title: S15_716 +DMSO 35d

value: DMSO for 35 days


title: Depletion-12w_tumor_Rep1_AB1138

status: Public on Dec 22 2024

type: SRA

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

country: Israel

institute: Tel Aviv University

library_source: transcriptomic single cell

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a). Reads with multiple mapping positions were excluded. We then assigned gene names for exonic, genomic and mitochondrial regions using featureCounts (v.2.0.0), processed the resulting BAM file using samtools (v.1.10) and finally created gene-cell UMI matrices using the UMI-tools software package (v.1.1.2). Using the Scanpy package (v.1.9.1), we loaded these files to a unified data object.
Assembly: GRCm39
Supplementary files format and content: FASTQ, R1 contains genomic data and R2 contains 8BP of cell barcode and 7BP of UMI barcode.

molecule: polyA RNA

organism: Mus musculus

source_name: Mammary gland

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mammary gland: The fourth pair of mammary glands was collected from MMTV-PyMT oncogene carrier and non-carrier females along 6 developmental and cancerous time points: postnatal day 10, and weeks 3, 6, 8, 10 and 12. The lymph nodes were removed from the dissected mammary glands. Both healthy and cancerous mammary tissues were suspended in Dulbecco’s modified Eagle medium/F12 medium (01-170-1A, Biological Industries) supplemented with collagenase IV (1 mg/ml, Worthington LS004188), collagenase II (1 mg/ml, Worthington LS004176), hyaluronidase I-S (800 U/ml, Sigma H3506) and DNase I (1.2 U/ml, Sigma D5021-15KU), cut into small pieces, mechanically dissociated by pipetting using different sizes of needles and incubated at 37ºC with agitation of 100 rpm for 30 minutes. Then, cells were washed with ice-cold sorting buffer (PBS supplemented with 0.2mM ethylene diamine tetra-acetic acid (EDTA), pH 8, and 0.5% BSA), filtered through a 100 µm cell strainer and centrifuged at 1500 rpm for 5 minutes at 4ºC. Flow cytometry was performed on the BD FACSAria III Cell sorter or BD FACSymphony S6, using a 100 µm nozzle, analyzed with BD FACSDIVA software (BD Biosciences) and FlowJo software. Cells suspended in ice-cold sorting buffer were incubated with anti-mouse CD16/32 (BD Bioscience) to block Fc receptors before labeling with fluorescent antibodies against cell-surface epitopes. Cells were stained with DAPI (Biolegend) and then with the following antibodies: eFLuor450-conjugated TER-119 (eBioscience), FITC-conjugated CD45 (Biolegend), APC-conjugated CD45 (Biolegend), PE-conjugated CD45 (Biolegend), APC/Cy7-conjugated EpCAM (, Biolegend), APC-conjugated EpCAM (Biolegend), FITC-conjugated F4/80 (Biolegend), FITC-conjugated Ly6G (Biolegend), PE-conjugated Ly6G (Biolegend), FITC-conjugated CD31 (Biolegend), PE-conjugated Pdgfr-a (Bioloegend), FITC-conjugated I-A/I-E (MHC II, Biolegend). For sorting, dead cells (DAPI+) and erythrocytes (TER119+) were excluded. First, total immune cells (CD45+) and non-immune cells (CD45-) were sorted from DAPI-/TER119- gate (Live cells). For enrichment of immune-epithelial/cancer cell PICs, we sorted the double positive population from live cells by using immune and epithelial markers (CD45+EpCAM+) and their respective singlet background, singlet immune (CD45+EpCAM-) and epithelial cells (CD45-EpCAM+). For enrichment of neutrophils-epithelial PICs, we gated the Ly6G+EpCAM+ population from general immune-tumor cell PICs (CD45+EpCAM+). For enrichment of singlet neutrophils, we sorted Ly6G+ cells from CD45+ gate. Singlet EpCAM+ cells used for analysis as tumor cell background were isolated from tumor carrier mice as described above. Singlets and PICs were sorted into 384-well cell capture plates. These plates contain 2μl of lysis solution along with barcoded poly (T) reverse-transcription primers for single-cell RNA-seq. As no-cell control for the data analysis, four wells were left empty. Immediately after sorting, each plate was spun down and stored at -80°C until further processing. Peripheral blood: Peripheral blood was collected by cardiac puncture from MMTV-PyMT+ female mouse. Peripheral blood was diluted in PBS and layered on top of Histopaque-1077, centrifuge at 400g, 30min, no break and acceleration. Buffy coat was diluted 10 times with PBS, centrifuged at 400 g, 7min at 4°C and resuspended in FACS buffer. Peripheral blood neutrophils were stained and sorted (CD45+ or CD45+Ly6G+).
The library preparation was conducted following the previously reported protocol {Jaitin, 2014}. In brief, mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol {Jaitin, 2014}. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

treatment_protocol: Mice were sacrified by CO2. For depletion/isotype samples, MMTV-PyMT+ female mice at the age of 10.5 weeks old were treated daily for 9 days via intraperitoneal injection with 12.5 μg per mouse of rat anti-Ly6G antibody (BioXcell, clone 1A8, BE0075-1-5AC) in PBS or rat IgG2a isotype control (BioXcell, BE0089-25AC).

tag: tissue

value: Mammary gland

tag: cell type

tag: strain

value: FVB/n MMTV-PyMT+

tag: age


title: 3w_tumor_CD45+_Rep2_AB143


title: S14_715 +DMSO 35d

city: Tel-Aviv

first: Amit

last: Levon

address: Ramat Aviv

institute: Tel-Aviv University

library_source: transcriptomic

data_processing:
The processed reads were aligned to the mouse genome (mm10) using Rsubread v2.0.0 ‘align’ function (sortReadsByCoordinates=True, detectSV=False), with the mouse GENCODE mm10 vM10 GTF as an external annotation file.
Gene expression was calculated using Rsubread ‘featureCounts’ (countMultiMappingReads=False) to count the number of reads that map to each gene, with the GENCODE mm10 vM10 GTF as an external annotation file.
The reads were then normalized by TPM (Transcripts Per Kilobase Million) using the total exonic length acquired from the same GENCODE database.
In order to remain with only genes that have been robustly expressed in the samples, we continued only with genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts only for genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset (txt file).

molecule: total RNA

source_name: Primary lung fibroblasts

growth_protocol: Cells were grown in complete Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin and 1% (v/v) L-glutamine. The cultures were maintained at 37°C in a humidified atmosphere with 5% CO2 and 3% O2

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (QIAGEN) and purified with the MiRNeasy Kit (QIAGEN), according to the manufacturer’s protocol. The RNA purity (260/230 and 280/260) was measured by nanodop.  RNA concentration was measured by Qbit and the integrity was measured using the Tapstation instrument. The purified RNA was used for subsequent library preparation and sequencing.
TruSeq RNA sample prep

treatment_protocol: Cells were treated with either KU60019 or DMSO at a final concentration of 3uM for 15 or 35 days.For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .

tag: genotype

value: Wild-type

tag: treatment

value: Primary lung fibroblasts


title: PBMCs, Japanese cohort, B003_L001, H037

city: Singapore

first: Boxiang

last: Liu

address: 12 Science Drive 2, MD1 - Tahir Foundation Building, Level 5

country: Singapore

institute: National University of Singapore

description: Library name: JP_RIK_B003_L001_5GEX_H037

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

organism: Homo sapiens

source_name: blood

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction

value: blood

tag: cell line

value: human

value: PBMCs


title: 3w_tumor_CD45+_Rep2_AB142


title: PBMCs, Japanese cohort, B003_L001, H042

description: Library name: JP_RIK_B003_L001_5GEX_H042


title: Depletion-12w_tumor_Rep1_AB1136


title: 10w_normal_CD45-_Rep2_AB141

value: FVB/n MMTV-PyMT-


title: S13_705 +DMSO 35d


title: S12_716 -KU 20d (15)

value: Removal of KU60019 after 15d and incubation for 20d


title: 10w_normal_CD45-_Rep2_AB140


title: PBMCs, Japanese cohort, B003_L001, H035

description: Library name: JP_RIK_B003_L001_5GEX_H035


title: Depletion-12w_tumor_Rep1_AB1135


title: 10w_normal_EPCAM_Rep2_AB139

value: EPCAM


title: PBMCs, Japanese cohort, B003_L001, H034

description: Library name: JP_RIK_B003_L001_5GEX_H034


title: S11_715 -KU 20d (15)


title: PBMCs, Japanese cohort, B003_L001, H033

description: Library name: JP_RIK_B003_L001_5GEX_H033


title: 10w_normal_CD45+_Rep2_AB138


title: S10_705 -KU 20d (15)


title: S16_705 +KU 35d

value: KU60019 for 35 days


title: Depletion-12w_tumor_Rep1_AB1133


title: PBMCs, Japanese cohort, B003_L001, H032

description: Library name: JP_RIK_B003_L001_5GEX_H032


title: S9_716 -DMSO 20d (15)

value: Removal of DMSO after 15d and incubation for 20d


title: 10w_tumor_CD45-_Rep2_AB136


title: Depletion-12w_tumor_Rep1_AB1132


title: S8_715 -DMSO 20d (15)


title: PBMCs, Japanese cohort, B003_L001, H036

description: Library name: JP_RIK_B003_L001_5GEX_H036


title: PBMCs, Japanese cohort, B003_L001, H031

description: Library name: JP_RIK_B003_L001_5GEX_H031


title: Depletion-12w_tumor_Rep1_AB1137


title: PBMCs, Caucasian, B002_L002, LONZA3038097

description: Library name: JP_RIK_B002_L002_5GEX_LONZA3038097


title: 12w_tumor_Rep6_AB868


title: 10w_tumor_CD45+_Rep2_AB134


title: PBMCs, Japanese cohort, B002_L002, H030

description: Library name: JP_RIK_B002_L002_5GEX_H030


title: 12w_tumor_Rep6_AB866


title: S5_715 +KU 15d

value: KU60019 for 15 days


title: PBMCs, Japanese cohort, B002_L002, H029

description: Library name: JP_RIK_B002_L002_5GEX_H029


title: PBMCs, Japanese cohort, B002_L002, H028

description: Library name: JP_RIK_B002_L002_5GEX_H028


title: S6_716 +KU 15d


title: Depletion-12w_tumor_Rep1_AB1131


title: 10w_normal_CD45+_Rep2_AB137


title: 10w_tumor_CD45-_Rep1_AB132


title: 12w_tumor_Rep6_AB865


title: S4_705 +KU 15d


title: S3_716 +DMSO 15d

value: DMSO for 15 days


title: 10w_tumor_CD45-_Rep1_AB131


title: PBMCs, Japanese cohort, B002_L002, H027

description: Library name: JP_RIK_B002_L002_5GEX_H027


title: 10w_tumor_EPCAM_Rep1_AB130


title: S2_715 +DMSO 15d


title: Depletion-12w_tumor_Rep1_AB1134


title: S7_705 -DMSO 20d (15)


title: 10w_tumor_EPCAM_Rep2_AB135


title: 12w_tumor_Rep6_AB864


title: 12w_tumor_Rep6_AB863


title: PBMCs, Japanese cohort, B002_L002, H025

description: Library name: JP_RIK_B002_L002_5GEX_H025


title: 10w_tumor_CD45+_Rep1_AB129


title: PBMCs, Japanese cohort, B002_L002, H026

description: Library name: JP_RIK_B002_L002_5GEX_H026


title: 12w_tumor_Rep6_AB867


title: S1_705 +DMSO 15d


title: 10w_tumor_CD45+_Rep2_AB133


title: 3w_normal_CD45-_Rep3_AB296


title: 10w_tumor_CD45+_Rep1_AB128


title: PBMCs, Japanese cohort, B002_L002, H024

description: Library name: JP_RIK_B002_L002_5GEX_H024


title: 3w_normal_CD45-_Rep3_AB295


title: 3w_normal_EPCAM_Rep1_AB127


title: PBMCs, Japanese cohort, B002_L002, H023

description: Library name: JP_RIK_B002_L002_5GEX_H023


title: 3w_tumor_CD45-_Rep3_AB290


title: SKBR3, biosimilar treated mRNA sample, replicate 8

city: Waterloo

first: Karsten

last: Rinas

state: ON

address: 200 University Ave W

department: Biology

country: Canada

institute: University of Waterloo

description: Library name: Sample24

data_processing:
Initial quality assessment of the raw sequencing reads was performed with FastQC v3.2 3 before and after adapter and low-quality bases trimming with the BBDuk method from the BBTools suite 4. A k-mer size of 23 was used for trimming the 3’ ends of the reads.
The reads were aligned to the human reference genome assembly GRCh38.p12 in combination with ENSEMBL v95 gene annotation reference database. This process was performed with the STAR aligner v2.5.05 using the tuned parameters recommended for STAR aligner by G. Baruzzo et al. in a benchmark study.
quantification of gene expression levels was carried out using RSEM (RNA-Seq by Expectation-Maximization) v1.3.07 adhering to default parameters.
Assembly: GRCh38.p12
Supplementary files format and content: xlsx file containing RSEM read estimates unfiltered

source_name: Breast cancer

growth_protocol: SKBR3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific, San Jose, USA) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco, Mississauga, Canada) and 1% (v/v) penicillin/streptomycin [10,000 U/ml penicillin, 10,000 µg/ml streptomycin] (Gibco, Mississauga, Canada). The cultures were maintained at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from the samples using the commercial Quick-RNA™ MiniPrep kit (Zymo Research, Irvine, USA) adhering to the protocol provided by the manufacturer. Before shipping the RNA concentration was quantified with the Qubit fluorometer, ensuring a minimum concentration threshold of 100 ng/μl prior to further processing.
The cDNA library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA) and sequenced at the Next Generation Sequencing Facility of The Hospital for Sick Children in Toronto, Canada. A HiSeq 2500 platform (Illumina, San Diego, USA) was used to generate 2 x 126 bp paired end reads.

treatment_protocol: the SKBR3 cell line were cultured in 6 well plates at an initial seeding density of 6,500 cells/cm2. To ensure consistency, eight replicates for each control and treatments group were established on Day 0. The culture media was refreshed on Days 1 and 4. Treatment groups were administered with either 4 μg/ml Herceptin (Genentech, San Francisco, USA) or ApoTras (Apobiologix, Toronto, Canada)1 in 1xPBS. The control group received no treatment. This design evaluates the efficacy of Herceptin and ApoTras on SKBR3 cell proliferation and viability. Total RNA extraction took place on Day 7.

value: Breast cancer


title: SKBR3, biosimilar treated mRNA sample, replicate 4

description: Library name: Sample20


title: 3w_normal_CD45-_Rep1_AB124


title: SKBR3, biosimilar treated mRNA sample, replicate 5

description: Library name: Sample21


title: 3w_tumor_CD45-_Rep3_AB289


title: 3w_tumor_CD45+_Rep3_AB287


title: PBMCs, Japanese cohort, B002_L002, H022

description: Library name: JP_RIK_B002_L002_5GEX_H022


title: PBMCs, Japanese cohort, B002_L002, H018

description: Library name: JP_RIK_B002_L002_5GEX_H018


title: SKBR3, biosimilar treated mRNA sample, replicate 3

description: Library name: Sample19


title: PBMCs, Japanese cohort, B002_L002, H019

description: Library name: JP_RIK_B002_L002_5GEX_H019


title: SKBR3, biosimilar treated mRNA sample, replicate 6

description: Library name: Sample22


title: PBMCs, Japanese cohort, B002_L002, H020

description: Library name: JP_RIK_B002_L002_5GEX_H020


title: 3w_normal_CD45-_Rep1_AB125


title: 3w_tumor_CD45+_Rep3_AB286


title: PBMCs, Japanese cohort, B002_L002, H021

description: Library name: JP_RIK_B002_L002_5GEX_H021


title: 3w_tumor_CD45-_Rep1_AB122


title: 8w_normal_CD45-_Rep2_AB282


title: 8w_normal_CD45-_Rep2_AB283


title: 8w_normal_CD45+_Rep2_AB279


title: 3w_tumor_CD45-_Rep1_AB120


title: SKBR3, biosimilar treated mRNA sample, replicate 2

description: Library name: Sample18


title: SKBR3, Herceptin treated mRNA sample, replicate 8

description: Library name: Sample16


title: PBMCs, Japanese cohort, B002_L002, H017

description: Library name: JP_RIK_B002_L002_5GEX_H017


title: 3w_tumor_CD45-_Rep1_AB121


title: 8w_normal_CD45+_Rep2_AB278


title: SKBR3, biosimilar treated mRNA sample, replicate 1

description: Library name: Sample17


title: 3w_tumor _EPCAM_Rep1_AB126


title: SKBR3, biosimilar treated mRNA sample, replicate 7

description: Library name: Sample23


title: 3w_normal_CD45+_Rep1_AB123


title: 8w_tumor_CD45-_Rep2_AB276


title: 3w_tumor_CD45+_Rep1_AB119


title: PBMCs, Japanese cohort, B002_L001, H030

description: Library name: JP_RIK_B002_L001_5GEX_H030


title: SKBR3, Herceptin treated mRNA sample, replicate 6

description: Library name: Sample14


title: SKBR3, Herceptin treated mRNA sample, replicate 7

description: Library name: Sample15


title: PBMCs, Caucasian, B002_L001, LONZA3038097

description: Library name: JP_RIK_B002_L001_5GEX_LONZA3038097


title: PBMCs, Japanese cohort, B002_L002, H016

description: Library name: JP_RIK_B002_L002_5GEX_H016


title: 3w_tumor_CD45+_Rep1_AB118


title: 8w_tumor_CD45+_Rep2_AB272


title: SKBR3, Herceptin treated mRNA sample, replicate 4

description: Library name: Sample12


title: 6w_normal_CD45-_Rep2_AB116


title: 8w_tumor_CD45+_Rep2_AB271


title: PBMCs, Japanese cohort, B002_L001, H028

description: Library name: JP_RIK_B002_L001_5GEX_H028


title: PBMCs, Japanese cohort, B002_L001, H027

description: Library name: JP_RIK_B002_L001_5GEX_H027


title: SKBR3, Herceptin treated mRNA sample, replicate 3

description: Library name: Sample11


title: SKBR3, Herceptin treated mRNA sample, replicate 5

description: Library name: Sample13


title: 6w_normal_CD45+_Rep2_AB115


title: 6w_tumor_CD45-_Rep2_AB114


title: PBMCs, Japanese cohort, B002_L001, H026

description: Library name: JP_RIK_B002_L001_5GEX_H026


title: 6w_normal_CD45-_Rep2_AB112


title: 10w_normal_CD45-_Rep3_AB267


title: SKBR3, Herceptin treated mRNA sample, replicate 2

description: Library name: Sample10


title: PBMCs, Japanese cohort, B002_L001, H025

description: Library name: JP_RIK_B002_L001_5GEX_H025


title: 10w_normal_CD45+_Rep3_AB266


title: 6w_tumor_CD45+_Rep2_AB113


title: SKBR3, Herceptin treated mRNA sample, replicate 1

description: Library name: Sample9


title: PBMCs, Japanese cohort, B002_L001, H029

description: Library name: JP_RIK_B002_L001_5GEX_H029


title: SKBR3, Untreated Control mRNA sample, replicate 8

description: Library name: Sample8


title: 6w_normal_CD45+_Rep2_AB111


title: 10w_normal_CD45+_Rep3_AB265


title: 8w_tumor_CD45-_Rep2_AB275


title: 6w_normal_EPCAM_Rep2_AB117


title: SKBR3, Untreated Control mRNA sample, replicate 7

description: Library name: Sample7


title: PBMCs, Japanese cohort, B002_L001, H023

description: Library name: JP_RIK_B002_L001_5GEX_H023


title: SKBR3, Untreated Control mRNA sample, replicate 6

description: Library name: Sample6


title: 10w_tumor_CD45-_Rep3_AB260


title: 10w_tumor_CD45+_Rep3_AB256


title: 10w_tumor_CD45-_Rep3_AB259


title: PBMCs, Japanese cohort, B002_L001, H022

description: Library name: JP_RIK_B002_L001_5GEX_H022


title: 6w_tumor _CD45-_Rep2_AB110


title: 6w_tumor _CD45+_Rep2_AB109


title: SKBR3, Untreated Control mRNA sample, replicate 4

description: Library name: Sample4


title: SKBR3, Untreated Control mRNA sample, replicate 5

description: Library name: Sample5


title: PBMCs, Japanese cohort, B002_L001, H021

description: Library name: JP_RIK_B002_L001_5GEX_H021


title: 10w_normal_CD45-_Rep3_AB268


title: PBMCs, Japanese cohort, B002_L001, H020

description: Library name: JP_RIK_B002_L001_5GEX_H020


title: PBMCs, Japanese cohort, B002_L001, H019

description: Library name: JP_RIK_B002_L001_5GEX_H019


title: 10d_tumor _EPCAM_Rep1_AB016


title: 10d_normal_CD45-_Rep1_AB015


title: PBMCs, Japanese cohort, B002_L001, H018

description: Library name: JP_RIK_B002_L001_5GEX_H018


title: 10d_normal_CD45-_Rep2_AB252


title: SKBR3, Untreated Control mRNA sample, replicate 2

description: Library name: Sample2


title: PBMCs, Japanese cohort, B002_L001, H024

description: Library name: JP_RIK_B002_L001_5GEX_H024


title: SKBR3, Untreated Control mRNA sample, replicate 1

description: Library name: Sample1

value: Control


title: PBMCs, Japanese cohort, B002_L001, H017

description: Library name: JP_RIK_B002_L001_5GEX_H017


title: 10d_normal_CD45+_Rep2_AB250


title: 10d_tumor _CD45-_Rep1_AB013


title: PBMCs, Japanese cohort, B002_L001, H016

description: Library name: JP_RIK_B002_L001_5GEX_H016


title: 10d_normal_CD45+_Rep1_AB014


title: 10d_tumor _CD45+_Rep1_AB012


title: 10d_normal_CD45-_Rep2_AB251


title: 10w_tumor_CD45+_Rep3_AB255


title: 10d_normal_EPCAM_Rep1_AB017


title: ITP7

city: Suzhou

first: Shuhong

last: Hu

address: No.188 Shizi Street

country: China

institute: The First Affiliated Hospital of Soochow University

data_processing:
FastQC software was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the refernce genome sequences.
Stringtie software was used to the assembly the reads that mapped the genome.
Stringtie software was used to caculate the expression amount readcount. Then caculate the FPKM of the gene and transcript.
Assembly: GRCh38.p14 Primary Assembly
Supplementary files format and content: tab-delimited text files include p-value for each Sample

source_name: Bone marrow

extract_protocol:
The total RNA was extrated for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard lllumina protocols

value: Bone marrow

value: Nucleated BM cells


title: 10d_normal_CD45+_Rep2_AB249

value: Mammary gland


title: 10d_tumor_CD45-_Rep2_AB245

value: FVB/n MMTV-PyMT+


title: ITP6


title: ITP5


title: 10d_tumor _CD45-_Rep1_AB010


title: SKBR3, Untreated Control mRNA sample, replicate 3

description: Library name: Sample3


title: Rattus norvegicus, ratonis epidermis Limbal niche, biol rep2

city: Wuhan

first: Bei

last: Wang

address: 1277 Jiefang Avenue, Wuhan, Hubei Province, China

institute: Huazhong University of Science and Technology

description:
Library name: T2
Column name fpkm.xls: T2

data_processing:
Raw sequencing data underwent quality control assessment using FastQC, and adapter sequences were trimmed with Trim Galore. Differential expression analysis was performed using DESeq2, identifying genes with |log2FC| > 1 and a Q value ≤ 0.05 as significantly differentially expressed.
Assembly: Norway rat Ensembl release 113
Supplementary files format and content: Tab delimited FPKM values for each sample

organism: Rattus norvegicus

source_name: ratonis epidermis

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific) and subsequently converted to cDNA using a reverse transcription kit (GeneCopoeia, Rockville, MD, USA). (1) After passing the Total RNA sample detection, eukaryotic mRNA was enriched using Oligo (dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) Using mRNA as a template, synthesize the first and second strands of cDNA and purify the cDNA; (4) Purified double stranded cDNA was subjected to end repair, base A was added, sequencing adapters were added, and fragment screening was performed to recover cDNA of approximately 350bp; (5) Finally, PCR enrichment was performed to obtain a cDNA library.
For library preparation, 1 µg of total RNA per sample from rat tissues was subjected to poly(A) selection using oligo(dT) beads, followed by reverse transcription into cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with random hexamer primers. The resulting cDNA was then processed for end repair, phosphorylation, and adenylation according to Illumina's library preparation protocol. Size selection of 300 bp fragments was performed using 2% Low Range Ultra Agarose gel electrophoresis, followed by PCR amplification with Phusion DNA Polymerase (NEB) for 15 cycles. Library quantification was carried out using a TBS380 fluorometer (Turner Biosystems).

value: ratonis epidermis

value: Limbal niche


title: Rattus norvegicus, ratonis epidermis Limbal niche, biol rep1

description:
Library name: T1
Column name fpkm.xls: T1


title: Rattus norvegicus, ratonis epidermis primary keratinocyte progenitors, biol rep3

description:
Library name: NC3
Column name fpkm.xls: NC3

value: primary keratinocyte progenitors


title: Rattus norvegicus, ratonis epidermis Limbal niche, biol rep3

description:
Library name: T3
Column name fpkm.xls: T3


title: 10d_tumor _CD45+_Rep1_AB009


title: ITP4


title: 10d_tumor_CD45+_Rep2_AB243


title: Rattus norvegicus, ratonis epidermis primary keratinocyte progenitors, biol rep2

description:
Library name: NC2
Column name fpkm.xls: NC2


title: 8w_normal_CD45+_Rep1_AB008


title: 10d_tumor_CD45+_Rep2_AB242


title: ITP3


title: Rattus norvegicus, ratonis epidermis primary keratinocyte progenitors, biol rep1

description:
Library name: NC1
Column name fpkm.xls: NC1


title: 10d_tumor_CD45+_Rep2_AB241


title: 8w_normal_CD45+_Rep1_AB007


title: Huh7 cells KO3

city: Chongqing

first: Feng

last: Li

address: No.30, Gaotanyanzheng Street

institute: Army Medical University

description: Library name: Huh7_KO_3

data_processing:
Mapping genome
Assembly: GRCh38 ensembl_111
Supplementary files format and content: xls fils include FPKM valus fo each example

source_name: cell line

extract_protocol:
RNA was harvested using RNAiso Plus (TaKaRa), 1 μg of total RNA was used for construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols

value: Hepatocellular carcinoma cell

value: FBXO32 knockout


title: 8w_normal_CD45-_Rep1_AB006

value: FVB/n MMTV-PyMT-


title: ITP2


title: 10d_tumor_CD45-_Rep2_AB244


title: ITP1


title: Huh7 cells KO2

description: Library name: Huh7_KO_2


title: Adipocytes, Cre virus, Rbm43 siRNA, rep 2

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

country: USA

institute: University of California, San Francisco

description: Normalized reads Column: PAD8

data_processing:
Sequenced reads were trimmed using fastp (v0.23.2)
Reads were aligned to reference genome mm10 (RefSeq gene annotations) and counted using STAR (v2.7.8)
Differential gene expression testing was performed using DEseq2 (v.2.11.40.7)
Assembly: mm10
Supplementary files format and content: Normalized counts table was prepared using DEseq2 (v2.11.40.7)

source_name: Primary adipocytes

extract_protocol:
Total RNA isolated using trizol followed by RNeasy column and subsequent DNase treatment using DNA-free turbo.
Libraries were prepared using Kapa stranded mRNA Hyper Prep sample preparation kits from 500 ng of total RNA isolated using RNeasy columns (Qiagen). The finished dsDNA libraries were quantified by Qubit fluorometer (Thermo Fisher), TapeStation 2200 (Agilent), and RT-qPCR using the Kapa Biosystems library quantification kit. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NovaSeq with paired-end 150 bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: Primary adipocytes

value: Cre virus, Rbm43 siRNA


title: 10d_normal_CD45+_Rep1_AB011


title: 8w_normal_CD45-_Rep1_AB005


title: Healthy control4

description: Healthy control4


title: Adipocytes, Cre virus, Rbm43 siRNA, rep 1

description: Normalized reads Column: PAD7


title: Adipocytes, GFP virus, Rbm43 siRNA, rep 2

description: Normalized reads Column: PAD4

value: GFP virus, Rbm43 siRNA


title: Huh7 cells KO1

description: Library name: Huh7_KO_1


title: 8w_tumor _CD45-_Rep1_AB004


title: Healthy control3

description: Healthy control3


title: 8w_tumor _CD45-_Rep1_AB003


title: Huh7 cells WT2

description: Library name: Huh7_WT_2

value: WT

value: negative control


title: Adipocytes, GFP virus, Rbm43 siRNA, rep 1

description: Normalized reads Column: PAD3


title: Huh7 cells WT3

description: Library name: Huh7_WT_3


title: Healthy control2

description: Healthy control2


title: Healthy control1

description: Healthy control1


title: 8w_tumor _CD45+_Rep1_AB002


title: Huh7 cells WT1

description: Library name: Huh7_WT_1


title: 8w_tumor _CD45+_Rep1_AB001


title: Adipocytes, GFP virus, Control siRNA, rep 1

description: Normalized reads Column: PAD1

value: GFP virus, control siRNA


title: Adipocytes, GFP virus, Control siRNA, rep 2

description: Normalized reads Column: PAD2


title: CHM13, low-risk GTN

status: Public on Dec 21 2024

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a txt file includes TPM counts of each sample

source_name: Complete hydatidiform mole

extract_protocol:
We collected CHM tissues from patients who underwent uterine evacuation. The total RNA of archival fresh frozen tissues was extracted using the miRNeasy® Mini Kit (QIAGEN, Hilden, Germany).
The library construction and pair-end sequencing were conducted by Rarevariant, Inc. (Tokyo, Japan).

value: Complete hydatidiform mole

tag: prognosis

value: Development of low-risk gestational trophoblast neoplasia


title: CHM11, low-risk GTN


title: CHM10, low-risk GTN


title: CHM12, low-risk GTN


title: CHM9, low-risk GTN


title: CHM6, control

value: Spontanous remission


title: CHM5, control


title: CHM4, control


title: CHM7, control


title: CHM8, low-risk GTN


title: CHM2, control


title: CHM3, control


title: 3 hours anti-CD40 stimulated B cells, A20 deficient, biological rep1

type: RNA

city: München

first: Marc

last: Schmidt-Supprian

address: Isamninger Str. 22

department: Klinikum rechts der Isar

country: Germany

institute: Technical University of Munich (TUM)

hyb_protocol: cRNA was hybridized on GeneChip Mouse Genome 430A 2.0 Array according to manufacturer's protocol (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000, Microarray Analysis Suite V5.0

data_processing: Data was filtered by MAS detection call to remove transcripts that were not present in any sample, Microarray data was processed with the RMA method following quantile normalization as implemented in the affy package (Gautier, L. et al., Bioinformatics 20 (2004))

label: biotin

source_name: B cells isolated from mouse spleen

label_protocol: cRNA was prepared according to the standard Affymetrix protocol from 6 total RNA (Affymetrix)

growth_protocol: Cells were extracted from mouse spleens. Per biological replicate, splenocytes from three mice were pooled and follicular B cells were enriched by depletion of CD9+ (marginal zone B) and CD43+ (T) cells.

extract_protocol: After 3 hours or overnight incubation (14 hours), cells were harvested through pelleting, resuspended in 800µl Trizol and cell lysate was frozen until further processing. RNA was extracted using RNeasy Mini Kit (Qiagen) and eluted in RNAse-free water

treatment_protocol: 7 million cells were seeded in 1 ml B cell medium (RPMI, 10% FCS (Gibco), 10 mM HEPES (Gibco), 2 mM L-Glutamine (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), Penicillin/Streptomycin (Gibco)), supplemented with 10 µg/mL anti-IgM (Jackson ImmunoResearch Laboratories, polyclonal), 2.5 µg/ml anti-CD40 (eBioscience, clone HM40–3) or 20 µg/mL lipopolysaccharide (LPS; Sigma-Aldrich) or without supplement.

value: B cells isolated from mouse spleen

value: 3 hours anti-CD40 stimulated


title: 3 hours LPS stimulated B cells, control, biological rep2

value: wild type

value: 3 hours LPS stimulated


title: 14 hours anti-CD40 stimulated B cells, control, biological rep1

value: 14 hours anti-CD40 stimulated


title: 14 hours anti-IgM stimulated B cells, control, biological rep1

value: 14 hours anti-IgM stimulated


title: 3 hours anti-CD40 stimulated B cells, A20 deficient, biological rep2


title: CHM1, control


title: 14 hours anti-CD40 stimulated B cells, A20 deficient, biological rep2


title: 14 hours LPS stimulated B cells, A20 deficient, biological rep2

value: 14 hours LPS stimulated


title: 14 hours LPS stimulated B cells, A20 deficient, biological rep1


title: 3 hours anti-CD40 stimulated B cells, control, biological rep1


title: 14 hours anti-CD40 stimulated B cells, control, biological rep2


title: 3 hours LPS stimulated B cells, A20 deficient, biological rep2


title: 14 hours LPS stimulated B cells, control, biological rep2


title: 14 hours anti-IgM stimulated B cells, A20 deficient, biological rep2


title: 14 hours anti-CD40 stimulated B cells, A20 deficient, biological rep1


title: 3 hours anti-IgM stimulated B cells, control, biological rep2

value: 3 hours anti-IgM stimulated


title: unstimulated B cells, A20 deficient, biological rep1

value: unstimulated


title: 3 hours anti-IgM stimulated B cells, A20 deficient, biological rep2


title: 14 hours anti-IgM stimulated B cells, control, biological rep2


title: 14 hours LPS stimulated B cells, control, biological rep1


title: 3 hours LPS stimulated B cells, A20 deficient, biological rep1


title: 3 hours anti-CD40 stimulated B cells, control, biological rep2


title: 3 hours LPS stimulated B cells, control, biological rep1


title: 3 hours anti-IgM stimulated B cells, control, biological rep1


title: 3 hours anti-IgM stimulated B cells, A20 deficient, biological rep1


title: unstimulated B cells, A20 deficient, biological rep2


title: 14 hours anti-IgM stimulated B cells, A20 deficient, biological rep1


title: mESC_H3K36me3

city: Beijing

first: Min

state: Beijing

address: Yan  yuan street

institute: 北京大学

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to human genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 20 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: mm10
Supplementary files format and content: The processed files were aggregate bigwig file.

molecule: genomic DNA

source_name: mESC

extract_protocol:
Following TACIT protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Cells were collocted by centrifugation at 300g for 3 minutes

tag: cell statement

value: Fixed by methanol

tag: chip antibody


title: KOC7

city: Changsha

first: Jie

last: Ma

address: street of nongda road

institute: Hunan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: adipose tissue

extract_protocol:
Adipose tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruseqTM RNA sample prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

value: post natal week 21


title: KOC4


title: WTC9


title: mESC_H3K4me3


title: KOC6


title: KOC5


title: unstimulated B cells, control, biological rep1


title: KOC3


title: mESC_H3K27me3


title: CACO2shADAR1-2.Input

city: Guangzhou

first: Yu

last: Lin

state: China

address: No. 1838, Guangzhou Dadao North, Baiyun District, Guangzhou

institute: Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital

description: Library name: treat2

data_processing:
Pairing reads were quality controlled using a quality criterion of 1/1000 (Q30) error base call probability in the Illumina HiSeq 4000 sequencer: Q30>80% indicates good sequencing quality. After quality control, trim the 3/adapter using Cutadapt software (v1.9.3) and remove low-quality reads, and harvest high-quality clean reads. Align a clean read of the input library with a reference genome (GRCh38.Geocoding v32) using STAR software (Domin et al., 2013) and identify mRNA peaks using DCC software(Cheng et al., 2016) . Next, align clean reads of all libraries with reference genomes using Hisat2 software (v2.0.4)(Kim et al., 2015). Identify o8G peaks on mRNA using MACS software(Zhang et al., 2008). In addition, different methylation peaks were identified using DiffReps software (Shen et al., 2013): o8G peaks with a fold change of >2 or <0.5 (P<0.00001) in CRC were considered to be up-regulated methylation or down-regulated methylation.(Shen et al., 2013)Peaks that overlap exons of protein-coding genes identified using software and o8G sections were selected using internally developed scripts for further annotation.
Assembly: hg19
Supplementary files format and content: excel format

source_name: colorectum

extract_protocol:
We extracted total RNA using Trizol reagent (Invitrogen, California, USA) following the manufacturer's instructions. Use the Ribo-Zero rRNA Removal Kit (Illumina, Inc., CA, USA) to reduce rRNA content. The quality of RNA is assessed using its OD260/OD280 ratio, which is a measure of nucleotide-to-protein ratio based on optical density measured using spectrophotometry. RNA purity with OD260/OD280 values in the range of 1.8-2.1 is considered acceptable, and RNA extracted from all samples meets this standard.
Total RNA was cleaved into 100 base pair fragments using the GenSeqTM O8G RNA IP Kit (GenSeq Inc, China), followed by O8G immunoprecipitation using the NEBNext® Ultra II Directed RNA Library Preparation Kit (New England Biolaboratories, USA), followed by RNA-seq library generation.The cDNA library was evaluated using the Bioanalyzer 2100 System (Agilent Technologies USA) and the library was sequenced using an Illumina Hiseq instrument with 150 bp pairing readings.

value: colorectum

value: CACO2 Cell

value: cancer cell

value: ADAR1 knockdown


title: KOC1


title: CACO2shADAR1-2.IP

description: Library name: treat4

data_processing:
Pairing reads were quality controlled using a quality criterion of 1/1000 (Q30) error base call probability in the Illumina HiSeq 4000 sequencer: Q30>80% indicates good sequencing quality. After quality control, trim the 3/adapter using Cutadapt software (v1.9.3) and remove low-quality reads, and harvest high-quality clean reads. Align a clean read of the input library with a reference genome (GRCh38.Geocoding v32) using STAR software (Domin et al., 2013) and identify mRNA peaks using DCC software(Cheng et al., 2016) . Next, align clean reads of all libraries with reference genomes using Hisat2 software (v2.0.4)(Kim et al., 2015). Identify o8G peaks on mRNA using MACS software(Zhang et al., 2008). In addition, different methylation peaks were identified using DiffReps software (Shen et al., 2013): o8G peaks with a fold change of >2 or <0.5 (P<0.00001) in CRC were considered to be up-regulated methylation or down-regulated methylation.(Shen et al., 2013)Peaks that overlap exons of protein-coding genes identified using software and o8G sections were selected using internally developed scripts for further annotation.
Assembly: hg19
Supplementary files format and content: excel format
Library strategy: MeRIP-seq

value: anti-O8G immunoprecipitation


title: KOC2


title: CACO2NC-2.IP

description: Library name: control4

value: WT


title: CACO2NC-1.Input

description: Library name: control1


title: WTC3


title: CACO2shADAR1-1.Input

description: Library name: treat1


title: CACO2NC-2.Input

description: Library name: control2


title: CACO2NC-1.IP

description: Library name: control3


title: CACO2shADAR1-1.IP

description: Library name: treat3


title: unstimulated B cells, control, biological rep2

value: B cells isolated from mouse spleen


title: WTC7

value: wild type


title: pulmonary carcinoid tumor, patient S01590

type: genomic

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

hyb_protocol: Bisulfite conversion was carried out using the EZ-96 DNA Methylation-GoldTM kit following the manufacturer's recommendations for Infinium assays. Bisulfite converted DNA was hybridised to Illumina Infinium HumanMethylation850 BeadChip following the manufacturer’s protocol (Illumina Inc.).

scan_protocol: Signal intensity was measured with the Illumina iScan.

data_processing:
Methylation intensities were determined using the RnBeads R package (version 2.10.0) and hg19 annotations. Probes on sex chromosomes were removed and normlized with the BMIQ method. All other parameters were set to the default values.
processed_data.txt:  BMIQ normalized beta values
signal_intensities.txt:  Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

value: pulmonary carcinoid tumors

tag: histopathology

value: typical

tag: Stage

value: Ia

tag: tert expr

tag: gender

value: Male


title: pulmonary carcinoid tumor, patient S01666

value: IIb

value: Female


title: pulmonary carcinoid tumor, patient S01605

value: IIIa


title: pulmonary carcinoid tumor, patient S01573


title: pulmonary carcinoid tumor, patient S01582


title: pulmonary carcinoid tumor, patient S01546

value: Ib


title: pulmonary carcinoid tumor, patient S01545

value: IIa


title: pulmonary carcinoid tumor, patient S01572

value: atypical


title: WTC8

value: adipose tissue

value: post natal week 21


title: pulmonary carcinoid tumor, patient S01543


title: WTC5


title: pulmonary carcinoid tumor, patient S01541


title: WTC4


title: WTC6


title: pulmonary carcinoid tumor, patient S01532


title: pulmonary carcinoid tumor, patient S01540


title: pulmonary carcinoid tumor, patient S01060


title: pulmonary carcinoid tumor, patient S01202


title: pulmonary carcinoid tumor, patient S00516


title: pulmonary carcinoid tumor, patient S00515


title: pulmonary carcinoid tumor, patient S01521


title: pulmonary carcinoid tumor, patient S00520


title: pulmonary carcinoid tumor, patient S00089


title: pulmonary carcinoid tumor, patient S00128


title: pulmonary carcinoid tumor, patient S01583


title: pulmonary carcinoid tumor, patient S00118


title: pulmonary carcinoid tumor, patient S00076

value: IIIb


title: mycelia - MNase_rsc1_rep2_IP

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

description: Library name: Sample 30

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: MG8
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph

organism: Pyricularia oryzae

growth_protocol: The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) or anti-H3K4ac (Active Motif, 39381) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

value: mycelia


title: mycelia - MNase_rsc1_rep1_IP

description: Library name: Sample 29


title: mycelia - MNase_WT_rep2_IP

description: Library name: Sample 28


title: mycelia - MNase_WT_rep1_IP

description: Library name: Sample 27


title: mycelia - H3_WT

description: Library name: Sample 26


title: mycelia - H3_rsc1

description: Library name: Sample 24


title: mycelia - H3_jmj1

description: Library name: Sample 25


title: mycelia - H3K18ac_rsc1_rep2_IP

description: Library name: Sample 23


title: mycelia - H3K27ac_rsc1_rep2_IP

description: Library name: Sample 19


title: mycelia - H3K27ac_rsc1_rep1_IP

description: Library name: Sample 18


title: mycelia - H3K18ac_rsc1_rep1_IP

description: Library name: Sample 22


title: mycelia - H3K18ac_WT_rep2_IP

description: Library name: Sample 21


title: mycelia - H3K27me3_jmj1_rep2_IP

description: Library name: Sample 15


title: mycelia - H3K27ac_WT_rep2_IP

description: Library name: Sample 17


title: mycelia - H3K18ac_WT_rep1_IP

description: Library name: Sample 20


title: pulmonary carcinoid tumor, patient S00094


title: mycelia - H3K27me3_rsc1_rep1_IP

description: Library name: Sample 12


title: mycelia - H3K27me3_WT_rep2_IP

description: Library name: Sample 11


title: mycelia - H3K27me3_rsc1_rep2_IP

description: Library name: Sample 13


title: mycelia - H3K27me3_WT_rep1_IP

description: Library name: Sample 10


title: mycelia - GFP_JMJ1_rep2_IP

description: Library name: Sample 9


title: mycelia - GFP_JMJ1_rep1_IP

description: Library name: Sample 8


title: mycelia - GFP_RSC1-kmt6_Input

description: Library name: Sample 4


title: mycelia - GFP_RSC1_rep1_IP

description: Library name: Sample 2


title: mycelia - GFP_RSC1-kmt6_rep2_IP

description: Library name: Sample 6


title: mycelia - GFP_JMJ1_Input

description: Library name: Sample 7


title: mycelia - GFP_RSC1_rep2_IP

description: Library name: Sample 3


title: mycelia - GFP_RSC1_Input

description: Library name: Sample 1


title: rsc1 mycelia 2 days rep2

description: Library name: Sample 5

data_processing:
RNAs were sequenced separately at Novogene, using Illumina NovaSeq 6000 with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of M. oryzae (MSU release 7) using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test (the total number of genes in the M. oryzae genome used was 14317). (http://nemates.org/MA/progs/overlap_stats.html).
Assembly: MG8
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 4-5 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
Total RNA was extracted from mycelia cultured in the liquid CM for 2 days from three biological repeats using the TRIzol (Invitrogen, USA) reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mutant


title: rsc1 mycelia 2 days rep1

description: Library name: Sample 4


title: WT mycelia 2 days rep2

description: Library name: Sample 2


title: mycelia - H3K27ac_WT_rep1_IP

description: Library name: Sample 16


title: WT mycelia 2 days rep1

description: Library name: Sample 1


title: WT mycelia 2 days rep3

description: Library name: Sample 3


title: mycelia - H3K27me3_jmj1_rep1_IP

description: Library name: Sample 14


title: 293T_3

city: fuzhou

first: Zhihua

last: Feng

state: Fujian

address: Fujian Normal University, Qishan Campus, No.8 Xuefu South Road, Shangjie, Minhou, Fuzhou, Fujian,China

institute: Fujian Normal University

description: Library name: Sample 3

data_processing:
Clean reads were obtained by removing adapter sequences, poly-N stretches, and low-quality reads from the raw data. The quality of the clean data was assessed by calculating Q20, Q30, GC content, and sequence duplication levels. Clean reads were aligned to the reference genome (GRCh38.p14) using HISAT2 (v2.2.1), and gene expression levels for each sample were quantified with featureCounts (v2.0.6).
Assembly: Clean reads were aligned to the reference genome (GRCh38.p14).
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: kidney

growth_protocol: 293T cell cultured in Dulbecco's Modified Eagle's Medium (DMEM) (Cytiva, Shanghai, China) supplemented with 10% (v/v) fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA), 10 μg/ml streptomycin, and 100 U/ml penicillin (BasalMedia, Shanghai, China). The cultures were maintained at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using TRIzol™ reagent (Sigma-Aldrich) following the manufacturer’s instructions. The total amount of 2 μg RNA was used as the starting material for RNA sample preparation.
Sequencing libraries were constructed using the NEBNext Ultra™ RNA Library Preparation Kit (New England BioLabs, USA) according to the manufacturer’s guidelines.

value: kidney

value: Epithelial cells

value: Wild type

value: Untreated


title: 293T_2

description: Library name: Sample 2


title: 293T_1

description: Library name: Sample 1


title: D2_VSV_12h_2

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

description: Library name: Sample 8

data_processing:
Sequencing data were analyzed with our in-house pipeline (Fu et al. 2011, 2015)
Sequencing reads were mapped to the human hg38 reference genomes, and internal priming was filtered.
poly(A) sites were defined for each sample by clustering the unique mapped reads, and then, the poly(A) sites were merged together across samples.
Assembly: hg38
Supplementary files format and content: Wiggle Track format files containing a graphical trace on a genome

growth_protocol: THP-1 cells were maintained in 1640 (Gibco) supplemented with 10% FBS (ExCell Bio) at 37ºC with 5% CO2 incubation.

extract_protocol:
Cells were harvested and total RNA was extracted with TRIzol
1 ug total RNA was used to prepare the IVT-SAPAS library according to the previous report (Fu et al., 2015). The quality of the library was evaluated with a Qsep400 Advance.

treatment_protocol: THP-1 cells were treated with PMA (50 ng/ml) for 48h and then replaced with 1640 complete medium and continued to be cultured for 24h.

value: monocytes

value: VSV virus infection for 12 h

value: VSV virus infection


title: D2_VSV_CPSF6_K161R_K185R

description: Library name: Sample 12

value: Overexpression of amino acid mutant CPSF6 at position 161 and 185


title: D2_VSV_CPSF6_WT

description: Library name: Sample 9

value: Overexpression of wild-type CPSF6


title: D2_VSV_CPSF6_K161R

description: Library name: Sample 10

value: Overexpression of amino acid mutant CPSF6 at position 161


title: D2_VSV_4h_2

description: Library name: Sample 6

value: VSV virus infection for 4 h


title: D2_VSV_CPSF6_K185R

description: Library name: Sample 11

value: Overexpression of amino acid mutant CPSF6 at position 185


title: D2_VSV_8h_2

description: Library name: Sample 7

value: VSV virus infection for 8 h


title: mycelia - GFP_RSC1-kmt6_rep1_IP

description: Library name: Sample 5


title: D2_VSV_0h_2

description: Library name: Sample 5

value: VSV virus infection for 0 h


title: D2_VSV_0h_1

description: Library name: Sample 1


title: D2_VSV_8h_1

description: Library name: Sample 3


title: rsc1 mycelia 2 days rep3

description: Library name: Sample 6


title: HT29, Cas13 CCAT1 targeting guide2, Replicate1, H3K27ac HiChIP

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
We mapped HiChIP paired end reads to hg19 using HiC-Pro (Servant 2015). Default settings were using to remove duplicate reads, identify valid interactions, and generate contact maps.
We identified statistically significant contacts using FitHiChIPat a 1% FDR. We used H3K27ac ChIP-seq data as a reference set of peaks in the FitHiChIP pipeline.
Assembly: hg19
Supplementary files format and content: allValidPairs, bed
Library strategy: H3K27ac HiChIP

growth_protocol: A375 and A549 cells were cultured in Dulbecco’s Modified Eagle Medium + 10% v/v FBS + 1% Pen/Strep. HT29 cells were cultured in McCoy's 5A (Modified) Medium + 10% v/v FBS + 1% Pen/Strep. K562 cells were cultured in Iscove's Modified Dulbecco's Medium + 10% v/v FBS + 1% Pen/Strep. MDAMB231 and PC( cells were cultured in RPMI-1640 + 10% v/v FBS + 1% Pen/Strep. All cells were cultured in a humidified enviornment with 5% CO2 at 37C.

extract_protocol:
For H3K27ac HiChIP libraries, we grew NIH3T3 (mouse) cells and human cell lines A375, A549, HT29, K562, MDA-MB-231 and PC-9 in the appropriate media.  We fixed cells in 1% formaldehyde for 10min and quenched to a final concentration of 125nM glycine. We mixed 2 million fixed mouse cells with 10 million of each fixed human cancer cell line. The cells were lysed in 0.5% SDS, quenched with 10% Triton X-100, and digested with MboI (NEB R0147M). The DNA overhangs were blunted, biotinylated (ThermoFisher 19524016), and ligated. Nuclei were spun down, resuspended in nuclear lysis buffer and sonicated using a Covaris LE220 with the following conditions: Fill level 10, PIP 450, Duty factor 30, CPB 200. We incubated the sheared DNA with Dynabeads Protein A (ThermoFisher 10001D) for 2 hours at 4 °C. We then placed the tubes on a magnet and the supernatant was kept. We performed immunoprecipitation with a cross-species reactive H3K27ac antibody (Active Motif 39133). The samples were incubated with the antibody overnight at 4 °C. We then washed, eluted and treated the samples and treated with Proteinase K. We purified the samples using Zymo DNA Clean & Concentrator
Biotin capture was performed with Dynabeads M-280 Streptavidin (ThermoFisher 11205D), followed by library preparation as previously described (Gryder, Khan and Stanton, 2020). We purified the amplified libraries with Illumina Sample Purification Beads. We sequenced the libraries using paired-end reads with NovaSeq 6000 or NextSeq 500.

treatment_protocol: HT29 cells with inducible RfxCas13d were transduced with a nontargeting guide or one of two CCAT1 targeting guides. We performed H3K27ac HiChIP 72 hours after induction with 1 ug/mL  doxycycline.

value: Cas13 CCAT1 targeting guide2


title: HT29, Cas13 CCAT1 targeting guide2, Replicate2, H3K27ac HiChIP


title: HT29, Cas13 CCAT1 targeting guide1, Replicate2, H3K27ac HiChIP

value: Cas13 CCAT1 targeting guide1


title: HT29, Cas13 CCAT1 nontargeting guide, Replicate3, H3K27ac HiChIP

value: Cas13 nontargeting guide


title: HT29, Cas13 CCAT1 targeting guide2, Replicate3, H3K27ac HiChIP


title: HT29, Cas13 CCAT1 nontargeting guide, Replicate2, H3K27ac HiChIP


title: HT29, Cas13 CCAT1 nontargeting guide, Replicate1, H3K27ac HiChIP


title: PC9, Replicate1, H3K27ac HiChIP

value: No treatment


title: PC9, Replicate2, H3K27ac HiChIP


title: HT29, Cas13 CCAT1 targeting guide1, Replicate1, H3K27ac HiChIP


title: K562, Replicate1, H3K27ac HiChIP


title: K562, Replicate2, H3K27ac HiChIP


title: MDAMB231, Replicate2,  H3K27ac HiChIP


title: D2_VSV_12h_1

description: Library name: Sample 4


title: PBMCs, Batch 7, Feature barcodes

city: Nashville

first: Kaushik

last: Amancherla

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

description: 10X Genomics

library_source: other

data_processing:
CellRanger 6.1.2 was used and demultiplexing was done using HTODemux() in Seurat (v4.3).
Assembly: GRCh38
Supplementary files format and content: Seurat object

molecule: protein

source_name: PBMC

extract_protocol:
PBMCs
Samples labeled with TotalSeq C hashtag antibodies were pooled together to generate mixtures of 5 samples per batch (total 8 batches). Pooled samples were loaded into a 10X Genomics microfluidic platform (Single Cell 5’ v2 Reagent Kit), targeting 12,000 – 16,000 cells per batch. Sequencing was performed on the NovaSeq6000 S4 flow cell targeting 50,000 reads per cell for the gene expression libraries and 5,000 reads per cell for the feature barcode libraries. Libraries were processed according to manufacturer’s instructions.
10X scRNA-seq using 5' v2 chemistry

treatment_protocol: 22 patients with CAV and 18 patients without

value: PBMC

tag: library type

value: HTO


title: HT29, Replicate1, H3K27ac HiChIP


title: D2_VSV_4h_1

description: Library name: Sample 2


title: A549, Replicate1, H3K27ac HiChIP


title: PBMCs, Batch 8, Feature barcodes

description: 10X Genomics


title: A549, Replicate2, H3K27ac HiChIP


title: PBMCs, Batch 2, Feature barcodes

description: 10X Genomics


title: PBMCs, Batch 4, Feature barcodes

description: 10X Genomics


title: PBMCs, Batch 8, GEX

description: 10X Genomics

value: mRNA


title: PBMCs, Batch 7, GEX

description: 10X Genomics


title: PBMCs, Batch 1, Feature barcodes

description: 10X Genomics


title: PBMCs, Batch 5, GEX

description: 10X Genomics


title: PBMCs, Batch 3, GEX

description: 10X Genomics


title: HT29, Cas13 CCAT1 targeting guide1, Replicate3, H3K27ac HiChIP


title: PBMCs, Batch 2, GEX

description: 10X Genomics


title: PBMCs, Batch 4, GEX

description: 10X Genomics


title: HT29, Replicate2, H3K27ac HiChIP


title: PBMCs, Batch 1, GEX

description: 10X Genomics


title: MDAMB231, Replicate1,  H3K27ac HiChIP


title: RNAseq_Zfp91_HS_neg_Rep2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
ChIP and RNA: Raw BCL output files were processed using bcl2fastq (Illumina, version 2.20)
ChIP and RNA: Quality trimming was performed using using CutAdapt1.14
ChIP: Trimmed ChIP-seq reads were aligned to the human genome (University of California at Santa Cruz [UCSC] hg38 build) using Bowtie v2.2.6
ChIP: Peak calling was performed using MACS2 with the  default (narrow) option. Called peaks were annotated with HOMER program annotatePeaks.pl
ChIP: Heatmaps and metaplots from bigwig files were generated using deepTools v3.1.1
RNA: RNA-seq reads were aligned to the hg38 human genome using STAR aligner v2.5.2
RNA: Outputted bam files were sorted using samtools v1.6
RNA: exonic reads were assigned to specific genes from Ensembl release 72 and genome assembly GRCh38.p13 using the python package HTSeq-0.6.1
Assembly: hg38
Supplementary files format and content: bigwig files for ChIP-seq data

growth_protocol: Human HCT116 cells were cultured in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (GIBCO #15140-122) in incubators set to 37°C and 5% CO2.

extract_protocol:
For RNA: RNA from HCT116 cells was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
For ChIP: Immunoprecipitated DNA was purified using a ChIP DNA Clean&Concentrator kit (Zymo Research, D5205).
ChIP libraries were prepared using the KAPA HTP library preparation kit (KAPA Biosystems). RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, # E7760L).

treatment_protocol:
100mM biotin (Sigma-Aldrich, B4501) stock prepared in DMSO was added directly to tissue culture media at a final concentration of 100-500µM for immunostaining experiments and at 500µM for immunoblotting and proteomics experiments. Cells were incubated in biotin for 30 minutes at 37°C and 5% CO2 in the tissue culture incubator. Following this, media was removed and cells were washed with ice-cold PBS 5 times to quench the biotinylation reaction before fixation for immunostaining or harvest for endpoint assays.
Cells were either incubated at 37C (non-heat shock, HS_neg)  and 5% CO2 or 42C and 5% CO2 (heat shock/HS_pos)

value: human colorectal carcinoma cells

value: Zfp91 knockdown

value: 37C 3 hours (no heat shock)


title: RNAseq_Zfp91_HS_pos_Rep2

value: 42C 3 hours (heat shock)


title: RNAseq_Zfp91_HS_neg_Rep1


title: RNAseq_Yy1_HS_pos_Rep2

value: Yy1 knockdown


title: PBMCs, Batch 6, GEX

description: 10X Genomics


title: PBMCs, Batch 6, Feature barcodes

description: 10X Genomics


title: PBMCs, Batch 3, Feature barcodes

description: 10X Genomics


title: RNAseq_Zfp91_HS_pos_Rep1


title: RNAseq_Yy1_HS_neg_Rep2


title: RNAseq_Yy1_HS_neg_Rep1


title: RNAseq_Trim28_HS_pos_Rep2

value: Trim28 knockdown


title: RNAseq_Trim28_HS_neg_Rep2


title: IVF35h_Late2cell_embryo_barcoded_TACIT_H3K27ac

last: Liu

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to human genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: mm10
Supplementary files format and content: The processed files were aggregate bigwig file.

source_name: embryo

growth_protocol: Cells were collected from frash embryos.

treatment_protocol: Cells were collocted by centrifugation at 150-1,500g for 3 minutes

value: embryo

value: embryonic cells

value: WT

tag: antibody

value: fixed by methanol


title: IVF20h_Early2cell_embryo_barcoded_TACIT_H3K27ac


title: RNAseq_Trim28_HS_pos_Rep1


title: skin_RRpreMDT.group_s51_1_RR12

city: Los Angeles

first: Priscila

middle: Ribeiro

last: Andrade

state: CALIFORNIA

address: 615 Charles E Young Drive South, room 246

department: Medicine

institute: UCLA

data_processing:
Sequenced reads were demultiplexed and aligned to the human reference genome hg19 (UCSC) using TopHat (version 2.0.6) and Bowtie2 (version 2.0.2)
Once raw counts were generated using HTSeq, data normalization was performed using the DESeq2 (Bioconductor package).
Assembly: human reference genome hg19 (UCSC)
Supplementary files format and content: tab-limited file includes raw counts for each sample
Supplementary files format and content: tab-limited file includes normalized counts for each sample

source_name: skin

extract_protocol:
Frozen leprosy skin biopsy specimens were cut into forty 4µm sections and lysed in RLT Buffer (Qiagen, cat n°79216) supplemented with 1% β-mercaptoethanol, followed by immediate storage at -80°C. For RNA extration, samples were added to Lysing Matrix B tubes containing 100µm zirconium beads (OPS Diagnostics, cat n°PFLB 100-100 06U) and sonicated in FastPrep®-24 instrument (MP Biomedicals) at 4°C for 2 cycles of 45 seconds at 4m/s with five minutes intervals on ice after each cycle. Total RNA was then isolated using the RNeasy Micro kit (Qiagen, cat n°74004) according to the manufacturer’s protocol and quantified by NanoDrop spectrophotomer and Qubit Fluorometer. All samples had RNA integrity numbers above 8.0 as determined by Bioanalyzer quality assessment (Agilent Technologies).
Depletion of ribosomal RNA and library preparation were performed using Ribozero Gold Human/Rat/Mouse (Illumina, cat n°MRZG126) and KAPA Stranded RNA-Seq Library prep Kit (Kapa Biosystems, cat n°KR0934) according to the manufacturer’s protocols. Final libraries were reassessed for quality (Qubit and Bioanalyzer), barcoded, multiplexed at eight samples per lane (10µM each library), and sequenced on a HiSeq 4000 sequencer (Illumina) at single-end 100bp reads.

treatment_protocol: Forty-five skin biopsy specimens (6 mm) were obtained from leprosy patients classified according to Ridley & Jopling criteria (1966) at the Souza Araújo Outpatient Unit (Oswaldo Cruz Foundation, Rio de Janeiro, Brazil) and immediately frozen in liquid nitrogen. The clinical diagnosis of the patients included in this study were supported by the histopathological analysis of hematoxylin & eosin-stained skin lesion sections and acid-fast staining of bacilli. The pre-RR group (paired) was comprised of biopsy specimens of six borderline-lepromatous (BL), one borderline-borderline (BB) and two lepromatous-lepromatous (LL) patients (n=9) obtained at the time of leprosy diagnosis and before multidrug therapy (MDT) initiation. The RR group (paired) included nine (n=9) skin lesions from the same pre-RR patients obtained at the RR clinical diagnosis, before prednisone treatment. Eight RR samples were obtained during MDT (n=8) and one sample was acquired after the completion of MDT treatment (n=1).The T-lep group was composed of ten (n=10) borderline-tuberculoid (BT) skin biopsy specimens obtained at the time of leprosy diagnosis and before MDT administration. The L-lep group included five new LL (n=5) skin lesions obtained at the time of leprosy diagnosis and before MDT administration, as well as 2 LL skin lesions from the pre-RR group. The RR pre-MDT group was comprised of twelve (n=12) patients that were officially diagnosed with RR at the same time of the leprosy clinical diagnosis, and therefore, were not given any treatment for leprosy or the reactional episode.

value: skin

value: skin cell populations

value: RR pre-MDT


title: IVF35h_Late2cell_embryo_barcoded_TACIT_H3K4me3


title: skin_RRpreMDT.group_s50_1_RR11


title: skin_RRpreMDT.group_s49_1_RR10


title: IVF20h_Early2cell_embryo_barcoded_TACIT_H3K4me3


title: skin_RRpreMDT.group_s48_1_RR9


title: skin_RRpreMDT.group_s47_1_RR8


title: RNAseq_Supt16h_HS_pos_Rep1

value: Supt16h knockdown


title: skin_RRpreMDT.group_s46_1_RR7


title: 8cell_CoTACIT_group2

value: H3K27ac, H3K36me3, H3K4me3


title: RNAseq_Yy1_HS_pos_Rep1


title: skin_RRpreMDT.group_s43_1_RR5


title: skin_RRpreMDT.group_s45_1_RR6


title: RNAseq_Supt16h_HS_neg_Rep1


title: 8cell_CoTACIT_group1

value: H3K27ac, H3K4me3, H3K4me1


title: skin_RRpreMDT.group_s38_1_RR1


title: skin_RRpreMDT.group_s37_1_RR4


title: RNAseq_Sumo2_HS_pos_Rep1

value: Sumo2 knockdown


title: 2cell_CoTACIT_group2


title: skin_RRpreMDT.group_s21_1_RR2


title: RNAseq_Trim28_HS_neg_Rep1

value: human colorectal carcinoma cells


title: skin_RRpreMDT.group_s13_1_RR3


title: 2cell_CoTACIT_group1


title: RNAseq_Supt16h_HS_pos_Rep2


title: RNAseq_Sumo2_HS_neg_Rep2


title: skin_RR.group_s85_1_RR.BL1

value: RR group (paired)


title: skin_RR.group_s84_1_RR.BL3


title: 2cell_h3k36me3

value: 1% FA


title: RNAseq_Sumo2_HS_neg_Rep1

value: 37C 3 hours (no heat shock)


title: 2cell_h3k4me1


title: skin_RR.group_s82_1_RR.BL5


title: RNAseq_Sumo2_HS_pos_Rep2

value: 42C 3 hours (heat shock)


title: RNAseq_Smarcd2_HS_pos_Rep2

value: Smarcd2 knockdown


title: RNAseq_Smarcd2_HS_pos_Rep1


title: skin_RR.group_s25_1_RR.BL6


title: skin_RR.group_s23_1_RR.LL2


title: skin_RR.group_s24_1_RR.BB1


title: skin_preRR.group_s30_1_BB1

value: preRR (paired)


title: GV_oocyte_h3k9me3

value: embryo

value: embryonic cells


title: RNAseq_Smarcd2_HS_neg_Rep2


title: RNAseq_Smarcd2_HS_neg_Rep1


title: skin_RR.group_s31_1_RR.BL4


title: zygote_h3k4me1

value: WT


title: PBMCs, Batch 5, Feature barcodes

description: 10X Genomics

value: PBMC

value: HTO


title: skin_preRR_BL.group_s86_1_LL1

value: skin

value: skin cell populations


title: skin_RR.group_s83_1_RR.LL1


title: skin_preRR_BL.group_s26_1_LL2


title: GV_oocyte_h3k36me3


title: skin_preRR_BL.group_s87_1_BL4


title: GV_oocyte_h3k4me1


title: RNAseq_Sdad1_HS_pos_Rep2

value: Sdad1 knockdown


title: skin_preRR_BL.group_s34_1_BL3


title: RNAseq_Sdad1_HS_pos_Rep1


title: single_embryo_RNA_KD

value: native


title: zygote_h3k36me3


title: skin_RR.group_s28_1_RR.BL2


title: RNAseq_Sdad1_HS_neg_Rep2


title: scRNA_zygote_to_blastocyst


title: RNAseq_Sdad1_HS_neg_Rep1


title: skin_preRR_BL.group_s35_1_BL2


title: embryo_barcode_tacit_late2cell_h3k4me3

value: fixed by methanol


title: skin_LL.group_s78_1_LL5

value: LL group


title: RNAseq_Scrambled_HS_pos_Rep2

value: human colorectal carcinoma cells

value: Scrambled control


title: embryo_barcode_tacit_early2cell_h3k4me3


title: skin_LL.group_s75_1_LL7


title: skin_LL.group_s76_1_LL6


title: skin_LL.group_s36_1_LL3


title: skin_BT.group_s79_1_BT2

value: BT group


title: RNAseq_Scrambled_HS_pos_Rep1

value: 42C 3 hours (heat shock)


title: embryo_barcode_tacit_late2cell_h3k27ac


title: embryo_barcode_tacit_early2cell_h3k27ac


title: RNAseq_Scrambled_HS_neg_Rep2

value: 37C 3 hours (no heat shock)


title: skin_BT.group_s77_1_BT7


title: skin_BT.group_s14_1_BT1


title: skin_preRR_BL.group_s33_1_BL5

value: preRR (paired)


title: skin_preRR_BL.group_s29_1_BL6


title: skin_BT.group_s10_1_BT3


title: cotacit_blastocyst

value: embryo


title: skin_preRR_BL.group_s32_1_BL1


title: RNAseq_Scrambled_HS_neg_Rep1


title: RNAseq_Ranbp2_HS_pos_Rep1

value: Ranbp2 knockdown


title: skin_BT.group_s8_1_BT6


title: cotacit_morula

value: embryonic cells

value: WT


title: RNAseq_Ranbp2_HS_pos_Rep2


title: skin_BT.group_s7_1_BT9


title: cotacit_8cell


title: skin_BT.group_s5_1_BT8


title: RNAseq_Ranbp2_HS_neg_Rep2


title: skin_LL.group_s80_1_LL4


title: cotacit_2cell


title: cotacit_4cell


title: MDAMB231, 2

city: sadel crick road

first: Mohd

middle: wasim

last: Nasser

state: Omaha

address: 42 and Emile

department: BMB

institute: UNMC

data_processing:
The alignment was performed using HISAT2 using GRCh37 human genome index. The read assignment was done using featureCounts and normalization was done using DESeq2 R package.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

extract_protocol:
Cells were grow in DMEM supplemented with 10% FBS and PS, and RNA was isolated by mir VANA kit
RNA was harvested using Mir vana kit (invitrogen).

value: Breast cancer


title: RNAseq_Rad50_HS_pos_Rep2

value: Rad50 knockdown


title: skin_BT.group_s11_1_BT4

value: skin

value: skin cell populations


title: MDAMB231, 1


title: RNAseq_Rad50_HS_pos_Rep1


title: cotacit_zygote


title: brain tissue, wild-type, male, PBS-treated, rep4 [S39_wtmp4]

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned with STAR v2.5.1a, and quantitated with Subread:featureCount v1.4.6-p5
Assembly: Mouse Ensembl GRCm38.76
Supplementary files format and content: all_40_samples_gene_counts.txt, tab-separated value, contains gene counts of all samples
Supplementary files format and content: per sample genecounts.sf, tab-separated value, contains gene counts with TPM values

source_name: brain

growth_protocol: Wild-type (C57BL/6J) and ch25h-/- (CKO) mice from the Jackson Laboratory were used in this study.

extract_protocol:
Animals were perfused 24 hours after the last injection. Left hemisphere was fixed in 4% paraformaldehyde for immunostaining. Hippocampus from the right hemisphere was flash frozen and stored at -80˚C until RNA isolation using Zymo Research Quick-RNA MiniPrep Plus kit (Cat. #: R1058).
an oligo-dT based SMARTer Ultra Low RNA kit from the Takara-Clontech was used to prepare the libraries

treatment_protocol: At 23-26 weeks of age, mice were intraperitoneally (i.p.) administered LPS (2 mg/kg per dose) or vehicle (PBS) twice with a 24-hours interval.

value: brain

value: male

value: 23-26 weeks

value: wild-type

value: PBS-gtreated


title: RNAseq_Rad50_HS_neg_Rep2

value: human colorectal carcinoma cells


title: brain tissue, wild-type, male, PBS-treated, rep5 [S40_wtmp5]


title: skin_BT.group_s4_1_BT5

value: BT group


title: RNAseq_Rad50_HS_neg_Rep1

value: 37C 3 hours (no heat shock)


title: MDAMB231Br, 2

value: BC Brain metastasis


title: brain tissue, wild-type, male, PBS-treated, rep3 [S38_wtmp3]


title: RNAseq_Prpf40a_HS_pos_Rep2

value: Prpf40a knockdown

value: 42C 3 hours (heat shock)


title: RNAseq_Prpf40a_HS_pos_Rep1


title: skin_BT.group_s6_1_BT10


title: brain tissue, wild-type, male, PBS-treated, rep1 [S36_wtmp1]


title: brain tissue, wild-type, male, LPS-treated, rep5 [S35_wtml5]

value: LPS-treated


title: brain tissue, wild-type, male, PBS-treated, rep2 [S37_wtmp2]


title: brain tissue, wild-type, male, LPS-treated, rep4 [S34_wtml4]


title: RNAseq_Prkdc_HS_pos_Rep2

value: Prkdc knockdown


title: RNAseq_Prkdc_HS_pos_Rep1


title: RNAseq_Prpf40a_HS_neg_Rep1


title: brain tissue, wild-type, male, LPS-treated, rep3 [S33_wtml3]


title: MDAMB231Br, 1


title: RNAseq_Ranbp2_HS_neg_Rep1

value: Ranbp2 knockdown


title: RNAseq_Prkdc_HS_neg_Rep1


title: brain tissue, wild-type, male, LPS-treated, rep2 [S32_wtml2]


title: RNAseq_Nono_HS_pos_Rep2

value: Nono knockdown


title: RNAseq_Nono_HS_pos_Rep1


title: RNAseq_Nono_HS_neg_Rep2


title: brain tissue, wild-type, female, PBS-treated, rep5 [S30_wtfp5]

value: female


title: RNAseq_Nono_HS_neg_Rep1


title: RNAseq_Nkap_HS_pos_Rep2

value: Nkap knockdown


title: brain tissue, wild-type, female, PBS-treated, rep2 [S27_wtfp2]

value: brain


title: brain tissue, wild-type, female, PBS-treated, rep3 [S28_wtfp3]


title: brain tissue, wild-type, female, PBS-treated, rep4 [S29_wtfp4]


title: brain tissue, wild-type, female, LPS-treated, rep4 [S24_wtfl4]


title: brain tissue, wild-type, male, LPS-treated, rep1 [S31_wtml1]

value: male


title: RNAseq_Nat10_HS_pos_Rep2

value: Nat10 knockdown


title: RNAseq_Nkap_HS_neg_Rep2


title: brain tissue, wild-type, female, PBS-treated, rep1 [S26_wtfp1]

value: 23-26 weeks

value: wild-type


title: RNAseq_Nat10_HS_neg_Rep2

value: human colorectal carcinoma cells


title: brain tissue, wild-type, female, LPS-treated, rep2 [S22_wtfl2]


title: RNAseq_Nkap_HS_neg_Rep1


title: RNAseq_Nat10_HS_pos_Rep1


title: brain tissue, wild-type, female, LPS-treated, rep3 [S23_wtfl3]


title: brain tissue, Ch25h-knockout, male, PBS-treated, rep5 [S20_komp5]

value: PBS-gtreated


title: brain tissue, Ch25h-knockout, male, PBS-treated, rep4 [S19_komp4]


title: RNAseq_Kpna2_HS_pos_Rep1

value: Kpna2 knockdown


title: brain tissue, wild-type, female, LPS-treated, rep1 [S21_wtfl1]


title: brain tissue, Ch25h-knockout, male, PBS-treated, rep3 [S18_komp3]


title: RNAseq_Nat10_HS_neg_Rep1

value: 37C 3 hours (no heat shock)


title: brain tissue, wild-type, female, LPS-treated, rep5 [S25_wtfl5]


title: RNAseq_Kpna2_HS_neg_Rep2


title: RNAseq_Kpna2_HS_neg_Rep1


title: brain tissue, Ch25h-knockout, male, PBS-treated, rep2 [S17_komp2]


title: RNAseq_Hspa9_HS_pos_Rep2

value: Hspa9 knockdown


title: brain tissue, Ch25h-knockout, male, PBS-treated, rep1 [S16_komp1]


title: brain tissue, Ch25h-knockout, male, LPS-treated, rep4 [S14_koml4]


title: RNAseq_Hspa9_HS_pos_Rep1

value: 42C 3 hours (heat shock)


title: brain tissue, Ch25h-knockout, male, LPS-treated, rep5 [S15_koml5]

value: LPS-treated


title: brain tissue, Ch25h-knockout, male, LPS-treated, rep3 [S13_koml3]


title: RNAseq_Hspa8_HS_pos_Rep2

value: Hspa8 knockdown


title: RNAseq_Hspa9_HS_neg_Rep2


title: brain tissue, Ch25h-knockout, female, PBS-treated, rep5 [S10_kofp5]


title: RNAseq_Hspa9_HS_neg_Rep1


title: brain tissue, Ch25h-knockout, male, LPS-treated, rep2 [S12_koml2]


title: brain tissue, Ch25h-knockout, male, LPS-treated, rep1 [S11_koml1]


title: RNAseq_Hspa6_HS_pos_Rep2

value: Hspa6 knockdown


title: brain tissue, Ch25h-knockout, female, PBS-treated, rep3 [S08_kofp3]


title: RNAseq_Hspa8_HS_pos_Rep1


title: brain tissue, Ch25h-knockout, female, PBS-treated, rep4 [S09_kofp4]


title: RNAseq_Hspa8_HS_neg_Rep1


title: RNAseq_Hspa6_HS_pos_Rep1


title: brain tissue, Ch25h-knockout, female, PBS-treated, rep2 [S07_kofp2]


title: brain tissue, Ch25h-knockout, female, LPS-treated, rep5 [S05_kofl5]


title: RNAseq_Hspa6_HS_neg_Rep2


title: brain tissue, Ch25h-knockout, female, LPS-treated, rep4 [S04_kofl4]


title: brain tissue, Ch25h-knockout, female, PBS-treated, rep1 [S06_kofp1]


title: RNAseq_Hspa1b_HS_pos_Rep2

value: Hspa1b knockdown


title: RNAseq_Hspa6_HS_neg_Rep1


title: RNAseq_Hspa1b_HS_pos_Rep1


title: RNAseq_Hspa1b_HS_neg_Rep2


title: brain tissue, Ch25h-knockout, female, LPS-treated, rep3 [S03_kofl3]

value: female


title: RNAseq_Hspa1b_HS_neg_Rep1


title: brain tissue, Ch25h-knockout, female, LPS-treated, rep2 [S02_kofl2]


title: brain tissue, Ch25h-knockout, female, LPS-treated, rep1 [S01_kofl1]


title: RNAseq_Hsp90aa1_HS_pos_Rep1

value: Hsp90aa1 knockdown


title: RNAseq_Nkap_HS_pos_Rep1

value: Nkap knockdown


title: RNAseq_Hsp90aa1_HS_pos_Rep2


title: H3K36me3_blastocyst

description: sample 3_H3K36me3_blastocyst

value: embryo

value: embryonic cells

value: blastocyst

value: WT

value: fixed by methanol


title: H3K36me3_morula

description: sample 3_H3K36me3_morula

value: morula


title: RNAseq_Hsp90aa1_HS_neg_Rep2

value: human colorectal carcinoma cells


title: H3K36me3_8cell

description: sample 3_H3K36me3_8cell


title: RNAseq_Hsp90aa1_HS_neg_Rep1

value: 37C 3 hours (no heat shock)


title: H3K36me3_2cell

description: sample 3_H3K36me3_2cell


title: H3K36me3_4cell

description: sample 3_H3K36me3_4cell


title: H3K36me3_zygote

description: sample 3_H3K36me3_zygote

value: zygote


title: RNAseq_Fubp3_HS_neg_Rep1

value: Fubp3 knockdown


title: RNAseq_Fubp3_HS_pos_Rep1

value: 42C 3 hours (heat shock)


title: H3K9me3_blastocyst

description: sample 2_H3K9me3_blastocyst


title: RNAseq_Fubp3_HS_neg_Rep2


title: H3K9me3_8cell

description: sample 2_H3K9me3_8cell


title: RNAseq_Eef1g_HS_pos_Rep1

value: Eef1g knockdown


title: RNAseq_Eef1g_HS_pos_Rep2


title: H3K9me3_4cell

description: sample 2_H3K9me3_4cell


title: H3K9me3_2cell

description: sample 2_H3K9me3_2cell


title: RNAseq_Bag2_HS_pos_Rep2

value: Bag2 knockdown


title: H3K9me3_zygote

description: sample 2_H3K9me3_zygote


title: RNAseq_Bag2_HS_pos_Rep1


title: RNAseq_Fubp3_HS_pos_Rep2


title: RNAseq_Bag2_HS_neg_Rep2


title: H3K4me3_blastocyst

description: sample 1_H3K4me3_blastocyst


title: H3K9me3_morula

description: sample 2_H3K9me3_morula


title: H3K4me3_morula

description: sample 1_H3K4me3_morula


title: RNAseq_Bag2_HS_neg_Rep1


title: RNAseq_Atad3a_HS_pos_Rep1

value: Atad3a knockdown


title: H3K4me3_4cell

description: sample 1_H3K4me3_4cell


title: RNAseq_Atad3a_HS_pos_Rep2


title: H3K4me3_8cell

description: sample 1_H3K4me3_8cell


title: H3K4me3_2cell

description: sample 1_H3K4me3_2cell


title: RNAseq_Eef1g_HS_neg_Rep1


title: RNAseq_Atad3a_HS_neg_Rep1


title: RNAseq_Atad3a_HS_neg_Rep2


title: H3K4me3_zygote

description: sample 1_H3K4me3_zygote


title: RNAseq_Amot_HS_pos_Rep2

value: Amot knockdown


title: CoTACIT_blastocyst

description: sample 5_CoTACIT_blastocyst

value: H3K9me3, H3K27me3, H3K27ac


title: RNAseq_Amot_HS_pos_Rep1


title: CoTACIT_early2cell

description: sample 5_CoTACIT_early2cell

value: H3K4me3, H3K27me3, H3K27ac


title: H2A.Z_blastocyst

description: sample 4_H2A.Z_blastocyst

value: embryo


title: H2A.Z_4cell

description: sample 4_H2A.Z_4cell


title: RNAseq_Amot_HS_neg_Rep2


title: H2A.Z_2cell

description: sample 4_H2A.Z_2cell


title: RNAseq_Amot_HS_neg_Rep1


title: RNAseq_Acacb_HS_pos_Rep1

value: Acacb


title: H2A.Z_8cell

description: sample 4_H2A.Z_8cell


title: RNAseq_Acacb_HS_neg_Rep2


title: H2A.Z_zygote

description: sample 4_H2A.Z_zygote


title: RNAseq_Acacb_HS_pos_Rep2


title: H3K27me3_zygote

description: sample 3_H3K27me3_zygote


title: H3K27me3_2cell

description: sample 3_H3K27me3_2cell


title: RNAseq_Acaca_HS_pos_Rep2

value: Acaca


title: RNAseq_Acacb_HS_neg_Rep1


title: H2A.Z_morula

description: sample 4_H2A.Z_morula


title: RNAseq_Acaca_HS_pos_Rep1


title: NMuMG, biol rep 2, LaminB1, CUT&RUN

city: Pasadena

first: Yodai

last: Takei

address: 1200 E California Blvd

institute: Caltech

data_processing:
*library strategy: CUT&RUN
Sequencing data was processed using the cutnrun pipeline v3.1 from nf-core (https://nf-co.re/cutandrun/3.1) with Nextflow v 24.04.1
Reads were aligned to the UCSC mm10 genome using bowtie2 v.2.4.2, keeping only reads with a minimum alignment q score of 20.
Aligned reads were masked using the mm10 blacklist from ENCODE.
Bigwigs were generated from masked alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: NMuMG

growth_protocol: E14 mouse embryonic stem cells (E14Tg2a.4) (RRID:MMRRC_015890-UCD) from Mutant Mouse Regional Resource Centers were maintained on 0.1% gelatin (Sigma-Aldrich G1393) coated 6-well plates under the serum/LIF condition containing 15% ES-grade FBS (Gibco 16141061), 1,000 units/mL leukemia inhibitory factor (LIF) (Sigma-Aldrich ESG1106), 1× non-essential amino acids (Gibco 11140050), 1 mM sodium pyruvate (Gibco 11360070), 55 μM 2-mercaptoethanol (Gibco 21985023), 1× penicillin and streptomycin (Gibco 15140122) in DMEM GlutaMAX (Gibco 10566016). NMuMG mammary gland cells (ATCC CRL-1636) were maintained on 6-well plates (Thermo Scientific 150687) in 10% FBS (Corning 35-010-CV), 10 μg/mL insulin (Gibco 12585014), 1× penicillin and streptomycin (Gibco 15140122), and DMEM (Corning 10-013-CV).

extract_protocol:
Unfixed nuclei were extracted and bound to concanavalin A beads (EpiCypher), followed by an addition of primary antibody. For CUT&Tag, secondary antibody was applied, followed by an addition of pAG-Tn5 (EpiCypher). Tagmentation was then performed by an addition of magnesium. The DNA fragments were then extracted by 0.1% SDS. For CUT&RUN, pAG-MNase was applied, washed, and then activated by calcium chloride. Then DNA fragments were purified from supernatant using the column purification (EpiCypher).
The CUT&Tag libraries were prepared with i5 and i7 primers (IDT) and Q5 High-Fidelity 2× Master Mix (NEB) and amplified using 15 cycles (RNAPIISer5-P and H3K27me3) or 17 cycles (IgG) on the thermocycler. The CUT&RUN libraries were prepared with CUT&RUN Library Prep Kit (EpiCypher) and amplified using 12 cycles on the thermocycler. Post amplification libraries were purified by using magnetic beads (Omega Bio-Tek), followed by a gel electrophoresis with 1% agarose gels (Invitrogen) and a column purification (Zymo Research). Libraries were validated using the High Sensitivity DNA kit (Agilent).

value: NMuMG

value: mammary gland cell

value: Lamin B1 (Abcam ab16048)


title: NMuMG, biol rep 1, LaminB1, CUT&RUN


title: H3K27me3_4cell

description: sample 3_H3K27me3_4cell

value: fixed by methanol


title: RNAseq_Acaca_HS_neg_Rep1

value: human colorectal carcinoma cells

value: 37C 3 hours (no heat shock)


title: NMuMG, biol rep 2, IgG, CUT&RUN

value: IgG (Epicypher 13-0042)


title: NMuMG, biol rep 1, IgG, CUT&RUN


title: H3K27me3_morula

description: sample 3_H3K27me3_morula


title: H3K27ac_zygote

description: sample 2_H3K27ac_zygote


title: NMuMG, biol rep 2, H3K9me3, CUT&RUN

value: H3K9me3 (Diagenode C15410193)


title: H3K27ac_4cell

description: sample 2_H3K27ac_4cell


title: RNAseq_Abcf2_HS_neg_Rep1


title: NMuMG, biol rep 2, H3K4me3, CUT&RUN

value: H3K4me3 (Cell Signaling 9751T)


title: RNAseq_Acaca_HS_neg_Rep2


title: H3K27ac_blastocyst

description: sample 2_H3K27ac_blastocyst


title: NMuMG, biol rep 1, H3K9me3, CUT&RUN


title: H3K27me3_blastocyst

description: sample 3_H3K27me3_blastocyst


title: H3K27ac_morula

description: sample 2_H3K27ac_morula


title: ChIP-seq-Ser2P-DLD1-shScr-HS-Rep2

data_processing:
ChIP and RNA: Raw BCL output files were processed using bcl2fastq (Illumina, version 2.20)
ChIP and RNA: Quality trimming was performed using using CutAdapt1.14
ChIP: Trimmed ChIP-seq reads were aligned to the human genome (University of California at Santa Cruz [UCSC] hg38 build) using bowtie 2.4.5 with --sensitive option. Where spike-in is indicated, mm10 assembly was used for alignment. The bigwig files with reference-normalized coverage were generated using deepTools 3.5.1 bamCoverage.
ChIP: Peak calling was performed using MACS2 with the  default (narrow) option. Called peaks were annotated with HOMER program annotatePeaks.pl
ChIP: Heatmaps and metaplots from bigwig files were generated using deepTools v3.1.1
RNA: RNA-seq reads were aligned to the hg38 human genome using STAR aligner v2.5.2
RNA: Outputted bam files were sorted using samtools v1.6
RNA: exonic reads were assigned to specific genes from Ensembl release 72 and genome assembly GRCh38.p13 using the python package HTSeq-0.6.1
Assembly: hg38
Supplementary files format and content: bigwig files for ChIP-seq data

growth_protocol: Human HCT116 cells were cultured in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (GIBCO #15140-122) in incubators set to 37°C and 5% CO2. Human DLD-1 cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Pen-Strep in CO2 incubators.

extract_protocol:
For RNA: RNA from HCT116 cells was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
For ChIP: Immunoprecipitated DNA was purified using a ChIP DNA Clean&Concentrator kit (Zymo Research, D5205). Cells were crosslinked with 1% formaldehyde (Thermo Scientific, Cat# 28908) in PBS for 10 min at r.t. To shear chromatin, sonication was performed using the E220 ultrasonicator (Covaris). The mouse embryonic fibroblast spike-in chromatin was added to the sample chromatin. Immunoprecipitation was performed using anti-Ser2P Pol II CTD (Active motif, Cat# 61083) and Dynabeads Protein G (ThermoFisher, Cat# 10004D) at 4°C. Protein degradation using proteinase K (Roche, Cat# 3115828001) and reverse crosslinking were performed at 65°C overnight. The immunoprecipitated DNA was purified using QIAquick PCR Purification Kit (Qiagen, Cat# 28106).
ChIP libraries were prepared using the KAPA HTP library preparation kit (KAPA Biosystems). RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, # E7760L).

treatment_protocol:
100mM biotin (Sigma-Aldrich, B4501) stock prepared in DMSO was added directly to tissue culture media at a final concentration of 100-500µM for immunostaining experiments and at 500µM for immunoblotting and proteomics experiments. Cells were incubated in biotin for 30 minutes at 37°C and 5% CO2 in the tissue culture incubator. Following this, media was removed and cells were washed with ice-cold PBS 5 times to quench the biotinylation reaction before fixation for immunostaining or harvest for endpoint assays.
Cells were either incubated at 37C (non-heat shock, HS_neg)  and 5% CO2 or 42C and 5% CO2 (heat shock/HS_pos). DLD-1 cells were treated with heat shock at 42°C for 2 h, following shRNA knockdown.

value: Colorectal adenocarcinoma

value: shScr-HS

value: pSer2 (ActiveMotif, # 61083)


title: RNAseq_Abcf2_HS_neg_Rep2


title: ChIP-seq-Ser2P-DLD1-shFUBP3-HS-Rep2


title: E14, biol rep 2, IgG, CUT&RUN

value: embryonic stem cell


title: ChIP-seq-Ser2P-DLD1-shScr-NonHS-Rep2

value: shScr-NonHS


title: H3K27ac_2cell

description: sample 2_H3K27ac_2cell

value: embryo


title: NMuMG, biol rep 1, H3K4me3, CUT&RUN


title: ChIP-seq-Ser2P-DLD1-shFUBP3-NonHS-Rep2


title: RNAseq_Abcf2_HS_pos_Rep2

value: 42C 3 hours (heat shock)


title: H3K27ac_8cell

description: sample 2_H3K27ac_8cell


title: RNAseq_Abcf2_HS_pos_Rep1


title: E14, biol rep 1, H3K9me3, CUT&RUN


title: H3K4me1_morula

description: sample 1_H3K4me1_morula


title: H3K4me1_blastocyst

description: sample 1_H3K4me1_blastocyst


title: H3K4me1_8cell

description: sample 1_H3K4me1_8cell


title: E14, biol rep 2, H3K9me3, CUT&RUN


title: E14, biol rep 2, H3K4me3, CUT&RUN


title: E14, biol rep 1, IgG, CUT&RUN


title: ChIP-seq-Ser2P-DLD1-shFUBP3-HS-Rep1


title: H3K4me1_4cell

description: sample 1_H3K4me1_4cell


title: ChIP-seq-Ser2P-DLD1-shScr-NonHS-Rep1


title: E14, biol rep 1, H3K4me3, CUT&RUN


title: ChIP-seq-Ser2P-DLD1-shFUBP3-NonHS-Rep1


title: H3K4me1_zygote

description: sample 1_H3K4me1_zygote


title: ChIPseq_HCT116_TC_LGP_HS_pos_input

value: TurboCas no guide control

value: None (input)


title: NMuMG, biol rep 2, IgG, CUT&Tag

data_processing:
*library strategy: CUT&Tag
Sequencing data was processed using the cutnrun pipeline v3.1 from nf-core (https://nf-co.re/cutandrun/3.1) with Nextflow v 24.04.1
Reads were aligned to the UCSC mm10 genome using bowtie2 v.2.4.2, keeping only reads with a minimum alignment q score of 20.
Aligned reads were masked using the mm10 blacklist from ENCODE.
Bigwigs were generated from masked alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10
Supplementary files format and content: Bigwig

value: NMuMG

value: mammary gland cell


title: NMuMG, biol rep 2, H3K27me3, CUT&Tag

value: H3K27me3 (Cell Signaling 9733S)


title: ChIPseq_HCT116_TC_LGP_HS_pos_ChIP_dCas9

value: human colorectal carcinoma cells


title: RS_MM_4BAT_KODDB1

city: shanghai

first: Guosheng

last: Hu

state: shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai

institute: fudan university

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using STAR.
Genome_build: mm10

source_name: mice brown adipocyte tissue

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA-Seq analysis of global gene expression profiling was conducted at Anoroad (Beijing, China). Briefly, 3 µg RNA pooled from 3 different samples of the same treatment was used to generate sequencing libraries using UltraTM RNA Library Prep Kit for Illumina (NEB, #7530L). Sequencing was performed at 125 bp/150 bp paired-end reads on an Illumina Hiseq platform. Paired-end clean reads were aligned to the reference genome using Tophat (v2.1.1). To quantify the expression level of each gene, Cuffdiff (v2.2.1) was used to count the reads numbers mapped to each gene, and genes with a FPKM greater than 0.5 in any group were kept for further analysis. Genes which were induced more than 1.5 fold after the induction were considered as immediate-early responsive genes (IEGs) during adipogenesis. In DDB1 or ELK1 knockdown cells, IEGs with an induction fold less than 67% of those in the control cells were defined as DDB1 and ELK1 downstream genes, respectively. Gene ontology analysis were performed using the cluster Profiler R package.

value: mice brown adipocyte tissue

value: BAT tissues harvested  from DDB1-BKO mice at 4oC


title: RNAseq_Kpna2_HS_pos_Rep2

value: Kpna2 knockdown


title: RS_MM_22BAT_KODDB1

value: BAT tissues harvested  from DDB1-BKO mice at 22oC


title: NMuMG, biol rep 1, H3K27me3, CUT&Tag


title: NMuMG, biol rep 2, RNAPIISer5-P, CUT&Tag

value: RNAPIISer5-P (Cell Signaling 13523S)


title: RS_MM_4BAT_WT

value: BAT tissues harvested  from DDB1f/f mice at 4oC


title: ChIPseq_HCT116_TC_EX1_HS_pos_input

value: TurboCas FOS-EX1


title: RS_MM_22BAT_WT

value: BAT tissues harvested  from DDB1f/f mice at 22oC


title: H3K4me1_2cell

description: sample 1_H3K4me1_2cell

extract_protocol:
Following TACIT protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: fixed by methanol


title: E14, biol rep 2, IgG, CUT&Tag

value: embryonic stem cell

value: IgG (Epicypher 13-0042)


title: ChIPseq_HCT116_TC_EX1_HS_neg_input

value: 37C 3 hours (no heat shock)


title: CS_MM_4BAT_PolIIser2_KODDB1

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: mm10

growth_protocol: BAT cells, were cultured in Medium B (Dulbecco’s modified Eagle’s medium (4.5 g/L glucose)

extract_protocol:
BAT adipocytes with forskolin treatments were used for ChIP-Seq analysis. For ChIP with anti-DDB1  antibodies, cells were fixed with 1% glutaraldehyde for 15 min at RT. For BAT tissue ChIP with  anti-Pol II and anti-Pol II-S2P antibodies, Tissue were fixed with 1% formaldehyde for 15 min at RT.Fixation was stopped by adding glycine to a final concentration of 0.14 M and incubating at RT for 10 min, followed by two washes with cold PBS.    For each ChIP, 1×107 cells or BAT tissue of 3 mice  were resuspended in Buffer A (50 mM Hepes, pH7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) supplemented with protease inhibitors (Roche), incubated on ice for 10 min, and spun at 1,000 g for 10 min at 4oC. Pellet (nuclear fractions) was washed twice with Buffer B (10 mM Tris, pH7.8, 200 mM NaCl, 1 mM EDTA and 1 mM EGTA) supplemented with protease inhibitors, and resuspended in 0.3 ml Buffer C (50 mM Tris, pH7.8, 10 mM EDTA and 1% SDS) supplemented with protease inhibitors. Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 3 μg anti-DDB1 (Abcam, ab109027),  5 μg anti-Pol II (Bethyl, A300-653A), 5 μg anti-Pol II-S2P (Abcam, ab5095) antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight, . DNA was isolated using Qiagen PCR product purification kit (#28104).
Library was generated using a KAPA Hyper Prep Kit (Roche, KK8503) following manufacturer’s instructions. Adaptors and primer sequences from Roche were used for library construction and amplification. After PCR amplification, the 250-450 bp fragments were purified using KAPA pure beads (Roche, KK8000) following manufacturer’s instructions.

treatment_protocol: 10 uM forskolin treatment for 1 hour

tag: cell line or tissue

value: anti-Pol II-S2P (Abcam, ab5095)


title: NMuMG, biol rep 1, IgG, CUT&Tag

value: NMuMG


title: E14, biol rep 1, IgG, CUT&Tag


title: CS_MM_4BAT_PolIIser2_WT


title: E14, biol rep 2, H3K27me3, CUT&Tag