title: 32-134D-1% O2 rep2 [134D1pct-2_S10]

first: Shaima

last: Salman

state: MD

address: 733 N. Broadway

department: Institute for Cell Engineering

institute: JHU

data_processing:
The Fastq files were QCed and analyzed by Genialis (https://www.genialis.com/)
Reads were preprocessed by BBDuk to remove adapters and trim reads for quality at the 3'-end and discard reads that are too short. Preprocessed reads are aligned by STAR aligner. Aligned reads were summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics and rRNA/globin depletion rate QC information were automatically summarized by the MultiQC tool.
The dataset was normalised within DESEq2, and fold change and log2(FC) were reported/computed from that.
Genome_build: Homo sapiens_GRCh38_ens92
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, Matrix table with raw gene counts for every gene and every sample

source_name: Hep3B liver cancer cell line

growth_protocol: Hep3B cells were maintained DMEM/F12 (50:50) medium. The culture media were supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin-streptomycin. Cells were cultured at 37°C in a 5% CO2, 95% air incubator.

extract_protocol:
RNA was extracted using TRIzol Reagent (ThermoFisher) and treated with DNase (Qiagen)
Library preparation and sequencing using the NovaSeq6000 platform (Illumina) were performed by Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

treatment_protocol: Hep3B cells were seeded on 6-well plates in three biological replicates and treated with compounds the following day and exposed to 20% or 1% O2 for 24 hours

tag: cell type

value: liver cancer

value: 32-134D and 1% O2 treated


title: 32-134D-1% O2 rep3 [134D1pct-3_S9]

status: Public on Nov 25 2025

type: SRA

city: Baltimore

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: wild typeZT8 rep2

city: Irvine

first: Kousha

last: Changizi

state: California

address: Donald Bren Hall

department: ICS/IGB

institute: University of California, Irvine

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

molecule: polyA RNA

organism: Mus musculus

source_name: Colon

extract_protocol:
Total RNA was extracted from the colon with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

tag: tissue

value: Colon

tag: genotype

value: wild type

value: ad libitum normal chow diet


title: FIS x luh 8DAI rep1

city: Berlin

first: Cezary

last: Smaczniak

address: Philippstr. 13

department: Institute for Biology

country: Germany

institute: Humboldt-Universität zu Berlin

description: Library name: FISxluh_8DAI_rep1

data_processing:
Adapter sequences were removed from the sequencing reads using Trimmomatic and the quality of sequencing data was evaluated by FastQC. Trimmed reads were mapped to the Arabidopsis TAIR9 genome using STAR. Unmapped reads were removed using Samtools. Reads that map to genomic features were counted using featureCounts. DESeq2 was used to generate gene normalized counts and identify differentially expressed genes across the four developmental stages in a pairwise comparison between genotypes.
Assembly: TAIR9
Supplementary files format and content: Deseq2NormCounts.csv; DeSeq2 gene normalized counts

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plant seeds were sterilized, stratified and grown on soil at 22 °C in a 16/8 h light/dark cycles with light intesity at 150 μmol m-2 s-1.

extract_protocol:
Three biological replicates for each genotype in 4 different time points were prepared. Flowers were collected and immediately frozen in liquid nitrogen. The tissue was homogenized with the Precellys Homogenizer and the RNA was isolated with the QIAwave RNA Mini Kit (Qiagen). DNA was removed by DNase I digestion followed by LiCl precipitation. The RNA concentration was measured using the Qubit 4 (Invitrogen) and the RNA integrity was assessed on a 4200 TapeStation (Agilent). Samples with an RNA integrity number equivalent (RINe) higher than 6 were considered for further processing.
Total RNA (300 ng) served as input for library preparation using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). After library preparation, samples were run on the 4200 TapeStation (Agilent) for quality control.

treatment_protocol: When pLUH:LUH-GFP pAP1:AP1-GR ap1 cal plants (FIS) had developed a stem of 3-5 cm height, the DEX induction solution (2 μM dexametasone, 0.015% Silwet L-77) was pipetted onto the main shoot until the inflorescence turned dark green.  The first induction was applied at 10:00 and subsequent inductions were applied approximately every 24 h. Tissue was collected at 16:00 on the day of interest.

value: inflorescence

value: pAP1:AP1-GR ap1 cal luh

tag: ecotype

value: Landsberg

value: Dexamethasone

tag: time

value: 8 days


title: wild type ZT8 rep1


title: FIS x luh 4DAI rep3

description: Library name: FISxluh_4DAI_rep3

value: 4 days


title: HTP71 sample analyzed with HTG kit

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Profesor Beltran Baguena, 8

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

description: Library name: HTP71_HTP

data_processing:
HTG parser v5.3 and TempOSeqR v1.0
Assembly: hg38 (HTG) and HWT_2_1_BrCa_22575plex (ToS)
Supplementary files format and content: csv file includes read counts for HTG and TempOSeq analysis

source_name: Endometrial Cancer

extract_protocol:
HTG and TempOSeq are targeted RNA-seq methods without FFPE sample RNA extraction
HTG edgeseq HTP panel and TempOSeq Human Whole Transcriptome Assay

value: Endometrial Cancer

tag: batch

value: HTG


title: wild type ZT4 rep3


title: FIS x luh 4DAI rep2

description: Library name: FISxluh_4DAI_rep2


title: HTP72 sample analyzed with HTG kit

description: Library name: HTP72_HTP


title: wild type ZT4 rep2


title: V-1% O2 rep3 [V1pct-3_S27]

value: DMSO and 1% O2 treated


title: FIS x luh 4DAI rep1

description: Library name: FISxluh_4DAI_rep1


title: wild type ZT4 rep1


title: HTP70 sample analyzed with HTG kit

description: Library name: HTP70_HTP


title: DFCI283_scRNA

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: DFCI283_scRNA

library_source: transcriptomic single cell

data_processing:
Output from Illumina software is processed by the Picard data-processing pipeline to yield BAM files containing well-calibrated, aligned reads.
Feature-barcode matrices were generated from FASTQ files using Cell Ranger v3.1.0 with default parameters and the GRCh38-3.0.0 reference transcriptome.
Assembly: GRCh38
Supplementary files format and content: Tar zipped output of the variant calling performed by Mutect2 and filtered count matrix from cellranger

source_name: Patient Derived Model

growth_protocol: All cell lines except SW1271 were maintained in Roswell Park Memorial Institute (RPMI)-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin (P/S) (Gibco). SW1271 was grown in Dulbecco’s Modified Eagle Medium (Gibco) with 10% FBS. Gefitinib, osimertinib, AZD8055, ZSTK474, MK2206, EPZ6438, GSK126 and compounds listed in Supplementary Table S6 were purchased from Selleck Chemicals. Stock solutions of all drugs were prepared at either 5 or 10 mmol/L in dimethyl sulfoxide (DMSO, Sigma) and stored at -80°C. Cell lines were authenticated by single tandem repeat analysis at the Molecular Biology Core Facilities in 2021 and tested negative for mycoplasma as determined the Mycoplasma Plus PCR Primer set (Agilent). LIF neutralizing antibody, IL6 neutralizing antibody and control antibody were purchased from R & D systems. Human EGF recombinant protein was obtained from Life Technologies. The malignant pleural effusions were obtained from a patient with EGFR-mt SCLC transformed tumors. The sample was subjected to red blood cell lysis using RBC Lysis Buffer (Boston BioProducts) and the cells were suspended either in RPMI-1640 with 10% FBS or in ACL4 media (Gibco) either with or without 10% FBS. We carefully monitored the appearance of the cells during serial passage to minimize the loss of intra-tumor heterogeneity. Once the cell lines were established, ultra-low attachment plates were used for culturing NE tSCLC cell lines whereas the regular tissue culture plates were used for non-NE tSCLC cell lines. DFCI112F and DFCI112Ad were maintained in RPMI-1640 with 10% FBS and P/S. DFCI190F and DFCI283F were grown in ACL4 media with P/S without serum. DFCI190Ad and DFCI283Ad were cultured in ACL4 media with 10% FBS and P/S. The number of passages the cells have undergone during the establishment of the cell lines is as follows: DFCI112F/Ad, passage 5; DFCI163F, passage 13; DFCI163Ad, passage 10; DFCI190F, passage 27; DFCI190Ad, passage 15; and DFCI283F/Ad, passage 20.

extract_protocol:
Following sample preparation, libraries are quantified using PicoGreen. Based on PicoGreen quantification, libraries are normalized to equal concentration and pooled by equal volume. Library pools are then quantified using a Sybr Green-based qPCR assay, with PCR primers complementary to the ends of the adapters (kit purchased from Kapa Biosciences). After qPCR quantification, library pools are normalized to 2 nmol/L, denatured using 0.2 N NaOH, and diluted to 20 pmol/L, the working concentration for downstream cluster amplification and sequencing. Denatured library pools are spread across the number of sequencing lanes required to hit target coverage for all samples.
Libraries are constructed using the protocol described in Fisher et al. with several modifications: first, initial genomic DNA input into shearing has been reduced from 3µg to 100ng in 50µL of solution. Second, for adapter ligation, Illumina paired end adapters have been replaced with palindromic forked adapters with unique 8 base index sequences embedded within the adapter. These index sequences enable pooling of libraries prior to sequencing. Third, custom sample preparation kits from Kapa Biosciences are now used for all enzymatic steps of the library construction process.

value: Patient Derived Model

value: Tumor Cells


title: FIS x luh 2DAI rep2

description: Library name: FISxluh_2DAI_rep2

value: 2 days


title: DFCI190_scRNA

description: Library name: DFCI190_scRNA


title: V-20% O2 rep3 [V20pct-3_S6]

value: liver cancer

value: DMSO and 20% O2 treated


title: DFCI112_scRNA

description: Library name: DFCI112_scRNA


title: V-1% O2 rep2 [V1pct-2_S26]


title: HTP73 sample analyzed with HTG kit

description: Library name: HTP73_HTP


title: wild type ZT0 rep3

value: Colon


title: wild type ZT0 rep2

value: wild type


title: FIS x luh 2DAI rep1

description: Library name: FISxluh_2DAI_rep1


title: DFCI283ad

description: Library name: DFCI283ad

library_source: genomic

molecule: genomic DNA


title: DFCI283F

description: Library name: DFCI283F


title: wild type ZT0 rep1

value: ad libitum normal chow diet


title: V-20% O2 rep1 [V20pct-1_S19]


title: V-20% O2 rep2 [V20pct-2_S13]


title: FIS x luh 0DAI rep2

description: Library name: FISxluh_0DAI_rep2

value: inflorescence

value: 0 days


title: FIS x luh 0DAI rep3

description: Library name: FISxluh_0DAI_rep3

value: pAP1:AP1-GR ap1 cal luh

value: Landsberg


title: Bmal1 knock out ZT20 rep3

value: Bmal1 knock out


title: 32-134D-1% O2 rep1 [134D1pct-1_S18]

value: 32-134D and 1% O2 treated


title: Bmal1 knock out ZT20 rep2


title: DFCI190F

description: Library name: DFCI190F


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, Input, replicate 2

description: Library name: LUH-GFP FIS 8DAI Input rep2

data_processing:
Adapter sequences were removed from the sequencing reads using Trimmomatic and the quality of sequencing data was evaluated by FastQC. Trimmed reads were mapped to the Arabidopsis TAIR9 genome using Bowtie2. Unmapped reads and reads with MAPQ score lower than 40 were removed using Samtools. Peak calling was performed using MACS2 against the Input control samples. Merged regions were further evaluated with Deseq2 to produce list of significantly p-value < 0.05 enriched peaks. For data visualization,  genome alignment tracks (BigWig files) were generated from MASC2 treat_pileup bedGraph files using bedGraphToBigWig tool.
Assembly: TAIR9
Supplementary files format and content: .bw bigWig

extract_protocol:
Induced inflorescences were fixed in 2.5 mM DSG and in 1% formaldehyde each time for 20 min at room temperature in the vacuum. Fixed tissue was ground to a fine powder in liquid nitrogen and nuclei were isolated. The crude nuclei were sonicated using Covaris S220 and centrifuged. The input sample was collected at this step. The rest of the supernatant was incubated with the GFP antibodies (#ab290, Abcam) followed by a capture with magnetic protein A beads (Dynabeads, Thermo) for immunoprecipitation. Bound chromatin was eluted from the beads. ChIP and Input samples were de-crosslinked and purified.
The DNA sequencing libraries for both ChIP and Input samples were prepared using ThruPLEX DNA-Seq Kit (Takara Bio) and SMARTer DNA Unique Dual Index Kit (Takara Bio) following manufacturer’s instructions. DNA double size selection 100-700 bp was performed using AMPure XP beads (Beckman Coulter).

value: pLUH:LUH-GFP pAP1:AP1-GR ap1 cal

value: Input


title: FIS x luh 2DAI rep3

description: Library name: FISxluh_2DAI_rep3

value: Dexamethasone


title: FIS x lug 8DAI rep3

description: Library name: FISxlug_8DAI_rep3

value: pAP1:AP1-GR ap1 cal lug

value: 8 days


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, Input, replicate 1

description: Library name: LUH-GFP FIS 8DAI Input rep1


title: FIS x luh 0DAI rep1

description: Library name: FISxluh_0DAI_rep1


title: V-1% O2 rep1 [V1pct-1_S15]

value: DMSO and 1% O2 treated


title: DFCI190ad

description: Library name: DFCI190ad

value: Patient Derived Model

value: Tumor Cells


title: Bmal1 knock out ZT16 rep3

value: Colon


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, ChIP, replicate 2

description: Library name: LUH-GFP FIS 8DAI ChIP rep2

value: GFPab (Abcam, #ab290)


title: DFCI163ad

description: Library name: DFCI163ad


title: Bmal1 knock out ZT20 rep1

value: ad libitum normal chow diet


title: FIS x lug 8DAI rep2

description: Library name: FISxlug_8DAI_rep2

value: inflorescence


title: HepG2 cell, JQ1

city: Nanjing

first: Tao

last: Wu

address: 24 Tongjiaxiang

country: China

institute: China Pharmaceutical University

description: Library name: JQ1

data_processing:
Sequences were cleaned and processed by Cutadapt (V1.9.1). clean data were aligned to reference genome via software Hisat2 (v2.0.1). Finally, HTSeq (v0.6.1) was used to estimate gene and isoform expression levels from the pair-end clean data.
Assembly: hg19
Supplementary files format and content: csv files inlcude FPKM values for each sample

extract_protocol:
Total RNA of each sample was extracted using RNeasy Mini Kit (Qiagen). 1 μg total RNA was used for following library preparation.
The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan,China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).


title: HepG2 cell, DMSO

description: Library name: DMSO

value: DSMO


title: FIS x lug 8DAI rep1

description: Library name: FISxlug_8DAI_rep1


title: Bmal1 knock out ZT16 rep2


title: Bmal1 knock out ZT16 rep1


title: R-3

city: Chongqing

first: XinDi

last: Gao

state: Chongqing

address: No.183 Xinqiaozheng Street, Shapingba District, Chongqing, China.

institute: Army Medical University

description: Library name: Sample 12

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Bowtie 2 suite (version 4.1.2)
Assembly: Cryptococcus neoformans var. grubii H99, Saccharomyces cerevisiae S288C
Supplementary files format and content: tab-delimited text files include reads values for each Sample

organism: Saccharomyces cerevisiae

source_name: strain

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the preparations of RNA sample.
Sequencing libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: strain

value: Saccharomyces cerevisiae BY4741

value: rpd3(YNL330C) knock-out

value: grown at logarithmic phase in 100ml YPD broth at 39°C


title: FIS x lug 4DAI rep2

description: Library name: FISxlug_4DAI_rep2

value: Landsberg

value: 4 days


title: R-1

description: Library name: Sample 10


title: FIS x lug 4DAI rep3

description: Library name: FISxlug_4DAI_rep3

value: Dexamethasone


title: DCL1ci-IP_rep3

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2
FASTQ file generation and demultiplexing was done by Fasteris. Adapter sequences were removed from raw reads using fastx_clipper (options: -c -l 25 -Q 33 -a TGGAATTCTCGG)
Mapping to Arabidopsis genome using TopHat (v2.0.11) using the TAIR10 Ensembl genome index and genes annotation (http://ccb.jhu.edu/software/tophat/igenomes.shtml)
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files have then be generated using bamCoverage from deeptools (3.5.0) on the accepted_hits.bam files generated by TopHat with option --binSize 1.

source_name: inflorescences

growth_protocol: Heterozygous pDCL1:DCL1ci-HA/dcl1-7+/- and dcl1-7+/- plants were grown for 2 weeks in soil in a 16-h-light/8-h-dark regimen. Genotyping was performed, then Homozygous pDCL1:DCL1ci-HA/dcl1-7-/- and dcl1-7-/- plants were selected and grown for two more week at the same conditions.

extract_protocol:
Three independent pools of pDCL1:DCL1ci-HA/dcl1-7 and three independent pools of dcl1-7 (control plants) were fixed in formaldehyde 1%, frozen and ground in liquid nitrogen. Supernatants were sonicated, precleared and incubated with Pierce™ Anti-DYKDDDDK Magnetic Agarose (Thermo Scientific™). The beads were removed magnetically, washed four times and reversal crosslinked in NaCl 200mM and Proteinase K. RNA was then phenol-extracted and precipitated in isopropanol and glycogen, washed in ethanol 80% and re-suspended in RNase-free water.
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

tag: strain and genotype

value: Columbia dcl1-7 transformed with pDCL1-DCL1ci-HA

value: inflorescences

tag: development stage

value: Unopened flower buds


title: R-2

description: Library name: Sample 11


title: Bmal1 knock out ZT12 rep2

value: Bmal1 knock out


title: DCL1ci-IP_rep2


title: FIS x lug 4DAI rep1

description: Library name: FISxlug_4DAI_rep1

value: pAP1:AP1-GR ap1 cal lug


title: FIS x lug 2DAI rep3

description: Library name: FISxlug_2DAI_rep3

value: 2 days


title: Bmal1 knock out ZT12 rep1

value: Colon


title: C-2

description: Library name: Sample 8

value: wild-type


title: control_rep3

value: Columbia dcl1-7


title: control_rep2


title: FIS x lug 2DAI rep2

description: Library name: FISxlug_2DAI_rep2

value: inflorescence


title: C-1

description: Library name: Sample 7

value: strain


title: DCL1ci-IP_rep1


title: FIS x lug 2DAI rep1

description: Library name: FISxlug_2DAI_rep1


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, ChIP, replicate 1

description: Library name: LUH-GFP FIS 8DAI ChIP rep1

value: pLUH:LUH-GFP pAP1:AP1-GR ap1 cal

value: GFPab (Abcam, #ab290)


title: C-3

description: Library name: Sample 9

value: Saccharomyces cerevisiae BY4741

value: grown at logarithmic phase in 100ml YPD broth at 39°C


title: Bmal1 knock out ZT12 rep3

value: ad libitum normal chow diet


title: FIS x lug 0DAI rep3

description: Library name: FISxlug_0DAI_rep3

value: Landsberg

value: Dexamethasone

value: 0 days


title: Bmal1 knock out ZT8 rep1


title: fetal tissue_065

type: genomic

city: Jiaxing

first: Luming

last: Wang

state: Zhejiang

address: NO.2468 Zhonghuan East Road

institute: Jiaxing Maternity and Child Health Care Hospital

description: Hybridized to CytoScan814K Array

hyb_protocol: As per manufacturer (Affymetrix),prepare Hybridization Master Mix and add Hybridization Master Mix to the samples.Place the plate onto the pre-heated thermal cycler and run the CytoScan Hyb protocol.Using a P200 pipette, remove 200 µL of the first sample and immediately inject it into an array.Allow the arrays to rotate at 50°C, 60 rpm for 16 to 18 hours.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® System 3000Dx v.2

data_processing:
Using ChAS v4.4 for data analysis,Reference Model File Creation is done with fixed parameters in the Reference Creation workflow.Beginning with the raw signal data in the CEL file, the Single Sample CytoScan  Workflow implements a series of steps that perform probe set summarization,  normalization, removal of variation caused by known properties and residual variation, and completing with calling genotypes, copy number segments and LOH segments.For CytoScan arrays, markers are individually assigned a copy number call by a Hidden Markov model (HMM). The sample specific inputs to the HMM are the Weighted Log2 Ratios generated by the Signal Restoration module.
[primary data description]  The weighted Log2 Ratios are centered on copy number (CN) = 2. In theory, when Log2 Ratio = 0 then CN = 2, when Log2 Ratio = -1 the CN = 1, etc. In truth, microarrays, or any hybridization-based technology, exhibit Log2 Ratio compression due to many factors, so the Log2 Ratios never exhibit the amplitude expected by the math. The following table shows theoretical and actual Log2 Ratios for different Copy Number States.Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: fetal tissue

label_protocol: As per manufacturer (Affymetrix),prepare labeling Master Mix and add Labeling Master Mix to pre-chilled strip tubes on cooling block on ice.Place the labeling plate in thermal cycler and run CytoScan Label protocol.

extract_protocol: Genomic DNA was extracted from fetal tissue using the QIAamp DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: gestational age

value: 13 weeks


title: Bmal1 knock out ZT4 rep3

value: Bmal1 knock out


title: FIS x lug 0DAI rep2

description: Library name: FISxlug_0DAI_rep2

value: pAP1:AP1-GR ap1 cal lug


title: fetal tissue_064

description: Hybridized to CytoScan813K Array

value: 14 weeks


title: Bmal1 knock out ZT4 rep2

value: Colon


title: FIS x lug 0DAI rep1

description: Library name: FISxlug_0DAI_rep1


title: KO_d4_replicate2 (miRNA-Seq)

first: Nikolaos

last: Tsopoulidis

state: MA

address: 185 Cambridge Street, CPZN 4100

institute: MGH Molecular Biology

description:
Library name: Nudt21KO_d4_r2
miRNA_cpm.xlsx

data_processing:
Transcriptome mapping was performed with STAR using the UCSC annotation of the mm10 reference genome.
To align microRNAs to the reference database miRbase (mature.fa). The mature.fa file was U to T converted via: “sed '/^[^>]/s/U/T/g' mature.fa > mature_conv.fa”. And aligned with bowtie using the following attributes “-v 1 -a --best –strata”. Read counts for individual genes were generated using featureCounts from the Subread package. microRNA counts were generated with samtools idxstas. Differential expression analysis was carried out with EdgeR after normalizing read counts and including only genes with CPM > 1 in at least one sample. Differentially expressed genes or microRNAs were identified based on a >2-fold change in expression value, unless otherwise specified.
Assembly: mm10
Supplementary files format and content: Table with CPM values for each sample

source_name: Esophagus

growth_protocol: Complete SAGM medium, supplemented with 10 μM Y-27632 (Tocris), 1 μM CHIR99021 (Tocris), 1 μM A83-01, and 1 μM DMH-1, was used for culture. Cells were kept in the exponential growth phase (maximum 8,000 cells/cm²). Media changes were performed every 48 hours. Cells were dissociated from the flasks and dishes either by scraping or treatment with TrypLE (Gibco) for 10 minutes. Epithelial cells were collected in 1% BSA/PBS (Invitrogen) and spun down at 300 g.

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen).
Illumina HiSeq2500 as PE50, producing approximately 20-30 million reads per sample. microRNA-seq libraries were constructed with the NEBNext® Small RNA Library Prep Set (NEB) and sequenced on the Illumina HiSeq2500, producing approximately 10 million reads per sample as SR50

treatment_protocol: ETOH or 4OHT(0.05 µM)

value: Esophagus

value: Esophageal basel cells

value: Nudt21 fl/fl; R26CreER

value: Nudt21 KO


title: FIS 8DAI rep3

description: Library name: FIS_8DAI_rep3

value: inflorescence

value: pAP1:AP1-GR ap1 cal

value: 8 days


title: fetal tissue_062

description: Hybridized to CytoScan811K Array


title: Bmal1 knock out ZT4 rep1


title: fetal tissue_063

description: Hybridized to CytoScan812K Array


title: Floxed_d0_replicate3 (miRNA-Seq)

description:
Library name: Floxed_d0_r3
miRNA_cpm.xlsx

value: ETOH

value: Control


title: FIS 8DAI rep2

description: Library name: FIS_8DAI_rep2

value: Landsberg


title: Bmal1 knock out ZT8 rep2

value: ad libitum normal chow diet


title: Bmal1 knock out ZT8 rep3


title: fetal tissue_061

description: Hybridized to CytoScan810K Array

value: 18 weeks


title: FIS 8DAI rep1

description: Library name: FIS_8DAI_rep1

value: Dexamethasone


title: fetal tissue_066

description: Hybridized to CytoScan815K Array

value: 13 weeks


title: Floxed_d0_replicate2 (miRNA-Seq)

description:
Library name: Floxed_d0_r2
miRNA_cpm.xlsx


title: Bmal1 knock out ZT0 rep2

value: Bmal1 knock out


title: fetal tissue_060

description: Hybridized to CytoScan809K Array

value: 16 weeks


title: control_rep1

value: Columbia dcl1-7

value: inflorescences

value: Unopened flower buds


title: Bmal1 knock out ZT0 rep1

value: Colon


title: FIS 4DAI rep3

description: Library name: FIS_4DAI_rep3

value: 4 days


title: KO_d4_replicate3 (miRNA-Seq)

description:
Library name: Nudt21KO_d4_r3
miRNA_cpm.xlsx

value: Esophagus

value: Esophageal basel cells

value: Nudt21 fl/fl; R26CreER

value: Nudt21 KO


title: Hypo_d4_replicate3 (PAS-seq)

description:
Library name: Nudt21Hypo_d4_r3
PAS-seq.xlsx

data_processing:
Transcriptome mapping was performed with STAR using the UCSC annotation of the mm9 reference genome.
Read counts for individual genes were generated using featureCounts. Only genes with CPM > 2 for at least two samples were included in the analyses.
PAS-seq data analysis was conducted as described by (Wang et al., 2021).
Assembly: mm9
Supplementary files format and content: Table with differential PAS usage

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen).
1µg of total RNA was used for PAS-seq library preparation, adhering to the protocol detailed in our methodological paper (Yoon et al., 2021).

treatment_protocol: ETOH or 4OHT(0.05 µM) or 4OHT+DOX(50ng/ml)

value: Nudt21 Hypomorph


title: fetal tissue_059

description: Hybridized to CytoScan808K Array


title: FIS 4DAI rep2

description: Library name: FIS_4DAI_rep2

value: inflorescence

value: pAP1:AP1-GR ap1 cal

value: Landsberg


title: KO_d4_replicate1 (miRNA-Seq)

description:
Library name: Nudt21KO_d4_r1
miRNA_cpm.xlsx


title: fetal tissue_058

description: Hybridized to CytoScan807K Array

value: 14 weeks


title: MR knock out ZT20 rep3

value: MR knock out

value: ad libitum normal chow diet


title: Hypo_d4_replicate2 (PAS-seq)

description:
Library name: Nudt21Hypo_d4_r2
PAS-seq.xlsx


title: MR knock out ZT20 rep2


title: fetal tissue_057

description: Hybridized to CytoScan806K Array

value: 16 weeks


title: Hypo_d4_replicate1 (PAS-seq)

description:
Library name: Nudt21Hypo_d4_r1
PAS-seq.xlsx


title: Bmal1 knock out ZT0 rep3

value: Bmal1 knock out


title: MR knock out ZT20 rep1


title: FIS 2DAI rep3

description: Library name: FIS_2DAI_rep3

value: Dexamethasone

value: 2 days


title: KO_d4_replicate3 (PAS-seq)

description:
Library name: Nudt21KO_d4_r3
PAS-seq.xlsx


title: MR knock out ZT16 rep3

value: Colon


title: FIS 2DAI rep2

description: Library name: FIS_2DAI_rep2


title: fetal tissue_055

description: Hybridized to CytoScan804K Array


title: KO_d4_replicate2 (PAS-seq)

description:
Library name: Nudt21KO_d4_r2
PAS-seq.xlsx


title: fetal tissue_056

description: Hybridized to CytoScan805K Array


title: fetal tissue_054

description: Hybridized to CytoScan803K Array

value: 17 weeks


title: Floxed_d0_replicate1 (miRNA-Seq)

description:
Library name: Floxed_d0_r1
miRNA_cpm.xlsx

value: Esophagus

value: ETOH

value: Control


title: KO_d4_replicate1 (PAS-seq)

description:
Library name: Nudt21KO_d4_r1
PAS-seq.xlsx

value: Esophageal basel cells

value: Nudt21 fl/fl; R26CreER

value: Nudt21 KO


title: MR knock out ZT16 rep1


title: fetal tissue_053

description: Hybridized to CytoScan802K Array


title: FIS 0DAI rep3

description: Library name: FIS_0DAI_rep3

value: inflorescence

value: pAP1:AP1-GR ap1 cal

value: 0 days


title: FIS 2DAI rep1

description: Library name: FIS_2DAI_rep1

value: Landsberg


title: FIS 0DAI rep2

description: Library name: FIS_0DAI_rep2


title: fetal tissue_052

description: Hybridized to CytoScan801K Array

value: 20 weeks


title: MR knock out ZT12 rep3

value: MR knock out

value: ad libitum normal chow diet


title: Floxed_d0_replicate3 (PAS-seq)

description:
Library name: Floxed_d0_r3
PAS-seq.xlsx


title: MR knock out ZT12 rep2


title: FIS 4DAI rep1

description: Library name: FIS_4DAI_rep1

value: Dexamethasone

value: 4 days


title: FIS 0DAI rep1

description: Library name: FIS_0DAI_rep1


title: Floxed_d0_replicate1 (PAS-seq)

description:
Library name: Floxed_d0_r1
PAS-seq.xlsx


title: fetal tissue_051

description: Hybridized to CytoScan800K Array

value: 21 weeks


title: fetal tissue_050

description: Hybridized to CytoScan799K Array

value: 16 weeks


title: fetal tissue_049

description: Hybridized to CytoScan798K Array


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, ChIP, replicate 3

description: Library name: LUH-GFP FIS 8DAI ChIP rep3

value: pLUH:LUH-GFP pAP1:AP1-GR ap1 cal

value: GFPab (Abcam, #ab290)


title: MR knock out ZT8 rep3

value: Colon


title: Liver-41

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

description: Library name: Liver-41

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Assembly: GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Frozen samples were dissociated on a GentleMACS in 1mL of TST buffer (https://www.nature.com/articles/s41591-020-0844-1). Nuclei were counted and resuspended in PBS+BSA+RNAse inhibitor before loading on a 10x 3' v3.1 channel.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, after nuclei loading and gel bead-in-emulsion (GEM) formation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Samples were placed in cryo-tubes after removal of liquid by gently wiping it samples on the side of the container. Tubes were then covered in dry ice and transferred to −80 °C for long-term storage.

tag: age

tag: Sex

value: M

tag: disease state

value: Normal

value: Liver


title: MR knock out ZT8 rep2


title: MR knock out ZT16 rep2


title: LUH-GFP FIS inflorescences, 4 days after DEX induction, Input, replicate 2

description: Library name: LUH-GFP FIS 4DAI Input rep2

value: inflorescence

value: Input


title: fetal tissue_048

description: Hybridized to CytoScan797K Array

value: 14 weeks


title: Liver-39

description: Library name: Liver-39

value: F


title: LUH-GFP FIS inflorescences, 4 days after DEX induction, Input, replicate 1

description: Library name: LUH-GFP FIS 4DAI Input rep1


title: Liver-40

description: Library name: Liver-40


title: fetal tissue_047

description: Hybridized to CytoScan796K Array


title: fetal tissue_046

description: Hybridized to CytoScan795K Array


title: MR knock out ZT4 rep3


title: Floxed_d0_replicate2 (PAS-seq)

description:
Library name: Floxed_d0_r2
PAS-seq.xlsx

value: Esophagus

value: Esophageal basel cells

value: Nudt21 fl/fl; R26CreER

value: ETOH

value: Control


title: LUH-GFP FIS inflorescences, 4 days after DEX induction, ChIP, replicate 2

description: Library name: LUH-GFP FIS 4DAI ChIP rep2


title: MR knock out ZT4 rep2

value: MR knock out

value: ad libitum normal chow diet


title: fetal tissue_045

description: Hybridized to CytoScan794K Array

value: 20 weeks


title: LUH-GFP FIS inflorescences, 4 days after DEX induction, ChIP, replicate 1

description: Library name: LUH-GFP FIS 4DAI ChIP rep1

value: pLUH:LUH-GFP pAP1:AP1-GR ap1 cal

value: GFPab (Abcam, #ab290)


title: Liver-37

description: Library name: Liver-37

value: M


title: MR knock out ZT8 rep1

value: Colon


title: MR knock out ZT4 rep1


title: fetal tissue_044

description: Hybridized to CytoScan793K Array


title: LUH-GFP FIS inflorescences, 8 days after DEX induction, Input, replicate 3

description: Library name: LUH-GFP FIS 8DAI Input rep3


title: MR knock out ZT12 rep1


title: MR knock out ZT0 rep3


title: MR knock out ZT0 rep2


title: CD34, day 13, don003, rep6

city: Oxford

first: Simone

last: Riva

state: England

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington Oxford OX3 9DS

country: United Kingdom

institute: University of Oxford

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep6

data_processing:
Assembly: hg38
All data was processed using the CATCH-up pipeline (https://github.com/Hughes-Genome-Group/UpStreamPipeline/tree/main/genetics/catch-up)
aligner_algorithm: bowtie2 (bowtie2 v2.4.5)
samtools_sort_extra: -m 4G (samtools v1.15.1)
filtering_extra: -bShuF 4 -f 3 -q 30  (samtools v1.15.1)
bam_coverage: --binSize 1 --extendReads (deepTools v3.5.1)
Supplementary files format and content: bigwig

source_name: Erythroid

growth_protocol: CD34+ cells were isolated from fresh blood as previously described (Truch, 2022) and subject to a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017).

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 75,000 cells were used per biological replicate.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).

tag: donor id

value: Erythroid

tag: origin cell_line

value: CD34+ human erythroid

tag: differentiation day

value: Day 13

tag: selection antibody

value: CD34 microbead, Miltenyi Biotec #130-046-702


title: CD34, day 13, don003, rep7

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep7

tag: cell type


title: fetal tissue_043

description: Hybridized to CytoScan792K Array

value: 14 weeks


title: fetal tissue_042

description: Hybridized to CytoScan791K Array


title: CD34, day 13, don003, rep4

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep4


title: MR knock out ZT0 rep1

tag: treatment


title: LUH-GFP FIS inflorescences, 2 days after DEX induction, ChIP, replicate 2

description: Library name: LUH-GFP FIS 2DAI ChIP rep2

tag: tissue

value: inflorescence


title: CD34, day 13, don003, rep5

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep5


title: fetal tissue_041

description: Hybridized to CytoScan790K Array


title: fetal tissue_040

description: Hybridized to CytoScan789K Array


title: high salt night fed ZT20 rep3

value: high salt night fed


title: LUH-GFP FIS inflorescences, 0 days after DEX induction, Input, replicate 2

description: Library name: LUH-GFP FIS 0DAI Input rep2

tag: genotype

value: Input


title: LUH-GFP FIS inflorescences, 2 days after DEX induction, Input, replicate 2

description: Library name: LUH-GFP FIS 2DAI Input rep2


title: CD34, day 13, don003, rep2

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep2


title: fetal tissue_039

description: Hybridized to CytoScan788K Array


title: LUH-GFP FIS inflorescences, 0 days after DEX induction, Input, replicate 1

description: Library name: LUH-GFP FIS 0DAI Input rep1


title: CD34, day 13, don003, rep1

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep1


title: high salt night fed ZT20 rep1


title: LUH-GFP FIS inflorescences, 0 days after DEX induction, ChIP, replicate 2

description: Library name: LUH-GFP FIS 0DAI ChIP rep2


title: LUH-GFP FIS inflorescences, 0 days after DEX induction, ChIP, replicate 1

description: Library name: LUH-GFP FIS 0DAI ChIP rep1


title: fetal tissue_037

description: Hybridized to CytoScan786K Array

value: 22 weeks


title: high salt night fed ZT16 rep3


title: CD34, day 13, don002, rep6

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep6


title: high salt night fed ZT16 rep2


title: LUH-GFP FIS inflorescences, 2 days after DEX induction, ChIP, replicate 1

description: Library name: LUH-GFP FIS 2DAI ChIP rep1


title: WT_toti

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

institute: southwest medical university

description:
Library name: WT_toti
10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

growth_protocol: Cells were induced using a modified two-step protocol from primed hPSCs to 8CLCs

extract_protocol:
4CL and me4CL cells were lysed and the released RNA was barcoded through reverse transcription in individual gel beads in emulsion (GEMs). Reverse transcription was performed on a S1000 Touch Thermal Cycler (Bio-Rad) at 53 °C for 45 min, followed by 85 °C for 5 min, and then held at 4 °C. The cDNA was generated and then amplified, and quality-assessed using the Agilent 4200 system.
According to the manufacturer’s instructions, scRNA-seq libraries were constructed using the Single Cell 3′ Library and Gel Bead Kit V3.1.


title: fetal tissue_036

description: Hybridized to CytoScan785K Array


title: fetal tissue_035

description: Hybridized to CytoScan784K Array


title: CD34, day 13, don002, rep4

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep4


title: WT_4cl

description:
Library name: WT_4cl
10X Genomics


title: CD34, day 13, don003, rep3

description: Library name: Erythroid_day_13_CD34+_don003_ATAC-seq_rep3


title: high salt night fed ZT16 rep1


title: CD34, day 13, don002, rep5

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep5


title: high salt night fed ZT12 rep3


title: fetal tissue_034

description: Hybridized to CytoScan783K Array


title: CD34, day 13, don002, rep3

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep3


title: fetal tissue_033

description: Hybridized to CytoScan782K Array


title: high salt night fed ZT20 rep2


title: high salt night fed ZT12 rep2


title: KO_4cl

description:
Library name: KO_4cl
10X Genomics


title: KO_toti

description:
Library name: KO_toti
10X Genomics


title: CD34, day 13, don002, rep2

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep2


title: high salt night fed ZT12 rep1


title: fetal tissue_032

description: Hybridized to CytoScan781K Array


title: 184D, p16sh, YAP1, MYC, p21, BioRep3, Rep 3

city: Duarte

first: Tara

last: Fresques

state: CA

address: 1500 East Duarte Rd.

department: Beckman Research Institute

institute: City of Hope

description: Library name: Sample 41

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 with the single read mode of 51 cycles. Real-time analysis 2.2.38 software was used to process the image analysis. RNA-seq reads were trimmed to remove sequencing adapters using Trimmomatic45. The processed reads were mapped back to the human genome (hg19) using TOPHAT2 software46. HTSeq47 and RSeQC48 software packages were applied to generate the count matrices and strand information, respectively, using default parameters.
Assembly: HG19
Supplementary files format and content: Tab delimited text includes raw counts for each sample

source_name: Mammary epithelial

extract_protocol:
A Quick-RNA Miniprep kit (Zymo Research) was used to extract RNA for gene expression analyses.
A Kappa mRNA-Seq Kit (Roche) was used for library preparations.

value: Mammary epithelial

tag: specimen

value: Specimen 184D

tag: Stage

value: Non-clonal Immortal

tag: transductions

value: p16sh, YAP1, MYC

tag: passage

value: passage 21


title: 184D, p16sh, YAP1, MYC, p21, BioRep3, Rep 2

description: Library name: Sample 40

tag: batch


title: fetal tissue_038

description: Hybridized to CytoScan787K Array

tag: gestational age


title: CD34, day 13, don002, rep1

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep1


title: LUH-GFP FIS inflorescences, 2 days after DEX induction, Input, replicate 1

description: Library name: LUH-GFP FIS 2DAI Input rep1

value: pLUH:LUH-GFP pAP1:AP1-GR ap1 cal


title: high salt night fed ZT8 rep3


title: 184D, p16sh, YAP1, MYC, p21, BioRep3, Rep 1

description: Library name: Sample 39


title: fetal tissue_030

description: Hybridized to CytoScan779K Array


title: high salt night fed ZT8 rep1


title: fetal tissue_029

description: Hybridized to CytoScan778K Array


title: HIV-1 infected 5F9, Rep 2, poly(A) depleted, rRNA depleted, mock digested

city: New Haven

first: Grace

last: Chen

state: CT

address: 300 Cedar Street

institute: Yale School of Medicine

description: poly(A) depleted and rRNA depleted and mock digested

data_processing:
Raw FASTQ files derived from the same library were merged across sequencing lanes and both runs. The FASTQ files uploaded unto GEO represent these merged files before any further processing. After merging, the FASTQ files were were pre-processed using Trimmomatic (v0.39) to remove sequencing adapters (TruSeq3-SE.fa) and reads with low quality sequence. The resultant FASTQ files were used an input for the CIRCexplorer3/CLEAR pipeline (CIRCexplorer v2.3.8, Stringtie-2.1.4, Tophat-2.1.0, HISAT2 v2.1.0), which returns both raw and normalized read counts for circular and linear human transcripts. Viral circRNA expression was examined using the de novo circRNA prediction tool CIRI2 (BWA v0.7.17, CIRI2 v2.0.6) using the same input files. All pipelines were executed according to package instructions using mostly default parameters (additional detail and scripts available upon request). To facilitate simultaneous prediction of host and virally-encoded circRNAs, all alignments were performed to a concatenated reference genome consisting of the pNL4-3-d6-dsEGFP plasmid sequence appended as an extra chromosome to the UCSC hg38 reference genome. Likewise, a mixed genome annotation file was supplied consisting of the UCSC hg38 refGene GTF concatenated to a custom-generated viral GTF of the HIV-1 genome (available upon request).
Assembly: hg38
Supplementary files format and content: (Sample)_CE3_quant.txt; tab-delimited text file of raw and normalized read counts for circRNAs and linear RNAs obtained using CIRCexplorer3 pipeline.
Supplementary files format and content: (Sample)_CIRI2.txt; tab-delimited text file of raw read counts for circRNAs obtained using CIRI2  pipeline.

source_name: Jurkat

growth_protocol: Jurkat, 8B10, and 5F9 T-cell lines were maintained in RPMI media supplemented with 10% fetal bovine serum (FBS) in a humid tissue culture chamber at 37C, 5% CO2.

extract_protocol:
Jurkat, 8B10, and 5F9 cells were lysed with TriZol (Thermo Fisher) and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research). The poly(A)-enriched RNA fraction was then isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, and the remaining poly(A)-depleted fraction was further processed using the NEBNext® rRNA Depletion Kit. The resulting poly(A)-depleted and rRNA-depleted RNA was treated with RNase R (or mock-treated with water instead of enzyme) under the following conditions: 1 unit RNase R enzyme (Lucigen) per microgram input RNA in a 20-50 µL reaction volume supplemented with 10X potassium chloride RNase R reaction buffer (Lucigen) incubated at 37°C for 2 hours. RNA was then purified from the digestion reaction using RNAClean XP magnetic beads (Beckman Coulter) and yields were quantified by Qubit.
30 ng of RNA was used for preparation of each library using the NEBNext® Ultra™ II Directional RNA Library Prep Kit, following manufacturer's instructions. Libraries were indexed using the NEBNext Universal PCR Primer for Illumina and unique indices selected from the NEBNext Multiplex Oligos for Illumina (Index Primer Set 1 and 2).
Libraries were pooled and subjected to bulk RNA-sequencing on a NextSeq 500 platform using single-end 150 nt long reads, with a targeted depth of 15-20 million reads per poly(A)-enriched library and 50-60 million reads per rRNA-depleted library. The pooled library was sequenced twice to acheive the desired depth.

treatment_protocol: The 8B10 and 5F9 are stable clones generated by transduction of Jurkat T-cells with a single-round HIV-1 reporter virus (NL4-3-d6-dsEGFP) followed by sorting and expansion of single-cell clones. This reporter virus is a modified variant of the wild-type HIV-1 NL4-3 genome that expresses destabilized EGFP (dsEGFP) in place of the envelope protein. Furthermore, it contains loss-of-function mutations in the genes for all viral proteins except Tat and Rev, which allows for continuous transcription, splicing, and cytoplasmic export of all viral RNAs while still allowing the infected cell to propagate.

tag: cell line

value: Jurkat

value: CD4+ T lymphocyte

value: HIV-1 infected


title: fetal tissue_031

description: Hybridized to CytoScan780K Array


title: high salt night fed ZT8 rep2

value: Colon


title: HIV-1 infected 5F9, Rep 2, poly(A) depleted, rRNA depleted, RNase R digested

description: poly(A) depleted and rRNA depleted and digested with RNase R


title: 184D, p16sh, YAP1, MYC, p15, BioRep3, Rep 2

description: Library name: Sample 37

value: passage 15


title: 184D, p16sh, YAP1, MYC, p15, BioRep3, Rep 3

description: Library name: Sample 38


title: fetal tissue_028

description: Hybridized to CytoScan777K Array


title: high salt night fed ZT4 rep3


title: high salt night fed ZT4 rep2


title: HIV-1 infected 5F9, Rep 1, poly(A) depleted, rRNA depleted, RNase R digested


title: fetal tissue_027

description: Hybridized to CytoScan776K Array


title: HIV-1 infected 5F9, Rep 2, poly(A) enriched

description: poly(A) enriched


title: HIV-1 infected 5F9, Rep 1, poly(A) depleted, rRNA depleted, mock digested


title: fetal tissue_026

description: Hybridized to CytoScan775K Array


title: 184D, p16sh, YAP1, MYC, p15, BioRep3, Rep 1

description: Library name: Sample 36


title: 184D, p16sh, Ctrl, MYC, p21, BioRep3, Rep 3

description: Library name: Sample 35

value: p16sh, Ctrl, MYC


title: HIV-1 infected 5F9, Rep 1, poly(A) enriched

description: poly(A) enriched


title: high salt night fed ZT0 rep3


title: fetal tissue_025

description: Hybridized to CytoScan774K Array

value: 14 weeks


title: high salt night fed ZT0 rep2


title: HIV-1 infected 8B10, Rep 2, poly(A) depleted, rRNA depleted, RNase R digested


title: 184D, p16sh, Ctrl, MYC, p21, BioRep3, Rep 2

description: Library name: Sample 34


title: 184D, p16sh, Ctrl, MYC, p21, BioRep3, Rep 1

description: Library name: Sample 33


title: fetal tissue_024

description: Hybridized to CytoScan773K Array

value: 18 weeks


title: high salt night fed ZT0 rep1

value: high salt night fed


title: fetal tissue_023

description: Hybridized to CytoScan772K Array


title: HIV-1 infected 8B10, Rep 2, poly(A) depleted, rRNA depleted, mock digested


title: 184D, p16sh, Ctrl, MYC, p15, BioRep3, Rep 3

description: Library name: Sample 32


title: high salt day fed ZT20 rep3

value: high salt day fed


title: HIV-1 infected 8B10, Rep 2, poly(A) enriched

description: poly(A) enriched


title: fetal tissue_022

description: Hybridized to CytoScan771K Array


title: 184D, p16sh, Ctrl, MYC, p15, BioRep3, Rep 2

description: Library name: Sample 31


title: high salt night fed ZT4 rep1


title: fetal tissue_021

description: Hybridized to CytoScan770K Array


title: HIV-1 infected 8B10, Rep 1, poly(A) depleted, rRNA depleted, mock digested


title: high salt day fed ZT20 rep1


title: fetal tissue_020

description: Hybridized to CytoScan769K Array


title: 184D, p16sh, Ctrl, MYC, p15, BioRep3, Rep 1

description: Library name: Sample 30


title: 184D, p16sh, YAP1, p24, BioRep3, Rep 3

description: Library name: Sample 29

value: Clonal Immortal

value: p16sh, YAP1

value: passage 24


title: fetal tissue_019

description: Hybridized to CytoScan768K Array


title: high salt day fed ZT16 rep3


title: Uninfected, Rep 2, poly(A) depleted, rRNA depleted, RNase R digested

value: WT


title: 184D, p16sh, YAP1, p24, BioRep3, Rep 2

description: Library name: Sample 28

value: Mammary epithelial

value: Specimen 184D


title: high salt day fed ZT16 rep2


title: fetal tissue_018

description: Hybridized to CytoScan767K Array


title: HIV-1 infected 8B10, Rep 1, poly(A) enriched

description: poly(A) enriched


title: Uninfected, Rep 2, poly(A) depleted, rRNA depleted, mock digested


title: high salt day fed ZT16 rep1


title: 184D, p16sh, YAP1, p24, BioRep3, Rep 1

description: Library name: Sample 27


title: 184D, p16sh, YAP1, p20, BioRep3, Rep 3

description: Library name: Sample 26

value: passage 20


title: fetal tissue_017

description: Hybridized to CytoScan766K Array


title: high salt day fed ZT20 rep2


title: fetal tissue_016

description: Hybridized to CytoScan765K Array


title: HIV-1 infected 8B10, Rep 1, poly(A) depleted, rRNA depleted, RNase R digested

value: Jurkat


title: 184D, p16sh, YAP1, p20, BioRep3, Rep 2

description: Library name: Sample 25


title: Uninfected, Rep 2, poly(A) enriched

description: poly(A) enriched

value: CD4+ T lymphocyte


title: Uninfected, Rep 1, poly(A) depleted, rRNA depleted, RNase R digested


title: high salt day fed ZT12 rep2


title: fetal tissue_015

description: Hybridized to CytoScan764K Array

value: 16 weeks


title: 184D, p16sh, YAP1, p20, BioRep3, Rep 1

description: Library name: Sample 24


title: Uninfected, Rep 1, poly(A) depleted, rRNA depleted, mock digested


title: fetal tissue_014

description: Hybridized to CytoScan763K Array


title: high salt day fed ZT8 rep3

value: Colon


title: Uninfected, Rep 1, poly(A) enriched

description: poly(A) enriched


title: high salt day fed ZT12 rep1


title: 184D, p16sh, YAP1, p18, BioRep3, Rep 3

description: Library name: Sample 23

value: Mixed

value: passage 18


title: 184D, p16sh, YAP1, p18, BioRep3, Rep 2

description: Library name: Sample 22


title: fetal tissue_013

description: Hybridized to CytoScan762K Array

value: 14 weeks


title: 184D, p16sh, YAP1, p18, BioRep3, Rep 1

description: Library name: Sample 21


title: Ebf1+/-Pax5+/-, Op9DL1_24h, ATAC-seq, rep1

city: Linköping

first: Mikael

last: Sigvardsson

address: Lab1, Level 13

department: Department of Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description:
Library name: ATACseq_TH_BM_proB_Op9DL1_24h_rep1
ATAC_TH_BM_proB_Op9DL1_24h_pooled.bw
TH_proB_Op9DL1_24h_idr.optimal_peak.narrowPeak.gz

data_processing:
ATAC-seq data was preprocessed with ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) (v.2.2.1). For paired-end data from WT and Ebf1+/-Pax5+/- proB cells, the pipeline was run with the following argument: "atac.paired_end":true, "atac.auto_detect_adapter": true, "atac.multimapping": 4, "atac.mapq_thresh": 30, "atac.dup_marker": "picard", "atac.no_dup_removal": false, "atac.enable_idr": true, "atac.idr_thresh": 0.05, "atac.enable_count_signal_track": true, "atac.filter_chrs": ["chrM", "MT"].  Single-end data from transduced Ebf1-/- and Pax5-/- cells were analyzed as above with the exeption of: "atac.paired_end": false, "atac.no_dup_removal": false.
Assembly: mm10
Supplementary files format and content: bigWig, IDR peaks (except Input)

source_name: BM proB

growth_protocol: Up to 50.000 WT and Ebf1+/-Pax5+/- proB cells were ex vivo sorted for omni-ATAC-seq. From the same mice, proB cells were sorted for expansion in Op9 co-cultures for 8 days in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum , 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT-ligand, 10ng/ml FLT3-ligand and 10ng/ml IL-7.

extract_protocol:
Sorted cells are spun down (500xg, 4 °C, 5 min) and washed in 50 µl cold ATAC-RSB (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2), followed by 3 min incubation on ice in ATAC-RSB supplemented with 0.1% NP40, 0.1 % Tween-20 and 0.01 % digitonin. 1 ml ATAC-RSB containing 0.1 % Tween-20 only was added and the samples were spun down at 500xg, 4°C for 10 min. Supernatants were discarded and the nuclei were resuspended in transposition reaction mix (25 µl Tagment DNA buffer (Illumina, 15028212), 2.5 µl Tagment DNA enzyme (Illumna, 15028212), 16.5 µl PBS, 0.001 % Digitonin, 0.1 % Tween-20, and Nuclease free H20 waster up to 50µl) and the tagmentation reactions were run by incubating the samples at 37 °C for 30 min. Samples were purified using ChIP clean and Concentrator kit (Zymo Research, D5205) and eluted in 10 µl elution buffer.
To each sample, 25 µl NEBNext Ultra II Q5 Master mix (New England Biolabs, M0544L), 3 µl 10x SYBR green (Invitrogen, S-7563), 6.25 µl 10 µM Nextera primer 1 (no barcode) as well as 6.25 µl of 10 µM Nextera primer 2 (barcode) unique for each sample. The transposed elements were amplified by running the following thermo-cycler program: 72 °C 5min, 98 °C 30 s, N x (98 °C 10 s, 63 °C 30 s, 72°C 30 s). N are defined as the number of cycles that correspond to ¼ of max intensity and was determined by running 5 µl of sample after 5 rounds of amplification on q-PCR. Amplified libraries were purified with Ampure XP (1.2 x sample volume) and quality control were performed with using Qubit® dsDNA HS Assay Kit & assay tubes (ThermoFisher Scientific, Q32854/Q32856) and High Sensitivity DNA Kit (Agilent, 5067-4626). Omni-ATAC-seq libraries were subjected to 2x38 cycles of paired-end sequencing on a Nextseq500 (Illumina) using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906).

treatment_protocol: 1*106 expanded proB cells per sample were transferred to 6-well plates pre-coated with 75.000 Op9 or Op9DL1 stromal cells the previous day. Cells were briefly spun down (300xg, for 1 min) and incubated at 37 °C for 24h. 50.000 CD45+ cells were sorted for ATAC-seq.

value: BM proB

value: Op9DL1 24h


title: high salt day fed ZT8 rep1

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

extract_protocol:
Total RNA was extracted from the colon with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

value: high salt day fed


title: 184D, p16sh, YAP1, p17, BioRep3, Rep 3

description: Library name: Sample 20

value: passage 17


title: fetal tissue_011

description: Hybridized to CytoScan760K Array


title: fetal tissue_012

description: Hybridized to CytoScan761K Array


title: WT, Op9DL1_24h, ATAC-seq, rep2

description:
Library name: ATACseq_WT_BM_proB_Op9DL1_24h_rep2
ATAC_WT_BM_proB_Op9DL1_24h_pooled.bw
WT_proB_Op9DL1_24h_idr.optimal_peak.narrowPeak.gz


title: 184D, p16sh, YAP1, p17, BioRep3, Rep 2

description: Library name: Sample 19

value: p16sh, YAP1


title: fetal tissue_010

description: Hybridized to CytoScan759K Array


title: high salt day fed ZT4 rep2


title: WT, Op9DL1_24h, ATAC-seq, rep1

description:
Library name: ATACseq_WT_BM_proB_Op9DL1_24h_rep1
ATAC_WT_BM_proB_Op9DL1_24h_pooled.bw
WT_proB_Op9DL1_24h_idr.optimal_peak.narrowPeak.gz


title: 184D, p16sh, YAP1, p17, BioRep3, Rep 1

description: Library name: Sample 18


title: fetal tissue_009

description: Hybridized to CytoScan758K Array


title: high salt day fed ZT12 rep3


title: high salt day fed ZT4 rep3


title: fetal tissue_008

description: Hybridized to CytoScan757K Array


title: 184D, p16sh, YAP1, p12, BioRep3, Rep 3

description: Library name: Sample 17

value: Post-stasis

value: passage 12


title: Ebf1+/-Pax5+/-, Op9, ATAC-seq, rep2

description:
Library name: ATACseq_TH_BM_proB_Op9_rep2
ATAC_TH_BM_proB_Op9_pooled.bw
TH_proB_Op9_idr.optimal_peak.narrowPeak.gz

value: Op9 24h


title: fetal tissue_007

description: Hybridized to CytoScan756K Array


title: Ebf1+/-Pax5+/-, Op9, ATAC-seq, rep1

description:
Library name: ATACseq_TH_BM_proB_Op9_rep1
ATAC_TH_BM_proB_Op9_pooled.bw
TH_proB_Op9_idr.optimal_peak.narrowPeak.gz


title: 184D, p16sh, YAP1, p12, BioRep3, Rep 2

description: Library name: Sample 16

value: Mammary epithelial

value: Specimen 184D


title: high salt day fed ZT4 rep1


title: high salt day fed ZT0 rep2


title: Ebf1+/-Pax5+/-, Op9DL1_24h, ATAC-seq, rep2

description:
Library name: ATACseq_TH_BM_proB_Op9DL1_24h_rep2
ATAC_TH_BM_proB_Op9DL1_24h_pooled.bw
TH_proB_Op9DL1_24h_idr.optimal_peak.narrowPeak.gz


title: high salt day fed ZT8 rep2


title: WT, Op9, ATAC-seq, rep2

description:
Library name: ATACseq_WT_BM_proB_Op9_rep2
ATAC_WT_BM_proB_Op9_pooled.bw
WT_proB_Op9_idr.optimal_peak.narrowPeak.gz

value: WT


title: high salt day fed ZT0 rep3


title: fetal tissue_006

description: Hybridized to CytoScan755K Array


title: WT, Op9, ATAC-seq, rep1

description:
Library name: ATACseq_WT_BM_proB_Op9_rep1
ATAC_WT_BM_proB_Op9_pooled.bw
WT_proB_Op9_idr.optimal_peak.narrowPeak.gz


title: 184D, p16sh, YAP1, p12, BioRep3, Rep 1

description: Library name: Sample 15


title: high salt day fed ZT0 rep1


title: CD34, day 13, don002, rep7

description: Library name: Erythroid_day_13_CD34+_don002_ATAC-seq_rep7

value: Erythroid

value: CD34+ human erythroid

value: Day 13

value: CD34 microbead, Miltenyi Biotec #130-046-702


title: Ebf1+/-Pax5+/-, exvivo, ATAC-seq, rep1

description:
Library name: ATACseq_TH_BM_proB_exvivo_rep1
ATAC_TH_BM_proB_exvivo_pooled.bw
TH_proB_exvivo_idr.optimal_peak.narrowPeak.gz

value: exvivo


title: fetal tissue_003

description: Hybridized to CytoScan752K Array

value: 14 weeks


title: WT, exvivo, ATAC-seq, rep2

description:
Library name: ATACseq_WT_BM_proB_exvivo_rep2
ATAC_WT_BM_proB_exvivo_pooled.bw
WT_proB_exvivo_idr.optimal_peak.narrowPeak.gz

value: BM proB


title: 184D, p16sh, Ctrl, p12, BioRep3, Rep 3

description: Library name: Sample 11

value: p16sh, Ctrl


title: Ebf1+/-Pax5+/-, exvivo, ATAC-seq, rep2

description:
Library name: ATACseq_TH_BM_proB_exvivo_rep2
ATAC_TH_BM_proB_exvivo_pooled.bw
TH_proB_exvivo_idr.optimal_peak.narrowPeak.gz


title: fetal tissue_005

description: Hybridized to CytoScan754K Array


title: fetal tissue_001

description: Hybridized to CytoScan750K Array


title: low salt day fed ZT20 rep2

value: Colon

value: low salt day fed


title: fetal tissue_004

description: Hybridized to CytoScan753K Array


title: low salt day fed ZT16 rep3


title: Pax5KO, Ebf1, ATAC-seq, rep2

description:
Library name: ATACseq_Pax5KO_Ebf1_rep2
ATAC_Pax5KO_Ebf1_pooled.bw
Pax5KO_Ebf1_idr_optimal_peak.narrowPeak.gz

source_name: FL B cell progenitor

value: FL B cell progenitor


title: low salt day fed ZT20 rep3


title: 184D, p16sh, Ctrl, p17, BioRep3, Rep 2

description: Library name: Sample 13

value: Post-stasis

value: passage 17


title: low salt day fed ZT16 rep1


title: 184D, p16sh, Ctrl, p12, BioRep3, Rep 2

description: Library name: Sample 10

value: passage 12


title: Pax5KO, Ebf1, ATAC-seq, rep1

description:
Library name: ATACseq_Pax5KO_Ebf1_rep1
ATAC_Pax5KO_Ebf1_pooled.bw
Pax5KO_Ebf1_idr_optimal_peak.narrowPeak.gz


title: 240LB, p16sh, YAP1, p22, BioRep2

description: Library name: Sample 8

value: Mammary epithelial

value: Specimen 240LB

value: Clonal Immortal

value: p16sh, YAP1

value: passage 22


title: low salt day fed ZT12 rep3


title: 184D, p16sh, Ctrl, p17, BioRep3, Rep 3

description: Library name: Sample 14

value: Specimen 184D


title: 240LB, p16sh, YAP1, p16, BioRep2

description: Library name: Sample 7

value: passage 16


title: fetal tissue_002

description: Hybridized to CytoScan751K Array


title: low salt day fed ZT20 rep1


title: low salt day fed ZT16 rep2


title: Pax5KO, Ctrl, ATAC-seq, rep1

description:
Library name: ATACseq_Pax5KO_Ctrl_rep1
ATAC_Pax5KO_Ctrl_pooled.bw
Pax5KO_Ctrl_idr_optimal_peak.narrowPeak.gz

value: Ctrl


title: low salt day fed ZT12 rep1


title: 240LB, p16sh, Ctrl, p12, BioRep2

description: Library name: Sample 5


title: WT, exvivo, ATAC-seq, rep1

description:
Library name: ATACseq_WT_BM_proB_exvivo_rep1
ATAC_WT_BM_proB_exvivo_pooled.bw
WT_proB_exvivo_idr.optimal_peak.narrowPeak.gz

value: WT

value: exvivo


title: Ebf1KO, Ctrl, ATAC-seq, rep2

description:
Library name: ATACseq_Ebf1KO_Ctrl_rep2
ATAC_Ebf1KO_Ctrl_pooled.bw
Ebf1KO_Ctrl_idr_optimal_peak.narrowPeak.gz


title: Ebf1KO, Ctrl, ATAC-seq, rep1

description:
Library name: ATACseq_Ebf1KO_Ctrl_rep1
ATAC_Ebf1KO_Ctrl_pooled.bw
Ebf1KO_Ctrl_idr_optimal_peak.narrowPeak.gz


title: KOAZ2

city: St Lucia

first: Steven

last: Zuryn

state: QLD

address: The University of Queensland

country: Australia

institute: Queensland Brain Institute

description:
Library name: Sample 11
no71AZ-2

data_processing:
pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data
clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05
Assembly: WBcel235
Supplementary files format and content: csv. file contains fpkm for all samples

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Synchronised C. elegans were attained by egg pulse

extract_protocol:
Standard TRIzol extraction protocol following washing of animals. Sequencing library preparation, sequencing and data analysis were carried out commercially by Azenta
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrosegel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: NGM plates with OP50 lawns were treated with water or sodium azide

value: whole body

value: sodium azide


title: low salt day fed ZT12 rep2

value: Colon

value: low salt day fed


title: 240LB, p16sh, YAP1, p25, BioRep1

description: Library name: Sample 4

value: passage 25


title: KOAZ1

description:
Library name: Sample 10
no71AZ-1


title: Ebf1+/-Pax5+/-_BM_proB, Input, rep2

description:
Library name: ChIPmentation_TH_BM_proB_Input_rep2
TH_Input_merge.bw

data_processing:
*library strategy: ChIPmentation
ChIPmentation data was trimmed with TrimGalore (v0.6.7) using the following options: --paired --gzip --fastqc --clip_R1 5 --clip_R2 5 --three_prime_clip_R1 3 --three_prime_clip_R2 3. The trimmed reads were aligned against the mm10 reference genome (GRCm38.p5) with bowtie2 (v 2.4.4) with options: -X 1000 --dovetail --no-mixed. Picards MarkDuplicates (2.26.10) was used to filter out duplicates. Peak-calling and generation of pooled bigwigs for genome browser visualization was performed with a custom pipeline (https://github.com/Tingvall/macs2_idr). Peak were called against input control using macs2 (v2.2.7.1) in narrow mode for H3K4me3/H3K27ac and broad mode for H3K27me3 with the following options: --genome size 2652783500, --macs_q 0.05 -- idr_threshold 0.05. IDR optimal set was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigWig, IDR peaks (except Input)

growth_protocol: BM cells from two individual mice of WT and Ebf1+/-Pax5+/- mice were c-Kit enriched and expanded on Op9 stromal cells for 13-15 days in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT-ligand, 10ng/ml FLT3-ligand, and 10ng/ml IL-7. Phenotypic analysis by flow cytometry confirmed that >95% of the cells were CD19+.

extract_protocol:
Cells were cross-linked at RT in 1 % formaldehyde for 10 min, followed by quenching in 1/10 volume of 0.125 M glycine. Nuclei were isolated by incubation with Nuclei isolation buffer (50 mM Tris pH 8.0, 60 mM KCL, 0.5 % NP40) + protease inhibitor cocktail (PIC) for 10 min. Pelleted nuclei were dissolved in Lysis buffer (0.5 % SDS, 10 mM EDTA, 50 mM Tris-HCL pH 8) + PIC and sonicated (30 s max intensity, 30 s rest) for 18 min a Bioruptor Plus (Diagenode). Sonicated samples were diluted 5x with Dilution buffer (1 % Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8) + PIC. 1% input controls were collected for each replicate and MgCl2 to a final concentration of 10 mM was added to inactivate EDTA before tagmentation. 1 µg of each antibody was hybridized to 60 µl Dynabeads™ Protein A (Invitrogen, 10002D) per 1*107 cells by incubation in PBS/0.5%BSA at 4°C on a rotating platorm for 4-6h. Antibody-beads complex was added to the sonicated samples and chromatin immunoprecipitation (ChIP) was performed with 10M cells per sample over night at 4 °C with rotation. Immunoprecipitated bead-cound chromatin was washed 1 x Wash buffer I (50 mM Tris-HCl pH 8, 150 mM NaCl, 0.1 % SDS, 0.1 % NaDOC, 1 % Triton X-100, 1 mM EDTA), 1 x in Wash buffer II (50 mM Tris-HCl pH 8, 500 mM NaCl, 0.1 % SDS, 0.1 % NaDOC, 1 % Triton X-100, 1 mM EDTA) 1x in Wash buffer III (10 mM Tris-HCl pH 8, 250 mM LiCl, 0.5 % NP-40, 0.5 % NaDOC, 1 mM EDTA), 2 x in TE buffer (10 mM Tris-HCÖ pH 8, 1 mM EDTA) and finally 2 x in 10 mM Tris-Hcl pH 8. Tagmentation was performed by incubating input control and bead-bound chromatin in 30 µl Tagment DNA buffer + 1 µl Tagment DNA enzyme (Illumina, 20034197) followed by incubated at 37 °C for 10 min. EDTA was added to a final concertation of 1 mM and samples were washed 3 x in Wash buffer I and 2 x in TE buffer. Immunoprecipitated chromatin was eluted by incubation in 200 µl ChIPmentation elution buffer (10 mM Tris-HlL pH 8, 5 mM EDTA, 300 mM NaCl, 0.4 % SDS) + 50 µg proteinase K at 55 °C for 1h followed by 65 °C over night. Eluded DNA was extracted by magnetization (supernatant) and purified and with ChIP clean and Concentrator kit (Zymo Research, D5205).
Simultaneous attachment of Nextera dual index and library amplification with NEBNext Ultra II Q5 Master mix (New England Biolabs, M0544L) was run with the following cycling conditions: 72 °C 5 min, 98 °C 5min, (98 °C 10s, 55°C 30s, 72°C 30s) x N rounds, 72 °C 1 min. N is defined as number of cycles required to each 1/4 of max (determined by running 1/6 of eluted sample on qPCR). Libraries clean up and size selection (0.6x/0.9x sample volume for right and left sided selection). Library concertation and quality control was performed with Qubit (ThermoFisher Scientific) using Qubit® dsDNA HS Assay Kit & assay tubes (ThermoFisher Scientific, Q32854/Q32856) and High Sensitivity DNA Kit (Agilent, 5067-4626). ChIPmentation libraries were subject to 2x38 cycles of paired-end sequencing on a Nextseq500 (Illumina) using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906).

value: BM proB

tag: chip antibody


title: 184D, p16sh, Ctrl, p17, BioRep3, Rep 1

description: Library name: Sample 12

value: Post-stasis

value: p16sh, Ctrl

value: passage 17


title: KOcontrol2

description:
Library name: Sample 8
no71-2

value: water


title: low salt day fed ZT8 rep3


title: KOcontrol3

description:
Library name: Sample 9
no71-3


title: KOAZ3

description:
Library name: Sample 12
no71AZ-3


title: Ebf1+/-Pax5+/-_BM_proB, Input, rep1

description:
Library name: ChIPmentation_TH_BM_proB_Input_rep1
TH_Input_merge.bw


title: 240LB, p16sh, YAP1, p18, BioRep1

description: Library name: Sample 3

value: Mammary epithelial

value: Specimen 240LB

value: Clonal Immortal

value: p16sh, YAP1

value: passage 18


title: low salt day fed ZT8 rep2


title: WT_BM_proB, Input, rep2

description:
Library name: ChIPmentation_WT_BM_proB_Input_rep2
WT_Input_merge.bw

value: WT


title: KOcontrol1

description:
Library name: Sample 7
no71-1


title: low salt day fed ZT8 rep1


title: 240LB, p16sh, YAP1_p12, BioRep2

description: Library name: Sample 6

value: passage 12


title: low salt day fed ZT4 rep3


title: 240LB, p16sh, p11, BioRep1

description: Library name: Sample 1

value: passage 11


title: low salt day fed ZT4 rep2


title: 240LB, p16sh, YAP1_p12, BioRep1

description: Library name: Sample 2


title: SSCZ064(patient2) hiPSCs derived Cortical neurons maintained for 120 days

city: Mumbai

first: Dhanjit

middle: Kumar

last: Das

state: Maharashtra

address: JM Street

department: Stem Cell Biology

country: India

institute: ICMR-NIRRCH

description:
Library name: SSCZ064
SSCZ064

data_processing:
Raw reads were analyzed with FastQC and reads were trimmed with Cutadapt for producing high quality reads.The quality was then analyzed using FastQC
Trimmed sequence reads were mapped wih reference genome (hg38) using HISAT2. Further the expression of the genes were counted by using HTSeq.
DGE analysis was carried out using edgeR. The read counts were normalized in edgeR based on TMM normalization. For further analysis CPM transformed values of TMM normalized factors were used.
The up and down regulated genes were identified based on their logFC values. A gene is considered up-regulated when the p-value<0.05 and logFC>1 whereas for downregulated the p-value<0.05 and logFC<-1.
Further GO analysis was done and pathwat analysis was performed using KEGG. The enriched pathway was plotted using ShinyGo.
Assembly: hg38
Supplementary files format and content: Microsoft Excel format contain logFC, LogCPM, P value and FDR

source_name: hipSCs-derived cortical neurons

growth_protocol: hiPSCs were generated from PBMCs using CytoTune Sendai Virus kit (Invitrogen),The generated hiPSCs were then differentiated into cortical neurons using Dual SMAD inhibition protocol. The generated neurons were maintained in Neuronal Maintainence Medium (1X N2, 1X B27 with vitamin A, 10 ng/ml  BDNF, 10 ng/ml GDNF , 10 ng/ml IGF1, 50 µg/ml Ascorbic acid, 1X GlutaMAX, 1X NEAA, 25ng/ml di-butyl c-AMP, DMEM/F12) maintained for 120 days in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRiZol method.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, MA, USA) at M/s BioXplore Labs, India.

value: hipSCs-derived cortical neurons

value: Matured cortical neurons

tag: Sex

value: Female

tag: disease state

value: Affected

value: 14th November 2021


title: Ebf1+/-Pax5+/-_BM_proB, H3K27me3, rep2

description:
Library name: ChIPmentation_TH_BM_proB_H3K27me3_rep2
TH_H3K27me3_merge.bw
TH_H3K27me3_optimal_set.IDR0.05.broadPeak.gz

value: BM proB


title: WT_BM_proB, Input, rep1

description:
Library name: ChIPmentation_WT_BM_proB_Input_rep1
WT_Input_merge.bw


title: low salt day fed ZT4 rep1

last: Changizi

address: Donald Bren Hall

institute: University of California, Irvine

value: Colon

value: low salt day fed


title: SCZ064(patient1) hiPSCs derived Cortical neurons maintained for 120 days

description:
Library name: SCZ064
SCZ064


title: WTAZ1

description:
Library name: Sample 4
N2AZ-1

value: whole body

value: sodium azide


title: low salt day fed ZT0 rep3


title: Control2 hiPSCs derived Cortical neurons maintained for 120 days

description:
Library name: Ctrl2
Ctrl2

value: Control


title: WTcontrol3

description:
Library name: Sample 3
N2-3

value: water


title: WT_BM_proB, H3K27me3, rep2

description:
Library name: ChIPmentation_WT_BM_proB_H3K27me3_rep2
WT_H3K27me3_merge.bw
WT_H3K27me3_optimal_set.IDR0.05.broadPeak.gz


title: WTcontrol2

description:
Library name: Sample 2
N2-2


title: SSCZ064

description: Copy Number Variation data from SCZ064 (Schizophrenia affected patient)

hyb_protocol: Following labelling, DNA were hybridized for 16hrs at 50C on GeneChip Human Cytogenetic array. GenneChips were washed and stained in the Affymetrix Fluidics Station450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: The data were analyzed with Chromosome Analysis Suite version 4.0 (r28959) using default analysis settings and global scaling as normalization method.NetAffix Build 33.2 (hg19) genomic annotation version was used.

label: biotin

source_name: Schizophrenia Patient DNA

label_protocol: DNA samples were labelled using DNA labelling reagent provided by Affymetrix according to the standard Affymetrix protocol.

extract_protocol: Genomic DNA was isolated using Qiamp DNA blood mini Kit (Qiagen) according to the manufaturer's instructions.

value: blood

tag: gender

tag: age

value: 16 yrs


title: low salt day fed ZT0 rep2

source_name: Colon


title: Control1 hiPSCs derived Cortical neurons maintained for 120 days

description:
Library name: M2iPSCs
M2iPSCs


title: Liver-38

description: Library name: Liver-38

value: M

value: Normal

value: Liver


title: WTAZ2

description:
Library name: Sample 5
N2AZ-2


title: WT_BM_proB, H3K27me3, rep1

description:
Library name: ChIPmentation_WT_BM_proB_H3K27me3_rep1
WT_H3K27me3_merge.bw
WT_H3K27me3_optimal_set.IDR0.05.broadPeak.gz

value: WT


title: Ebf1+/-Pax5+/-_BM_proB, H3K27me3, rep1

description:
Library name: ChIPmentation_TH_BM_proB_H3K27me3_rep1
TH_H3K27me3_merge.bw
TH_H3K27me3_optimal_set.IDR0.05.broadPeak.gz


title: WTAZ3

description:
Library name: Sample 6
N2AZ-3


title: 39-6-3

description: Library name: Sample 6

organism: Cryptococcus neoformans

value: strain

value: Cryptococcus neoformans var.grubii H99

value: dac6 (CNAG_05276) knock-out

value: grown at logarithmic phase in 100ml YPD broth at 39°C


title: low salt day fed ZT0 rep1


title: Ebf1+/-Pax5+/-_BM_proB, H3K27ac, rep2

description:
Library name: ChIPmentation_TH_BM_proB_H3K27ac_rep2
TH_H3K27ac_merge.bw
TH_H3K27ac_optimal_set.IDR0.05.narrowPeak.gz

value: BM proB

value: H3K27ac (Abcam, ab4729)


title: WTcontrol1

description:
Library name: Sample 1
N2-1


title: Small RNA-sequencing of CCL-125 cells infected with BZL mosquitoes

city: BOSTON

first: NELSON

middle: C

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: AeAeg_CCL125_BZL_sRNA

library_source: other

data_processing:
The Mosquioto Small RNA Genomics (MSRG)  pipeline published in PMIDs: 33419731 and 35796973. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt and Trimmomator. Total RNA reads were also further trimmed by length to 35 nt to be compatable for processing with the MSRG pipeline
Assembly: AaegL5
Supplementary files format and content: tab-delimited text file with Excel extension includes processed counts for each Sample for microRNA genes or protein-coding genes. csv files include RPM values for each Sample mapped to viruses

molecule: other

organism: Aedes aegypti

extract_protocol:
RNA was harvested using the NEB Monarch Total RNA extration kit.  0.5 to 1.0ug of total RNA was used for the construction of sequencing libraries.
Total RNA libraries for RNA-seq were prepared using Zymo RiboFree Zymo-Seq Library Prep Kit following manufacturer's protocols.  Small RNA libraries for microRNA-seq were prepared with the NEBNext Small RNA Library prep kit according to the manufacturer's protocols.

value: BZL mosquito virus-infected


title: WT_BM_proB, H3K27ac, rep2

description:
Library name: ChIPmentation_WT_BM_proB_H3K27ac_rep2
WT_H3K27ac_merge.bw
WT_H3K27ac_optimal_set.IDR0.05.narrowPeak.gz


title: low salt night fed ZT20 rep2

first: Kousha

value: Colon

value: low salt night fed


title: 39-6-1

description: Library name: Sample 4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Bowtie 2 suite (version 4.1.2)
Assembly: Cryptococcus neoformans var. grubii H99, Saccharomyces cerevisiae S288C
Supplementary files format and content: tab-delimited text files include reads values for each Sample

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the preparations of RNA sample.
Sequencing libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).


title: low salt night fed ZT20 rep3


title: Small RNA-sequencing of CCL-125 cells infected with AWK mosquitoes

description: Library name: AeAeg_CCL125_AWK_sRNA

value: AWK mosquito virus-infected


title: 30-6-3

description: Library name: Sample 3

value: grown at logarithmic phase in 100ml YPD broth at 30°C


title: WT_BM_proB, H3K27ac, rep1

description:
Library name: ChIPmentation_WT_BM_proB_H3K27ac_rep1
WT_H3K27ac_merge.bw
WT_H3K27ac_optimal_set.IDR0.05.narrowPeak.gz


title: 4_POU2F3IND-DOX

city: Charleston

first: Jorge

last: Munera

state: SC

address: 173 Ashley Avenue

institute: Medical University of South Carolina

description: Library name: 4_POU2F3IND-DOX

data_processing:
Raw sequencing data containing adapter sequences or low-quality reads were filtered to obtain valid, high-quality data. Data processing was performed using SOAPnuke, a tool developed by BGI, with the following filter parameters: -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 --minReadLen 100. The filtering process included several steps. First, reads were removed if 25.0% or more of the sequence matched an adapter, allowing a maximum of two mismatches. Second, reads shorter than 100 bp were discarded. Third, reads with N content accounting for 0.1% or more of the total sequence were removed. Fourth, reads containing a polyX sequence (A, T, G, or C) longer than 50 bp were discarded. Fifth, low-quality reads, where bases with a quality score below 20 comprised 40.0% or more of the sequence, were removed. Finally, clean reads were generated with quality values output in the Phred+33 format.
Assembly: hg38
Supplementary files format and content: TPM values for all samples are provided as a .csv file

source_name: colonoids

growth_protocol: Colonoids were grown in expansion media for 4 days. then switched to differentiation media contatining either vehicle (DMSO) or 1 μg/ml doxycycline (DOX) for 24 hours. Colonids were then switched to differentiation media.

extract_protocol:
RNA was extracted using NucleoSpin® RNA extraction kit (Macharey-Nagel) according to manufacturer's protocols.
Total RNA samples were first enriched for mRNA with poly-A tails using oligo dT beads. The enriched mRNA molecules were then fragmented into small pieces, which were subsequently used to synthesize first-strand cDNA with random primers. The second strand of cDNA was synthesized using dUTP in place of dTTP. The synthesized cDNA underwent end-repair and 3' adenylation, after which adaptors were ligated to the ends of the adenylated cDNA fragments. Following this, PCR amplification was performed, and the resulting library underwent quality control. The library was circularized and further amplified to produce DNA nanoballs (DNB), which were sequenced using the DNBSEQ platform.

treatment_protocol: Colonoids were then switched to differentiation media contatining either vehicle (DMSO) or 1 μg/ml doxycycline (DOX) for 24 hours. Colonids were then switched to differentiation media. Colonoids were grown for an additional 6 days for vehicle, 4 days for KLF4IND and POU2F3 colonoids +DOX and 6 days for NEUROG3-T2A-NKX6-3 +DOX.

value: colonoids

value: doxycyline

tag: time

value: 4 days post DOX pulse


title: low salt night fed ZT16 rep2

city: Irvine


title: low salt night fed ZT16 rep3


title: Ebf1+/-Pax5+/-_BM_proB, H3K4me3, rep2

description:
Library name: ChIPmentation_TH_BM_proB_H3K4me3_rep2
TH_H3K4me3_merge.bw
TH_H3K4me3_optimal_set.IDR0.05.narrowPeak.gz

tag: cell type


title: 39-6-2

description: Library name: Sample 5

tag: treatment


title: 30-6-1

description: Library name: Sample 1

tag: tissue


title: Ebf1+/-Pax5+/-_BM_proB, H3K27ac, rep1

description:
Library name: ChIPmentation_TH_BM_proB_H3K27ac_rep1
TH_H3K27ac_merge.bw
TH_H3K27ac_optimal_set.IDR0.05.narrowPeak.gz

tag: genotype


title: 30-6-2

description: Library name: Sample 2


title: Ebf1+/-Pax5+/-_BM_proB, H3K4me3, rep1

description:
Library name: ChIPmentation_TH_BM_proB_H3K4me3_rep1
TH_H3K4me3_merge.bw
TH_H3K4me3_optimal_set.IDR0.05.narrowPeak.gz


title: 3_POU2F3IND-DOX

description: Library name: 3_POU2F3IND-DOX


title: low salt night fed ZT20 rep1


title: low salt night fed ZT16 rep1


title: Small RNA-sequencing of CCL-125 cells uninfected

description: Library name: AeAeg_CCL125_Mock_sRNA

value: mock


title: 2_POU2F3IND-DOX

description: Library name: 2_POU2F3IND-DOX


title: EHT, atrial, WT/WT, rep 3

city: Vancouver

first: Kate

last: Huang

state: BC

address: 166-1081 Burrard Street

department: Department of Medicine - Centre for Heart Lung Innovation

country: Canada

institute: University of British Columbia

data_processing:
FASTQ files were aligned to the reference transcriptome with STAR version 2.6.0a.
Read counts were quantified with HTSEQ version 0.11.2.
Gene count normalization and differential expression were performed using DESEQ2 version 1.16.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts of samples (columns) by transcripts (rows).

source_name: iPSC-derived engineered heart tissue (3D)

growth_protocol: hiPSC-derived cardiomyocytes and engineered heart tissue constructs were cultured in RPMI 1640 with B27 supplement media and kept in an incubator at 37°C, 5% CO2.

extract_protocol:
Total RNA of hiPSC-CMs were extracted using the illustra RNAspin Mini Isolation Kit (GE Healthcare). Total RNA of engineered heart tissues were extracted using the Total RNA Purification Kit (Norgen Biotek). RNA integrity was assessed with the TapeStation 4200 (Agilent Technologies) and quantified with the Qubit RNA HS assay (Thermo Fisher Scientific).
200ng of total RNA was used as input for ribosomal RNA depletion using the MGIEasy rRNA Depletion Kit (MGI). Strand-specific libraries were prepared using the MGIEasy RNA Directional Library Prep Kit (MGI). Library quality and size were checked with the TapeStation 4200 D1000 Assay (Agilent Technologies) then quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific). Libraries were sequenced on a MGI DNB-G50 sequencer to generate approximately 40 million 100-bp paired-end reads per library.

value: Isogenic AF patient iPSCs

value: atrial-like

value: WT/WT


title: SCZ064

value: blood

value: Female

value: 18 yrs


title: WT_BM_proB, H3K4me3, rep2

description:
Library name: ChIPmentation_WT_BM_proB_H3K4me3_rep2
WT_H3K4me3_merge.bw
WT_H3K4me3_optimal_set.IDR0.05.narrowPeak.gz

value: BM proB

value: WT


title: low salt night fed ZT12 rep3


title: low salt night fed ZT12 rep2


title: EHT, ventricular, WT/WT, rep 3

value: iPSC-derived engineered heart tissue (3D)

value: ventricular-like


title: 5_NEUROG3-T2A-NKX6-3IND-DOX

description: Library name: 5_NEUROG3-T2A-NKX6-3IND-DOX

value: 6 days post DOX pulse


title: 4_NEUROG3-T2A-NKX6-3IND-DOX

description: Library name: 4_NEUROG3-T2A-NKX6-3IND-DOX


title: EHT, atrial, WT/WT, rep 2


title: p00_gprbxxxx_bc559

city: Santa Cruz

first: Bin

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

description: Library name: bc559

data_processing:
Paired end reads were trimmed to 25x25bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements plus the E.coli genome
Paired end reads that mapped to repeat elements or E.coli  were discarded. The remaining reads were mapped to the mm10 genome using Bowtie2 .
The set of Bowtie2 paired-end mappings was filtered, retaining only mappings having  genomic length less than or equal to 120bp.
The bam files of mappings were converted to coverage tracks across the genome with the bedtools programs, using options so that the end-to-end coverage of each paired-end read is used.
The coverage tracks were compressed into bigWig format.
The coverage was merged over groups of 3 samples of the same developmental stage, experiment date, and antibody (including the IgG control antibody).
For each developmental stage and experiment date, the 3-sample coverage of an antibody was compared to the 3-sample coverage of the IgG control antibody using the SEACR program with the "norm" and "stringent" parameters.
The SEACR bed file of peaks was converted to a track in the bigBed format
Assembly: mm10
Supplementary files format and content: bigWig coverage tracks of the end-to-end mappings of the paired-end reads
Supplementary files format and content: bigBed track of SEACR stringent peak loci
Library strategy: CUT&Tag

source_name: cerebral cortex

extract_protocol:
Cortices were dissected, and cells were isolated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. 100,000 cells were used for each experiment
CUT&RUN, DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7335L, E7500L).

value: cerebral cortex

tag: develpmental stage

tag: antibody

value: guinea pig and rabbit IgG

value: wildtype

value: Cut&Run


title: low salt night fed ZT12 rep1

value: Colon

value: low salt night fed


title: EHT, ventricular, WT/WT, rep 2

value: Isogenic AF patient iPSCs


title: low salt night fed ZT8 rep3


title: EHT, ventricular, WT/WT, rep 1


title: EHT, atrial, WT/WT, rep 1

value: atrial-like


title: 5_KLF4IND-DOX

description: Library name: 5_KLF4IND-DOX

value: colonoids

value: doxycyline

value: 4 days post DOX pulse


title: e13_gprbxxxx_bc570

description: Library name: bd570


title: p00_gprbxxxx_bc558

description: Library name: bc558


title: low salt night fed ZT8 rep1


title: WT_BM_proB, H3K4me3, rep1

description:
Library name: ChIPmentation_WT_BM_proB_H3K4me3_rep1
WT_H3K4me3_merge.bw
WT_H3K4me3_optimal_set.IDR0.05.narrowPeak.gz


title: p00_gprbxxxx_bc557

description: Library name: bc557


title: EHT, ventricular, WT/TTNtv, rep 3

value: WT/TTNtv (p.Ser21134Trpfs*25)


title: e13_gprbxxxx_bc569

description: Library name: bc569


title: e13_gprbxxxx_bc568

description: Library name: bc568


title: 3_KLF4IND-DOX

description: Library name: 3_KLF4IND-DOX


title: EHT, atrial, WT/TTNtv, rep 3


title: low salt night fed ZT4 rep2


title: EHT, atrial, WT/TTNtv, rep 2


title: p00_wtn_rbiggxxxx_bc938

description: Library name: bc938

value: rabbit IgG


title: 2_KLF4IND-DOX

description: Library name: 2_KLF4IND-DOX


title: 3_NEUROG3-T2A-NKX6-3IND-DOX

description: Library name: 3_NEUROG3-T2A-NKX6-3IND-DOX


title: EHT, ventricular, WT/TTNtv, rep 2


title: 2_NEUROG3-T2A-NKX6-3IND-DOX

description: Library name: 2_NEUROG3-T2A-NKX6-3IND-DOX


title: 1_POU2F3IND-VEH

description: Library name: 1_POU2F3IND-VEH

value: vehicle

value: pooled 1-4

value: 6 days post VEH pulse


title: low salt night fed ZT8 rep2


title: p00_wtn_rbiggxxxx_bc937

description: Library name: bc937


title: low salt night fed ZT0 rep3


title: EHT, atrial, WT/TTNtv, rep 1

value: iPSC-derived engineered heart tissue (3D)


title: 1_NEUROG3-T2A-NKX6-3IND-VEH

description: Library name: 1_NEUROG3-T2A-NKX6-3IND-VEH


title: p00_wtn_rbiggxxxx_bc936

description: Library name: bc936

value: cerebral cortex


title: low salt night fed ZT0 rep2


title: 4_KLF4IND-DOX

description: Library name: 4_KLF4IND-DOX


title: low salt night fed ZT4 rep3


title: EHT, ventricular, WT/TTNtv, rep 1

value: ventricular-like


title: e15_gprbxxxx_bc646

description: Library name: bc646

value: guinea pig and rabbit IgG

value: wildtype


title: iPSC-CM, atrial, WT/WT, rep 3

value: WT/WT


title: low salt night fed ZT0 rep1

value: Colon

value: low salt night fed


title: CUTAC_combo_8h_2_(240722_CD_Hs_1230)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: CUTAC_combo_8h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig

source_name: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: 184D, p16sh, Ctrl, p12, BioRep3, Rep 1

description: Library name: Sample 9

value: Mammary epithelial

tag: specimen

value: Specimen 184D

tag: Stage

value: Post-stasis

tag: transductions

value: p16sh, Ctrl

value: passage 12


title: e15_gprbxxxx_bc645

description: Library name: bc645

value: Cut&Run


title: CUTAC_combo_8h_1_(240722_CD_Hs_1229)

description:
Library name: CUTAC_combo_8h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 8 hours.

value: MDA-MB-231 human breast cancer epthileal cells  (ATCC HTB-26).


title: WT_RTX_72H_2

city: Cambridge

first: Ya-Chieh

last: Hsu

address: 7 Divinity Ave, sherman-fairchild

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: RNA sequencing of treated and control samples

data_processing:
Data was processed using Cell Ranger v7.1.0, including demultiplexing, barcode processing, gene counting, and aggregation of single-cell gene expression data.
Assembly: mm10
Supplementary files format and content: H5 files - gene exression matrix

source_name: Skin

extract_protocol:
Cells were isolated from C57BL/6J mice in first anagen after 12 hr injection with saline (control) or RTX, and after 72 hr injection with RTX. Mouse back skin containing the damaged regions was dissected, and the fat layer was removed by scraping with a surgical scalpel. The dermal fraction was isolated by incubating the skin in a collagenase solution in HBSS on an orbital shaker for 45-60 minutes at 37°C with scraping of the dermis. Following collection of the dermis, the remaining skin was incubated in trypsin-EDTA for 25-30 minutes at 37°C to collect the epidermis. Single cell suspensions of each fraction were obtained by filtering through a 70-mm and 40-mm filter. Cell suspensions were then centrifuged for 8 minutes at 350g at 4°C and resuspended in 5% FBS with a CD16/F32 Fc blocking antibody (BioLegend 101302, 1:100).
Libraries were constructed according to the 10x Genomics Single Cell v3.1 protocol
For scRNAseq, a small aliquot of the epidermal and dermal fractions was set aside containing fibroblasts. The fibroblasts were depleted from the remainder of each fraction by incubating with CD140A-biotin antibody (eBioscience 13-1401-82, 1:200) and then removing CD140A-bound cells with magnetic beads. The aliquoted fractions were then added back to respective samples, and cells were stained for 45-60 minutes on ice using the following antibodies: CD34-e660 (eBioscience 0-0341-82, 1:100), Ly-6A/E (Sca-1)-PerCp-Cy5.5 (eBioscience 45-5981-82, 1:1000), CD45-eF450 (eBioscience 48-0451-82, 1:250), a6-PE (eBioscience 12-0495-82, 1:250). DAPI (1:1000) was used to exclude dead cells. FACS was used to enrich for cell populations of interest at a ratio of 2:1:3:1:2 (immune cells: fibroblasts: hair follicle: general cells: HFSCs) that were isolated as follows: immune cells (CD45+), fibroblasts (Sca1+, CD34+, a6-), hair follicle (Sca1-, CD34-,a6low-high), general cells (DAPI-, CD45-, Sca1-, CD34-,a6-), HFSCs (Sca1-, CD34+,a6+).

value: Skin

tag: strain

value: Wild-type

value: RTX


title: WT_RTX_72H_1


title: e15_gprbxxxx_bc644

description: Library name: bc644

value: cerebral cortex


title: iPSC-CM, atrial, WT/WT, rep 2

tag: cell line

value: Isogenic AF patient iPSCs

value: atrial-like


title: Pax5KO, Ctrl, ATAC-seq, rep2

description:
Library name: ATACseq_Pax5KO_Ctrl_rep2
ATAC_Pax5KO_Ctrl_pooled.bw
Pax5KO_Ctrl_idr_optimal_peak.narrowPeak.gz

value: FL B cell progenitor

value: Ctrl


title: e12_gprbxxxx_bc544

description: Library name: bc544

value: guinea pig and rabbit IgG

value: wildtype


title: CUTAC_combo_4h_1_(240722_CD_Hs_1227)

description:
Library name: CUTAC_combo_4h_1
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.

value: Anti-RNA Polymerase CTD repeat YSPTSPS (phospho S5) antibody [4H8] from abcam (ab5408).


title: CUTAC_combo_4h_2_(240722_CD_Hs_1228)

description:
Library name: CUTAC_combo_4h_2
RNA Polymerase II Serine-5P-based CUTAC in MDA-MB-231 cells co-treated with 400nM THZ531 and 1uM FHT1015 for 4 hours.


title: WT_RTX_12H_1


title: e12_gprbxxxx_bc543

description: Library name: bc543


title: iPSC-CM, ventricular, WT/WT, rep 2

value: ventricular-like

value: WT/WT


title: WT_RTX_12H_2


title: 1_KLF4IND-VEH

description: Library name: 1_KLF4IND-VEH

value: colonoids

value: vehicle

tag: batch

value: pooled 1-4

value: 6 days post VEH pulse


title: e12_gprbxxxx_bc542

description: Library name: bc542

value: Cut&Run


title: p00_rbsatb2x_bc547

description: Library name: bc547