title: TG+De-2d-3

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description:
Library name: TG+De-2d-3
TG+De-2d-3

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422. Data were then preprocessed using the Cumulus SMART-Seq2v2.6.1 workflow on Terra (https://terra.bio/). The workflow employs histat2 v2.1.0 to align read to mm10 mouse genome, and the RSEM v1.3.3 to calculate raw counts and TPM. The workflow computes the TPM-normalized count for each gene, defined as TPM_i / 10^6 * c rounded to the nearest integer, where TPM_i is the TPM for gene i, and c is the total number of reads achieved for the sample.
Assembly: mm10
Supplementary files format and content: comma-separated values (CSV) files include TPM-normalized count for every gene (rows)  in every sample (columns)

source_name: in vitro; originally from spleen and dLN

extract_protocol:
For the CYP11A1 WT vs. cKO and GR WT vs. cKO experiments, EAE mice were euthanized and perfused intracardially with ice-cold PBS. The brain and spinal cord were finely minced using a razor blade and digested with 2.5 mg/ml collagenase D (Roche Diagnostics) at 37°C for 20 minutes. The digested tissue was then passed through a 70-μm strainer. Mononuclear cells were isolated by density gradient centrifugation using a Percoll (Amersham Biosciences) gradient of 37% and 70%. The mononuclear cells were collected from the interphase for further analysis. 2,000 CNS-infiltrating 2D2+ cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).  For the in vitro Dex and TGF-β1 treatment experiment, in vitro–differentiated Th17Inf cells were treated with dexamethasone (Dex), TGF-β1, or a combination of both for 2 days. 2,000 live Th17 cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).
Libraries were prepared using a modified SMART-Seq2 protocol, including RNA secondary structure denaturation at 72 °C for 3 min, reverse transcription with Maxima Reverse Transcriptase (Thermo Fischer Scientific) and whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix 2× (KAPA Biosystems) for 12 cycles. Whole-transcriptome amplification product quality was confirmed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 (Agilent, G2939BA) and quantified using a Qubit dsDNA HS Assay kit (Thermo Scientific). Libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina) and sequenced using a high-output V2 75 cycle kit (Illumina) on a NextSeq 500 sequencer (Illumina) with 2 × 38 paired-end reads.

value: T cell


title: TTchemSeq 1 hour recovery after Menadione replicate 1 exp2

status: Public on Jun 12 2026

type: SRA

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: TT2_m60_MND_1

library_source: transcriptomic

data_processing:
Raw fastq files for Read 1 were labelled with appropriate UMI reads using UMItools
adapter trimming with cutadapt (v4.5) within trim_galore (v0.6.10) and read length filtering > 19nt
samples were mapped with STAR75 (v2.7.11b) against a merged human-yeast genome assemblies (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Genome alignments BAM files were filtered for multimapped reads with samtools (v1.21) view function (-q 10)
UMI duplicates were then removed with UMItools dedup function. A yeast gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate yeast size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific and spike-in normalised BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/ yeast size-factor) with bin size of 25 nt (-bs 25)
Assembly: (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Supplementary files format and content: bigwig forward and reverse strands

molecule: nuclear RNA

organism: Homo sapiens

source_name: HEK293 Flp-in T-Rex

growth_protocol: Flp-InTM T-REx HEK293 cells (HEK293, R78007, ThermoFisher Scientific, human embryonic kidney epithelial, female origin) were cultured at 37C with 5% CO2 in high glucose DMEM (Biowest, Cat#L0104) supplemented with 10% v/v FBS (Gibco, Cat#10270106), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco, 10378016) 2 mM L-glutamine.

extract_protocol:
80% confluent cells RNA were labelled in vivo for 15 min with 4sU by adding it directly to the tissue culture media to a final concentration of 1 mM. Per samples 80-100 μg of total RNA resuspended in 100 μL RNAse-free H2O was complemented with 1 % (relative to total RNA concentration) of S. cerevisiae 4tU-labelled RNA spike-in. Total RNA was fragmented by adding 20 μL of freshly prepared 1 M NaOH per sample, thoroughly mixed and incubated for 40 min on ice to < 400 nt fragments. Resuspended and purified 4sU labelled RNA in RNAse-free water was biotinylated in 10 mM Tris-HCl pH = 7.4; 1 mM EDTA complemented with 0.5 mg/ μL MTSEA biotin-XX linker (Biotum, Cat# BT90066) for 30 min in the dark at room temperature. Biotinylated RNA was immediately purified by ROTI®Aqua-P/C/I extraction and isopropanol precipitation and resuspended in 50 μL RNAse-free water. and isolated with μMACS Streptavidin Kit (Miltenyi, Cat#130-074-101). A total of 100uL μMACS Streptavidin MicroBeads were added to denatured 4sU total RNA and incubated for 15 min at room temperature with agitation. Beads bound to 4sU biotinylated RNA were applied to magnetic μColumns and transferred to the magnetic field of the μMACS magnetic separator (Miltenyi).
Approx. 30 ng of purified 4sU biotinylated RNA was used to prepare libraries with NEBNext® Ultra™ II RNA library prep kit (NEB, Cat#E7760) according to manufacturer’s protocol (protocol 5 for fragmented RNA) with ligation of two barcodes of 8 nt and 11 nt UMIs (NEB, Cat#E7416).

treatment_protocol: Inhibitors treatments were carried out by direct addition to the cell culture media with the following concentration 100 μM DRB (Sigma, D1916) or/and 10 μM Olaparib (PARPi, MedchemExpress, Cat#HY-10162) or/and 10 μM TH5487 (OGG1i, MedchemExpress, Cat#HY-125276). Oxidative stress induction treatments were carried out for 15 min (or 30 min for EU-labelling) with direct addition of freshly prepare 1000x concentrate to cell culture media, fresh H2O2 (maximum 3 month old kept at 4CC) to final concentration of 1 mM H2O2 (Sigma, H1009) or freshly resuspended Menadione sodium bisulfite (MND, Sigma, M5750) in water to final concentration of 0.25 mM.

tag: cell line

value: HEK293 Flp-in T-Rex


title: 1501_W10_treatment

city: Duarte

first: Russell

last: Rockne

state: CA

address: 1500 E Duarte Rd

department: Beckman Research Institute

country: USA

institute: City of Hope

description:
Library name: COHP_51169
1501_W10_CML_KO

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, CA) using the S4 Reagent Kit v1.5, 200 cycles (Part no 20028313). Illumina Real-Time Analysis (RTA3) v3.4.4 was used for base calling and quality scores and Illumina BCL Convert v3.9.3 to export FASTQ files. All protocols were performed according to the manufacturer’s instructions. Comprehensive library quality assessment was performed using v2.1.0 of the nf-core/scrnaseq pipeline34 and reads (including those from introns) counted using 10X Genomics Cellranger count v7.0.0 implemented therein. We used the Gencode M28 reference annotation and genome (https://www.gencodegenes.org/, downloaded 22 March 2022) augmented with a custom BRC::ABL transcript (GenBank accession forthcoming) prepared using the default parameters and preprocessing described for Cellranger mkref. To perform quality control, each library was filtered to remove genes expressed in fewer than 3 cells, and cells with fewer than 200 genes expressed, with more than 20% mitochondrial transcripts, or with fewer than 5% ribosomal transcripts, then merged into a single v5 Seurat33 object for downstream analysis. Cell types were assigned with the default parameters of SingleR34 (v2.6.0) using reference expression profiles from the Immunological Genome Project, accessed through the celldex package (v0.1.16.0).
Assembly: GENCODEm28
Supplementary files format and content: counts matrix csv
Supplementary files format and content: Seurat v5 RDS

molecule: total RNA

organism: Mus musculus

source_name: PBMC

extract_protocol:
Approximately 10,000 cells per sample were captured using a Chromium X (10X Genomics, Pleasanton, CA), with the Chromium Next GEM Single Cell 3’ Reagent Kit V3.1 (10X Genomics, Cat. PN-1000268).
Prior to sequencing, library quality was assessed using a High Sensitivity DNA Chip (Agilent, Santa Clara, CA, Cat. 5067-4626) and quantified with the Qubit High Sensitivity DNA Assay Kit (Thermo,Fisher Scientific, Waltham, MA, Cat. Q32854).

treatment_protocol: The SCLtTA/BCR::ABL and Mir142−/−SCLtTA/BCR::ABL mice in B6 background were maintained on tetracycline (tet) water at 0.5 g/L. Tet withdrawal (tet-off) results in expression of BCR::ABL and generation of a CP CML-like disease in SCLtTA/BCR::ABL mice with a median survival of approximately 55 days and of a BC CML-like disease in Mir142−/−SCLtTA/BCR::ABL mice with a median survival of approximately 32 days, after induction of BCR::ABL. Blood (100μl) was collected from six to eight weeks old male (n=1) and female (n=2) SCLtTA/BCR::ABL or Mir142−/−SCLtTA/BCR::ABL mice weekly, i.e., before BCR::ABL induction (t = 0) and after induction up to 9 weeks (t = 1 to 9) or when the mouse developed leukemia and became moribund, whichever event occurred first. After red cell lysis, an aliquot of the PBMCs was stained with anti-mouse antibodies and analyzed for hematopoietic cell subpopulations and the remaining cells were subjected to scRNA-seq.

tag: tissue

value: PBMC

tag: genotype

value: 142KO positive

tag: treatment

tag: Sex

value: female

tag: timepoint

tag: batch


title: TTchemSeq 30min recovery after Menadione replicate 2 exp2

description: Library name: TT2_m30_MND_2


title: TG+De-2d-2

city: Boston

description:
Library name: TG+De-2d-2
TG+De-2d-2

molecule: polyA RNA

value: in vitro; originally from spleen and dLN

tag: cell type


title: B186-03

first: Allegra

middle: A

last: Petti

state: Massachusetts

address: 185 Cambridge St.

department: Department of Neurosurgery

institute: Massachusetts General Hospital

description:
Library name: TWBK-B186-03
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT

data_processing:
Demultiplexing, image and transcript alignment, and transcript quantification was performed using the Spaceranger pipeline (10x Genomics, v1.2, GRCh38 reference)
Assembly: GRCh38
Supplementary files format and content: Filtered feature matrices output from spaceranger
Supplementary files format and content: fiducial images and json files from spaceranger
Library strategy: Spatial Transcriptomics

source_name: Brain tumor section (IDH wildtype Glioblastoma)

extract_protocol:
Using image-guided surgical biopsies and 5-aminolevulinic acid (5-ALA) fluorescence, we collected 22 samples from tumor regions ranging from the core to the margin in nine patients with IDHWT GBM undergoing surgical resection of radiographic, primary high-grade glioma. Each section (i.e. sample) was preserved, stained with hematoxylin and eosin (H&E), imaged, and processed to generate a spatial transcriptomic library. The first 13 samples were fresh-frozen and OCT-embedded, and cDNA libraries were constructed according to the Visium Spatial 3’ Gene Expression User Guide Rev. D. The next nine samples were preserved in FFPE, and cDNA libraries were generated according to the Visium Spatial Gene Expression for FFPE User Guide Rev. E.
All libraries were sequenced on an Illumina Novaseq S2 flow cell to a target depth of 50,000 reads/spot and yielded high quality transcriptome data (median values: 2300 spots under tissue, 55917 mean reads under tissue spot, 2275 panel genes per spot, 4544 median panel UMIs/spot, and 22508 (OCT) or 16334 (FFPE) total genes detected)


title: 909_W10_control

description:
Library name: COHP_51168
909_W10_CML

value: positive

value: CML


title: TTchemSeq 30min recovery after Menadione replicate 1 exp2

description: Library name: TT2_m30_MND_1


title: 1501_W9_treatment

description:
Library name: COHP_51112
1501_W9_CML_KO


title: B186-02

description:
Library name: TWBK-B186-02
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT

value: Brain tumor section (IDH wildtype Glioblastoma)


title: B186-01

description:
Library name: TWBK-B186-01
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: TTchemSeq Menadione Treated replicate 2 exp2

description: Library name: TT2_no_MND_2


title: TG+De-2d-1

description:
Library name: TG+De-2d-1
TG+De-2d-1


title: TGF-2d-3

description:
Library name: TGF-2d-3
TGF-2d-3


title: 911_W9_control

description:
Library name: COHP_51111
911_W9_CML

value: male


title: B185-03

description:
Library name: TWBK-B185-03
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: TTchemSeq Menadione Treated replicate 1 exp2

description: Library name: TT2_no_MND_1


title: TGF-2d-2

description:
Library name: TGF-2d-2
TGF-2d-2


title: 909_W9_control

description:
Library name: COHP_51110
909_W9_CML


title: TTchemSeq 2 hours recovery after low dose h2o2 replicate 2 exp2

description: Library name: TT2_m120_lowdose_2


title: B185-02

description:
Library name: TWBK-B185-02
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: TGF-2d-1

description:
Library name: TGF-2d-1
TGF-2d-1


title: 1501_W8_treatment

description:
Library name: COHP_51079
1501_W8_CML_KO


title: TTchemSeq 2 hours recovery after low dose h2o2 replicate 1 exp2

description: Library name: TT2_m120_lowdose_1


title: Dex-2d-3

description:
Library name: Dex-2d-3
Dex-2d-3


title: TTchemSeq 1 hour recovery after low dose h2o2 replicate 2 exp2

description: Library name: TT2_m60_lowdose_2


title: 911_W8_control

description:
Library name: COHP_51078
911_W8_CML


title: Dex-2d-2

description:
Library name: Dex-2d-2
Dex-2d-2


title: B185-01

description:
Library name: TWBK-B185-01
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: B178-02-01

description:
Library name: TWBK-B178-02-01
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: 909_W8_control

description:
Library name: COHP_51077
909_W8_CML


title: TTchemSeq 1 hour recovery after low dose h2o2 replicate 1 exp2

description: Library name: TT2_m60_lowdose_1


title: B176-02-04

description:
Library name: TWBK-B176-02-04
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: Dex-2d-1

description:
Library name: Dex-2d-1
Dex-2d-1


title: 1507_W7_treatment

description:
Library name: COHP_50980
1507_W7_CML_KO


title: Ctrl-2d-3

description:
Library name: Ctrl-2d-3
Ctrl-2d-3


title: TTchemSeq 30min recovery after low dose h2o2 replicate 2 exp2

description: Library name: TT2_m30_lowdose_2


title: B176-02-01

description:
Library name: TWBK-B176-02-01
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: 1501_W7_treatment

description:
Library name: COHP_50979
1501_W7_CML_KO


title: E110_rep2

city: Xianyang City

first: Guanghui

last: Tan

address: No.22, Xinong Road, Yangling Demonstration Zone, Yangling District, Xianyang City

country: China

institute: Northwest A&F University

description: Library name: C5_3_TP_rep2

data_processing:
Raw sequencing data were demultiplexed and processed with Cell Ranger (v7.1.0) against the ARS-UCD2.0 bovine reference genome.
Assembly: Bovine reference genome ARS-UCD2.0 (Ensembl release) was used for read alignment and downstream analyses.
Supplementary files format and content: Processed expression matrices are provided in Matrix Market format (MTX) along with barcodes and feature annotation files. Additional processed data are provided as Seurat R objects (RDS format) containing metadata, normalized counts, dimensionality reduction coordinates, and cell type annotations.

organism: Bos taurus

source_name: placenta

growth_protocol: All experimental animals were healthy Holstein heifers (Bos taurus) with normal estrous cycles. Estrus synchronization was performed by hormone treatment, followed by embryo transfer on day 7 after estrus as previously described (Moraes et al., 2018). Pregnant animals were humanely euthanized at different gestational stages (E60, E85, E110, E180, E240, and E280) for placenta collection.

extract_protocol:
Frozen placental tissues were minced into 2 mm pieces and homogenized in EZ lysis buffer supplemented with protease and RNase inhibitors using a Dounce homogenizer. The nuclear fraction was isolated by filtration and centrifugation steps, stained with 7-AAD, and sorted by FACS to remove debris and doublets. Nuclei were resuspended at 700–1200 nuclei/μl in PBS + 0.07% BSA + RNase inhibitor before loading.
Single-nucleus suspensions were processed using the Chromium Single Cell 3' v3 Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Libraries were quality checked and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: placenta

tag: characteristics [gestation_stage]


title: TTchemSeq 30min recovery after low dose h2o2 replicate 1 exp2

description: Library name: TT2_m30_lowdose_1


title: TTchemSeq low dose h2o2 Treated replicate 2 exp2

description: Library name: TT2_no_lowdose_2


title: 911_W7_control

description:
Library name: COHP_50978
911_W7_CML


title: B172-02

description:
Library name: TWBK-B172-02
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: Ctrl-2d-1

description:
Library name: Ctrl-2d-1
Ctrl-2d-1


title: B176-01-02

description:
Library name: TWBK-B176-01-02
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: 914_W7_control

description:
Library name: COHP_50977
914_W7_CML


title: TTchemSeq low dose h2o2 Treated replicate 1 exp2

description: Library name: TT2_no_lowdose_1


title: GR-CNS-KO-4

description:
Library name: GR-CNS-KO-4
GR-CNS-KO-4

source_name: CNS

value: CNS

value: GR KO (C57/B6)


title: B172-01

description:
Library name: TWBK-B172-01
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: 909_W7_control

description:
Library name: COHP_50976
909_W7_CML


title: SC-beta cells + SC-Mreg macrophages, seq2

city: Vancouver

first: Bruno

middle: Felipe de Abreu

last: Freitas

state: British Columbia

address: 938 W 28th Ave

department: Surgery

country: Canada

institute: University of British Columbia - BC Children's Hospital Research Institute

description:
Library name: sample 6
10X genomics

data_processing:
Data processing followed using the Seurat (v5.3.0) R package. To reduce background RNA contamination from within our samples, the SoupX R package was used, where cells identified as having contamination levels > 0.25 were removed from our analysis. Additionally, cells with high volumes of mitochondrial genes (percent.mt > 0.25), low unique RNA transcripts (nCount_RNA < 1000), low total RNA transcripts (nFeature_RNA < 2000), and cells identified as doublets through the DoubletFinder R package, were also removed from our analysis. After quality control (QC) steps, 17,576 cells remained for downstream analysis. Cell clustering was then performed using a graph-based approach on the FastMNN-integrated space, generating UMAP visualizations using 30 principal components and a resolution of 1.2.
Assembly: human hg38
Supplementary files format and content: tab-separate values files and matrix files

source_name: Human embryonic stem cells

extract_protocol:
SC-beta  alone, SC-M alone, and SC-beta + SC-M co-aggregates were dissociated with TrypLE Express (Gibco) for 6 minutes at 37oC. The TrypLE Express was then diluted 3X with PBS + 10% FBS and the cells were spun down in a 15 mL Falcon tube at 450xG for 5 minutes. The cells were then washed in PBS and viable cells were counted using Trypan blue.
Library preparation was performed according to manufacturer's instructions (single cell 3' v3; 10X Genomix). The samples were then delivered to the School of Biomedical Engineering (SBME) Sequencing Core at University of British Columbia’s Biomedical Research Centre (UBC-BRC) for sequencing with the NovaSeq 6000 System (Illumina). After sequencing, BCL files were converted using the CellRanger software.

value: Human embryonic stem cells

value: WA01 H1 hESC

value: SC-beta cells + SC-Macrophages

value: INS-GFP (SC-beta), CD68-mScarlet (SC-Mreg)


title: GR-CNS-KO-3

description:
Library name: GR-CNS-KO-3
GR-CNS-KO-3

value: T cell


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 25

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: Library name: Sample329

library_source: genomic

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 genome. As mESCs tend to have karyotype abnormality on chr 8 and chr 11, these chromosomed were removed from the reference genome.
Duplicated reads were filtered out.
For quality control of scRepli-seq data, we applied median-absolute-deviation (MAD) score evaluation to filter out cells with problematic RT (MAD scores = 0 or >1.0).
For generating log2[(mappability-corrected S-phase reads)/median] scores (log2median RT score) to obtain single-cell RT profiles using cells that passed MAD score evaluation, we counted the reads in sliding windows of 200-kb at 40-kb intervals after normalizing S-phase data with AneuFinder’s correctMappability command based on G1 control without karyotype defects in each strain. (Miura et al., 2020).
The binarization for each 80-kb was performing find CNVs command in AneuFinder (Miura et al., 2020). We applied the 1-somy mode for early S-phase cells. Repliscore as a percentage of replicated bins in the total number of replicated and unreplicated bins was calculated from binarized scRepli-seq data (Miura et al., 2020).
Assembly: mm9
Supplementary files format and content: Binarized bedGraph
Supplementary files format and content: Log2median bedGraph

molecule: genomic DNA

growth_protocol: C57BL/6N mESCs were grown in serum free medium NDiff 227 (Cellartis, Y40002), 1 μM PD0325901 (Wako, 162-25291) and 3 μM CHIR99021 (Wako, 034-23103), 0.1 mM 2-mercaptoethanol and 1000 U/ml mLIF on iMatrix-511 (Matrixome, 892012) coated dishes.

extract_protocol:
We followed the scRepli-seq protocol as described (Miura et al., 2020). Early-S phase cell population were sorted by a Sony SH800 cell sorter (thymidine/5-Ph-IAA removed cells: ultra-purity mode, G1/early-S cells: single-cell mode). Thymidine/5-Ph-IAA removed cells were manually collected after EdU signal observation and cells were transferred into lysis buffer using mouth pipette. G1/early-S cells were directly sorted into lysis buffer.
Extracted gDNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed WGA DNA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were synchronized at the G1/S boundary by treating with 2.5 mM thymidine for 12 hours. After thymidine release, late-replicating DNA was pulse-labeled with EdU, followed by mitotic arrest using 50 ng/ml nocodazole. Nocodazole was replaced with 5-Ph-IAA solution, and cells were cultured for 15 hours, then switched to normal medium for an additional 4 hours. EdU and DNA were stained using Click-iT Plus EdU Alexa Fluor 594 Imaging Kit (Invitrogen) and  FxCycle™ Violet Stain (Invitrogen), respectively, then early-S phase cells were sorted, and EdU signals were observed. Selected cells were manually picked for library preparation using mouth pipette under the microscopy.

value: embryonic stem cells

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: SC-Mreg macrophages alone, seq2

description:
Library name: sample 5
10X genomics

value: SC-Macrophages


title: GR-CNS-KO-2

description:
Library name: GR-CNS-KO-2
GR-CNS-KO-2


title: 1501_W6_treatment

description:
Library name: COHP_50861
1501_W6_CML_KO

value: PBMC

value: 142KO positive

value: female


title: GR-CNS-KO-1

description:
Library name: GR-CNS-KO-1
GR-CNS-KO-1


title: TTchemSeq 1 hour recovery after h2o2 replicate 3 exp1

description: Library name: TT1_H2O2_1hr_recovery_r3

value: HEK293 Flp-in T-Rex


title: 911_W6_control

description:
Library name: COHP_50860
911_W6_CML

value: positive

value: CML

value: male


title: TTchemSeq 1 hour recovery after h2o2 replicate 2 exp1

description: Library name: TT1_H2O2_1hr_recovery_r2


title: 914_W6_control

description:
Library name: COHP_50859
914_W6_CML


title: GR-CNS-WT-5

description:
Library name: GR-CNS-WT-5
GR-CNS-WT-5

value: CNS

value: GR WT (C57/B6)


title: TTchemSeq 1 hour recovery after h2o2 replicate 1 exp1

description: Library name: TT1_H2O2_1hr_recovery_r1


title: GR-CNS-WT-4

description:
Library name: GR-CNS-WT-4
GR-CNS-WT-4


title: SC-Mreg macrophages alone, seq1

description:
Library name: sample 2
10X genomics

value: Human embryonic stem cells

value: WA01 H1 hESC


title: TTchemSeq 30min recovery after h2o2 replicate 3 exp1

description: Library name: TT1_H2O2_30m_recovery_r3


title: 909_W6_control

description:
Library name: COHP_50858
909_W6_CML


title: GR-CNS-WT-3

description:
Library name: GR-CNS-WT-3
GR-CNS-WT-3


title: TTchemSeq 30min recovery after h2o2 replicate 2 exp1

description: Library name: TT1_H2O2_30m_recovery_r2


title: C&R_Rh30_MED13_BI1347-24hr_rep2

first: Susu

last: Zhang

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Library name: C_R_Rh30_MED13_BI1347-24hr_rep2

data_processing:
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9). Raw FASTQ data were trimmed using Trimmomatic-v0.38 and paired end reads were aligned to human hg38 genome using Bowtie2 (v2.3.5) in very sensitive local mode --dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using MAXS2 (v2.1.4) with a threshold of q<0.01 and peak were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were normalized and generated using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig file
Library strategy: CUT&Run

growth_protocol: Rh30 is cultured in DMEN containing 10% FBS, 1% L-Glutamin, and 1% P.S.

extract_protocol:
CUT&RUN+NEB DNA clean up
NEB Next Ultra II library prep kit

treatment_protocol: DMSO or BI1347 were added to cell after adhering.

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: 1501_W5_treatment

description:
Library name: COHP_50741
1501_W5_CML_KO


title: TTchemSeq 30min recovery after h2o2 replicate 1 exp1

description: Library name: TT1_H2O2_30m_recovery_r1


title: GR-CNS-WT-1

description:
Library name: GR-CNS-WT-1
GR-CNS-WT-1

value: T cell


title: 911_W5_control

description:
Library name: COHP_50740
911_W5_CML


title: C&R_Rh30_MED13_DMSO_rep2

description: Library name: C_R_Rh30_MED13_DMSO_rep2


title: CHD1_KO_dLN_4

description: Library name: CHD1_KO_dLN_4

source_name: dLN

extract_protocol:
For the CHD1 WT vs. cKO and GR WT vs. cKO experiments, EAE mice were euthanized and perfused intracardially with ice-cold PBS. The brain and spinal cord were finely minced using a razor blade and digested with 2.5 mg/ml collagenase D (Roche Diagnostics) at 37°C for 20 minutes. The digested tissue was then passed through a 70-μm strainer. Mononuclear cells were isolated by density gradient centrifugation using a Percoll (Amersham Biosciences) gradient of 37% and 70%. The mononuclear cells were collected from the interphase for further analysis. 2,000 CNS-infiltrating 2D2+ cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich). At the same time, draining lymph nodes (dLNs) cells were obtained by mechanically dispersing the organs through a 70-μm strainer. 2,000 2D2+ cells were sorted from dLN by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).  For the in vitro Dex treatment experiment, naive T cells from WT or IL-23R KO mice were differentiated into Th17Inf cells in vitro and treated with or without dexamethasone (Dex) for two days. 2,000 live Th17 cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).
Libraries were prepared using a modified SMART-Seq2 protocol, including RNA secondary structure denaturation at 72 °C for 3 min, reverse transcription with Maxima Reverse Transcriptase (Thermo Fischer Scientific) and whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix 2× (KAPA Biosystems) for 12 cycles. Whole-transcriptome amplification product quality was confirmed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 (Agilent, G2939BA) and quantified using a Qubit dsDNA HS Assay kit (Thermo Scientific). Libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina) and sequenced using a high-output V2 75 cycle kit (Illumina) on a NextSeq 500 sequencer (Illumina) with 2 × 38 paired-end reads.

value: dLN

value: Chd1 KO (C57/B6)


title: 914_W5_control

description:
Library name: COHP_50739
914_W5_CML


title: TTchemSeq 15min recovery after h2o2 replicate 2 exp1

description: Library name: TT1_H2O2_15min_recovery_r2


title: C&R_Rh30_MED13_DMSO_rep1

description: Library name: C_R_Rh30_MED13_DMSO_rep1


title: CHD1_KO_dLN_3

description: Library name: CHD1_KO_dLN_3


title: TTchemSeq 15min recovery after h2o2 replicate 1 exp1

description: Library name: TT1_H2O2_15min_recovery_r1


title: 909_W5_control

description:
Library name: COHP_50738
909_W5_CML


title: C&R_Rh30_MED12_BI1347-24hr_rep2

description: Library name: C_R_Rh30_MED12_BI1347-24hr_rep2


title: CHD1_KO_dLN_2

description: Library name: CHD1_KO_dLN_2


title: 1510_W4_treatment

description:
Library name: COHP_50691
1510_W4_CML_KO


title: C&R_Rh30_MED12_BI1347-24hr_rep1

description: Library name: C_R_Rh30_MED12_BI1347-24hr_rep1


title: 1507_W4_treatment

description:
Library name: COHP_50690
1507_W4_CML_KO


title: CHD1_KO_dLN_1

description: Library name: CHD1_KO_dLN_1


title: TTchemSeq h2o2 Treated replicate 2 exp1

description: Library name: TT1_H2O2_no_recovery_r2


title: C&R_Rh30_MED12_DMSO_rep2

description: Library name: C_R_Rh30_MED12_DMSO_rep2


title: CHD1_WT_dLN_3

description: Library name: CHD1_WT_dLN_3

value: Chd1 WT (C57/B6)


title: TTchemSeq Untreated replicate 1 exp2

description: Library name: TT2_untreated_1


title: 1501_W4_treatment

description:
Library name: COHP_50689
1501_W4_CML_KO

value: PBMC


title: TTchemSeq h2o2 Treated replicate 1 exp1

description: Library name: TT1_H2O2_no_recovery_r1


title: C&R_Rh30_MED12_DMSO_rep1

description: Library name: C_R_Rh30_MED12_DMSO_rep1


title: CHD1_WT_dLN_2

description: Library name: CHD1_WT_dLN_2


title: 911_W4_control

description:
Library name: COHP_50688
911_W4_CML


title: TTchemSeq Untreated replicate 3 exp1

description: Library name: TT1_UNT_r3


title: C&R_Rh30_CCNC_BI1347-24hr_rep2

description: Library name: C_R_Rh30_CCNC_BI1347-24hr_rep2


title: 914_W4_control

description:
Library name: COHP_50687
914_W4_CML


title: C&R_Rh30_CCNC_BI1347-24hr_rep1

description: Library name: C_R_Rh30_CCNC_BI1347-24hr_rep1


title: TTchemSeq Untreated replicate 2 exp1

description: Library name: TT1_UNT_r2


title: 909_W4_control

description:
Library name: COHP_50686
909_W4_CML


title: TTchemSeq Untreated replicate 1 exp1

description: Library name: TT1_UNT_r1


title: C&R_Rh30_CCNC_DMSO_rep2

description: Library name: C_R_Rh30_CCNC_DMSO_rep2


title: 1510_W3_treatment

description:
Library name: COHP_50685
1510_W3_CML_KO

value: 142KO positive


title: CHD1_KO_CNS_3

description: Library name: CHD1_KO_CNS_3


title: first ELCAP rpb3-flag 2 hours recovery replicate 1

description: Library name: ELCAP_120minRec_rep1

data_processing:
reads were mapped with STAR (–-alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT) against a human genome assembly merged with drosophila melanogaster genome assembly (GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46)
Genome alignment BAM files were deduplicated using UMItools dedup function and subsequently filtered with samtools view function for low quality mapped reads (-q 10,)
For HEK parental samples complemented with Drosophila spike-in, a Drosophila gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate drosophila spike-in size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific, spike-in normalised (for HEK parental cells) or RPKM (for RPB3-FLAG cells)
single-nucleotide BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/size-factor or --normalizeUsing RPKM ) with bin size of 1 nt (-bs 1).
Assembly: GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46
Supplementary files format and content: bigwig for forward and reverse strands

source_name: HEK293 Flp-in T-Rex - RPB3-FLAG

growth_protocol: For RNAPII IPs from the RPB3-FLAG expressing cell line 4x15cm plates of cells were induced with 100 ng/mL doxycycline for 16 hours and grown to 80-90% confluency. For RNAPII IPs with 4H8 and 8WG16 antibodies for ELCAP-seq, triplicates of 2x15cm and 6x15cm plates HEK293 parental cells were used. Drosophila spike-ins were used. For this Drosophila S2 cells were grown at 27oC in Schneider’s medium (Gibco, Cat#21720024) complemented with heat inactivated 10% v/v FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Normalised parental HEK293 chromatin fractions were spiked-in with 10% protein/protein of Drosophila S2 chromatin extract and added to ab-conjugated magnetic Dynabeads for 3 hours at 4oC with agitation. The beads were washed 4 times with ELCAP wash buffer (10 mM Tris-HCl pH = 7.5; 250 mM NaCl; 0.5% (v/v) NP-40; 0.5 mM EDTA; fresh protease inhibitor; protease Inhibitors cocktail and fresh phosphatase inhibitors). Short RNA fragments trapped by RNAPII complexes were extracted with the Quick-RNA MicroPrep kit (Zymo, Cat#R1050) according to the manufacture’s instruction for short RNA extraction (17-200 nt). Briefly, RNPAII bound beads were incubated for 5 min at RT in extraction buffer (per 100 μL sample; 100 μL of supplied Zymo RNA lysis Buffer, 100 μL of IP wash buffer,100 μL ethanol). RNA was isolated using kit supplied Zymo-Spin™ IC columns following the manufacturer’s instructions.
Library were prepared using 5 ul of short RNAs with NEBNext® Small RNA library preparation kit (NEB, Cat# E7300) according to the manufacturer’s protocol with the only modification being inclusion of a UMI containing adapter; the initial ligation was carried with the custom ligation adapter ‘5'-App-NNNNNNAGATCGGAAGAGCACACGTCT-3' (IDT) with the same ligation conditions as manufacturer’s protocol. Libraries were amplified with 8 cycles of PCR and the whole library was separated by size with Novex™ TBE Gels, 10% (Invitrogen, ThermoFischer Scientific, Cat# EC62752BOX), stained with 1/50.000 SYBRTMgold (Invitrogen, ThermoFischer Scientific, Cat# S11494) and fragment size ranging from 147 nt to 190 nt were excised from the gel and purified according to NEBNext® Small RNA library preparation kit protocol.

treatment_protocol: In all cases oxidative stress was induced by treatment with 1 mM H2O2 for 15 min. And for some samples let to recovery for indicated times after media change.

value: HEK293 Flp-in T-Rex - RPB3-FLAG


title: C&R_Rh30_CCNC_DMSO_rep1

description: Library name: C_R_Rh30_CCNC_DMSO_rep1


title: CHD1_KO_CNS_2

description: Library name: CHD1_KO_CNS_2


title: 1507_W3_treatment

description:
Library name: COHP_50684
1507_W3_CML_KO

value: female


title: C&R_Rh30_CDK8_BI1347-24hr_rep2

description: Library name: C_R_Rh30_CDK8_BI1347-24hr_rep2


title: CHD1_KO_CNS_1

description: Library name: CHD1_KO_CNS_1


title: 1501_W3_treatment

description:
Library name: COHP_50683
1501_W3_CML_KO


title: C&R_Rh30_CDK8_BI1347-24hr_rep1

description: Library name: C_R_Rh30_CDK8_BI1347-24hr_rep1


title: first ELCAP rpb3-flag 30min recovery replicate 1

description: Library name: ELCAP_30minRec_rep1


title: CHD1_WT_CNS_3

description: Library name: CHD1_WT_CNS_3


title: 911_W3_control

description:
Library name: COHP_50682
911_W3_CML

value: positive


title: first ELCAP rpb3-flag 30min recovery replicate 2

description: Library name: ELCAP_30minRec_rep2


title: C&R_Rh30_CDK8_DMSO_rep2

description: Library name: C_R_Rh30_CDK8_DMSO_rep2


title: CHD1_WT_dLN_1

description: Library name: CHD1_WT_dLN_1


title: CHD1_WT_CNS_2

description: Library name: CHD1_WT_CNS_2


title: 914_W3_control

description:
Library name: COHP_50681
914_W3_CML

value: CML


title: first ELCAP rpb3-flag 1 hour recovery replicate 1

description: Library name: ELCAP_60minRec_rep1


title: CHD1_KO_CNS_4

description: Library name: CHD1_KO_CNS_4


title: C&R_Rh30_CDK8_DMSO_rep1

description: Library name: C_R_Rh30_CDK8_DMSO_rep1


title: CHD1_WT_CNS_1

description: Library name: CHD1_WT_CNS_1


title: 909_W3_control

description:
Library name: COHP_50680
909_W3_CML


title: first ELCAP rpb3-flag 1 hour recovery replicate 2

description: Library name: ELCAP_60minRec_rep2


title: C&R_Rh30_H3K27ac_BI1347-72hr_rep2

description: Library name: C_R_Rh30_H3K27ac_BI1347-72hr_rep2


title: WiDr GSK715 ONT full-length cDNA sequencing replicate 2

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

description:
Library name: WiDr_ONT_GSK715_2
WiDr cells were treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h and subjected to ONT full-length cDNA sequencing. Processed data file(s): ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.

data_processing:
Short-read RNA-seq: Adapters and low-quality reads were removed with Cutadapt. Clean reads were aligned to GRCh38 using HISAT2, and transcript abundance was quantified as FPKM using StringTie. Differential expression analysis was performed with DESeq2 (adjusted P < 0.05, |log2FC| >= 1).
ONT full-length cDNA sequencing: Raw pod5/fast5 signals were base-called with Dorado (--no-trim) to generate FASTQ reads. Reads passing the basecalling quality filter (Q >= 10) were retained as clean reads. Full-length cDNA reads were identified, oriented and trimmed using Pychopper (-Q 7 -z 50), followed by additional filtering with NanoFilt (-q 7 -l 50). Filtered full-length reads were aligned to GRCh38 using minimap2 (-ax splice -uf -k14). Consensus transcript sets were constructed using Pinfish, and transcript reconstruction and merging were performed with StringTie. Transcript abundance was quantified as TPM using Salmon. Differentially expressed transcripts and genes were identified using DESeq2 (P < 0.05 and |log2FoldChange| > 2). Poly(A) sites were identified, clustered and annotated using QuantifyPoly(A) to analyze 3'-end heterogeneity.
Processed matrices prepared for GEO: hct116_gene_count_matrix.tsv.gz; widr_gene_count_matrix.tsv.gz; ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.
Assembly: GRCh38
Supplementary files format and content: hct116_gene_count_matrix.tsv.gz and widr_gene_count_matrix.tsv.gz are gzip-compressed tab-delimited gene-level count matrices for short-read RNA-seq samples.
Supplementary files format and content: ont_widr_gene_counts_matrix.tsv.gz is a gzip-compressed tab-delimited gene-level count matrix for ONT full-length cDNA sequencing samples; ont_widr_full_length_stats.tsv.gz contains full-length read summary statistics.

source_name: colon

growth_protocol: HCT116 and WiDr cells were cultured under standard mammalian cell culture conditions before treatment.

extract_protocol:
Total RNA was extracted from treated cells and assessed for quality before library construction.
Total RNA from WiDr and HCT-116 cells treated with DMSO, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction by Lianchuan Biotechnology (Hangzhou) and paired-end sequencing on an Illumina NovaSeq 6000. WiDr cells treated with DMSO or 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h were subjected to Oxford Nanopore Technologies (ONT) full-length cDNA sequencing on a PromethION platform by Benagen (Wuhan).

treatment_protocol: Cells were treated for 96 h with DMSO vehicle control, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor), as applicable.

value: colon

value: WiDr

value: colorectal carcinoma cell line

value: ONT full-length cDNA sequencing


title: 1510_W2_treatment

description:
Library name: COHP_50625
1510_W2_CML_KO

value: male


title: first ELCAP rpb3-flag h2o2 treated replicate 1

description: Library name: ELCAP_NoRec_rep1


title: C&R_Rh30_H3K27ac_BI1347-72hr_rep1

description: Library name: C_R_Rh30_H3K27ac_BI1347-72hr_rep1

value: Rhabdomyosarcoma


title: 1507_W2_treatment

description:
Library name: COHP_50624
1507_W2_CML_KO


title: WiDr GSK715 ONT full-length cDNA sequencing replicate 1

description:
Library name: WiDr_ONT_GSK715_1
WiDr cells were treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h and subjected to ONT full-length cDNA sequencing. Processed data file(s): ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.


title: first ELCAP rpb3-flag h2o2 treated replicate 2

description: Library name: ELCAP_NoRec_rep2


title: first ELCAP rpb3-flag 2 hours recovery replicate 2

description: Library name: ELCAP_120minRec_rep2


title: C&R_Rh30_H3K27ac_BI1347-24hr_rep2

description: Library name: C_R_Rh30_H3K27ac_BI1347-24hr_rep2

value: PAX3::FOXO1 fusion


title: WiDr DMSO ONT full-length cDNA sequencing replicate 2

description:
Library name: WiDr_ONT_DMSO_2
WiDr cells were treated with DMSO vehicle control for 96 h and subjected to ONT full-length cDNA sequencing. Processed data file(s): ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.

value: DMSO vehicle control for 96 h


title: Ctrl-2d-2

description:
Library name: Ctrl-2d-2
Ctrl-2d-2

value: in vitro; originally from spleen and dLN

value: T cell


title: 1501_W2_treatment

description:
Library name: COHP_50623
1501_W2_CML_KO


title: C&R_Rh30_H3K27ac_BI1347-24hr_rep1

description: Library name: C_R_Rh30_H3K27ac_BI1347-24hr_rep1


title: first ELCAP rpb3-flag untreated replicate 1

description: Library name: ELCAP_UNT_rep1


title: WiDr DMSO ONT full-length cDNA sequencing replicate 1

description:
Library name: WiDr_ONT_DMSO_1
WiDr cells were treated with DMSO vehicle control for 96 h and subjected to ONT full-length cDNA sequencing. Processed data file(s): ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.


title: 911_W2_control

description:
Library name: COHP_50622
911_W2_CML


title: TTchemSeq Untreated replicate 2 exp2

description: Library name: TT2_untreated_2

value: HEK293 Flp-in T-Rex


title: first ELCAP rpb3-flag untreated replicate 2

description: Library name: ELCAP_UNT_rep2


title: 1507_W6_treatment

description:
Library name: COHP_50862
1507_W6_CML_KO

value: PBMC


title: C&R_Rh30_H3K27ac_DMSO_rep2

description: Library name: C_R_Rh30_H3K27ac_DMSO_rep2


title: SC-beta cells alone, seq2

description:
Library name: sample 4
10X genomics

value: Human embryonic stem cells

value: WA01 H1 hESC

value: SC-beta cells

value: INS-GFP


title: 914_W2_control

description:
Library name: COHP_50621
914_W2_CML

value: positive

value: CML

value: female


title: PET-8

city: Lanzhou City, Gansu Province

first: Yanbin

last: Zhu

address: No.1 Yingmen Village, Anning District

institute: Gansu Agricultural University

description:
Library name: PET-8
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 8

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to BosGru3.0 / 3.1  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: BosGru3.0 / 3.1
Supplementary files format and content: tab-delimited text files include gene count and fpkm for each Sample

organism: Bos grunniens

source_name: jejunal tissue

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: jejunal tissue


title: SC-beta cells + SC-Mreg macrophages, seq1

description:
Library name: sample 3
10X genomics

value: SC-beta cells + SC-Macrophages

value: INS-GFP (SC-beta), CD68-mScarlet (SC-Mreg)


title: ELCAP rpb3-flag untreated replicate 3

description: Library name: Rpb3-Unt-3

value: HEK293 Flp-in T-Rex - RPB3-FLAG


title: 909_W2_control

description:
Library name: COHP_50620
909_W2_CML


title: PET-7

description:
Library name: PET-7
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 7


title: C&R_Rh30_H3K27ac_DMSO_rep1

description: Library name: C_R_Rh30_H3K27ac_DMSO_rep1

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: C&R_Rh30_H3K4me3_BI1347-72hr_rep2

description: Library name: C_R_Rh30_H3K4me3_BI1347-72hr_rep2


title: PET-6

description:
Library name: PET-6
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 6


title: ELCAP rpb3-flag untreated replicate 2

description: Library name: Rpb3-Unt-2


title: 1510_W1_treatment

description:
Library name: COHP_50551
1510_W1_CML_KO

value: 142KO positive

value: male


title: 1507_W5_treatment

description:
Library name: COHP_50742
1507_W5_CML_KO


title: SC-beta cells alone, seq1

description:
Library name: sample 1
10X genomics


title: ELCAP rpb3-flag untreated replicate 1

description: Library name: Rpb3-Unt-1


title: C&R_Rh30_H3K4me3_BI1347-72hr_rep1

description: Library name: C_R_Rh30_H3K4me3_BI1347-72hr_rep1


title: PET-5

description:
Library name: PET-5
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 5


title: Rex1-EmGFPd2 Tardbp gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_47_Tardbp_9_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
15_Tardbp_mean_w200ks40k.bedGraph

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 genome.
Duplicated reads were filtered out.
Reads per million (rpm) normalization were calculated for early- and late-S-phase BrdU-IP samples in sliding windows of 200-kb at 40-kb intervals and a nonoverlapping 200-kb bins for Robust scaling analysis, respectively.
The ratio of early-S-phase to total read counts [(early-S reads)/(early-S reads + late-S reads)] was calculated for each bin, and their distribution was converted to fit within a ±1 scale. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: BrdU-IP Repli-seq

extract_protocol:
We followed the BrdU-IP-based protocol as described (Ryba et al., 2011). 75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early-S phase and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 cell sorter (ultra-purity mode). For nocodazole/5-Ph-IAA removal experiments, only early-S phase cells were collected. Extracted DNA was sonicated by a Bioruptor BR2012A (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: (1) Transfection of gRNA-carrying vector was performed with Lipofectamine LTX&PLUS (ThermoFisher, 15338100) according to the manufacturer’s instructions. Cells were collected 4 days after transfection. (2) 5-Ph-IAA treatment: 5-Ph-IAA solution was added at a final concentration of 1 µM to the medium. (3) Nocodazole removal: after 15 hours of 50 ng/ml nocodazole treatment, the medium containintg nocodazole was replaced with normal culture medium. (4) 5-Ph-IAA removal: after 15 hours of 1 µM 5-Ph-IAA treatment, the medium containing 5-Ph-IAA was replaced with normal culture medium.

value: embryonic stem cells

tag: strain

tag: genetic modification

value: EmGFPd2 knockin at Rex1 locus, Cas9 knockin at Rosa26 locus


title: Rex1-EmGFPd2 Tbcc gRNA#2 mESCs, BrdU-IP Early

description:
DEP_01_066_45_Tbcc_7_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
16_Tbcc_mean_w200ks40k.bedGraph

value: pU6-Tbcc-gRNA#2-CBA-PuroR transfection


title: L-fHP_85

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Library name: 79147250

data_processing:
Clusters were generated using ExAmp chemistry on patterned flow cells and sequenced with the NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles) on the NovaSeq 6000 system (Illumina, San Diego, CA), following the manufacturer's instructions. Approximately 60 million reads by were generated for each cDNA library by 150bp paired end (PE) sequencing cycle.
Assembly: hg38
Supplementary files format and content: .csv file includes raw counts for each Sample

source_name: venous blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA kit (Qiagen, cat#762164) following manufacturer’s protocol. RNA quality and integrity were confirmed by Quant-iT RiboGreen RNA Assay Kit (ThermoFisher, cat#R11490) and TapeStation RNA ScreenTape (Agilent, Santa Clara, CA)
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, cat# 470-2020-003-A).

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

value: Female

tag: age blood_draw

tag: smoking history

value: No

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months

value: venous blood


title: H1 CLYBL-AB9 R3

first: Beth

last: Stevens

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: Sample 6

data_processing:
In accordance with sharing guidelines by Jackson Laboratory, fastq data files were processed before alignment and deposition to remove Y chromosome reads.
Reads were aligned to the human genome with STAR using Ensembl genome files: ‘Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz’ and ‘Homo_sapiens.GRCh38.115.gtf.gz’. Output BAM files were processed with samtools48 to identify Y chromosome reads. Fastq files were filtered to remove Y chromosome reads using custom shell scripts.
Salmon was used to quantify transcript abundances from filtered fastq files. Salmon index was built using ‘gencode.v48.transcripts.fa.gz’. pytximport was used to process salmon output ‘quant.sf’ files into RNA counts matrix (Table S3).
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz, gencode.v48.transcripts.fa.gz
Supplementary files format and content: Table S1.xlsx sheet name "This study" includes processed counts matrix.

source_name: H1 CLYBL-AB9

growth_protocol: iAstrocytes were cultured in maturation medium until day 21. KOLF2.1J uninduced iPSCs were cultured in E8 medium until near confluency.

extract_protocol:
Cells were lysed in Buffer RLT (Qiagen) with DTT. RNA was isolated using RNAeasy kits (Qiagen).
Bulk RNA-seq was performed using Novogene commercial sequencing service. Directional mRNA libraries were prepared using ultra-low input total RNA directional library preparation. Sequencing was performed using NovaSeq X Plus Series (PE150).

tag: cell line

value: H1 CLYBL-AB9

tag: cell type

value: iAstrocyte


title: KOLF2.1J CLYBL-AB9 R1

description: Library name: Sample 13

source_name: KOLF2.1J CLYBL-AB9

value: KOLF2.1J CLYBL-AB9


title: GR-CNS-WT-2

description:
Library name: GR-CNS-WT-2
GR-CNS-WT-2

tag: tissue

value: CNS

value: T cell

tag: genotype

value: GR WT (C57/B6)


title: L-fHP_82

description: Library name: 79141850

tag: diagnosis

tag: endotype

tag: Sex

value: Male


title: H1 CLYBL-AB9 R1

description: Library name: Sample 4


title: ELCAP rpb3-flag h2o2 treated replicate 3

description: Library name: Rpb3-Treated-3

value: HEK293 Flp-in T-Rex - RPB3-FLAG


title: 1507_W1_treatment

description:
Library name: COHP_50550
1507_W1_CML_KO

value: PBMC

value: 142KO positive

tag: treatment

value: female

tag: timepoint

tag: batch


title: C&R_Rh30_H3K4me3_BI1347-24hr_rep2

description: Library name: C_R_Rh30_H3K4me3_BI1347-24hr_rep2

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: KOLF2.1J CLYBL-NBS9 R3

description: Library name: Sample 12

source_name: KOLF2.1J CLYBL-NBS9

value: KOLF2.1J CLYBL-NBS9


title: PET-4

description:
Library name: PET-4
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 4

value: jejunal tissue


title: C&R_Rh30_H3K4me3_BI1347-24hr_rep1

description: Library name: C_R_Rh30_H3K4me3_BI1347-24hr_rep1


title: ELCAP rpb3-flag h2o2 treated replicate 2

description: Library name: Rpb3-Treated-2


title: PET-3

description:
Library name: PET-3
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 3


title: 911_W1_control

description:
Library name: COHP_50548
911_W1_CML

value: positive

value: CML

value: male


title: C&R_Rh30_H3K4me3_DMSO_rep2

description: Library name: C_R_Rh30_H3K4me3_DMSO_rep2


title: PET-2

description:
Library name: PET-2
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 2


title: PET-1

description:
Library name: PET-1
P. pentosaceus NQ0729-pretreated group followed by ETEC challenge, replicate biosample 1


title: C&R_Rh30_TADA2B_BI1347-72hr_rep2

description: Library name: C_R_Rh30_TADA2B_BI1347-72hr_rep2


title: C&R_Rh30_H3K4me3_DMSO_rep1

description: Library name: C_R_Rh30_H3K4me3_DMSO_rep1


title: 1510_W0_treatment

description:
Library name: COHP_50363
1510_W0_CML_KO


title: ELCAP 8WG16 untreated replicate 1

description: Library name: 8WG16-Unt-1

value: HEK293 Flp-in T-Rex


title: C&R_Rh30_TADA2B_BI1347-72hr_rep1

description: Library name: C_R_Rh30_TADA2B_BI1347-72hr_rep1


title: ELCAP 8WG16 h2o2 treated replicate 3

description: Library name: 8WG16-Treated-3


title: C&R_Rh30_TADA2B_BI1347-24hr_rep2

description: Library name: C_R_Rh30_TADA2B_BI1347-24hr_rep2


title: 1501_W0_treatment

description:
Library name: COHP_50361
1501_W0_CML_KO


title: ELCAP 8WG16 h2o2 treated replicate 2

description: Library name: 8WG16-Treated-2


title: 911_W0_control

description:
Library name: COHP_50360
911_W0_CML


title: ELCAP 8WG16 h2o2 treated replicate 1

description: Library name: 8WG16-Treated-1


title: 914_W0_control

description:
Library name: COHP_50359
914_W0_CML


title: C&R_Rh30_TADA2B_DMSO_rep1

description: Library name: C_R_Rh30_TADA2B_DMSO_rep1


title: ETEC-3

description:
Library name: ETEC-3
ETEC-challenged group, replicate biosample 3


title: 909_W0_control

description:
Library name: COHP_50358
909_W0_CML


title: ETEC-4

description:
Library name: ETEC-4
ETEC-challenged group, replicate biosample 4


title: ELCAP 4H8 untreated replicate 2

description: Library name: 4H8-Unt-2


title: C&R_Rh30_SIX4_BI1347-72hr_rep2

description: Library name: C_R_Rh30_SIX4_BI1347-72hr_rep2


title: ETEC-2

description:
Library name: ETEC-2
ETEC-challenged group, replicate biosample 2


title: LDB1KO_EB_2_ATAC

city: Bethesda

first: HeungSun

last: Kwon

state: MD

address: 50 South Drive Building 50

department: NIDDK

institute: NIH

description: EB, LDB1KO, replicate 2

data_processing:
Paired-end raw fastq reads were trimmed using cutadapt (v4.4)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.5.1)
Uniquely mapped, properly paired, non-supplementary, non-mitochondrial alignments were retained using samtools view command with options “-F 2048 -f 2 -q 20” piped with “grep -v chrM”.
Duplicated reads were cleaned using picard MarkDuplicates (v2.27.5) with “REMOVE_DUPLICATES=true”.
Peaks were called using MACS2 (v2.2.7.1) with the settings “-f BAMPE --keep-dup all -g 2.3e9” at default cutoffs.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig

growth_protocol: ESC were maintained and differentiated as described, with modifications (Carotta et al. 2004). Undifferentiated ESC were cultured on 0.1% gelatin-coated plates in EmbryoMax DMEM (MilliporeSigma, SLM-220-M supplemented with 10% fetal bovine serum (MilliporeSigma), 2-β-mercaptoethanol (MilliporeSigma, ES-007-E), GlutaMax, penicillin/streptomycin, non-essential amino acids, and ESGRO-2i (MilliporeSigma, cat# SF016-200. To generate EB, cultures were adjusted to 1 × 10^5 cells/ml and incubated in EB medium (STEMCELL TECH, Aggrewell EB formation medium) for 3 to 5 days in Aggrewell plates (STEMCELL TECH, 34421). After 4 days, EB were pooled and grown in suspension in non-adherent plates, with media changed daily. EB were collected on days 3 and 5.

extract_protocol:
Genomic DNA was extracted by QIAquick PCR purification kit (Quiagen 28104).
ATAC-seq was performed with the ATAC-Seq Kit (Active Motif, 53150), according to manufacturer’s protocol.

treatment_protocol: gRNAs targeting Ldb1 were cloned into the CRISPR-Cas9 and gRNA expression vector pSpCas9(BB)-2A-GFP (PX458) (Addgene, cat #48138). ES cells were transfected with Mouse ES Cell Nucleofector® Kit (Lonza, cat # VPH-1001) according to the manufacturer’s instructions. Fluorescent cells were sorted 48 hours later and plated at limiting dilution to isolate single clones harboring the LDB1 gene knockout.

value: mEB


title: ELCAP 4H8 untreated replicate 1

description: Library name: 4H8-Unt-1


title: ETEC-1

description:
Library name: ETEC-1
ETEC-challenged group, replicate biosample 1


title: C&R_Rh30_SIX4_BI1347-72hr_rep1

description: Library name: C_R_Rh30_SIX4_BI1347-72hr_rep1


title: LDB1KO_EB_1_ATAC

description: EB, LDB1KO, replicate 1


title: ELCAP 4H8 h2o2 treated replicate 3

description: Library name: 4H8-Treated-3


title: CON-8

description:
Library name: CON-8
control group, replicate biosample 8


title: WT_EB_2_ATAC

description: EB, WT, replicate 2


title: C&R_Rh30_SIX4_BI1347-24hr_rep1

description: Library name: C_R_Rh30_SIX4_BI1347-24hr_rep1


title: CON-7

description:
Library name: CON-7
control group, replicate biosample 7


title: ELCAP 4H8 h2o2 treated replicate 1

description: Library name: 4H8-Treated-1


title: C&R_Rh30_SIX4_DMSO_rep2

description: Library name: C_R_Rh30_SIX4_DMSO_rep2


title: CON-6

description:
Library name: CON-6
control group, replicate biosample 6


title: C&R_Rh30_SIX4_DMSO_rep1

description: Library name: C_R_Rh30_SIX4_DMSO_rep1


title: ChIP-seq of totalRNAPII with D8L4Y treated with H2o2

description: Library name: ChIP_totPolII_treated

data_processing:
reads were mapped with STAR (–-alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT) against a human genome assembly merged with drosophila melanogaster genome assembly (GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46)
Genome alignment BAM files were deduplicated using UMItools dedup function and subsequently filtered with samtools view function for low quality mapped reads (-q 10,)
For HEK parental samples complemented with Drosophila spike-in, a Drosophila gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate drosophila spike-in size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific, spike-in normalised (for HEK parental cells) or RPKM (for RPB3-FLAG cells)
single-nucleotide BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/size-factor or --normalizeUsing RPKM ) with bin size of 1 nt (-bs 1).
FE files were created with macs2 callpeak function, then macs2 bdgcmp, sorted and transformed to bigwig with ucsc bedGraphToBigWig
Assembly: GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46
Supplementary files format and content: bigwig for forward and reverse strands

growth_protocol: For each sample, 80 % confluent HEK293 cells in a 15 cm plate were crosslinked with 1% formaldehyde for 15 min and stopped with 125 mM glycine for 5 min

extract_protocol:
Fixed cells were then homogenized in cellular lysis buffer (5 mM Pipes pH = 8; 85 mM KCl; 0.5 % NP‐40). Nuclei were then resuspended in nuclear lysis buffer (50 mM Tris pH = 8.1; 10 mM EDTA; 1 % SDS) and sonicated to obtain DNA fragments between 50 bp and 500 bp (5 cycles; 30sec ON, 30sec OFF, with Bioruptor pico). Samples were diluted 10 times in dilution buffer (0.01 % SDS; 1.1 % Triton X‐100; 1.2 mM EDTA; 16.7 mM Tris pH = 8; 167 mM NaCl). Samples were pre-cleared with 25 µL proteins A/G beads (ThermoFisher Scientific, Cat#20422 ) and blocked with 500 µg BSA for each 200 µg of chromatin for 2 hours at 4°C. A volume of 100 µL pre-cleared chromatin was keep at -20°C for inputs and another volume of chromatin was then incubated overnight with either NELFE or total RPB1 (D8L4Y) antibodies at 4°C. Immunoprecipitation was performed using 35 µL proteins A/G beads (blocked with 500 µg BSA) for 2 hours at 4°C. Beads were then washed once with dialysis buffer (2 mM EDTA; 50 mM Tris-HCl pH=8.1; 0.2% Sarkosyl), once wash buffer (100 mM Tris pH = 8.8; 500 mM LiCl; 1% NP‐40; 1% NaDoc) and once with TE (10 mM Tris pH = 8; 0.5 mM EDTA). Immunoprecipitated complexes and inputs were resuspended in TE and incubated with 1 µL of RNase A (10 mg/mL, ThermoFisher Scientific, Cat#EN0531) for 30 min at 37°C. Reverse crosslinking was performed by incubating samples overnight at 70°C with 4 µL SDS (10%) and incubation with ProteinaseK (10 mg/mL, ThermoFisher Scientifc Cat#AM2548) for 1 hour 30 min at 45°C. DNA was purified by phenol/chlorophorm extraction followed by ethanol precipitation.
Libraries were prepared with NEBNext® Ultra™ II DNA library prep kit (NEB, Cat#E7604) with 12 nt UMIs adaptors (NEB, Cat#E7395) according to manufacturer’s protocol


title: CON-5

description:
Library name: CON-5
control group, replicate biosample 5


title: ChIP-seq of totalRNAPII with D8L4Y untreated control

description: Library name: ChIP_totPolII_NT


title: C&R_Rh30-P3F-FKBP_P3F-HA_BI1347-72hr_rep2

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_BI1347-72hr_rep2


title: CON-4

description:
Library name: CON-4
control group, replicate biosample 4


title: WT_ESC_2_ATAC

description: ESC, WT, replicate 2

value: mESC


title: ChIP-seq of totalRNAPII with D8L4Y 1 hour recovery after H2o2

description: Library name: ChIP_totPolII_1h


title: C&R_Rh30-P3F-FKBP_P3F-HA_BI1347-72hr_rep1

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_BI1347-72hr_rep1


title: C&R_Rh30-P3F-FKBP_P3F-HA_BI1347-24hr_rep2

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_BI1347-24hr_rep2


title: CON-2

description:
Library name: CON-2
control group, replicate biosample 2


title: Empty vector #2

status: Public on Jun 13 2026

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description:
Library name: WR2
column name in RNAseq_counts.tsv: WR2

data_processing:
Reads were aligned to the human transcriptome (Gencode r.28) using kallisto (Bray et al. 2016)
Transcript-level abundance estimates were summarized to gene-level expression values using the lengthScaledTPM method in tximport (Soneson et. al., 2015).
Data was normalized using edgeR’s TMM mormalization
log2CPM values were calculated using voom (from limma)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes raw counts. Samples are identified by the column header.

growth_protocol: Human adrenocortical HAC15 cell line was routinely cultured in growth media consisting of Dulbecco’s modified Eagle’s medium (DMEM)-F12 (Gibco) supplemented with 10 % cosmic calf serum (Hyclone), 1 % ITS (insulin-transferrin-selenium; Corning), and antibiotics, 1 % penicillin/streptomycin (Gibco) and 0.1 % gentamicin (Gibco). Cells were grown at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini kit (Qiagen; Cat#: 74134) and eluted in nuclease-free H2O.
Poly(A) Tail RNA Selection 250-300 bp Insert cDNA Library Strand-Specific Preparation by LC Sciences. Library construction and sequencing is described by LCScience.com as: "Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the paired-end 2×150bp sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.

value: Adrenocortical carcinoma cell


title: ESC_H3K27ac_KO_rep2

description: Cut and Tag

data_processing:
Paired-end fastq reads were preprocessed using cutadapt (v2.7)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.3.5) with the settings reported for CUT&Tag (Kaya-Okur et al. 2019)..
Duplicated reads were cleaned using picard MarkDuplicates (v2.21.4) with “REMOVE_DUPLICATES=true”.
Peaks were called from bam files using MACS2 (v2.2.7.1) using default settings.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig
Library strategy: Cut&Tag

extract_protocol:
Genomic DNA was extracted by Cut&tag-it assay kit(Activemotif, 53170)
CUT&Tag library preparation was performed with the CUT&Tag-IT™ Assay Kit (Active Motif, 53170) according to manufacturer’s protocol. H3K27ac(Active motif, 39085), H3K4me3 (Active motif, 39016) and H3K27me3(Active motif, 39055) were used for IP.


title: control-1

city: 北京-Beijing

first: QING

last: Liu

state: 北京市

address: Department of Neurology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College (PUMC) & Chinese Academy of Medical Science (CAMS), Beijing, China

description: Library name: sample1

data_processing:
Data were processed using Cell Ranger and analyzed via Seurat (v4.0). Quality control metrics included filtering cells with <200 or >5,000 detected genes and mitochondrial gene expression >20%.
Assembly: GRCh38

source_name: brain

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and digested using Trypsin (Hyclone SH30042.01) as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using SeekMate Tinitan Fluorescence Cell Counter (SeekGene M002C) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI-1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI-1640 and 2% FBS (Gibco 10100147C).
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index.The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on illumina NovaSeq X Plus with PE150 read length.

value: brain

value: microglia


title: C&R_Rh30-P3F-FKBP_P3F-HA_BI1347-24hr_rep1

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_BI1347-24hr_rep1


title: CON-1

description:
Library name: CON-1
control group, replicate biosample 1


title: ESC_H3K27ac_KO_rep1

description: Cut and Tag


title: CON-3

description:
Library name: CON-3
control group, replicate biosample 3


title: WT_ESC_1_ATAC

description: ESC, WT, replicate 1


title: ChIP-seq of NELFE 1 hour recovery after H2o2

description: Library name: ChIP_NelfE_1h


title: ChIP-seq of NELFE treated with H2o2

description: Library name: ChIP_NelfE_treated


title: C&R_Rh30-P3F-FKBP_P3F-HA_DMSO_rep2

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_DMSO_rep2


title: Hindpaw BALB/c_Healthy, biological rep5

type: RNA

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: Gene expression data from hindpaw tissue of BALB/c healthy control mice

hyb_protocol: After fragmentation, 5500 ng of labeled ss-cDNA was hybridized to GeneChip Clariomª D Mouse Arrays for 16Ð18 hours at 45_¡C. Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were analyzed using the Transcriptome Analysis Console (TAC, Affymetrix) with default parameters. Global scaling was applied as the normalization method.

label: biotin

source_name: BALB/c mice Healthy

label_protocol: Biotinylated cRNA was prepared from 200 ng total RNA using the Affymetrix GeneChip WT PLUS Reagent Kit, following the manufacturerÕs protocol (User Guide: GeneChip Whole Transcript [WT] Expression Arrays).

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturerÕs protocol, optimized for lipid-rich and pulverized frozen tissues.

treatment_protocol: Dissected hindpaw tissues (tarsus to phalanges) were aseptically processed using sterile surgical instruments. Skin and nails were removed. Tissues were immediately snap-frozen in liquid nitrogen and manually pulverized using a stainless steel Biopulverizer (BioSpec Products) prior to RNA extraction.

tag: strain

value: BALB/c

tag: gender

tag: age of confinment

tag: age of euthanasia

value: 20 weeks

tag: condition

value: Healthy

value: Distal hindpaws (tarsus to phalanges), including joints, bone, cartilage, muscle; skin and nails removed


title: ESC_H3K27ac_WT_rep2

description: Cut and Tag


title: DMPA_10 meningioma, RNA-seq

city: Pittsburgh

first: Sakibul

last: Huq

state: PA

address: 200 Lothrop St, Suite B-400

department: Neurological Surgery

institute: University of Pittsburgh Medical Center

description: Library name: DMPA_10

data_processing:
fastp: adapter trimming and quality filtering.
HISAT2: alignment to the GRCh38 primary assembly; coordinate-sorted BAMs.
featureCounts v2.1.1 (Subread): gene-level counts, GENCODE v44, -t exon -g gene_id, unstranded (-s 0), paired-end (-p --countReadPairs -B -C).
Assembly: GRCh38 (GENCODE v44)
Supplementary files format and content: Tab-delimited gene-level raw count matrix (featureCounts v2.1.1); rows = Ensembl gene IDs (GENCODE v44); columns = DMPA-1..DMPA-10.

source_name: meningioma

extract_protocol:
Total RNA extracted from representative FFPE tumor blocks.
Illumina RNA exome-capture libraries (probes covering ~45 Mb of exonic coding regions).

value: meningioma

value: female

tag: who grade

tag: histologic subtype

value: Secretory

tag: mutation status (ngs panel)

tag: traf7 group


title: C&R_Rh30-P3F-FKBP_P3F-HA_DMSO_rep1

description: Library name: C_R_Rh30-P3F-FKBP_P3F-HA_DMSO_rep1

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: Hindpaw BALB/c_Healhty, biological rep4

tag: tissue


title: ESC_H3K27ac_WT_rep1

description: Cut and Tag


title: DMPA_09 meningioma, RNA-seq

description: Library name: DMPA_09

value: Metaplastic


title: CD105N

city: Guangzhou

first: Ren

last: Mao

address: 58 Zhongshan Road 2nd, Guangzhou

institute: The First Affiliated Hospital, Sun Yat-Sen University

description:
Library name: sample15
10× Genomics

data_processing:
Human mesenteric tissue single-nucleus RNA-seq data were processed using Cell Ranger software (v3.1.0; 10x Genomics). Raw sequencing reads were converted to FASTQ files, aligned to the human reference genome, and quantified to generate gene-barcode expression matrices for each sample. Low-quality barcodes and UMIs were filtered out. Reads uniquely mapped to the transcriptome and intersecting exonic regions were counted. UMI sequences were corrected for sequencing errors, and valid cell/nucleus barcodes were identified for downstream matrix generation. Cell-by-gene count matrices were generated by UMI counting and cell barcode calling. The filtered feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, are provided as processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Normal mesenteric adipose tissue in Crohn's disease

extract_protocol:
The samples were chopped on ice into 1-2 mm³ pieces, transferred to cryovials, snap-frozen in liquid nitrogen for 5 minutes, and then stored in an ultra-low temperature freezer and liquid nitrogen.. Then transfer the tissue from the cryovial to a Dounce homogenizer and add 500 μl of pre-chilled lysis buffer to thaw. Use a small and a tight pestle to press the tissue 15-20 times and 5-10 times, respectively, to create a homogenate. Add 700 μl of nuclear wash buffer, mix, and filter through a 70 μm cell strainer. Add 1 ml of 50% iodixanol to the filtrate, mix gently, and layer onto a gradient solution of 30% and 33% iodixanol. Centrifuge at 10,000×g for 20 minutes at 4°C. Extract the white nuclear layer at the interface, add nuclear wash buffer, mix, and centrifuge at 500×g for 8 minutes at 4°C. Transfer the supernatant, resuspend the nuclei, and repeat the wash. Filter through a 40 μm filter, centrifuge, resuspend the nuclei, and adjust the concentration to 700-1200 nuclei/μl using a microscope.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and equenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.


title: C&R_Rh4_CDK8_rep1

description: Library name: C_R_Rh4_CDK8_rep1

tag: genotype


title: Hindpaw BALB/c_Healthy, biological rep3

value: male


title: ESC_H3K4me3_KO_rep2

description: Cut and Tag


title: DMPA_08 meningioma, RNA-seq

description: Library name: DMPA_08

tag: Sex

value: Transitional

value: PIK3CA; FGFR1


title: ChIP-seq of NELFE untreated control

first: Lea

last: Gregersen

address: Blegdamsvej 3B,

description: Library name: ChIP_NelfE_NT

source_name: HEK293 Flp-in T-Rex

value: HEK293 Flp-in T-Rex


title: 1501_W1_treatment

first: Russell

last: Rockne

address: 1500 E Duarte Rd

description:
Library name: COHP_50549
1501_W1_CML_KO

data_processing:
Sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, CA) using the S4 Reagent Kit v1.5, 200 cycles (Part no 20028313). Illumina Real-Time Analysis (RTA3) v3.4.4 was used for base calling and quality scores and Illumina BCL Convert v3.9.3 to export FASTQ files. All protocols were performed according to the manufacturer’s instructions. Comprehensive library quality assessment was performed using v2.1.0 of the nf-core/scrnaseq pipeline34 and reads (including those from introns) counted using 10X Genomics Cellranger count v7.0.0 implemented therein. We used the Gencode M28 reference annotation and genome (https://www.gencodegenes.org/, downloaded 22 March 2022) augmented with a custom BRC::ABL transcript (GenBank accession forthcoming) prepared using the default parameters and preprocessing described for Cellranger mkref. To perform quality control, each library was filtered to remove genes expressed in fewer than 3 cells, and cells with fewer than 200 genes expressed, with more than 20% mitochondrial transcripts, or with fewer than 5% ribosomal transcripts, then merged into a single v5 Seurat33 object for downstream analysis. Cell types were assigned with the default parameters of SingleR34 (v2.6.0) using reference expression profiles from the Immunological Genome Project, accessed through the celldex package (v0.1.16.0).
Assembly: GENCODEm28
Supplementary files format and content: counts matrix csv
Supplementary files format and content: Seurat v5 RDS

source_name: PBMC

extract_protocol:
Approximately 10,000 cells per sample were captured using a Chromium X (10X Genomics, Pleasanton, CA), with the Chromium Next GEM Single Cell 3’ Reagent Kit V3.1 (10X Genomics, Cat. PN-1000268).
Prior to sequencing, library quality was assessed using a High Sensitivity DNA Chip (Agilent, Santa Clara, CA, Cat. 5067-4626) and quantified with the Qubit High Sensitivity DNA Assay Kit (Thermo,Fisher Scientific, Waltham, MA, Cat. Q32854).

value: PBMC

value: 142KO positive

tag: treatment


title: Hindpaw BALB/c_Healhty, biological rep2


title: C&R_Rh30_CDK8_rep1

description: Library name: C_R_Rh30_CDK8_rep1

extract_protocol:
CUT&RUN+NEB DNA clean up
NEB Next Ultra II library prep kit


title: ESC_H3K4me3_KO_rep1

description: Cut and Tag

value: mESC


title: DMPA_07 meningioma, RNA-seq

description: Library name: DMPA_07

value: Meningothelial


title: ELCAP rpb3-flag h2o2 treated replicate 1

description: Library name: Rpb3-Treated-1

value: HEK293 Flp-in T-Rex - RPB3-FLAG


title: ELCAP 8WG16 untreated replicate 2

description: Library name: 8WG16-Unt-2


title: 914_W1_control

description:
Library name: COHP_50547
914_W1_CML

value: positive

value: CML

tag: timepoint


title: ELCAP 8WG16 untreated replicate 3

description: Library name: 8WG16-Unt-3


title: 909_W1_control

description:
Library name: COHP_50546
909_W1_CML

tag: batch


title: Hindpaw BALB/c_Healthy, biological rep1

tag: strain

value: BALB/c

value: 20 weeks

value: Healthy

value: Distal hindpaws (tarsus to phalanges), including joints, bone, cartilage, muscle; skin and nails removed


title: C&R_Rh4_P3F_rep1

description: Library name: C_R_Rh4_P3F_rep1

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: ETEC-8

description:
Library name: ETEC-8
ETEC-challenged group, replicate biosample 8

value: jejunal tissue


title: ETEC-7

description:
Library name: ETEC-7
ETEC-challenged group, replicate biosample 7


title: DMPA_06 meningioma, RNA-seq

description: Library name: DMPA_06

value: meningioma

value: female

value: Meningothelial with myxoid features


title: 1507_W0_treatment

description:
Library name: COHP_50362
1507_W0_CML_KO

value: PBMC


title: ESC_H3K4me3_WT_rep2

description: Cut and Tag


title: C&R_Rh30_P3F_rep1

description: Library name: C_R_Rh30_P3F_rep1


title: Hindpaw DBA/1_SpAD without fasting (control), biological rep3

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, no fasting (control)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 12 week of age, no fasting (control group of fasting mice), euthanasia at 18 weeks of age

tag: gender

value: male

value: 12 weeks

value: 18 weeks

value: Spondyloarthritis (diseased)


title: ESC_H3K4me3_WT_rep1

description: Cut and Tag

value: mESC


title: DMPA_05 meningioma, RNA-seq

description: Library name: DMPA_05

value: Metaplastic


title: ETEC-6

description:
Library name: ETEC-6
ETEC-challenged group, replicate biosample 6


title: ATACseq_Rh30-BI1347-24hr-rep2

description: Library name: ATACseq_Rh30-BI1347-24hr-rep2

library_source: other

data_processing:
Raw FASTQ data were trimmed by Trimmomatic-v0.39, and paired end reads were aligned to a concatenated human genome hg38 using Bowtie2 (v2.3.5) ((--dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using Genrich (v. 0.6.1) (https://github.com/jsh58/Genrich) with the following options -j -y -r -e chrM -q 0.05 -a 20. Peaks were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were generated and normalized using the DESeq2 size factors using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: bigwig files

molecule: other

extract_protocol:
ATAC-seq kit (cat# 53150) column extraction
ATAC-seq kit (cat# 53150) library prep


title: C&R_Rh30_TADA2B_BI1347-24hr_rep1

description: Library name: C_R_Rh30_TADA2B_BI1347-24hr_rep1

data_processing:
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9). Raw FASTQ data were trimmed using Trimmomatic-v0.38 and paired end reads were aligned to human hg38 genome using Bowtie2 (v2.3.5) in very sensitive local mode --dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using MAXS2 (v2.1.4) with a threshold of q<0.01 and peak were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were normalized and generated using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig file
Library strategy: CUT&Run


title: ETEC-5

description:
Library name: ETEC-5
ETEC-challenged group, replicate biosample 5


title: DMPA_04 meningioma, RNA-seq

description: Library name: DMPA_04

value: Transitional with myxoid features


title: Hindpaw DBA/1_SpAD without fasting (control), biological rep2

tag: age of confinment


title: ATACseq_Rh30-BI1347-24hr-rep1

description: Library name: ATACseq_Rh30-BI1347-24hr-rep1


title: Hindpaw DBA/1_SpAD without fasting (control), biological rep1

tag: age of euthanasia


title: ESC_H3K27me3_KO_rep1

description: Cut and Tag


title: DMPA_03 meningioma, RNA-seq

description: Library name: DMPA_03

value: Meningothelial


title: Hindpaw DBA/1_SpAD with fasting, biological rep2

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, every-other-day fasting

source_name: DBA/1 mice with Spontaneous arthritis, confined at 12 week of age, every-other-day fasting for 6 weeks, euthanasia at 18 weeks of age

tag: condition

value: every-other-day fasting for 6 weeks


title: DMPA_02 meningioma, RNA-seq

description: Library name: DMPA_02

tag: who grade


title: Hindpaw DBA/1_SpAD with fasting, biological rep3

value: Distal hindpaws (tarsus to phalanges), including joints, bone, cartilage, muscle; skin and nails removed


title: ATACseq_Rh30-BI1347-4hr-rep1

description: Library name: ATACseq_Rh30-BI1347-4hr-rep1

value: Rhabdomyosarcoma


title: DMPA_01 meningioma, RNA-seq

description: Library name: DMPA_01

tag: histologic subtype


title: ATACseq_Rh30-DMSO-rep2

description: Library name: ATACseq_Rh30-DMSO-rep2

value: PAX3::FOXO1 fusion

value: DMSO


title: Hindpaw DBA/1_SpAD with fasting, biological rep1


title: mESC-LDB1-3_ChIPmentation

description: LDB1 ChIPmentation rep3

data_processing:
Raw fastq reads were preprocessed using cutadapt (v2.7)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.3.5) with the “--no-unal” option.
Duplicated reads were cleaned using picard MarkDuplicates (v2.21.4) with “REMOVE_DUPLICATES=true”.
Peaks were called from bam files using MACS2 (v2.2.7.1) using default settings.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig
Library strategy: ChIPmentation

extract_protocol:
Genomic DNA was extracted by QIAquick PCR purification kit (Quiagen 28104).
ChIPmentation libraries were prepaired as described (Nat Methods. 2015 Oct;12(10):963-965). LDB1 Ab(Abcam: ab 96799) was used for IP.


title: PROseq_Rh30-BI1347-72hr-rep2

description: Library name: PROseq_Rh30-BI1347-72hr-rep2

data_processing:
The sequences were aligned to hg38 using bowtie2 before using the Nascent RNA Sequencing Analysis (NRSA) pipeline31 to determine the gene body and eRNA changes.
Assembly: hg38
Supplementary files format and content: bedGraph files
Library strategy: PRO-Seq

extract_protocol:
ProNex Chemistry beads extraction
PROseq run-on library prep


title: mESC-LDB1-2_ChIPmentation

description: LDB1 ChIPmentation rep2


title: Hindpaw DBA/1_SpAD ossification, biological rep6

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 5-6 (severe)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 5-6 (severe)

value: 11 weeks

value: 21 weeks


title: ATACseq_Rh30-DMSO-rep1

description: Library name: ATACseq_Rh30-DMSO-rep1


title: RNAseq_Rh30_BI1347_D7_repeat_B

description:
Library name: RNAseq_Rh30_BI1347_D7_repeat_B
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt

data_processing:
FastQC was used to evaluate read quality on raw RNA-seq reads. Reads were aligned to the human genome (hg38) using STAR (v2.7.2b) (Dobin et al., 2013). Transcript-level quantifications were calculated using RSEM (v1.3.1) (Li et al. 2011). Gene counts from STAR were then used to quantify differentially expressed genes between the experimental and control conditions using the R Bioconductor package DESeq2 (Anders, et al., 2010) using the approximate posterior estimation for GLM coefficients (apeglm) method for effect size. Normalized expression values for individual samples were obtained from RSEM log2 TPM values with the RSEM log2(TPM+1) values used for GSEA and producing RNA-seq heat map plots.
Assembly: hg38

extract_protocol:
Trizol
Novogene library prep pipeline


title: Hindpaw DBA/1_SpAD ossification, biological rep4

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 3 (moderate)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 3 (moderate)


title: mESC-LDB1-1_ChIPmentation

description: LDB1 ChIPmentation rep1


title: RNAseq_Rh30_BI1347_D7_repeat_A

description:
Library name: RNAseq_Rh30_BI1347_D7_repeat_A
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: PROseq_Rh30-BI1347-24hr-rep2

description: Library name: PROseq_Rh30-BI1347-24hr-rep2


title: RNAseq_Rh30_Bi1347_D3_repeat_B

description:
Library name: RNAseq_Rh30_Bi1347_D3_repeat_B
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: PROseq_Rh30-BI1347-24hr-rep1

description: Library name: PROseq_Rh30-BI1347-24hr-rep1


title: Hindpaw DBA/1_SpAD ossification, biological rep2

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 1-1.5 (mild)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 1-1.5 (mild)


title: RNAseq_Rh30_BI1347_D3_repeat_A

description:
Library name: RNAseq_Rh30_BI1347_D3_repeat_A
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: PROseq_Rh30-DMSO-rep4

description: Library name: PROseq_Rh30-DMSO-rep4


title: Hindpaw DBA/1_SpAD ossification, biological rep1

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 0.5 (mild)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 0.5 (mild)


title: PROseq_Rh30-DMSO-rep3

description: Library name: PROseq_Rh30-DMSO-rep3


title: RNAseq_Rh30_BI1347_D1_repeat_B

description:
Library name: RNAseq_Rh30_BI1347_D1_repeat_B
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: RNAseq_Rh30_BI1347_D1_repeat_A

description:
Library name: RNAseq_Rh30_BI1347_D1_repeat_A
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: PROseq_Rh30-BI1347-4hr-rep2

description: Library name: PROseq_Rh30-BI1347-4hr-rep2


title: Hindpaw DBA/1_SpAD without exercise (control), biological rep3

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, no exercise (control)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, no exercised (control group of exercised mice), euthanasia at 22 weeks of age

value: 22 weeks


title: PROseq_Rh30-BI1347-4hr-rep1

description: Library name: PROseq_Rh30-BI1347-4hr-rep1


title: WT_DIF_3_RNA

data_processing:
RNA-seq fastq files were trimmed using the cutadapt program (v2.7)
Preprocessed reads were aligned to the mouse reference genome Gencode M18 using hisat2 (v2.1.0) with default parameters.
Aligned reads were then mapped to gene features using subread featureCounts (v1.6.4) with parameters “-p -s 0 -T 1”.
Differential expression between groups of samples was tested using R (v3.5.1) with DESeq2 package (v1.22.1).
Transcript quantitation was performed with salmon (v0.14.2) with parameters “--libType=A --gcBias --seqBias --validateMappings".
Assembly: mm10 (Gencode M18)
Supplementary files format and content: tab-delimited text file of featurecounts.

extract_protocol:
RNA was extracted by RNeasy plus kit (Quiagen, 74134).
RNA sequencing libraries were prepared from 1ug of total RNA from ESC, EB or differentiated cells using NEBNext Ultra TM RNA library Prep Kit (NEB, Cat #7770) for Illumina following manufacturer’s

value: Differntiated cells


title: WT_DIF_2_RNA


title: Hindpaw DBA/1_SpAD without exercise (control), biological rep2

value: male


title: RNAseq_Rh30_DMSO_repeat_A

description:
Library name: RNAseq_Rh30_DMSO_repeat_A
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt


title: PROseq_Rh30-DMSO-rep2

description: Library name: PROseq_Rh30-DMSO-rep2


title: Hindpaw DBA/1_SpAD without exercise (control), biological rep1


title: WT_DIF_1_RNA


title: PROseq_Rh30-DMSO-rep1

description: Library name: PROseq_Rh30-DMSO-rep1


title: RNAseq_Rh30_sgCDK8-3_rep3

description:
Library name: RNAseq_Rh30_sgCDK8-3_rep3
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt


title: Hindpaw DBA/1_SpAD with exercise, biological rep3

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, exercised for 8 weeks

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, treadmill familiarized for 3 weeks, exercised for 8 weeks, euthanasia at 22 weeks of age


title: LDB1KO_EB_3_RNA

value: mEB


title: RNA serum, advanced gastric cancer, GC0165

city: Punta Arenas

first: Yolanda

last: Espinosa-Parrilla

state: Magallanes

address: Manuel Bulnes 01855

country: Chile

institute: Universidad de Magallanes

description:
Library name: SV18664_0012
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0012_S12_R1_001.fastq

data_processing:
Data proccesing was perfomed with Norgen Biotek's pipelin based on exceRpt: Cutadapt for trimming and filtering, fastqc for QC, STAR for alignment and featurecounts for quantification.
miRNA Analysis used trimmed mean of M-values (TMM) normalization method for the statistical analysis (Robinson and Oshlack, 2010).
Assembly: hg38
Supplementary files format and content: comma-separated text file (CSV) miRNA read counts per sample

source_name: serum

extract_protocol:
RNA was isolated from 250 ul of serum  using Plasma/Serum RNA Purification Mini Kit (Cat. 55000, Norgen Biotek)
RNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit for Illumina (Cat. 63600, 63620)

value: serum


title: RNAseq_Rh30_sgCDK8-3_rep2

description:
Library name: RNAseq_Rh30_sgCDK8-3_rep2
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt


title: Hindpaw DBA/1_SpAD with exercise, biological rep2

value: Spondyloarthritis (diseased)

value: treadmill familiarized for 3 weeks, exercised for 8 weeks


title: LDB1KO_EB_2_RNA


title: RNA serum, advanced gastric cancer, GC0428

description:
Library name: SV18664_0011
Column name in exceRpt_miRNA_ReadCounts: SV18664_0011_S10_R1_001.fastq


title: RNAseq_Rh30_sgCDK8-3_rep1

description:
Library name: RNAseq_Rh30_sgCDK8-3_rep1
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt


title: Hindpaw DBA/1_SpAD with exercise, biological rep1


title: LDB1KO_EB_1_RNA


title: RNAseq_Rh30_sgChr2.2_rep3

description:
Library name: RNAseq_Rh30_sgChr2.2_rep3
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt