophila melanogaster spike-in


title: L26290_IL4_treated_2


title: Mix-IP-Replicate-6

description: Library name: X9

value: Mix-IP


title: ChIPseq_DMSO_Input_for_S5P_rep2

description:
Library name: 2511468_S5P_DMSO_Input
Drosophila melanogaster spike-in

value: DMSO


title: ChIPseq_DMSO_S5P_rep2

description:
Library name: 2511467_S5P_DMSO_IP
Drosophila melanogaster spike-in


title: L26289_IL4_treated_1


title: ChIPseq_SynTEF1_RGFP109_Input_for_S2P_rep2

description:
Library name: 2511466_S2P_SynTEF1_109_Input
Drosophila melanogaster spike-in


title: Mix-IP-Replicate-5

description: Library name: X8


title: ChIPseq_SynTEF1_RGFP109_S2P_rep2

description:
Library name: 2511465_S2P_SynTEF1_109_IP
Drosophila melanogaster spike-in

value: S2P, Active Motif 61083


title: ChIPseq_RGFP109_Input_for_S2P_rep2

description:
Library name: 2511464_S2P_109_Input
Drosophila melanogaster spike-in


title: Mix-IP-Replicate-4

description: Library name: X7


title: ChIPseq_RGFP109_S2P_rep2

description:
Library name: 2511463_S2P_109_IP
Drosophila melanogaster spike-in


title: L26288_TNFa_treated_3

value: TNFa


title: ChIPseq_SynTEF1_Input_for_S2P_rep2

description:
Library name: 2511462_S2P_SynTEF1_Input
Drosophila melanogaster spike-in


title: Mix-IP-Replicate-3

description: Library name: X12


title: L26287_TNFa_treated_2


title: ChIPseq_SynTEF1_S2P_rep2

description:
Library name: 2511461_S2P_SynTEF1_IP
Drosophila melanogaster spike-in


title: L26286_TNFa_treated_1


title: Mix-IP-Replicate-2

description: Library name: X11


title: ChIPseq_DMSO_Input_for_S2P_rep2

description:
Library name: 2511460_S2P_DMSO_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_Input_for_Pol2_rep2

description:
Library name: 2511458_Pol2_SynTEF1_109_Input
Drosophila melanogaster spike-in


title: L26294_Control_3

value: PBS


title: Mix-IP-Replicate-1

description: Library name: X10


title: ChIPseq_SynTEF1_RGFP109_Pol2_rep2

description:
Library name: 2511457_Pol2_SynTEF1_109_IP
Drosophila melanogaster spike-in

value: Pol2, Active Motif 61667


title: L26293_Control_2

value: Primary astroglia


title: ChIPseq_RGFP109_Input_for_Pol2_rep2

description:
Library name: 2511456_Pol2_109_Input
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_S2P_rep2

description:
Library name: 2511459_S2P_DMSO_IP
Drosophila melanogaster spike-in


title: Metronidazole-PO-Replicate-6

description: Library name: M6

value: Metronidazole-PO


title: L26292_Control_1

value: wild type


title: ChIPseq_SynTEF1_Input_for_Pol2_rep2

description:
Library name: 2511454_Pol2_SynTEF1_Input
Drosophila melanogaster spike-in


title: Metronidazole-PO-Replicate-5

description: Library name: M5


title: ChIPseq_SynTEF1_Pol2_rep2

description:
Library name: 2511453_Pol2_SynTEF1_IP
Drosophila melanogaster spike-in


title: 34622_K562_SMC3_rep1-1

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C.  Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA),  The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected.
Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.

value: IMDM

value: Benzonase ChIP-exo (6.1)


title: ChIPseq_RGFP109_Pol2_rep2

description:
Library name: 2511455_Pol2_109_IP
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_Input_for_Pol2_rep2

description:
Library name: 2511452_Pol2_DMSO_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_Input_for_S5P_rep1

description:
Library name: 2495083_S5P_Syn109_Input
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_Pol2_rep2

description:
Library name: 2511451_Pol2_DMSO_IP
Drosophila melanogaster spike-in


title: 34621_K562_RAD21_rep2-1


title: Metronidazole-PO-Replicate-4

description: Library name: M4

value: Whole colon

value: WT


title: ChIPseq_SynTEF1_RGFP109_S5P_rep1

description:
Library name: 2495082_S5P_Syn109_IP
Drosophila melanogaster spike-in


title: Metronidazole-PO-Replicate-3

description: Library name: M3


title: ChIPseq_RGFP109_Input_for_S5P_rep1

description:
Library name: 2495081_S5P_109_Input
Drosophila melanogaster spike-in


title: Metronidazole-PO-Replicate-2

description: Library name: M2


title: 32070_K562_RAD21_rep1-1


title: ChIPseq_RGFP109_S5P_rep1

description:
Library name: 2495080_S5P_109_IP
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_Input_for_S5P_rep1

description:
Library name: 2495079_S5P_SynTEF1_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_S5P_rep1

description:
Library name: 2495078_S5P_SynTEF1_IP
Drosophila melanogaster spike-in


title: Metronidazole-PO-Replicate-1

description: Library name: M1


title: 32119_K562_RAD21_rep1-2


title: 34598_K562_NFIA_rep2-1

value: NFIA


title: ChIPseq_DMSO_S5P_rep1

description:
Library name: 2495076_S5P_DMSO_IP
Drosophila melanogaster spike-in

value: B-Lymphocyte


title: 32116_K562_NFIA_rep1-2


title: Metronidazole-IV-Replicate-4

description: Library name: M18

value: Metronidazole-IV


title: Metronidazole-IV-Replicate-3

description: Library name: M17


title: ChIPseq_SynTEF1_RGFP109_Input_for_S2P_rep1

description:
Library name: 2495075_S2P_Syn109_Input
Drosophila melanogaster spike-in

value: Patient Derived B-Lymphocytes


title: ChIPseq_SynTEF1_RGFP109_S2P_rep1

description:
Library name: 2495074_S2P_Syn109_IP
Drosophila melanogaster spike-in


title: 32067_K562_NFIA_rep1-1


title: ChIPseq_DMSO_Input_for_S5P_rep1

description:
Library name: 2495077_S5P_DMSO_Input
Drosophila melanogaster spike-in


title: ChIPseq_RGFP109_Input_for_S2P_rep1

description:
Library name: 2495073_S2P_109_Input
Drosophila melanogaster spike-in


title: Metronidazole-IV-Replicate-2

description: Library name: M15


title: ChIPseq_RGFP109_S2P_rep1

description:
Library name: 2495072_S2P_109_IP
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_Input_for_S2P_rep1

description:
Library name: 2495071_S2P_SynTEF1_Input
Drosophila melanogaster spike-in


title: Metronidazole-IV-Replicate-1

description: Library name: M14


title: ChIPseq_SynTEF1_S2P_rep1

description:
Library name: 2495070_S2P_SynTEF1_IP
Drosophila melanogaster spike-in


title: 33924_K562_CTCF_rep2-1

value: CTCF


title: 28802_H4_2-2

data_processing:
*library strategy: ChIP-exo
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg19
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

growth_protocol: Growth protocol: K562 cells were grown in suspension at ~0.5-1.0 x 106 cell/mL in complete IMDM with ~10% FBS and ~1% PenStrep at 5% CO2 and 37oC.

extract_protocol:
Cells were poured into methanol-free formaldehyde (final 1% concentration) at room temperature with gentle mixing for 10 min (cells for Pol II ChIP-exo was crosslinked in 1x PBS for 5 mins). Reactions were quenched with 3M Tris (pH 8.0), with 2 moles of Tris per 1 mole of formaldehyde, for at least 5 min. Fixed cells were washed with PBS, lysed with detergent containing buffers and needle lysis. Chromatin for histones was digested with benzonase, while chromatin for Pol II was sonicated.
Benzonase digested or sonicated chromatin was centrifuged at 16,363 x g for 15 min at 4oC and the supernatant was used ChIP. ProteinA/G Sepharose beads were washed, pre-cleared with tRNA, and attached to antibodies against either histone, histone variants, histone modifications or Pol II. 10 million cell-equivalents of fixed, Benzonase-digested chromatin was added to antibody-coated beads and incubated overnight on rototorque at 4oC. Immunoprecipitated chromatin on resin was washed and then underwent A-tailing, ExA2_iNN/ExA2B oligo ligation with addition of PNK, Phi29-based Fill-in, Lambda exonuclease digestion, and overnight reverse crosslinking and protein digestion. DNA was then purified with Ampure beads, splint ligated to ExA1-58/ExA1-SSL_N5 adapters, purified again, and amplified by PCR with Illumina P1.3 and P2.1 primers for 18 cycles. Amplified libraries were size selected by gel electrophoresis in the range from 200-500 bp. Libraries were sequenced with the Illumina NextSeq 550, paired-end mode.

value: Benzonase ChIP-exo

tag: fraction

value: super

tag: benzonase digestion

tag: sonication

value: no


title: ChIPseq_DMSO_S2P_rep1

description:
Library name: 2495068_S2P_DMSO_IP
Drosophila melanogaster spike-in

tag: cell line

value: DMSO

value: S2P, Active Motif 61083


title: Metronidazole-IP-Replicate-4

description: Library name: M8

value: Metronidazole-IP


title: ChIPseq_DMSO_Input_for_S2P_rep1

description:
Library name: 2495069_S2P_DMSO_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_Input_for_Pol2_rep1

description:
Library name: 2495067_Pol2_Syn109_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_Pol2_rep1

description:
Library name: 2495066_Pol2_Syn109_IP
Drosophila melanogaster spike-in

value: Pol2, Active Motif 61667


title: 28797_H4_1-2


title: Metronidazole-IP-Replicate-2

description: Library name: M12


title: ChIPseq_RGFP109_Input_for_Pol2_rep1

description:
Library name: 2495065_Pol2_109_Input
Drosophila melanogaster spike-in


title: ChIPseq_RGFP109_Pol2_rep1

description:
Library name: 2495064_Pol2_109_IP
Drosophila melanogaster spike-in


title: 28457_H4_1-1


title: 28465_H4_2-1


title: ChIPseq_SynTEF1_Input_for_Pol2_rep1

description:
Library name: 2495063_Pol2_SynTEF1_Input
Drosophila melanogaster spike-in


title: Metronidazole-IP-Replicate-3

description: Library name: M7


title: Metronidazole-IP-Replicate-1

description: Library name: M10


title: ChIPseq_SynTEF1_Pol2_rep1

description:
Library name: 2495062_Pol2_SynTEF1_IP
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_Input_for_Pol2_rep1

description:
Library name: 2495061_Pol2_DMSO_Input
Drosophila melanogaster spike-in


title: 25973_H3K9ac_4-1


title: Ampicillin-PO-Replicate-6

description: Library name: A6

value: Ampicillin-PO


title: ChIPseq_DMSO_Pol2_rep1

description:
Library name: 2495060_Pol2_DMSO_IP
Drosophila melanogaster spike-in


title: 25966_H3K9ac_3-1


title: Ampicillin-PO-Replicate-5

description: Library name: A5


title: ChIPseq_SynTEF1_RGFP109_Input_for_H3K9me3_rep2

description:
Library name: 2495059_K9me3_Syn109_R3_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_H3K9me3_rep2

description:
Library name: 2495058_K9me3_Syn109_R3_IP
Drosophila melanogaster spike-in

value: H3K9me3, Abcam Ab8898


title: 25870_H3K9ac_2-1


title: Ampicillin-PO-Replicate-4

description: Library name: A4


title: ChIPseq_RGFP109_Input_for_H3K9me3_rep2

description:
Library name: 2495057_K9me3_109_R3_Input
Drosophila melanogaster spike-in


title: ChIPseq_RGFP109_H3K9me3_rep2

description:
Library name: 2495056_K9me3_109_R3_IP
Drosophila melanogaster spike-in


title: 25862_H3K9ac_1-1


title: ChIPseq_SynTEF1_H3K9me3_rep2

description:
Library name: 2495054_K9me3_SynTEF1_R3_IP
Drosophila melanogaster spike-in


title: 28809_H3K4me3_6-1


title: Ampicillin-PO-Replicate-3

description: Library name: A3


title: ChIPseq_SynTEF1_Input_for_H3K9me3_rep2

description:
Library name: 2495055_K9me3_SynTEF1_R3_Input
Drosophila melanogaster spike-in


title: Ampicillin-PO-Replicate-2

description: Library name: A2


title: ChIPseq_DMSO_Input_for_H3K9me3_rep2

description:
Library name: 2495053_K9me3_DMSO_R3_Input
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_H3K9me3_rep2

description:
Library name: 2495052_K9me3_DMSO_R3_IP
Drosophila melanogaster spike-in


title: Ampicillin-PO-Replicate-1

description: Library name: A1


title: 28805_H3K4me3_5-1


title: ChIPseq_SynTEF1_RGFP109_Input_for_H3K9me3_rep1

description:
Library name: 2495051_K9me3_Syn109_R2_Input
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_RGFP109_H3K9me3_rep1

description:
Library name: 2495050_K9me3_Syn109_R2_IP
Drosophila melanogaster spike-in


title: Ampicillin-IV-Replicate-6

description: Library name: A18

value: Ampicillin-IV


title: ChIPseq_RGFP109_Input_for_H3K9me3_rep1

description:
Library name: 2495049_K9me3_109_R2_Input
Drosophila melanogaster spike-in


title: ChIPseq_RGFP109_H3K9me3_rep1

description:
Library name: 2495048_K9me3_109_R2_IP
Drosophila melanogaster spike-in


title: 25965_H3K4me3_3-1


title: 25972_H3K4me3_4-1


title: Ampicillin-IV-Replicate-5

description: Library name: A17

value: Whole colon


title: OVCA-V026_H3K4me3_ChIPseq

status: Public on Jul 03 2026

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14 and MACS2

growth_protocol: All cell lines were expanded and maintained in specified growth medium from ATCC or MDACC.

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

value: Ovarian cancer cell line


title: ChIPseq_SynTEF1_H3K9me3_rep1

description:
Library name: 2495046_K9me3_SynTEF1_R2_IP
Drosophila melanogaster spike-in


title: ChIPseq_SynTEF1_Input_for_H3K9me3_rep1

description:
Library name: 2495047_K9me3_SynTEF1_R2_Input
Drosophila melanogaster spike-in


title: ChIPseq_DMSO_Input_for_H3K9me3_rep1

description:
Library name: 2495045_K9me3_DMSO_R2_Input
Drosophila melanogaster spike-in


title: 25869_H3K4me3_2-1


title: Ampicillin-IV-Replicate-4

description: Library name: A16

value: WT


title: ChIPseq_DMSO_H3K9me3_rep1

description:
Library name: 2495044_K9me3_DMSO_R2_IP
Drosophila melanogaster spike-in

value: B-Lymphocyte


title: 25861_H3K4me3_1-1


title: Ampicillin-IV-Replicate-3

description: Library name: A15


title: KI_3, Sample, Donor3

city: Granada

first: Karim

last: Benabdellah

state: Granada

address: Avenida de la Ilustración 114

country: Spain

institute: GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS Granada

description: Library name: KI_sample3

data_processing:
Quality control with fastQC v0.12.1 and MultiQC v1.25.1
Trimming of Illumina Multiplexing PCR Primer 2.01 performed with cutadapt v4.9
Reference gtf and fasta files  Homo_sapiens.GRCh38.113.gtf Homo_sapiens.GRCh38.dna.toplevel.fa, mapped with rsem v1.3.3 and STAR 2.7.11b
Files for lanes and reads where properly concatenated
Expression calculated with rsem and STAR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing each sample raw counts by columns

source_name: Peripheral blood

growth_protocol: Human T cells were cultured in TexMACS medium (Miltenyi Biotec) supplemented with 20 ng/mL IL-2 (Miltenyi Biotec), 5% human AB serum (Biowest), and 1% P/S (Biowest) at a density of 1x106 cells/mL, at 37°C with 5% CO2

extract_protocol:
Total RNA from edited and unedited CAR T cells was extracted after three days post αCD3-αCD28 activation with the High Pure RNA Isolation Kit (Roche) according to the manufacturer’s recommendation and later purified and concentrated with the RNA Cleanup Kit (Monarch). The RNA quantity and purity (A260/ A280) ratio were measured on a Nanodrop spectrophotometer (Thermo Fisher Scientific), and the RNA integrity number (RIN) was determined using a 2100 Bioanalyzer with an Agilent RNA 6000 Pico kit (Agilent).
mRNA-Sequencing was carried out by Novogene (UK) Company Ltd. Sample quality control, including RIN, was assessed with an Agilent 5400.  Subsequently , strand-specific library preparation, including polyA-enrichment, was performed according to their standard protocols and 30M paired-end reads were sequenced on an Illumina NovaSeq X Plus sequencer, using paired-end 150-bp sequencing strategy.

treatment_protocol: Edited and unedited CAR T cells was extracted after three days post αCD3-αCD28 activation

value: Peripheral blood

value: Human T cell

value: CAR T cell

value: T cell PD-1KIL-15 CAR T, Kock-In of IL-15 in PDCD1 locus


title: KI_2, Sample, Donor2

description: Library name: KI_sample2


title: 28463_H3K4me1_2-1

value: Benzonase ChIP-exo

value: super


title: Ampicillin-IV-Replicate-2

description: Library name: A14


title: KO_3, Sample, Donor3

description: Library name: KO_sample3

value: T cell PD-1 KO, Knock-out of PDCD1 locus

value: PD-1 KO CAR T cells was αCD3-αCD28 activated during three days


title: 28455_H3K4me1_1-1

value: no


title: Ampicillin-IV-Replicate-1

description: Library name: A13


title: 25974_H3K36me3_4-1


title: KO_1, Sample, Donor1

description: Library name: KO_sample1


title: KO_2, Sample, Donor2

description: Library name: KO_sample2


title: KI_1, Sample, Donor1

description: Library name: KI_sample1


title: WT_3, Control, Donor3

description: Library name: Ctrl_sample3

value: T cell WT, control

value: WT CAR T cells was αCD3-αCD28 activated during three days


title: Ampicillin-IP-Replicate-6

description: Library name: A9

value: Ampicillin-IP


title: 25967_H3K36me3_3-1


title: WT_2, Control, Donor2

description: Library name: Ctrl_sample2


title: WT_1, Control, Donor1

description: Library name: Ctrl_sample1


title: Ampicillin-IP-Replicate-5

description: Library name: A8


title: NCI-H69 cells, si-CSNK2B, input DNA for RBBP4 ChIP-seq

city: suzhou

first: Jiahao

last: Guo

address: Address: 16 Baita West Road, Gusu District, Suzhou

country: China

institute: SUZHOU MUNICIPAL HOSPITAL

description:
Library name: NCIH69_siCSNK2B_RBBP4_Input
Input DNA control for the RBBP4 ChIP-seq experiment after CSNK2B knockdown.

data_processing:
Raw reads were assessed by FastQC.
Low-quality reads (Phred score <20) and adapter sequences were removed using Trim Galore v0.6.7 to obtain clean reads.
Clean reads were aligned to the human reference genome GRCh38 using Bowtie2 v2.4.5.
Peaks were called with MACS2 v2.2.7.1 using q-value <0.05.
Differential binding peaks between si-CSNK2B and control samples were analyzed using DiffBind v3.4.11 with |log2(fold change)| >= 1 and FDR <0.05. Peaks were annotated using ChIPseeker v1.28.3 and GREAT v4.0.4; visualization used IGV v2.11.1 and ggplot2 v3.3.5.
Assembly: GRCh38
Supplementary files format and content: XLS file containing differential peaks and RPKM values for si-CSNK2B versus control samples.
Supplementary files format and content: FASTQ files contain raw paired-end sequencing reads.

source_name: lung

growth_protocol: NCI-H69 human small cell lung cancer cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2. Cells were routinely tested negative for mycoplasma.

extract_protocol:
NCI-H69 cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. Chromatin was sheared to 200-500 bp fragments. Immunoprecipitation was performed with anti-RBBP4 antibody (Abcam, ab79416; ChIP 1:100) or anti-P300 antibody (Abcam, ab275378; ChIP 1:100) and Protein A/G magnetic beads overnight at 4°C; input DNA was processed in parallel. Immunocomplexes were washed, reverse-crosslinked at 65°C for 8 h, digested with proteinase K, and ChIP DNA was purified.
ChIP DNA libraries were generated by end repair, A-tailing, adapter ligation, size selection of 250-350 bp fragments, and PCR amplification. Libraries were sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000 platform by Wuhan Kangce Biological Technology Co., Ltd.

treatment_protocol: NCI-H69 cells were transfected with siRNA targeting CSNK2B or non-targeting control siRNA using Lipofectamine RNAiMAX. Cells were harvested 48 h after transfection for ChIP-seq.

value: lung

value: small cell lung cancer cell line

value: siRNA-mediated CSNK2B knockdown

value: RBBP4 input


title: NCI-H69 cells, si-CSNK2B, RBBP4 ChIP-seq

description:
Library name: NCIH69_siCSNK2B_RBBP4_ChIP
Chromatin immunoprecipitated with anti-RBBP4 antibody (Abcam, ab79416; ChIP 1:100) after CSNK2B knockdown.


title: 25871_H3K36me3_2-1


title: Ampicillin-IP-Replicate-4

description: Library name: A7

value: Whole colon

value: WT


title: NCI-H69 cells, non-targeting siRNA, input DNA for RBBP4 ChIP-seq

description:
Library name: NCIH69_siNC_RBBP4_Input
Input DNA control for the RBBP4 ChIP-seq experiment.

value: non-targeting control siRNA


title: NCI-H69 cells, non-targeting siRNA, RBBP4 ChIP-seq

description:
Library name: NCIH69_siNC_RBBP4_ChIP
Chromatin immunoprecipitated with anti-RBBP4 antibody (Abcam, ab79416; ChIP 1:100).


title: 25863_H3K36me3_1-1


title: Ampicillin-IP-Replicate-3

description: Library name: A12


title: NCI-H69 cells, si-CSNK2B, input DNA for P300 ChIP-seq

description:
Library name: NCIH69_siCSNK2B_P300_Input
Input DNA control for the P300 ChIP-seq experiment after CSNK2B knockdown.

value: P300 input


title: NCI-H69 cells, si-CSNK2B, P300 ChIP-seq

description:
Library name: NCIH69_siCSNK2B_P300_ChIP
Chromatin immunoprecipitated with anti-P300 antibody (Abcam, ab275378; ChIP 1:100) after CSNK2B knockdown.


title: Ampicillin-IP-Replicate-2

description: Library name: A11


title: NCI-H69 cells, non-targeting siRNA, input DNA for P300 ChIP-seq

description:
Library name: NCIH69_siNC_P300_Input
Input DNA control for the P300 ChIP-seq experiment.


title: NCI-H69 cells, non-targeting siRNA, P300 ChIP-seq

description:
Library name: NCIH69_siNC_P300_ChIP
Chromatin immunoprecipitated with anti-P300 antibody (Abcam, ab275378; ChIP 1:100).


title: Ampicillin-IP-Replicate-1

description: Library name: A10


title: PeCa70_patient_tissue_sample

city: Homburg

first: Johannes

last: Linxweiler

address: Kirrberger Straße 100

country: Germany

institute: Saarland University

description: Library name: PeCa70_tissue

data_processing:
The reads of all probes were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2). Mapping was done against the Homo sapiens (hg38; GRCh38.107) (July 20, 2022) genome sequence.
Assembly: Mapping was done against the Homo sapiens (hg38; GRCh38.107) (July 20, 2022) genome sequence.
Supplementary files format and content: xlsx Tab including raw counts, RPKM, TPM and CPM values for all samples in seprarate columns

source_name: penile cancer

extract_protocol:
DNA and total RNA was isolated from patient tissue samples, matched primary cell cultures and first-generation xenograft tumors using RNeasy, RNeasy FFPE, QIAamp DNA and QIAamp DNA FFPE kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Concentration and purity of isolated DNA and RNA were analyzed with a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Schwerte, Germany). RNA-seq was performed as 3´-mRNA sequencing in a NovaSeq6000 sequencing system (Illumina, San Diego, CA, USA) with a QuantiSeq 3´-mRNA Library Prep (Lexogen, Vienna, Austria) and a 10M raw read coverage using 500 ng of highly pure RNA (A260 / A280 > 1.8, A260 / A230 > 2.0).
RNA-libraries for RNA-seq were prepared using a QuantiSeq 3´-mRNA Library Prep (Lexogen, Vienna, Austria) according to the manufacturers instructions.

value: penile cancer


title: 28796_H3K27me3_1-2

value: Benzonase ChIP-exo


title: PeCa70_primary_culture

description: Library name: PeCa70_culture

source_name: penile cancer primary culture

value: penile cancer primary culture


title: 28456_H3K27me3_1-1

value: super


title: PeCa65_primary_culture

description: Library name: PeCa65_culture


title: PeCa65_patient_tissue_sample

description: Library name: PeCa65_tissue


title: SPF Vancomycin ZT11 replicate 4

description: Library name: S32

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Mus_musculus.GRCm39) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text files include both ENSMUSG and gene name identifiers, and normalized expression levels per gene.

source_name: SPF

growth_protocol: Swiss Webster mice were bred and maintained under a 12-hour light/dark cycle and fed standard chow in either SPF or germ-free conditions at the Azrieli Faculty of Medicine of the Bar-Ilan University. 8- to 12-week-old mice were used for all experiments.

treatment_protocol: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via intraperitoneal injection. Mice received 2.5mg vancomycin in 100µl of PBS. Control mice received 100µl of PBS. For treatment of germ-free mice, mice were removed from sterile isolators into Tecniplast ISOchages, where they were maintained for the duration of the treatment.

value: Vancomycin


title: SPF Vancomycin ZT11 replicate 3

description: Library name: S31


title: PeCa60_primary_culture

description: Library name: PeCa60_culture


title: 28810_H3K27ac_6-1

value: no


title: SPF Vancomycin ZT11 replicate 2

description: Library name: S30


title: PeCa60_patient_tissue_sample

description: Library name: PeCa60_tissue


title: PeCa53_primary_culture

description: Library name: PeCa53_culture


title: 28806_H3K27ac_5-1


title: PeCa53_patient_tissue_sample

description: Library name: PeCa53_tissue


title: SPF Vancomycin ZT11 replicate 1

description: Library name: S29


title: DHT/TGFB5

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

description: Library name: Sample 8

data_processing:
Raw data QC (fastp/FastQC) → HISAT2 genome alignment → StringTie transcript assembly & FPKM quantification → rMATS alternative splicing analysis → SNP/InDel calling (samtools/bcftools) → DESeq2 differential gene analysis → GO/KEGG enrichment & GSEA → PPI network construction.
Assembly: GRCh38 (hg38), Ensembl v109
Supplementary files format and content: *.fastq.gz: clean filtered sequencing reads .bam/.bai: genome alignment data CSV/TXT matrix: gene FPKM expression values VCF: SNP & InDel variation information GTF: assembled novel transcripts TXT tables: alternative splicing, DEG, GO/KEGG, GSEA and PPI results PNG/PDF: all quality control and statistical visualization figures

source_name: Normal human renal cortex

extract_protocol:
Total RNA extraction with TRIzol reagent; RNA quality controlled by Agilent 2100 (RIN ≥ 6.8).
mRNA enrichment by oligo(dT); cDNA synthesis, adapter ligation, fragment selection and PCR amplification for Illumina PE library.

value: Normal human renal cortex

value: Primary human renal tubular epithelial cells (hTECs)

value: hTECs


title: DHT/TGFB3

description: Library name: Sample 6


title: 25969_H3K27ac_4-1


title: 25962_H3K27ac_3-1


title: DHT/TGFB2

description: Library name: Sample 5


title: SPF PBS ZT11 replicate 3

description: Library name: S27

value: PBS


title: 25866_H3K27ac_2-1


title: DHT/TGFB1

description: Library name: Sample 4


title: NC_3

description: Library name: Sample 3


title: SPF PBS ZT11 replicate 2

description: Library name: S26


title: NC_2

description: Library name: Sample 2


title: WT Day 6

city: shang hai

first: Hui

last: Wang

address: shang hai

institute: Tongji University

description: Library name: WT Day 6

library_source: transcriptomic single cell

data_processing:
The FASTQ files were processed and aligned to GRCm39 murine reference genome using Cell Ranger software (version 9.0.0) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzed using Seurat (version 4.0.0) R package.
To remove low-quality cells and likely multiplet captures, a set of criteria were conducted: Cells were filtered by (1) gene numbers (gene numbers < 200), (2) UMI (UMI <1000), (3) log10GenesPerUMI (log10GenesPerUMI < 0.7), (4) percentage of mitochondrial RNA UMIs (proportion of UMIs mapped to mitochondrial genes > 10%) and (5) percentage of hemoglobin RNA UMIs (proportion of UMIs mapped to hemoglobin genes > 5%). Subsequently, the DoubletFinder package (version 2.0.3) was used to identify potential doublets. To obtain the normalized gene expression data, library size normalization was processed using the NormalizeData function. Specifically, the global-scaling normalization method “ LogNormalize ” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and log-transformed the results.
Top 2000 highly variable genes (HVGs) were calculated using the Seurat function FindVariableGenes (mean.function=FastExpMean, dispersion.function= FastLogVMR). Principal-component analysis (PCA) was performed to reduce the dimensionality with RunPCA function.
Graph-based clustering was performed to cluster cells according to their gene expression profile with the FindClusters function. Cells were visualized using a 2-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm with the RunUMAP function. The FindAllMarkers function (test.use = presto) was used to identify marker genes of each cluster.
Differentially expressed genes (DEGs) were selected using the function FindMarkers (test.use = presto). Bonferroni correction was applied for multiple testing adjustments of P values. P value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R (version 4.0.3) based on the hypergeometric distribution. The sequencing and bioinformatics analysis were provided by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: GRCm39
Supplementary files format and content: matrix tables with raw genes counts for every gene and every cell

source_name: kidney tissue

extract_protocol:
Under sterile conditions, the freshly collected tissues were washed twice with pre-cooled RPMI 1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes. The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4 ° C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was discarded. The pellet was washed once with medium followed by another centrifugation at 300 × g for 5 minutes, and the final supernatant was removed. CD45+ immune cells were enriched using mouse CD45 MicroBeads (Miltenyi, cat.no.130-052-301） accordding to the manufacturer’s protocol. Finally，the cells were re-suspended with 1ml RPMI 1640 medium (Conring, cat.no.10-040-CVR) with 0.04% BSA added. Single-cell suspension concentration and cell viability were then evaluated by Luna-FL cell counter (Logos Biosystems，Korea) or Trypan Blue staining method.
The freshly prepared single-cell suspension was adjusted to a concentration of 700-1200 cells/μl. Library preparation and loading were performed following the manufacturer’s protocol for the 10× Genomics Chromium Next GEM Single Cell 3 ʹ Reagent Kits v3.1 (cat.no.PN-1000268). The constructed libraries were sequenced on the Illumina Nova 6000 PE150 platform for high-throughput sequencing.

value: kidney tissue

value: Day 6


title: WT Day 2

description: Library name: WT Day 2

value: Day 2


title: NC_1

description: Library name: Sample 1


title: 28808_H3_6-1


title: WT Naïve

description: Library name: WT Naïve

value: Naïve


title: 28804_H3_5-1


title: R3

description: Library name: Sample 6


title: 25971_H3_4-1


title: R2

description: Library name: Sample 5


title: scRNA-seq, DE BM Lin- KIThi-int cells, HTO

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: de_hto

library_source: other

data_processing:
Raw sequencing data were processed using Cell Ranger (v8.0.0) for alignment to the mm10 reference genome, barcode processing, UMI counting, and generation of the gene expression matrix.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: bone marrow

extract_protocol:
BM cells were harvested from three mice per genotype. Lineage-positive cells were depleted using antibodies against CD3e, CD8b, CD11b, CD19, B220, Ly-6G, and TER-119. The remaining cells were stained with fluorochrome-conjugated antibodies, labeled with unique Antibody Capture TotalSeq B antibodies (BioLegend), and sorted for lin- KIThi-int cells. Three samples from each genotype were pooled and resuspended in PBS containing 0.04% BSA at a final concentration of ~1,000 cells/uL. Single-cell suspensions were loaded onto a 10x Genomics Chromium Single Cell Controller at GTAC@MGI.
Library preparation, sequencing, and Cell Ranger processing were performed by GTAC@MGI. Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3 and sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads, targeting depths of 1 billion reads for the gene expression library and 100 million reads for the feature barcode library.

value: bone marrow

value: Lin- KIThi-int cells

value: DE

tag: library type

value: HTO

tag: hto

value: TotalSeq™-B0301 anti-mouse Hashtag 1, TotalSeq™-B0302 anti-mouse Hashtag 2, TotalSeq™-B0303 anti-mouse Hashtag 3


title: SPF Vancomycin ZT5 replicate 2

description: Library name: S22

value: Whole colon

value: WT


title: 25964_H3_3-1

tag: pegr id

tag: method

value: Benzonase ChIP-exo

value: super


city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Library name: zygotes_OneCell_multiome_h3k27me3_batch1

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: 10X-like UMI matrix of RNA counts :  zygotes_barcodes.tsv, zygotes_genes.tsv, zygotes_matrix.mtx
Supplementary files format and content: fragment files of DNA counts : Zygote_4_rH3K27me3_pA.fragments.tsv.gz,  Zygote_5_rH3K27me3_pA.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: Zygote_5_rH3K27me3_pA.fragments.tsv.gz.tbi, Zygote_4_rH3K27me3_pA.fragments.tsv.gz.tbi,
Supplementary files format and content: single-cell bigwigs, H3K27me3 (CPM-normalized) L548_Zygote_4_rH3K27me3_pA_Cell2.bigwig L548_Zygote_4_rH3K27me3_pA_Cell3.bigwig L548_Zygote_4_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell1.bigwig L548_Zygote_5_rH3K27me3_pA_Cell2.bigwig L548_Zygote_5_rH3K27me3_pA_Cell3.bigwig L548_Zygote_5_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell5.bigwig L548_Zygote_5_rH3K27me3_pA_Cell6.bigwig L548_Zygote_5_rH3K27me3_pA_Cell7.bigwig L548_Zygote_5_rH3K27me3_pA_Cell8.bigwig
Supplementary files format and content: single-cell bigwigs, RNA (CPM-normalized) D1888T0578_Zygote_4_cell2_RNA.bw D1888T0579_Zygote_4_cell3_RNA.bw D1888T0580_Zygote_4_cell4_RNA.bw D1888T0588_Zygote_5_cell1_RNA.bw D1888T0589_Zygote_5_cell2_RNA.bw D1888T0590_Zygote_5_cell3_RNA.bw D1888T0591_Zygote_5_cell4_RNA.bw D1888T0592_Zygote_5_cell5_RNA.bw D1888T0593_Zygote_5_cell6_RNA.bw D1888T0594_Zygote_5_cell7_RNA.bw D1888T0595_Zygote_5_cell8_RNA.bw
Supplementary files format and content: pseudobulk bigwigs, RNA (CPM-normalized)
Library strategy: CUT&Tag

source_name: zygote

growth_protocol: Zygotes were obtained from 6-week-old B6D2F1/J females mated with C57BL6/J males (3–6 months old) after hormonal induction with pregnant mare serum gonadotropin (5 IU) and human chorionic gonadotropin (hCG, 5 IU) 46–48-h later.

extract_protocol:
Zygotes were collected at 23 post-hCG treatment in M2 medium. Cumulus cells were removed using M2 media containing hyaluronidase (Merck-Millipore MR-051-F). The zona pellucida was removed with Pronase (SIGMA P8811), followed by two washes in M2 medium. Zygotes were then manually dispensed in 384-well plates filled with 2µl of M2 medium with 0.2µl Dynabeads Myone Carboxylic (Fisher, 10563775) and kept on ice. After centrifugation, M2 medium was replaced by 2µl of lysis buffer (0.2% Triton X-100, 1x Protease Inhibitor Cocktail, 1.2U/µl Recombinant RNAse Inhibitor, 9.2µM oligo-dT /5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN).
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Moutaux& Schwager et al., 2025) using manual OneCell CUT&Tag

value: zygote

value: no

value: DNA


title: R1

description: Library name: Sample 4

value: Normal human renal cortex

value: Primary human renal tubular epithelial cells (hTECs)

value: hTECs


title: SPF Vancomycin ZT5 replicate 1

description: Library name: S21

value: Vancomycin


title: 28801_H3K27me3_2-2

tag: target

tag: antibody


title: scRNA-seq, DC BM Lin- KIThi-int cells, HTO

description: Library name: dc_hto

value: DC


title: SPF PBS ZT 5 replicate 4

description: Library name: S20

value: PBS


title: 25868_H3_2-1

tag: biological replicate

tag: resequencing replicate


title: NC3

description: Library name: Sample 3

tag: tissue


title: scRNA-seq, DC BM Lin- KIThi-int cells, GEX

description: Library name: dc_gex

value: bone marrow

value: Lin- KIThi-int cells

tag: genotype

value: mRNA


title: NC2

description: Library name: Sample 2

tag: cell type


title: SPF PBS ZT 5 replicate 3

description: Library name: S19

tag: treatment


title: SPF PBS ZT 5 replicate 2

description: Library name: S18


title: 28800_H2B_2-2


title: scRNA-seq, WT BM Lin- KIThi-int cells, GEX

description: Library name: wt_gex


title: 28462_H2B_2-1


title: T522_SG_All

city: Tsukuba

first: Saori

last: Abe

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: Library name: Sample3_LSG

data_processing:
Demultiplexing of raw reads and quality control. Alignment to the TCR reference database. TCR clone identification and annotation of V, D, J, and C genes. Clonal abundance and diversity analysis.
Assembly: Human TCR reference database
Supplementary files format and content: .txt or .csv
Supplementary files format and content: A table containing columns for identified TCR clones, CDR3 amino acid sequences, V/J gene usage, and the number of reads for each clone.
Library strategy: TCR-Seq

source_name: minor salivary gland

extract_protocol:
mRNA in T-cell lysates were captured using Dynabeads M270 streptavidin bound to BioEcoP-dT25-adapter primers, followed by reverse transcription and template-switching.
TCR cDNA containing complementarity determining region 3 (CDR3) was amplified using nested PCR with KAPA Hifi Hotstart ReadyMix. PCR products were purified with AM Pure XP kit. A third PCR was performed to add adaptor sequences for the Illumina sequencer. Final libraries were quantified using KAPA SYBR Fast qPCR Kit and analyzed by Microchip Electrophoresis System MultiNA.

value: minor salivary gland

value: Tissue


title: SPF PBS ZT 5 replicate 1

description: Library name: S17

value: Whole colon

value: WT


title: DHT/TGFB4

description: Library name: Sample 7


title: SPF PBS ZT11 replicate 4

description: Library name: S28


title: 28795_H2B_1-2

value: Benzonase ChIP-exo

value: super


title: T522_Blood_Tfh17

description: Library name: Sample3_Tfh17

source_name: Blood

value: Blood

value: T cell


title: PeCa60_xenograft_tissue_sample

description: Library name: PeCa60_xeno

source_name: penile cancer xenograft tumor

value: penile cancer xenograft tumor


title: SPF Vancomycin ZT23 replicate 4

description: Library name: S16


title: PeCa53_xenograft_tissue_sample

description: Library name: PeCa53_xeno


title: 28454_H2B_1-1

value: no


title: 25858_H3K27ac_1-1


title: T522_Blood_Tfh2

description: Library name: Sample3_Tfh2


title: SPF Vancomycin ZT23 replicate 3

description: Library name: S15


title: SPF PBS ZT11 replicate 1

description: Library name: S25


title: SPF Vancomycin ZT5 replicate 4

description: Library name: S24


title: BCHT3

city: Chengdu

first: Susu

last: Xiao

address: No.37 Guoxue Alley, Wuhou District

institute: West China Hospital, Sichuan University

description: Library name: BCHT3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Tumor tissue

value: murine breast cancer cell line


title: 28799_H2A.Z_2-2


title: SPF Vancomycin ZT23 replicate 2

description: Library name: S14

value: Vancomycin


title: T522_Blood_Tfh1

description: Library name: Sample3_Tfh1


title: BCHT2

description: Library name: BCHT2


title: 28461_H2A.Z_2-1


title: SPF Vancomycin ZT5 replicate 3

description: Library name: S23


title: T522_Blood_Treg

description: Library name: Sample3_Treg


title: SPF Vancomycin ZT23 replicate 1

description: Library name: S13


title: BCHT1

description: Library name: BCHT1


title: scRNA-seq, DE BM Lin- KIThi-int cells, GEX

description: Library name: de_gex

value: DE


title: 28794_H2A.Z_1-2


title: T522_Blood_Th17

description: Library name: Sample3_Th17


title: SPF PBS ZT23 replicate 4

description: Library name: S12

value: PBS


title: Control3

description: Library name: Control3


title: ZBTB10KO_STB_Rep2

city: Seattle

first: Meagan

middle: Nicole

last: Esbin

state: WA

address: 850 Republican St. S280

department: Obstetrics & Gynecology

institute: University of Washington School of Medicine

description: Library name: Sample 16

data_processing:
Plasmidsaurus performed read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp
Plasmidsaurus aligned reads to the human hg38 reference genome using STAR aligner v2.7.1181 with non-canonical splice junction removal and output of unmapped reads.
Plasmidsaurus performed gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook with filtering for low-expressed genes with edgeR::filterByExpr. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by Ensembl Gene ID
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (logFC), p-value (pValue) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) comparing NEG (non-targeting sgRNA transfected) hTSCs to ZBTB10 KO hTSCs in Undifferentiated, STB-differentiated, and EVT-differentiated conditions. Comparisons are noted as (_KOvsWT) where positive FC values indicates higher gene expression in ZBTB10 KO cells compared to NEG control.

source_name: hTSC

growth_protocol: Naïve-derived human trophoblast stem cells were established previously and cultured in hypoxic conditions (37°C, 5% CO2, 5% O2) in TSC Media (DMEM/F12 supplemented with 0.1 mM β-mercaptoethanol, 0.2% FBS (Sigma, F4135), 0.5% Penicillin-Streptomycin (P/S; Gibco, 15140122), 0.3% BSA, 1% ITS-X (Gibco, 41400045), 1.5 μg/mL L-ascorbic acid, 50 ng/mL EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA, and 5 μM Y-27632).51 Media was changed every other day and TSCs were passaged using TrypLE Express (Gibco, 12605010) when 80% confluent (approximately every 4 days) at a ratio of 1:4–6 on Cultrex-coated plates. Cells from passage 10-25 were used.

extract_protocol:
hTSC RNA was harvested using the RNeasy mini kit (Qiagen, 74104).
RNA-sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology with custom analysis and annotation.

treatment_protocol: Human hTSCs were plated at a density of 1E5 cells/well in Cultrex-coated 6-well plates and differentiated for 6 days into EVT or STB and harvested at Day 7, or if undifferentiated were harvested when confluent at Day 4. For the induction of EVTs, Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to EVT1 medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 100ng/mL NRG1, 7.5uM A83-01, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) supplemented with 1% Geltrex (Day 1). On day 3, the medium was replaced with EVT2 medium (EVT1 medium without NRG1) supplemented with 0.5% Geltrex. On day 5, the medium was replaced with EVT2 medium. For the induction of STBs, TSCs were seeded identically as above. Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to STB medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 2.5 μM forskolin, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) on Day 1. The medium was replaced on day 4.

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells

value: polyclonal ZBTB10 KO

value: 6 day STB differentiation

tag: batch


title: Control 2

city: Stockholm

first: Danai

last: Zareifi

address: Nobels väg 6

department: Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: P23101_1046

data_processing:
Library preparation and sequencing were conducted on an Illumina platform, generating reads with Phred scores consistently above Q30. Quality and adapter trimming of reads was performed using Cutadapt (v2.8). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to the Ensembl GRCh38 reference genome using STAR (v2.7.9a). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: Ensembl GRCh38
Supplementary files format and content: txt file contains raw counts for all samples

source_name: human adipocytes

extract_protocol:
RNA isolation, cDNA synthesis and quantitative real-time PCR (qPCR) were performed as previously described11. Briefly, total RNA was purified using the NucleoSpin RNA kit (Macherey-Nagel #740955) and quantified with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). Reverse transcription and qPCR were performed using iScript (Bio-Rad #1708891) and iQ SYBR Green Supermix (Bio-Rad #1708882), respectively. Relative mRNA levels were calculated using the comparative 2-DDct method. Where indicated, z-score analysis was applied using the formula: (observed value - mean) / standard deviation.
The library pool was prepared with Illumina mRNA stranded ligation protocol.

value: human adipocytes

tag: Sex

value: male

value: control


title: AP d3, rep 1

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Initial mapping and counting of 10x Genomics scRNA-seq reads was performed using Cell Ranger v3.1.0.
Assembly: GRCm38.p6
Supplementary files format and content: Cell Ranger output containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Pancreas

extract_protocol:
Single-cell encapsulation was performed using the Chromium Single Cell B Chip Kit (10x Genomics, PN-1000073).
Library preparation was performed using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10x Genomics, PN-1000075).

treatment_protocol: Mice were treated with PBS (n=3) or repeated hourly doses of 75ng/g body weight of caerulein for 6 hours, and taken down at day 1 (n=2), day 3 (n=3), or day 7 (n=2).

value: Pancreas

value: Caerulein


title: T522_Blood_Th1

description: Library name: Sample3_Th1

value: Blood

value: T cell


title: IL13KO_coculture_3

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.9)
Raw sequence was trimmed for adapter content using Trimmomatic (version 0.39)
Reads were aligned to the GRCm38.p6 genome using STAR (v 2.7.7a)
Alignment quality was assess using Picard’s CollectAlignmentMetrics, CollectRnaSeqMetrics, MarkDuplicates and CollectInsertSizeMetrics tools (v 2.27.3)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Assembly: GRCm38.p6
Supplementary files format and content: Raw and DESeq2-normalised counts matrix (as .csv file)

source_name: Fibroblast

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen) and 5 to 15 ng used as input material for library preparation.
Libraries were generated with the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. The pooled libraries were quantified with KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and sequenced (paired end 50nt) on an Illumina NovaSeq 6000 system (Illumina).

value: Fibroblast

value: IL13KO ILC2 coculture


title: 28453_H2A.Z_1-1

city: Ithaca

first: B. Franklin

last: Pugh

address: 465 Biotechnology Building

institute: Cornell University

value: Benzonase ChIP-exo

tag: fraction

value: super

tag: benzonase digestion

value: no


title: DMSO treated 2

city: shanghai

first: Yong

middle: hui

last: Chen

address: 160, Pujian Road

institute: Renji hospital

description:
Library name: sample5
DMSO_2
D2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: PBMC

value: DMSO


title: SPF PBS ZT23 replicate 3

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

institute: Bar-Ilan University

description: Library name: S11

extract_protocol:
RNA from flash frozen colonic tissues was extracted using RNeasy Plus Universal mini kit (Qiagen). The integrity of the isolated RNA was analyzed using the Agilent TS HS RNA Kit and TapeStation 4200 at the Genome Technology Center at the Azrieli Faculty of Medicine, Bar-Ilan University. 1000 ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L).
RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L).  Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

value: Whole colon

value: WT

value: PBS


title: Control2

description: Library name: Control2

value: Tumor tissue

tag: cell line

value: murine breast cancer cell line


title: 28460_H2A_2-1

data_processing:
*library strategy: ChIP-exo
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg19
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

extract_protocol:
Cells were poured into methanol-free formaldehyde (final 1% concentration) at room temperature with gentle mixing for 10 min (cells for Pol II ChIP-exo was crosslinked in 1x PBS for 5 mins). Reactions were quenched with 3M Tris (pH 8.0), with 2 moles of Tris per 1 mole of formaldehyde, for at least 5 min. Fixed cells were washed with PBS, lysed with detergent containing buffers and needle lysis. Chromatin for histones was digested with benzonase, while chromatin for Pol II was sonicated.
Benzonase digested or sonicated chromatin was centrifuged at 16,363 x g for 15 min at 4oC and the supernatant was used ChIP. ProteinA/G Sepharose beads were washed, pre-cleared with tRNA, and attached to antibodies against either histone, histone variants, histone modifications or Pol II. 10 million cell-equivalents of fixed, Benzonase-digested chromatin was added to antibody-coated beads and incubated overnight on rototorque at 4oC. Immunoprecipitated chromatin on resin was washed and then underwent A-tailing, ExA2_iNN/ExA2B oligo ligation with addition of PNK, Phi29-based Fill-in, Lambda exonuclease digestion, and overnight reverse crosslinking and protein digestion. DNA was then purified with Ampure beads, splint ligated to ExA1-58/ExA1-SSL_N5 adapters, purified again, and amplified by PCR with Illumina P1.3 and P2.1 primers for 18 cycles. Amplified libraries were size selected by gel electrophoresis in the range from 200-500 bp. Libraries were sequenced with the Illumina NextSeq 550, paired-end mode.

tag: sonication


title: T513_SG_All

description: Library name: Sample2_LSG

value: minor salivary gland

value: Tissue


title: SPF PBS ZT23 replicate 2

description: Library name: S10


title: 28452_H2A_1-1


title: Control1

description: Library name: Control1


title: T513_Blood_Tfh17

description: Library name: Sample2_Tfh17


title: SPF PBS ZT23 replicate 1

description: Library name: S9


title: SC_342_KPS

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

description: Library name: SITTF12

data_processing:
CellRanger count (v7.0.1) : default parameters
Assembly: mm10 (2020-A)
Supplementary files format and content: raw_feature_bc_matrix

source_name: PDAC tumour

extract_protocol:
we submitted 35K cells in 43 uL
Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide; 10x Genomics single nuclei RNA-seq

value: PDAC tumour

tag: strain

value: T69a Smad4 KO g264


title: T513_Blood_Tfh2

description: Library name: Sample2_Tfh2

value: Blood

value: T cell


title: 19355_PolII_2-1

tag: pegr id

value: ChIP-exo

value: yes

value: Pol II


title: SC_341_KP

description: Library name: SITTE12

value: T69a Smad4 WT g265 ROSA


title: SPF Vancomycin ZT17 replicate 3

description: Library name: S7

value: Vancomycin


title: 19354_PolII_1-1

tag: method

value: super


title: SC_340_KP

description: Library name: SITTD12


title: SPF Vancomycin ZT17 replicate 4

description: Library name: S8

value: Whole colon


title: 33648_50U-10min_20-1

data_processing:
*library strategy: Benzonase-seq
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg19
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

extract_protocol:
Cells were poured into methanol-free formaldehyde (final 1% concentration) at room temperature with gentle mixing for 10 min. Reactions were quenched with 3M Tris (pH 8.0), with 2 moles of Tris per 1 mole of formaldehyde, for at least 5 min. Fixed cells were washed with PBS, lysed with detergent containing buffers and needle lysis. Chromatin was digested with benzonase.
Benzonase-fragmented chromatin was centrifuged at 16,363 x g for 15 min at 4˚C.  The supernatant and pellet were separately used for library preparation. The pellet was resuspended by needle lysis with increasing needle gauge to minimize clumps. In some cases, total, super, or pellet fractions underwent DNA purification before being used for library input. Depending on the preparation, typically 0.5-1.3 million cell-equivalents of Benzonase-digested chromatin was digested with ProteinaseK for approximately 16 hours. Reverse-crosslinked DNA was purified with Ampure beads at 1.8x ratio to starting material and eluted in pure water. DNA underwent end-repair, A-tailing, and ligation to fork adapters (annealed Multiplexing Read 2 Sequencing primer /Nextera Read 2 External Adapter) with 3’ Ts. Components for enzymatic reactions were added successively to the previous resulting DNA and the enzyme was then heat inactivated before adding the next master mix. The ligated DNA was purified again with Ampure beads at 1.8x ratio to the final volume of ligation reaction and then amplified by PCR using ExB2 and ExC1 primers. Amplified libraries were size selected by gel electrophoresis in the range from 200-500 bp. Libraries were sequenced with the Illumina NextSeq 550, paired-end mode.

value: no


title: SPF Vancomycin ZT17 replicate 2

description: Library name: S6

value: WT


title: T513_Blood_Treg

description: Library name: Sample2_Treg


title: 25860_H3_1-1

value: Benzonase ChIP-exo

tag: target


title: SC_339_KPS

description: Library name: SITTC12


title: T513_Blood_Tfh1

description: Library name: Sample2_Tfh1


title: T513_Blood_Th17

description: Library name: Sample2_Th17


title: SPF Vancomycin ZT17 replicate 1

description: Library name: S5


title: SC_338_KPS

description: Library name: SITTB12


title: 33646_50U-10min_18-1


title: 33647_50U-10min_19-1


title: T513_Blood_Th1

description: Library name: Sample2_Th1


title: NC1

description: Library name: Sample 1

value: Normal human renal cortex

value: Primary human renal tubular epithelial cells (hTECs)

value: hTECs


title: SPF PBS ZT17 replicate 4

description: Library name: S4

value: PBS


title: SC_337_KP

description: Library name: SITTA12

value: PDAC tumour


title: PBMC, Post-SR, replicate 4, scRNA-seq

first: Yumei

address: 1166 LiuTai

institute: Chengdu University of TCM

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: hg19
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: peripheral blood after taking SR

extract_protocol:
Prior to taking the initial vein blood sample, volunteers must refrain from smoking and drinking, continue with their regular work schedule, and get plenty of rest (Pre-SR groups). Consequently, they were giving SR boil-free granules for 7 days, 2.5 g each time, three times per day, and after that, their vein blood samples were once again taken as Post-SR groups. During the medication, volunteers must continue to abstain from alcohol and tobacco while taking the medicine, as well as maintain their regular schedule of work and rest. Peripheral blood mononuclear cells (PBMCs) were extracted from the refresh blood after it had been centrifuged utilizing standard density gradient centrifugation
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, PBMCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction. During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: peripheral blood after taking SR

value: PBMC

value: after taking SR


title: SPF PBS ZT17 replicate 3

description: Library name: S3


title: 36_PSC5_FIBRO27_MG1

description: Library name: UDP0240

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39) - kmer 23
Supplementary files format and content: Raw count data in tab-delimited salmon file

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent (15596018; Invitrogen). RNA was extracted using the PureLink RNA mini kit (12183018A; Invitrogen). RNA concentration was measured using a Qubit and RNA quality was assessed on a TapeStation 4200 (Agilent) using the Agilent RNA ScreenTape kit.
Illumina mRNA library

value: Multi-stroma


title: SPF PBS ZT17 replicate 2

description: Library name: S2

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Mus_musculus.GRCm39) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text files include both ENSMUSG and gene name identifiers, and normalized expression levels per gene.


title: 33163_50U-10min_16-2

value: pellet


title: SPF PBS ZT17 replicate 1

description: Library name: S1


title: 30_PSC4_FIBRO28_MH11

description: Library name: UDP0241


title: 33027_50U-10min_16-1


title: PBMC, Post-SR, replicate 1, scRNA-seq

description: 10× Genomics


title: GF Vancomycin ZT11 replicate 4

description: Library name: GF_S32

source_name: Germ Free (GF)


title: 33164_50U-10min_17-2


title: 26_PSC4_FIBRO27_MH11

description: Library name: UDP0229


title: 34_PSC5_FIBRO27_MG1

description: Library name: UDP0235


title: GF Vancomycin ZT11 replicate 3

description: Library name: GF_S31


title: GF Vancomycin ZT11 replicate 2

description: Library name: GF_S30


title: Female,Adlib,Insulin,Adult,rep4

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 16A.8_Female_Adlib_Insulin_mPFC_Adult
16A.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

organism: Rattus norvegicus

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: 13_PSC5_FIBRO27_MG1

description: Library name: UDP0236


title: PBMC, Pre-SR, replicate 3, scRNA-seq

description: 10× Genomics

source_name: peripheral blood before taking SR

value: peripheral blood before taking SR

value: before taking SR


title: 33161_50U-10min_14-2

value: super


title: GF Vancomycin ZT11 replicate 1

description: Library name: GF_S29

value: Whole colon

value: Vancomycin


title: 11_PSC5_FIBRO27_MG1

description: Library name: UDP0225


title: 33025_50U-10min_14-1

value: no


title: GF PBS ZT11 replicate 4

description: Library name: GF_S28

value: WT


title: PBMC, Pre-SR, replicate 1, scRNA-seq

description: 10× Genomics


title: 33160_50U-10min_13-2

value: total


title: PBMC, Pre-SR, replicate 2, scRNA-seq

description: 10× Genomics


title: GF PBS ZT11 replicate 3

description: Library name: GF_S27


title: ChIPseq_DMSO_BRD4_IP_rep1

city: Memphis

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

institute: St. Jude Childrens Research Hospital

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000. Samples with Drosophila melanogaster spike-in (BRD4 ChIP-seq) were mapped the the human-fly hybrid genome instead, and reads mapping to human reference were further extracted.
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: hg38 (GRCh38.p12), dm6
Supplementary_files_format_and_content: bigwig

source_name: B-Lymphocyte

extract_protocol:
Chromatin was immunoprecipitated using the standard Covaris protocol and purified on silica columns. Samples with Drosophila melanogaster spike-in (BRD4) were processed using a common ChIP protocol and purified using phenol-chloroform extraction
Libraries were constructed using standard Illumina protocols

value: Patient Derived B-Lymphocytes

tag: spike in

value: Drosophila melanogaster spike-in

tag: chip antibody

value: DMSO


title: GF PBS ZT11 replicate 2

description: Library name: GF_S26

value: PBS


title: 16_PSC4_FIBRO28_MH11

description: Library name: UDP0243


title: 33159_50U-10min_12-2

tag: biological replicate

tag: resequencing replicate


title: ChIPseq_SynTEF1_BRD4_IP_rep1


title: GF PBS ZT11 replicate 1

description: Library name: GF_S25

tag: tissue

tag: genotype


title: 33023_50U-10min_12-1


title: ChIPseq_DMSO_BRD4_Input_rep1

tag: cell type

tag: treatment


title: 07_PSC5_FIBRO27_MG1

description: Library name: UDP0233

tag: batch


title: 28820_50U-10min_11-1

tag: fraction


title: ChIPseq_SynTEF1_HP1y_IP_rep2

value: HP1y (Millipore 05-690)


title: GF Vancomycin ZT5 replicate 4

description: Library name: GF_S24


title: Nras+C-myc+IL-2/CD25, HCC 4

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

description: Library name: Sample 7

data_processing:
Raw sequencing data were converted to FASTQ format using Illumina bcl2fastq (v5.0.1). Cell counting and gene expression profiling were performed with CellRanger (v7.0.0) and scRNA-seq data were aligned to the Ensembl reference genome.
Assembly: Ensembl mouse v105
Supplementary files format and content: matrix files with barcode、features and matrix for each sample

source_name: HCC tissue

extract_protocol:
Cells were loaded into the Chromium Controller on a Chromium Next GEM Chip G Single Cell Kit (10X Genomics, PN-1000127) and processed to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000315). cDNA amplification.
library construction were performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics, PN-1000268) according to the manufacturer's manual.

value: HCC tissue


title: ChIPseq_SynTEF1_HP1y_IP_rep1


title: 28473_50U-10min_10-1

tag: benzonase digestion


title: GF Vancomycin ZT5 replicate 2

description: Library name: GF_S22


title: 28464_H3K27me3_2-1

tag: cell line

value: Benzonase ChIP-exo

tag: antibody


title: ChIPseq_SynTEF1_HP1y_Input_rep2


title: GF Vancomycin ZT5 replicate 1

description: Library name: GF_S21


title: Nras+C-myc+IL-2/CD25, HCC 2

description: Library name: Sample 5


title: 28471_50U-10min_8-1

value: super (purified DNA)

tag: sonication


title: GF PBS ZT 5 replicate 4

description: Library name: GF_S20


title: Nras+C-myc+IL-2/CD25, HCC 1

description: Library name: Sample 4


title: PBMC, Post-SR, replicate 3, scRNA-seq

description: 10× Genomics

value: peripheral blood after taking SR

value: PBMC

value: after taking SR


title: 28469_50U-10min_7-1

tag: pegr id

value: pellet (purified DNA)


title: GF PBS ZT 5 replicate 3

description: Library name: GF_S19

value: Whole colon


title: ChIPseq_SynTEF1_HP1b_IP_rep2

value: HP1b (Cell Signaling 8676S)


title: Nras+C-myc, HCC 3

description: Library name: Sample 3

value: Control


title: PBMC, Pre-SR, replicate 4, scRNA-seq

description: 10× Genomics

value: peripheral blood before taking SR

value: before taking SR


title: 28468_50U-10min_6-1

value: total (purified DNA)

value: no


title: ChIPseq_SynTEF1_HP1b_IP_rep1

value: Patient Derived B-Lymphocytes


title: GF PBS ZT 5 replicate 2

description: Library name: GF_S18

value: WT

value: PBS


title: 04_PSC4_FIBRO27_MH11

description: Library name: UDP0242V3

value: Multi-stroma


title: GF PBS ZT 5 replicate 1

description: Library name: GF_S17


title: ChIPseq_SynTEF1_HP1b_Input_rep2


title: Nras+C-myc, HCC 1

description: Library name: Sample 1

value: HCC tissue


title: ChIPseq_SynTEF1_HP1b_Input_rep1


title: 40_PSC4_FIBRO28_MH11

description: Library name: UDP0223V3


title: si-NFkB-2-3, IL-17

city: Sakai

first: Kosuke

last: Murakami

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

institute: Kindai University

description: Library name: siNFkB2-IL17-3

data_processing:
FASTQ files were quality-checked (FastQC) and quantified at the transcript level using Salmon against the mouse reference transcriptome. Transcript abundances were summarized to gene-level TPM and counts using tximport.
Assembly: mm10
Supplementary files format and content: csv file

source_name: CCC

extract_protocol:
Total RNA was extracted from cultured murine ovarian clear cell carcinoma (OCCC) cells following siRNA transfection and IL-17 stimulation using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol and homogenized by passing through a QIAshredder column. Lysates were applied to silica membrane spin columns, and on-column DNase I digestion was performed to remove residual genomic DNA contamination. After sequential washing steps, total RNA was eluted in RNase-free water. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was assessed using an Agilent Bioanalyzer prior to library preparation. Only samples meeting quality control criteria were used for downstream sequencing.
RNA sequencing libraries were generated from high-quality total RNA using a stranded mRNA library preparation protocol. Poly(A)+ RNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to generate first-strand cDNA. Second-strand synthesis was performed to produce double-stranded cDNA, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were purified, quantified, and quality-checked prior to sequencing.

value: CCC


title: 28326_50U-10min_3-1

value: super


title: ChIPseq_SynTEF1_HP1a_IP_rep2

value: HP1a (Cell Signaling 2616S)


title: GF Vancomycin ZT23 replicate 3

description: Library name: GF_S15

value: Vancomycin


title: si-NFkB-2-2, IL-17

description: Library name: siNFkB2-IL17-2


title: 25976_50U-10min_2-1


title: ChIPseq_SynTEF1_HP1a_IP_rep1


title: GF Vancomycin ZT23 replicate 2

description: Library name: GF_S14


title: si-NFkB-2-1, IL-17

description: Library name: siNFkB2-IL17-1


title: ChIPseq_SynTEF1_HP1a_Input_rep2


title: 25769_50U-10min_1-1


title: GF Vancomycin ZT23 replicate 1

description: Library name: GF_S13


title: ChIPseq_SynTEF1_HP1a_Input_rep1


title: GF PBS ZT23 replicate 4

description: Library name: GF_S12


title: si-NFkB-1-2, IL-17

description: Library name: siNFkB1-IL17-2


title: 28393_50U-30min_1-1


title: ChIPseq_SynTEF1_H3K9me3_IP_rep2

value: H3K9me3 (Abcam Ab8898)


title: si-NFkB-1-1, IL-17

description: Library name: siNFkB1-IL17-1


title: GF PBS ZT23 replicate 3

description: Library name: GF_S11

value: Whole colon


title: ChIPseq_SynTEF1_H3K9me3_IP_rep1


title: GF PBS ZT23 replicate 2

description: Library name: GF_S10


title: si-negative control-3, IL-17

description: Library name: siNC-IL17-3


title: 28385_50U-3min_1-1


title: ChIPseq_SynTEF1_H3K9me3_Input_rep2


title: GF PBS ZT23 replicate 1

description: Library name: GF_S9


title: si-negative control-2, IL-17

description: Library name: siNC-IL17-2


title: G146C3 head

city: Los Angeles

first: Lauryn

last: Higginson

state: CA

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

description: Library name: Sample 18

data_processing:
Raw sequencing data were basecalled in real time using MinKNOW (V6.8.11) with Dorado (v7.11.2) employing default cDNA-PCR basecalling model
Gene-level counts were quantified using featureCounts
Assembly: Reads were aligned to Drosophila melanogaster reference genome (FlyBase release r6.66) using minimap2 (v2.30).
Supplementary files format and content: csv of raw counts from each sample

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Total RNA was extracted from fly thorax using standard phenol-chloroform protocol
Total RNA samples were subjected to in vitro polyadenylation using E. coli Poly(A) polymerase (New England Biolabs, M0276S) according to the manufacturer’s instructions. Polyadenylated RNA was subsequently purified by phenol-chloroform extraction followed by ethanol precipitation. Sequencing libraries were generated from approximately 200 ng of in vitro polyadenylated RNA using Oxford Nanopore Technologies (ONT) PCR-cDNA Barcoding Kit (SQK-PCB111.24) following the manufacturer’s protocol.

value: head


title: ChIPseq_SynTEF1_H3K9me3_Input_rep1


title: si-NFkB-1-3, IL-17

description: Library name: siNFkB1-IL17-3


title: 28394_50U-30min_2-1


title: 33028_50U-10min_17-1

value: pellet


title: GF Vancomycin ZT17 replicate 4

description: Library name: GF_S8


title: PBMC, Post-SR, replicate 2, scRNA-seq

last: Wang

description: 10× Genomics

value: peripheral blood after taking SR

value: PBMC

value: after taking SR


title: si-negative control-1, IL-17

description: Library name: siNC-IL17-1


title: 18_PSC4_FIBRO28_MH11

description: Library name: UDP0239


title: 33162_50U-10min_15-2

value: no


title: 33026_50U-10min_15-1


title: GF Vancomycin ZT17 replicate 3

description: Library name: GF_S7


title: si-negative control-3, control

description: Library name: siNC-control-3


title: ChIPseq_SynTEF1_H3K4me3_IP_rep2

value: Patient Derived B-Lymphocytes

value: H3K4me3 (Abcam Ab8540)


title: G146C1 head

description: Library name: Sample 16


title: 28386_50U-3min_2-1


title: G146C2 head

description: Library name: Sample 17


title: ChIPseq_SynTEF1_H3K4me3_IP_rep1


title: GF Vancomycin ZT17 replicate 2

description: Library name: GF_S6

value: WT


title: ChIPseq_SynTEF1_BRD4_Input_rep1

value: Drosophila melanogaster spike-in


title: si-negative control-2, control

description: Library name: siNC-control-2


title: GF Vancomycin ZT17 replicate 1

description: Library name: GF_S5


title: si-negative control-1, control

description: Library name: siNC-control-1


title: ChIPseq_SynTEF1_H3K4me3_Input_rep2


title: G11A2 head

description: Library name: Sample 14


title: G11A3 head

description: Library name: Sample 15


title: ChIPseq_SynTEF1_H3K4me3_Input_rep1


title: 33024_50U-10min_13-1

value: total


title: GF PBS ZT17 replicate 4

description: Library name: GF_S4

value: PBS


title: P_65_70K

description: Library name: SITTH11

data_processing:
CellRanger count (v8.0.1) : default parameters
Assembly: mm10-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Pancreatitis

extract_protocol:
For samples from batch 1 and 2 : Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide. For samples from batch 3 and 4 : Chromium GEM-X Single Cell 3' Kit v4,  PN-1000691; Chromium GEM-X Single Cell 3' Chip Kit v4, PN-1000690, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium GEM-X Single Cell 3' v4 Gene Expression User Guide (Revision B).
10x Genomics single nucleus RNA-seq

treatment_protocol: submitted 35-55-70K nuclei

value: Pancreatitis

value: Wild-type


title: ChIPseq_DMSO_HP1y_IP_rep2

value: HP1y (Millipore 05-690)

value: DMSO


title: G11A1 head

description: Library name: Sample 13


title: 09_PSC5_FIBRO27_MG1

description: Library name: UDP0232

value: Multi-stroma


title: GF PBS ZT17 replicate 3

description: Library name: GF_S3

value: Whole colon


title: WT3 head

description: Library name: Sample 12

value: head


title: P_64_70K_batch4

description: Library name: SITTG11


title: GF PBS ZT17 replicate 2

description: Library name: GF_S2


title: WT2 head

description: Library name: Sample 11


title: KPC_14.3f_35K

description: Library name: SITTB6

source_name: PDAC tumors

value: PDAC tumors

value: KrasLSL-G12D/+; Trp53LSL-R172H/+;Cre


title: ChIPseq_DMSO_HP1y_IP_rep1


title: ChIPseq_DMSO_HP1y_Input_rep2


title: KPC_7.2b_35K

description: Library name: SITTA6


title: GF PBS ZT17 replicate 1

description: Library name: GF_S1


title: GF Vancomycin ZT5 replicate 3

description: Library name: GF_S23

value: Vancomycin