title: pola-1, H3K9me3 input, rep4

city: Cambridge

first: Juan

middle: Carlos

last: Rueda Silva

address: 80 Tennis Ct Rd

department: Biochemistry

institute: University of Cambridge

description: Library name: pola-1_H3K9me3_rep4_input

data_processing:
ChIP-Seq- Quality and Adaptor Trimming - Cutadapt
ChIP-Seq- Read aligment- BWA
ChIP-Seq- Peak calling and bdg generations- MACS3
ChIP-Seq- BigWig generation- bedGraphtoBigWig
ChIP-Seq- Differential enrichment analysis- DiffBind
RNA-Seq- Libraries were mapped, quality controlled, quantified and BigWigs were prepared using the standard Squire pipeline
sRNA-Seq- Quality and Adaptor Trimming - Cutadapt
sRNA-Seq- Mapping - STAR
sRNA-Seq- Count table generation - featureCounts
sRNA-Seq- Differential expression analysis - DeSEQ2
Assembly: Ensembl - WBCel235
Supplementary files format and content: .bw- library size normalized bigwigs for the sequencing tracks
Supplementary files format and content: .broadPeaks- MACS3 called broad peaks
Supplementary files format and content: .counts.tsv - raw gene and repeat RNA counts
Supplementary files format and content: .exon_norm_counts.txt - normalized 22G-RNA counts

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Worms were grown at 20C on HB101 Escherichia coli plates. Worms were synchronized by bleaching and synchronized young adults collected

extract_protocol:
RNA-Seq and sRNA-Seq samples were extracted with Trizol, in the case of sRNA-seq samples with treated with RppH. ChIP-Seq samples were crosslinked by 1% formalaldehyde and sonicated using a Diagenode Bioruptor Pico.
ChIP libraries were prepared using a standard paired ended DNA 150bp library. RNA libraries were prepared using a standard protocol with polyA enrichment. sRNA libraries were enriched for 22G-RNAs with RppH and sequenced using a standard sRNA library preparation protocol.

value: Whole animal

tag: developmental stage

value: Young adult


title: Hep3B SOX4-/- 1

status: Public on Mar 05 2026

type: SRA

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

description:
Hep3B_SOX4_KO-1
raw_counts-1.txt

library_source: transcriptomic

data_processing:
The data processing steps were performed in the Partek Flow RNA toolkit, starting with mRNA samples. Base trimming was performed to generate trimmed reads, followed by alignment using STAR, resulting in aligned reads. Pre-alignment quality control (Pre-alignment QA/QC) was conducted before the alignment. The aligned reads were then quantified to an annotation model, producing transcript counts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene level count values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: MEM, 10% fetal bovine serum, 1x non-essential amino acid 1 mM sodium pyruvate. Cells were cultured at 5% CO2 at 37⁰C.

extract_protocol:
RNA was purified by TRIzol reagent
RNA-seq libraries were generated by illumina stranded mRNA prep (illumina, 20040534)

tag: cell line

tag: cell type

value: Liver cancer

tag: genotype

value: SOX4 knockout


title: MC4R KO mouse, normal diet, small intestine contents, sample 7

city: Fujisawa

first: Akira

last: Mitsui

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: DMPK & Safety Business Unit

country: Japan

institute: Axcelead Drug Discovery Partners, Inc.

description: Library name: Intestine-19

library_source: genomic

data_processing:
Read sequences (39,000 – 60,000 paired-end reads) whose starting sequences perfectly matched the primer sequences used were extracted using the fastx_barcode_splitter tool from FASTX-Toolkit (ver. 0.0.14). When the primer sequences contained N-mix, this process was repeated, considering the number of Ns (six types on the forward side × six types on the reverse side = 36 types). The extracted reads were trimmed to remove primer sequences using fastx_trimmer from the FASTX-Toolkit. Sequences with a quality score <20 were removed using Sickle (ver. 1.33), and sequences shorter than 130 bases along with their paired sequences were discarded. Paired-end read merging was performed using FLASH script (ver. 1.2.11). After removing chimeric and noisy sequences using the DADA2 plugin in Qiime2 (ver. 2021.4), 23,000 – 35,000 amplicon sequence variants (ASVs) and their feature table were generated. Taxonomic classification was performed by assigning the ASV sequences against Greengenes database (ver. 13_8) using a feature classifier plugin.
Assembly: Greengenes database (ver. 13_8)
Supplementary files format and content: Microsoft Excel file includes ASV counts for each Sample
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: Mus musculus

source_name: small intestine contents

extract_protocol:
Approximately 100-200 mg of small intestine or large intestine contents from WD-fed or ND-fed MC4RKO and WT mice were freeze-dried using a VD-250R Freeze Dryer (TAITEC). The freeze-dried samples were homogenized at 1,500 rpm for 2 min using a multi-bead shocker (Yasui Kikai, Osaka, Japan). The DNA was extracted as follows: Lysis Solution F (Nippon Gene, Tokyo, Japan) was added to the crushed samples and incubated at 65 °C for 10 min. The samples were then centrifuged at 12,000 × g for 2 min, and the supernatant was collected. DNA was purified from the collected solution using the MPure-12 system and MPure Bacterial DNA Extraction Kit (MP Biomedicals, Tokyo, Japan). The concentration of the purified DNA was measured using Synergy LX (BioTek, Winooski, Vermont, USA) and QuantiFluor dsDNA System (Promega, Madison, WI, USA).
The concentration of the purified DNA was measured using Synergy LX (BioTek, Winooski, Vermont, USA) and QuantiFluor dsDNA System (Promega, Madison, WI, USA). The sequencing library was prepared using a 2-step tailed PCR method. In the first PCR, 16S region-specific primers were used to amplify the V3-V4 region: 341f_MIX:5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNCCTACGGGNGGCWGCAG-3' 805r_MIX:5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNGACTACHVGGGTATCTAATCC-3' Each 10 μL reaction contained 0.05 U/μL of RxTaq HS (Takara Bio, Shiga, Japan), 0.5 μM of each primer, and 1 ng of template DNA. The PCR conditions were as follows: initial denaturation at 94°C for 2 min; 30 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 30 s; followed by a final extension at 72°C for 5 min. PCR products were cleaned using AMPure XP beads (Beckman Coulter, CA, USA) following the manufacturer’s protocol. A second PCR was performed using the following indexed primers: F:5’-AATGATACGGCGACCACCGAGATCTACAC-Index2 ACACTCTTTCCCTACACGACGC-3' R:5’-CAAGCAGAAGACGGCATACGAGAT-Index1 GTGACTGGAGTTCAGACGTGTG-3' In this step, cleaned amplicons from the first PCR served as templates in 10 μL reactions with 0.05 U/μL of RxTaq HS (Takara Bio) and 0.5 μM of each indexed primer. Amplification was conducted for 10 cycles under the same cycling conditions as the first PCR. The concentration of the library was measured using Synergy H1 (BioTek) and QuantiFluor dsDNA System. Library quality was assessed using a Fragment Analyzer and a dsDNA 915 Reagent Kit (Advanced Analytical Technologies, Orangeburg, NY, USA).

tag: tissue

value: small intestine contents


title: Ensheathing Glia, Control, Batch 1, Replicate 1

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: Library name: Control 1 Rep 1

data_processing:
FASTQ files were cleaned with fastp with default settings.Aligning and counting were carried out with STAR and the 4th 2020 FlyBase Drosophila melanogaster release (r6.35) with the –quantMode flag set as GeneCounts.
For differential gene expression testing we used DESeq2, where we fit a negative binomial model and carried out the Wald-test. We removed experimental batch as a covariate according to the design formula ∼date+genotype. All genes below a Benjamini-Hochberg corrected p-value of 0.05 were considered deregulated.
Assembly: FlyBase Drosophila melanogaster release (r6.35)
Supplementary files format and content: All_Samples_Combined_Counts.csv: Comma seperated value table for raw counts
Supplementary files format and content: Metadata.csv: Comma separated value table for sample metadata

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ensheathing Glia

growth_protocol: Fruit flies were maintained in an incubator at 25°C under a 12:12 light-dark cycle, and provided with a standard diet consisting of cornmeal and molasses. For experiments, only fly males were used. Flies were raised in parallel on the same batch of food, which was exchanged every three to four days and kept in only male population of similar density.

extract_protocol:
Ten brains of flies 5 ± 1 days old were collected, with most of the laminae removed. Dissections were performed in ice-cold PBS that contained 5 μM Actinomycin D (Sigma) to inhibit changes in gene expression during tissue processing. For the dissociation of brain tissue, a mix of Dispase I (0.6 mg/ml) (Sigma), Collagenase I (30 mg/ml) (Thermo Fisher), Trypsin (0.5x) (Thermo Fisher), and 5 μM Actinomycin D was used. Immediately after dissociation, cells were sorted using a FACSAria Fusion (BD Biosciences) flow cytometer with a 100 µm nozzle at 20 psi. Live (DAPI-negative), GFP-positive cells were sorted into 96-well PCR plates at 300 cells per well (3 wells per genotype) using a 4-way purity mask.
3 ul of cell lysis buffer (0.1% Triton X-100, Sigma Aldrich; 1U/ul of RNase Inhibitor, RNase OUT, Thermo Fisher; 2.5 uM Oligo dT(25), IDT; and 2.5 mM dNTP, Promega) was aliquoted in triplicate to 96 well plates (4titude, Cat. No. 4TI-0960/C). Roughly 300 cells were sorted into the wells with lysis buffer and the plate was spun down at 2000xg for 1 min prior to storage at - 80*C. For the first strand synthesis, the Smart-Seq 2 plates were thawed to room temperature for a minute and subsequently spun down at 2000 xg for minute. The RNA denaturation is carried out at 72*C for 10 mins and then flash cooled on ice for 5 mins. First strand synthesis mix (1X SuperScript II first strand synthesis buffer, Thermo Fisher; 5 mM DTT, Thermo Fisher; 100 U SuperScript II reverse transcriptase enzyme, Thermo Fisher; 10 U RNAse OUT, Thermo Fisher; 1M Betaine, Sigma Aldrich; 6 mM MgCl2, Thermo Fisher; and 1 uM TSO, IDT Technologies) is added to the cell lysis mix to a total volume of 10 ul. The First strand synthesis reaction was carried out with following program: 42*C for 90 mins; 10 cycles of {50*C for 2 mins; 42*C for 2 mins}; 72*C for 15 mins; 4*C indefinite hold. PCR amplification of the first strand product was performed by adding 15 ul of the PCR mix to the first strand product (1X KAPA HiFi HotStart Ready Mix, Roche; and 0.1 uM of IS PCR primer, IDT Technologies). 22 cycles of the following PCR program was used to amplify the first strand product: 98*C for 3 mins; 22 cycles of {98*C for 20 secs; 67*C for 15 secs; 72*C for 6 mins}; 72*C for 5 mins; 4*C indefinite hold. 20 ul of Ampure XP was added to each well and mixed. Standard Ampure XP purification was carried out as per manufacturer’s recommendation and the cDNA library was eluted in 17.5 ul of Elution buffer. 17 ul of the eluted library was transfered to fresh 96 well plate (4titude, Cat. No. 4TI-0960/C). 5 ul of Tn5 tagmentation mix (1X Tagment DNA buffer, Illumina; ATM mix, Illumina and cDNA library 1 ng) was prepared for cDNA fragmentation. Tn5 tagmentation was performed with following program: 55*C for 10 mins; 4*C indefinite hold. Tagementation reaction was stopped by quenching the reaction with 1.25ul of NT buffer for 5 mins (Illumina). 1.25 ul of the i5 and i7 Illumina indexes were added to the plates. Finally 3.75 ul of NPM master mix was added to the plate and mixed well and put for the index PCR amplification: 72*C for 3 mins; 95*C for 30 secs; 12 cycles of {95*C for 10 secs; 55*C for 30 secs; 72*C for 30 secs}; 72*C for 5 mins, and 4*C indefinite hold. The indexed PCR products were pooled in a single tube, and 0.8X Ampure XP purification (Beckman Coulter) was carried out as per the manufacturer’s recommendation, and finally, the sequencing library was eluted in 35.5 μl of Elution buffer (Qiagen). SMART seq 2 libraries were sequenced on the NextSeq 500 (Illumina) sequencing platform. Sequencing was done as per the protocol recommendations: paired-end read of 76 bps (read 1), 76 bps (read 2), 8 bps (index 1) and 8 bps (index 2). For a targeted sequencing depth of ~30 million reads per sample.

value: Ensheathing Glia

tag: batch


title: Top 20% cells in Jurkat transduced with rAAV6-M2 batch3

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

data_processing:
The sequencing reads were undergone adapter removal by 'cutadapter' with parameters '-n 1 -e 0.11 -O 15 -m 16'.
The sequences were then aligned to the designed CRISPR library sequences using bowtie2 with '–np 0 –n-ceil L,0,0.2 –very-sensitive'.
We counted the reads number of each gRNA from the Brunello CRISPR library in both the top 20% and bottom 20% fluorescent samples.
The read numbers were then normalized according to the sequencing depth of each NGS library, and an enrichment score was calculated for each gRNA (thus the targeted gene) using MAGeCK.
Assembly: Designed CRISPR library
Supplementary files format and content: The xlsx file, enrichment score for each gRNA.
Library strategy: CRISPR Screen

source_name: Jurkat

extract_protocol:
After sorting, genomic DNA was extracted by TIANamp Genomic DNA Kit (TIANGEN, DP304-03). Then, sgRNA sequences were amplified using Q5 master mix (2×) (NEB #M0544S) and purified using SPRI beads (Beckman #A63882) for NGS.
The CRISPR screening NGS libraries were sequenced as 150-bp paired-ends.

treatment_protocol:
Human CRISPR Brunello lentiviral pooled library targeting 19114 genes (a total of 76441 sgRNAs) was packaged and transduced in Jurkat with stable Cas9 expression (Jurkat-Cas9).
The screening was performed in two Jurkat-Cas9 mono clones. For each replicate, 7E7 Cas9-expressing Jurkat cells (300X coverage) were transduced with the lentiviral library at MOI=0.3 by spinfection and incubated overnight.
Transduction efficiencies at around 30% were confirmed in each replicate by flow cytometry for mKate2+% expression at 72h after lentivirus transduction.
Then, the transduced Jurkat-Cas9 cells were selected and expanded in culture medium with puromycin. When mKate2+% achieved above 95%, 2.3×10^7 cells per replicate were transduced with scrAAV-WT-EGFP or scrAAV-M-EGFP at indicated MOI.
At 72 h after rAAV transduction, cells were collected for top 20% and bottom 20% sorting via Flow Cytometer.

value: Jurkat

value: Human T cell

tag: raav

tag: cell population

value: Top 20%


title: Col-0, 12h, DMSO, rep 1

first: Hannah

middle: Rae

last: Thomas

address: 866 Yuhangtang Road

department: Horticulture

institute: Zhejiang University

data_processing:
Library quality was accessed with Fastqc v0.11.8
Libraries were trimmed using Trim_galore v0.5.0 and Cutadapt v1.7
Libraries were aligned to the Arabidopsis genome using Hisat2 v2.1.0 or STAR 2.5.a in the case of mapping to the transgene, mCherry.
Libraries were converted to SAM and BAM files using Samtools v1.4.1.
Transcripts were assembled using Stringtie v1.3.3.
Raw read counts were extracted using the Stringtie python script, Deprep.py
Assembly: TAIR10 https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Supplementary files format and content: tab-delimited csv file with includes raw counts for each sample from hisat aligner and STAR aligner

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Three  Arabidopsis thaliana lines, Columbia-0 wild-type, icals3m, and PD-plug, were grown on MS media (1% sucrose, 0.8% agar) for 5 weeks in 50mm diameter petri dishes at 10 h light at 22 °C.

extract_protocol:
Two leaves from four plants (either DMSO or estradiol treated) were harvested 12 h, 24 h, 48 h and 72 h post treatment. Three biological replicates for each genotype/treatment/time point were collected.
Leaves were flash frozen in liquid nitrogen. Leaf tissue was homogenised using a Genogrinder and each Eppendorf tube contained 2 steel ball bearings.
RNA was extracted from leaf tissue using the Qiagen Plant RNeasy mini kit.
Rigorous treatment with Turbo DNase was undertaken to remove genomic DNA contamination.
Libraries were constructed by Novogene Co., Ltd using Illumina NovaSeq 6000

treatment_protocol: Leaves were painted on both the abaxial and adaxial side with either 0.1% DMSO (mock treatment) or 20 µM β-Estradiol 17-acetate (estradiol treatment) containing 0.01% Silwet L-77 in ddH2O, using a fine paint brush

tag: time

tag: treatment

value: DMSO

value: leaves


title: MC4R KO mouse, western diet, small intestine contents, sample 3

description: Library name: Intestine-23


title: Col-0, 12h, estradiol, rep 2

value: estradiol


title: Col-0, 12h, estradiol, rep 3


title: pola-1, H3K9me3 input, rep3

country: United Kingdom

description: Library name: pola-1_H3K9me3_rep3_input

tag: chip antibody


title: Hep3B 1

description:
Hep3B-1
raw_counts-1.txt

value: WT


title: MC4R KO mouse, normal diet, small intestine contents, sample 5

description: Library name: Intestine-17


title: MC4R KO mouse, normal diet, small intestine contents, sample 6

description: Library name: Intestine-18


title: pola-1, H3K9me3 ChIP, rep4

description: Library name: pola-1_H3K9me3_rep4


title: MC4R KO mouse, normal diet, small intestine contents, sample 4

description: Library name: Intestine-16


title: Top 20% cells in Jurkat transduced with rAAV6-M2 batch2


title: Hep3B SOX4-/- 2

description:
Hep3B_SOX4_KO-2
raw_counts-1.txt


title: pola-1, H3K9me3 ChIP, rep3

description: Library name: pola-1_H3K9me3_rep3


title: Grade 4 glioblastoma primary tumor sample

city: Evanston

first: Timothy

last: Pan

state: IL

address: 633 Clark St

country: USA

institute: Northwestern University

description:
Library name: GBM02PR
snNanoRNA-seq

library_source: transcriptomic single cell

data_processing:
Processing of raw fastq files were performed using scNanoGPS (v2.0), which produced the gene expression matrix. The isoform matrix was generated by IsoQuant using the 'nanopore' data type setting and 'unique_only' transcript quantification setting.
Assembly: GRCh38 (GENCODE v44/Ensembl110 annotations)
Supplementary files format and content: "matrix_gene.tsv" is a TSV file of the single cell gene expression matrix output by scNanoGPS.
Supplementary files format and content: "matrix_isoform.tsv" is a TSV file the single cell isoform expression matrix output by IsoQuant.
Supplementary files format and content: "annotation.gtf" is the GTF file from isoform quantification output by IsoQuant.

source_name: Brain tumor

extract_protocol:
Single nuclei suspensions were prepared from fresh frozen tissue using the Chromium Nuclei Isolation Kit (10X Genomics).
Libraries were prepared using the 10X Genomics Chromium Controller on Chip J with expected recovery of 3,000 nuclei. cDNA was amplified and enriched for long fragments. Final libraries were pepared using the SQK-LSK14 ligation sequencing kit (Oxford Nanopore Technologies).

value: Brain tumor


title: scNanoRNAseq of VCaP

city: Chicago

first: Ruli

last: Gao

address: Simpson Querrey, 7th Floor

department: Department of Biochemistry and Molecular Genetics

description:
Library name: scNanoRNAseq of VCaP
Long-read single cell RNAseq of VCaP cell suspension using scNanoRNA-seq; Cell line was purchased from ATCC (cat. no. CRL-2876).

data_processing:
Data were processed using scNanoGPS and LongFUSE
Assembly: GRCh38
Supplementary files format and content: gene expression formats are compatible with single cell experiment object

source_name: Prostate tumor

extract_protocol:
Single cell capture was performed by following the 10X Genomics  protocol (3' scRNAseq V3.1).
scNanoRNAseq protocol with ONT LSK114 and R10.4 flow cell

value: Prostate tumor

value: VCaP

value: tumor cell line


title: Top 20% cells in Jurkat transduced with rAAV6-M2 batch1


title: MC4R KO mouse, normal diet, small intestine contents, sample 3

description: Library name: Intestine-15


title: Col-0, 12h, estradiol, rep 1


title: Hep3B 2

description:
Hep3B-2
raw_counts-1.txt


title: MC4R KO mouse, normal diet, small intestine contents, sample 2

description: Library name: Intestine-14


title: Bottom 20% cells in Jurkat transduced with rAAV6-M2 batch3

value: Bottom 20%


title: N2, H3K9me3 ChIP, rep4

description: Library name: N2_H3K9me3_rep4

value: Whole animal

value: Young adult


title: HK-2 Cells CDC42 KO-3-Control

city: Chongqing

first: Xue

last: Zhou

address: 重庆医科大学

institute: College of Pharmacy

data_processing:
Homo sapiens Genomics
Sequence reads were trimmed for adaptor sequence/low-quality sequence using RSeQC benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to Homo sapiens using HISAT2 benchwork
Read count extraction and normalization were performed using String Tile benchwork
Assembly: Homo sapiens
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: kidney

extract_protocol:
RNA sequencing was performed by Sangon Biotech (China, Shanghai) after total RNA extraction from HK-2 cells by TRIzol reagent
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: kidney

value: human renal cortical proximal tubular epithelial cells.

value: CDC42 knockout


title: Bottom 20% cells in Jurkat transduced with rAAV6-M2 batch2

value: Jurkat


title: HK-2 Cells CDC42 KO-2-Control


title: MC4R KO mouse, normal diet, small intestine contents, sample 1

description: Library name: Intestine-13

value: small intestine contents


title: Bottom 20% cells in Jurkat transduced with rAAV6-M2 batch1

value: Human T cell


title: N2, H3K9me3 ChIP, rep3

description: Library name: N2_H3K9me3_rep3


title: N2, H3K9me3 input, rep3

description: Library name: N2_H3K9me3_rep3_input


title: WT mouse, western diet, small intestine contents, sample 5

description: Library name: Intestine-11


title: N2, H3K9me3 input, rep4

description: Library name: N2_H3K9me3_rep4_input


title: N2, H3K9me3 input, rep2

description: Library name: N2_H3K9me3_rep2_input


title: HK-2 Cells CDC42 KO-1-Control


title: HK-2 Cells NC-2-Control


title: HK-2 Cells NC-3-Control


title: WT mouse, western diet, small intestine contents, sample 6

description: Library name: Intestine-12


title: Top 20% cells in Jurkat transduced with rAAV9-M1 batch2

value: Top 20%


title: WT mouse, western diet, small intestine contents, sample 4

description: Library name: Intestine-10


title: WT mouse, western diet, small intestine contents, sample 3

description: Library name: Intestine-9


title: Bottom 20% cells in Jurkat transduced with rAAV9-M1 batch2


title: HK-2 Cells NC-1-Control


title: N2, H3K9me3 ChIP, rep2

description: Library name: N2_H3K9me3_rep2


title: Top 20% cells in Jurkat transduced with rAAV9-M1 batch1


title: ATAC-T

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

description: Library name: ATAC-T

data_processing:
Raw sequencing reads from ATAC-seq, ChIP-seq and ChIRP-seq experiments were processed using a unified bioinformatics pipeline. Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.33). Clean reads were aligned to the appropriate reference genome (hg19) using Bowtie (v1.1.2). PCR duplicates were removed. Peaks were identified using MACS2 (v2.1.0) with default parameters.
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: peripheral blood

extract_protocol:
Cells were harvested and washed with cold PBS. Nuclei were isolated using ATAC lysis buffer according to standard ATAC-seq protocols. Approximately 50,000 nuclei were used for downstream transposition reactions.
ATAC-seq libraries were prepared following the protocol described by Buenrostro et al. with minor modifications. Isolated nuclei were subjected to Tn5 transposition reaction. Following DNA fragmentation and purification, libraries were amplified by PCR for 14 cycles. Library fragment size distribution was assessed using an Agilent Bioanalyzer. Libraries were sequenced on an Illumina HiSeq 2500 platform.
Cells were crosslinked with 1% formaldehyde and lysed. Chromatin was fragmented by sonication to generate DNA fragments of approximately 200–500 bp.
Chromatin Isolation by RNA Purification (ChIRP) was performed according to the manufacturer’s protocol (APE×BIO, China). Biotin-labeled probes targeting IRF1-AS1 were hybridized with chromatin lysates at 37°C. RNA–protein–DNA complexes were captured using streptavidin-coated magnetic beads. After stringent washing and reverse cross-linking, DNA was purified and used for library preparation. Libraries were sequenced on an Illumina platform. An irrelevant probe was used as a negative control.
Crosslinked cells were lysed and chromatin was sheared by sonication at 4°C using a Bioruptor 300 to generate fragments of approximately 200–400 bp. Soluble chromatin was precleared with protein A agarose beads prior to immunoprecipitation.
The precleared chromatin was incubated overnight at 4°C with antibodies. After washing, immunoprecipitated chromatin was eluted and reverse cross-linked at 65°C for 12 hours. DNA was purified by phenol–chloroform extraction followed by ethanol precipitation. Sequencing libraries were prepared using standard Illumina-compatible protocols and sequenced on an Illumina platform.

value: peripheral blood

value: primary cells

value: T

value: ARDS


title: WT mouse, western diet, small intestine contents, sample 2

description: Library name: Intestine-8


title: ATAC-C

description: Library name: ATAC-C

value: C


title: Bottom 20% cells in Jurkat transduced with rAAV9-M1 batch1


title: N2, H3K9me3 ChIP, rep1

description: Library name: N2_H3K9me3_rep1

value: WT


title: WT mouse, western diet, small intestine contents, sample 1

description: Library name: Intestine-7


title: N2, H3K9me3 input, rep1

description: Library name: N2_H3K9me3_rep1_input


title: Bottom 20% cells in Jurkat transduced with rAAV9-WT batch2


title: pole-3;pole-4, H3K9me3 input, rep2

description: Library name: pole-3pole-4_H3K9me3_rep2_input


title: Patient104,CD14+,IRF1-AS1(ChIRP)

description: Library name: IRF1-AS1

data_processing:
Raw sequencing reads from ATAC-seq, ChIP-seq and ChIRP-seq experiments were processed using a unified bioinformatics pipeline. Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.33). Clean reads were aligned to the appropriate reference genome (hg19) using Bowtie (v1.1.2). PCR duplicates were removed. Peaks were identified using MACS2 (v2.1.0) with default parameters.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: ChIRP-seq


title: Patient104,CD14+,AS1-input(input)

description: Library name: AS1-input


title: WT mouse, normal diet, small intestine contents, sample 6

description: Library name: Intestine-6


title: Top 20% cells in Jurkat transduced with rAAV9-WT batch1


title: pole-3;pole-4, H3K9me3 ChIP, rep2

description: Library name: pole-3pole-4_H3K9me3_rep2


title: Patient104,CD14+,H3K4m3-T(ChIP)

description: Library name: H3K4m3-T


title: Top 20% cells in Jurkat transduced with rAAV9-WT batch2


title: Bottom 20% cells in Jurkat transduced with rAAV9-WT batch1


title: mcm-2, H3K9me3 input, rep2

description: Library name: mcm-2_H3K9me3_rep2_input


title: Top 20% cells in Jurkat transduced with rAAV6-WT batch2


title: WT mouse, normal diet, small intestine contents, sample 3

description: Library name: Intestine-3


title: Patient104,CD14+,H3K4m3-C(ChIP)

description: Library name: H3K4m3-C


title: Patient104,CD14+,H3K4m1-T(ChIP)

description: Library name: H3K4m1-T


title: Bottom 20% cells in Jurkat transduced with rAAV6-WT batch2


title: WT mouse, normal diet, small intestine contents, sample 2

description: Library name: Intestine-2


title: Top 20% cells in Jurkat transduced with rAAV6-WT batch1


title: pole-3;pole-4, H3K9me3 input, rep1

description: Library name: pole-3pole-4_H3K9me3_rep1_input


title: mcm-2, H3K9me3 input, rep1

description: Library name: mcm-2_H3K9me3_rep1_input


title: Patient104,CD14+,H3K4m1-C(ChIP)

description: Library name: H3K4m1-C


title: WT mouse, normal diet, small intestine contents, sample 1

description: Library name: Intestine-1


title: pole-3;pole-4, H3K9me3 ChIP, rep1

description: Library name: pole-3pole-4_H3K9me3_rep1


title: WT mouse, normal diet, small intestine contents, sample 4

description: Library name: Intestine-4


title: Patient104,CD14+,DNMT3a1(ChIP)

description: Library name: DNMT3A1


title: mcm-2, H3K9me3 ChIP, rep2

description: Library name: mcm-2_H3K9me3_rep2


title: Bottom 20% cells in Jurkat transduced with rAAV6-WT batch1


title: Barcode association

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: Barcode_association
R1: read1, R2: barcode index, R3: read2

data_processing:
Data was processed using MPRAflow and MPRAnalyze, as previously decribed (Achuach et al. 2019).
Assembly: hg38
Supplementary files format and content: tab-delimeted file

source_name: Barcode

extract_protocol:
Genomic DNA from MPRA barcode association
Sequencing libraries were generated as previously described (Gordon et al. 2020).

value: Barcode


title: WT mouse, normal diet, small intestine contents, sample 5

description: Library name: Intestine-5


title: rabbit ovary,night-restriced feeding,11:00 pm,night_9A

status: Public on Mar 04 2026

city: Beijing

first: Mengqi

last: Zhu

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

description:
Library name: NN night_9A
Column name in raw counts gene_count.txt: night_9A

data_processing:
The raw data was filtered with SOAPnuke (v1.4.0) [1] by 1) Removing readscontaining adapters (adapter contamination); 2) Removing reads whose unknown base('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio(Base quality less than or equal to 15) is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT2
Within-group differential gene analysis was performed using DESeq2
Annotating assembled Unigene with functional databases (KEGG, GO), and predicting the transcription factors.
Assembly: OryCun2.0 (GCA_000003625.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Oryctolagus cuniculus

source_name: ovary

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

treatment_protocol: 35-day-old female IRA rabbits divided into two groups: DF (daytime feeding) and NRF (night-restricted feedin).  The DF group had access to food all day (with feed provided at 6:30 am). The NRF group could only access food during the night (from 6:30 pm to 6:30 am, with feed provided at 6:30 pm).

value: ovary

value: night-restriced feeding


title: rabbit ovary,night-restriced feeding,11:00 pm,night_7A

description:
Library name: NN night_7A
Column name in raw counts gene_count.txt: night_7A


title: rabbit ovary,night-restriced feeding,11:00 pm,night_11A

description:
Library name: NN night_11A
Column name in raw counts gene_count.txt: night_11A


title: rabbit ovary,night-restriced feeding,11:00 am,day_5A

description:
Library name: ND day_5A
Column name in raw counts gene_count.txt: day_5A


title: mcm-2, H3K9me3 ChIP, rep1

description: Library name: mcm-2_H3K9me3_rep1

value: Whole animal

value: Young adult


title: rabbit ovary,night-restriced feeding,11:00 am,day_9A

description:
Library name: ND day_9A
Column name in raw counts gene_count.txt: day_9A


title: rabbit ovary,night-restriced feeding,11:00 pm,night_5A

description:
Library name: NN night_5A
Column name in raw counts gene_count.txt: night_5A


title: rabbit ovary,night-restriced feeding,11:00 pm,night_3A

description:
Library name: NN night_3A
Column name in raw counts gene_count.txt: night_3A


title: rabbit ovary,night-restriced feeding,11:00 am,day_7A

description:
Library name: ND day_7A
Column name in raw counts gene_count.txt: day_7A


title: rabbit ovary,night-restriced feeding,11:00 am,day_3A

description:
Library name: ND day_3A
Column name in raw counts gene_count.txt: day_3A


title: rabbit ovary,night-restriced feeding,11:00 pm,night_1A

description:
Library name: NN night_1A
Column name in raw counts gene_count.txt: night_1A


title: rabbit ovary,daytime feeding,11:00 am,day_12A

description:
Library name: DD day_12A
Column name in raw counts gene_count.txt: day_12A

value: daytime feeding


title: rabbit ovary,daytime feeding,11:00 pm,night_12A

description:
Library name: DN night_12A
Column name in raw counts gene_count.txt: night_12A


title: rabbit ovary,daytime feeding,11:00 am,day_4A

description:
Library name: DD day_4A
Column name in raw counts gene_count.txt: day_4A


title: rabbit ovary,daytime feeding,11:00 pm,night_4A

description:
Library name: DN night_4A
Column name in raw counts gene_count.txt: night_4A


title: rabbit ovary,daytime feeding,11:00 pm,night_2A

description:
Library name: DN night_2A
Column name in raw counts gene_count.txt: night_2A


title: leukocyte DNA from hypertensive patients 98

type: genomic

city: Shanghai

first: Yan

last: Wang

address: 197 Ruijin 2nd Road, Shanghai

institute: Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: Minfi and lmerTest package in R environment (v4.0.0)

label: Cy3 and Cy5

source_name: leukocyte

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from peripheral leukocytes using a DNeasy Blood and Tissue Kit (Qiagen) according to standard instructions

value: leukocyte


title: rabbit ovary,night-restriced feeding,11:00 am,day_1A

description:
Library name: ND day_1A
Column name in raw counts gene_count.txt: day_1A


title: Patient104,CD14+,input(input)

description: Library name: input1


title: rabbit ovary,daytime feeding,11:00 am,day_8A

description:
Library name: DD day_8A
Column name in raw counts gene_count.txt: day_8A


title: rabbit ovary,daytime feeding,11:00 pm,night_8A

description:
Library name: DN night_8A
Column name in raw counts gene_count.txt: night_8A


title: rabbit ovary,daytime feeding,11:00 am,day_6A

description:
Library name: DD day_6A
Column name in raw counts gene_count.txt: day_6A


title: leukocyte DNA from hypertensive patients 97


title: leukocyte DNA from hypertensive patients 96


title: leukocyte DNA from hypertensive patients 986


title: leukocyte DNA from hypertensive patients 988


title: rabbit ovary,daytime feeding,11:00 am,day_2A

description:
Library name: DD day_2A
Column name in raw counts gene_count.txt: day_2A


title: leukocyte DNA from hypertensive patients 934


title: leukocyte DNA from hypertensive patients 937


title: leukocyte DNA from hypertensive patients 921


title: leukocyte DNA from hypertensive patients 941


title: rabbit ovary,daytime feeding,11:00 pm,night_10A

description:
Library name: DN night_10A
Column name in raw counts gene_count.txt: night_10A


title: leukocyte DNA from hypertensive patients 943


title: leukocyte DNA from hypertensive patients 9


title: leukocyte DNA from hypertensive patients 925


title: leukocyte DNA from hypertensive patients 919


title: leukocyte DNA from hypertensive patients 886


title: leukocyte DNA from hypertensive patients 89


title: leukocyte DNA from hypertensive patients 910


title: leukocyte DNA from hypertensive patients 911


title: leukocyte DNA from hypertensive patients 894


title: leukocyte DNA from hypertensive patients 857


title: rabbit ovary,daytime feeding,11:00 am,day_10A

description:
Library name: DD day_10A
Column name in raw counts gene_count.txt: day_10A


title: leukocyte DNA from hypertensive patients 855


title: leukocyte DNA from hypertensive patients 85


title: leukocyte DNA from hypertensive patients 829


title: leukocyte DNA from hypertensive patients 841


title: leukocyte DNA from hypertensive patients 860


title: leukocyte DNA from hypertensive patients 868


title: leukocyte DNA from hypertensive patients 853


title: leukocyte DNA from hypertensive patients 880


title: leukocyte DNA from hypertensive patients 815


title: leukocyte DNA from hypertensive patients 818


title: leukocyte DNA from hypertensive patients 800


title: leukocyte DNA from hypertensive patients 789


title: leukocyte DNA from hypertensive patients 854


title: leukocyte DNA from hypertensive patients 874


title: leukocyte DNA from hypertensive patients 773


title: leukocyte DNA from hypertensive patients 852


title: leukocyte DNA from hypertensive patients 772


title: leukocyte DNA from hypertensive patients 808


title: leukocyte DNA from hypertensive patients 765


title: leukocyte DNA from hypertensive patients 717


title: leukocyte DNA from hypertensive patients 819


title: leukocyte DNA from hypertensive patients 704


title: leukocyte DNA from hypertensive patients 691


title: leukocyte DNA from hypertensive patients 716


title: leukocyte DNA from hypertensive patients 801


title: leukocyte DNA from hypertensive patients 677


title: leukocyte DNA from hypertensive patients 705


title: leukocyte DNA from hypertensive patients 66


title: leukocyte DNA from hypertensive patients 79


title: leukocyte DNA from hypertensive patients 734


title: leukocyte DNA from hypertensive patients 687


title: leukocyte DNA from hypertensive patients 663


title: leukocyte DNA from hypertensive patients 723


title: leukocyte DNA from hypertensive patients 788


title: leukocyte DNA from hypertensive patients 799


title: leukocyte DNA from hypertensive patients 7


title: leukocyte DNA from hypertensive patients 782


title: leukocyte DNA from hypertensive patients 643


title: leukocyte DNA from hypertensive patients 75


title: leukocyte DNA from hypertensive patients 646


title: leukocyte DNA from hypertensive patients 749


title: leukocyte DNA from hypertensive patients 763


title: leukocyte DNA from hypertensive patients 694


title: leukocyte DNA from hypertensive patients 625


title: leukocyte DNA from hypertensive patients 709


title: leukocyte DNA from hypertensive patients 697


title: leukocyte DNA from hypertensive patients 659


title: leukocyte DNA from hypertensive patients 688


title: leukocyte DNA from hypertensive patients 68


title: leukocyte DNA from hypertensive patients 693


title: leukocyte DNA from hypertensive patients 601


title: leukocyte DNA from hypertensive patients 597


title: leukocyte DNA from hypertensive patients 623


title: leukocyte DNA from hypertensive patients 599


title: leukocyte DNA from hypertensive patients 586


title: leukocyte DNA from hypertensive patients 585


title: leukocyte DNA from hypertensive patients 651


title: leukocyte DNA from hypertensive patients 561


title: leukocyte DNA from hypertensive patients 67


title: leukocyte DNA from hypertensive patients 634


title: leukocyte DNA from hypertensive patients 658


title: leukocyte DNA from hypertensive patients 640


title: leukocyte DNA from hypertensive patients 560


title: leukocyte DNA from hypertensive patients 650


title: leukocyte DNA from hypertensive patients 624


title: leukocyte DNA from hypertensive patients 636


title: leukocyte DNA from hypertensive patients 546


title: leukocyte DNA from hypertensive patients 621


title: leukocyte DNA from hypertensive patients 591


title: leukocyte DNA from hypertensive patients 592


title: leukocyte DNA from hypertensive patients 61


title: leukocyte DNA from hypertensive patients 587


title: leukocyte DNA from hypertensive patients 626


title: leukocyte DNA from hypertensive patients 575


title: leukocyte DNA from hypertensive patients 578


title: leukocyte DNA from hypertensive patients 603


title: leukocyte DNA from hypertensive patients 655


title: leukocyte DNA from hypertensive patients 657


title: leukocyte DNA from hypertensive patients 459


title: leukocyte DNA from hypertensive patients 619


title: leukocyte DNA from hypertensive patients 570


title: leukocyte DNA from hypertensive patients 454


title: leukocyte DNA from hypertensive patients 559


title: leukocyte DNA from hypertensive patients 555


title: leukocyte DNA from hypertensive patients 503


title: leukocyte DNA from hypertensive patients 530


title: leukocyte DNA from hypertensive patients 539


title: leukocyte DNA from hypertensive patients 437


title: leukocyte DNA from hypertensive patients 512


title: leukocyte DNA from hypertensive patients 53


title: leukocyte DNA from hypertensive patients 434


title: leukocyte DNA from hypertensive patients 502


title: leukocyte DNA from hypertensive patients 471


title: leukocyte DNA from hypertensive patients 467


title: leukocyte DNA from hypertensive patients 458


title: leukocyte DNA from hypertensive patients 469


title: leukocyte DNA from hypertensive patients 48


title: leukocyte DNA from hypertensive patients 442


title: leukocyte DNA from hypertensive patients 455


title: leukocyte DNA from hypertensive patients 423


title: leukocyte DNA from hypertensive patients 420


title: leukocyte DNA from hypertensive patients 428


title: leukocyte DNA from hypertensive patients 536


title: leukocyte DNA from hypertensive patients 465


title: leukocyte DNA from hypertensive patients 440


title: leukocyte DNA from hypertensive patients 42


title: leukocyte DNA from hypertensive patients 448


title: leukocyte DNA from hypertensive patients 427


title: leukocyte DNA from hypertensive patients 47


title: leukocyte DNA from hypertensive patients 445


title: leukocyte DNA from hypertensive patients 480


title: leukocyte DNA from hypertensive patients 500


title: leukocyte DNA from hypertensive patients 41


title: leukocyte DNA from hypertensive patients 393


title: leukocyte DNA from hypertensive patients 375


title: leukocyte DNA from hypertensive patients 412


title: leukocyte DNA from hypertensive patients 374


title: leukocyte DNA from hypertensive patients 421


title: leukocyte DNA from hypertensive patients 422


title: leukocyte DNA from hypertensive patients 360


title: leukocyte DNA from hypertensive patients 337


title: leukocyte DNA from hypertensive patients 414


title: leukocyte DNA from hypertensive patients 335


title: leukocyte DNA from hypertensive patients 32


title: leukocyte DNA from hypertensive patients 373


title: leukocyte DNA from hypertensive patients 399


title: leukocyte DNA from hypertensive patients 351


title: leukocyte DNA from hypertensive patients 348


title: leukocyte DNA from hypertensive patients 384


title: leukocyte DNA from hypertensive patients 392


title: leukocyte DNA from hypertensive patients 314


title: leukocyte DNA from hypertensive patients 342


title: leukocyte DNA from hypertensive patients 333


title: leukocyte DNA from hypertensive patients 308


title: leukocyte DNA from hypertensive patients 364


title: leukocyte DNA from hypertensive patients 323


title: leukocyte DNA from hypertensive patients 328


title: leukocyte DNA from hypertensive patients 345


title: leukocyte DNA from hypertensive patients 280


title: leukocyte DNA from hypertensive patients 286


title: leukocyte DNA from hypertensive patients 268


title: leukocyte DNA from hypertensive patients 319


title: leukocyte DNA from hypertensive patients 289


title: leukocyte DNA from hypertensive patients 287


title: leukocyte DNA from hypertensive patients 309


title: leukocyte DNA from hypertensive patients 265


title: leukocyte DNA from hypertensive patients 254


title: leukocyte DNA from hypertensive patients 270


title: leukocyte DNA from hypertensive patients 29


title: leukocyte DNA from hypertensive patients 327


title: leukocyte DNA from hypertensive patients 291


title: leukocyte DNA from hypertensive patients 264


title: leukocyte DNA from hypertensive patients 252


title: leukocyte DNA from hypertensive patients 281


title: leukocyte DNA from hypertensive patients 257


title: leukocyte DNA from hypertensive patients 307


title: leukocyte DNA from hypertensive patients 226


title: leukocyte DNA from hypertensive patients 234


title: leukocyte DNA from hypertensive patients 260


title: leukocyte DNA from hypertensive patients 222


title: leukocyte DNA from hypertensive patients 248


title: leukocyte DNA from hypertensive patients 223


title: leukocyte DNA from hypertensive patients 201


title: leukocyte DNA from hypertensive patients 216


title: leukocyte DNA from hypertensive patients 221


title: leukocyte DNA from hypertensive patients 172


title: leukocyte DNA from hypertensive patients 18


title: leukocyte DNA from hypertensive patients 16


title: leukocyte DNA from hypertensive patients 202


title: leukocyte DNA from hypertensive patients 147


title: leukocyte DNA from hypertensive patients 215


title: leukocyte DNA from hypertensive patients 183


title: leukocyte DNA from hypertensive patients 19


title: leukocyte DNA from hypertensive patients 191


title: leukocyte DNA from hypertensive patients 125


title: leukocyte DNA from hypertensive patients 13


title: leukocyte DNA from hypertensive patients 120


title: leukocyte DNA from hypertensive patients 132


title: leukocyte DNA from hypertensive patients 154


title: leukocyte DNA from hypertensive patients 142


title: leukocyte DNA from hypertensive patients 143


title: leukocyte DNA from hypertensive patients 156


title: leukocyte DNA from hypertensive patients 148


title: leukocyte DNA from hypertensive patients 123


title: leukocyte DNA from hypertensive patients 127


title: leukocyte DNA from hypertensive patients 131


title: leukocyte DNA from hypertensive patients 162


title: leukocyte DNA from hypertensive patients 135


title: leukocyte DNA from hypertensive patients 204


title: whole worm, day 1 adult, flp-17oe x egl-6(lof), rep 5

city: Bethesda

first: Ashley

last: Frakes

state: MD

address: 9000 Rockville Pike, 10N219

department: NIDDK, Genetics & Biochemistry Branch

institute: National Institutes of Health

description: Library name: CS-10557-25_S25

data_processing:
Sequencing performed on NovoseqX 1.5B reads, 300cycles
Alignment performed using STAR (v2.7.11b)
Assembly: ce11
Supplementary files format and content: Matrix, one column of gene ids (gene.names), remaining columns are samples (headed with Sample IDs) with rows corresponding to raw counts per gene

source_name: Whole worm

growth_protocol: C. elegans were grown on NGM plates and fed with OP50-1. Animals were age synchronized. Samples collected at day 1 of adulthood.

extract_protocol:
RNA isolation was done with a Trizol prep followed by cleanup using a Qiagen Rneasy Micro Kit.
Illumina RNA seq, polyA select, 150-10-10-150, 325 bp, C. elegans

treatment_protocol: Two strains- AEF148 and AEF237- contain extrachromasomal arrays and thus do not have full penetrance across the population. Because of this, 24 hours before samples were collected for RNA isolation, control worms without arrays were washed with M9 buffer and replated onto fresh NGM plates (N2, AEF236, and AEF243). Worms with arrays (AEF148 and AEF237) were collected in M9 and sorted for the fluorescent co-expression marker using a large particle biosorter before replating.

value: Whole worm

tag: strain id

tag: sample id

tag: group


title: leukocyte DNA from hypertensive patients 112


title: whole worm, day 1 adult, flp-17oe x egl-6(lof), rep 4

description: Library name: CS-10557-20_S20


title: whole worm, day 1 adult, N2, rep 5

description: Library name: CS-10557-21_S21


title: leukocyte DNA from hypertensive patients 113


title: leukocyte DNA from hypertensive patients 12


title: leukocyte DNA from hypertensive patients 1023


title: whole worm, day 1 adult, N2, rep 4

description: Library name: CS-10557-16_S16


title: leukocyte DNA from hypertensive patients 115


title: leukocyte DNA from hypertensive patients 106


title: whole worm, day 1 adult, egl6(lof), rep 3

description: Library name: CS-10557-13_S13


title: leukocyte DNA from hypertensive patients 101


title: leukocyte DNA from hypertensive patients 102


title: whole worm, day 1 adult, flp-17oe, rep 5

description: Library name: CS-10557-24_S24


title: whole worm, day 1 adult, flp-17oe, rep 2

description: Library name: CS-10557-9_S9


title: leukocyte DNA from hypertensive patients 10


title: whole worm, day 1 adult, egl6(lof), rep 5

description: Library name: CS-10557-23_S23


title: whole worm, day 1 adult, N2, rep 2

description: Library name: CS-10557-6_S6


title: whole worm, day 1 adult, flp-17oe, rep 4

description: Library name: CS-10557-19_S19


title: leukocyte DNA from hypertensive patients 107


title: whole worm, day 1 adult, N2, rep 3

description: Library name: CS-10557-11_S11


title: whole worm, day 1 adult, flp-17oe x egl-6(lof), rep 1

description: Library name: CS-10557-5_S5


title: whole worm, day 1 adult, flp17(lof), rep 4

description: Library name: CS-10557-17_S17


title: whole worm, day 1 adult, flp17(lof), rep 5

description: Library name: CS-10557-22_S22


title: whole worm, day 1 adult, flp-17oe x egl-6(lof), rep 3

description: Library name: CS-10557-15_S15


title: whole worm, day 1 adult, AEF149, rep 3

description: Library name: AEF149_3

data_processing:
Sequencing performed by Novogene on NovoseqXPlus, 150PE, 6Gb per sample
Alignment performed using STAR (v2.7.11b)
Assembly: ce11 appended with sequence for GFP
Supplementary files format and content: Matrix, one column of gene ids (gene.names), remaining columns are samples (headed with Sample IDs) with rows corresponding to raw counts per gene

extract_protocol:
RNA isolation was done with a Trizol prep followed by cleanup using a Qiagen Rneasy Micro Kit.
Library prep performed by Novogene. mRNA library preparation (poly A enrichment)

treatment_protocol: Three strains- AEF378, AEF373, and AEF149- contain extrachromasomal arrays and thus do not have full penetrance across the population. Because of this, 24 hours before samples were collected for RNA isolation, control worms without arrays were washed with M9 buffer and replated onto fresh NGM plates (AEF231 and AEF276). Worms with arrays (AEF378, AEF373, and AEF149) were collected in M9 and sorted for the fluorescent co-expression marker using a large particle biosorter before replating.


title: whole worm, day 1 adult, N2, rep 1

description: Library name: CS-10557-1_S1


title: whole worm, day 1 adult, flp-17oe, rep 3

description: Library name: CS-10557-14_S14


title: whole worm, day 1 adult, flp17(lof), rep 2

description: Library name: CS-10557-7_S7


title: whole worm, day 1 adult, flp-17oe x egl-6(lof), rep 2

description: Library name: CS-10557-10_S10


title: whole worm, day 1 adult, egl6(lof), rep 4

description: Library name: CS-10557-18_S18


title: whole worm, day 1 adult, AEF149, rep 5

description: Library name: AEF149_5


title: whole worm, day 1 adult, flp-17oe, rep 1

description: Library name: CS-10557-4_S4


title: whole worm, day 1 adult, egl6(lof), rep 2

description: Library name: CS-10557-8_S8


title: whole worm, day 1 adult, AEF373, rep 3

description:
Library name: YUW133_3
Naming convention (YUW133) was used to distinguish the two flp-17p::flp-17 strains during the experiment. YUW133 is the original strain ID received from Dr. Jin Lee before crossing into AEF231. In the process, a flp-17null background was removed.

value: zcls4[hsp-4p::GFP]V; Ex[flp17p::FLP-17::flp-17 3UTR + unc-122p::mCherry]


title: whole worm, day 1 adult, egl6(lof), rep 1

description: Library name: CS-10557-3_S3


title: whole worm, day 1 adult, AEF149, rep 1

description: Library name: AEF149_1


title: whole worm, day 1 adult, flp17(lof), rep 1

description: Library name: CS-10557-2_S2


title: whole worm, day 1 adult, gcy31, rep 3

description: Library name: gcy31_3


title: whole worm, day 1 adult, AEF373, rep 2

description:
Library name: YUW133_2
Naming convention (YUW133) was used to distinguish the two flp-17p::flp-17 strains during the experiment. YUW133 is the original strain ID received from Dr. Jin Lee before crossing into AEF231. In the process, a flp-17null background was removed.


title: whole worm, day 1 adult, AEF373, rep 5

description:
Library name: YUW133_5
Naming convention (YUW133) was used to distinguish the two flp-17p::flp-17 strains during the experiment. YUW133 is the original strain ID received from Dr. Jin Lee before crossing into AEF231. In the process, a flp-17null background was removed.


title: whole worm, day 1 adult, flp17(lof), rep 3

description: Library name: CS-10557-12_S12


title: whole worm, day 1 adult, gcy31, rep 4

description: Library name: gcy31_4


title: whole worm, day 1 adult, AEF373, rep 1

description:
Library name: YUW133_1
Naming convention (YUW133) was used to distinguish the two flp-17p::flp-17 strains during the experiment. YUW133 is the original strain ID received from Dr. Jin Lee before crossing into AEF231. In the process, a flp-17null background was removed.


description: Library name: flp17null_5

value: flp-17(n4894)IV; zcls4[hsp-4p::GFP]V


title: whole worm, day 1 adult, AEF373, rep 4

description:
Library name: YUW133_4
Naming convention (YUW133) was used to distinguish the two flp-17p::flp-17 strains during the experiment. YUW133 is the original strain ID received from Dr. Jin Lee before crossing into AEF231. In the process, a flp-17null background was removed.


description: Library name: flp17null_4


title: whole worm, day 1 adult, gcy31, rep 2

description: Library name: gcy31_2


title: whole worm, day 1 adult, gcy31, rep 5

description: Library name: gcy31_5


title: whole worm, day 1 adult, gcy31, rep 1

description: Library name: gcy31_1


description: Library name: flp17null_3


title: whole worm, day 1 adult, AEF149, rep 4

description: Library name: AEF149_4


title: whole worm, day 1 adult, AEF231, rep 4

description: Library name: AEF231_4


title: whole worm, day 1 adult, AEF149, rep 2

description: Library name: AEF149_2


title: whole worm, day 1 adult, AEF231, rep 6

description: Library name: AEF231_6


description: Library name: flp17null_1


title: whole worm, day 1 adult, AEF231, rep 5

description: Library name: AEF231_5


title: whole worm, day 1 adult, AEF231, rep 1

description: Library name: AEF231_1


title: RUES2 proprioceptor protocol DIV60 biol rep 3

city: New York

first: Joriene

middle: C

last: de Nooij

state: NY

address: 650 West 168th Street

department: Neurology

institute: Columbia University

description:
Library name: JB025
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.

data_processing:
We use bases2fastq version 1.7.0.1196148384 for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v113, Human:GRCh38.p14) using kallisto (0.50.1).
Assembly: GRCh38
Supplementary files format and content: txt files with raw counts for each gene
Supplementary files format and content: txt file with counts for each transcript isoform/exon

source_name: hESC-derived neurons

growth_protocol: hESC culturing and differentiation as described in the accompanying publication

extract_protocol:
RNA was extracted using Trizol. RNA concentration and integrity was assessed by bioanalyzer. The Clontech Ultra Low v4 kit was used for cDNA synthesis.
NexteraXT

value: hESC-derived neurons

value: sensory neuron'

value: proprioceptor protocol


title: whole worm, day 1 adult, AEF231, rep 3

description: Library name: AEF231_3


description: Library name: flp17null_2


title: RUES2 proprioceptor protocol DIV60 biol rep 2

description:
Library name: JB022
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.

treatment_protocol: hESC culturing and differentiation as described in the accompanying publication


title: RUES2 proprioceptor protocol DIV60 biol rep 1

description:
Library name: JB019
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.


title: whole worm, day 1 adult, AEF231, rep 2

description: Library name: AEF231_2


title: RUES2 mechanoreceptor protocol DIV60 biol rep 2

description:
Library name: JB021
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.

value: mechanoreceptor protocol


title: RUES2 nociceptor protocol DIV60 biol rep 3

description:
Library name: JB023
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.

value: nociceptor protocol


title: RUES2 nociceptor protocol DIV60 biol rep 2

description:
Library name: JB020
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.


title: RUES2 mechanoreceptor protocol DIV60 biol rep 1

description:
Library name: JB018
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.


title: RUES2 nociceptor protocol DIV60 biol rep 4

description:
Library name: JB026
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.


title: RUES2 mechanoreceptor protocol DIV60 biol rep 3

description:
Library name: JB024
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.


title: Sample 1(Lane1) HashTagOligos

city: Munich

first: Linda

last: Warmuth

address: Trogerstr. 30

country: Germany

institute: Technical University Munich

description: Library name: Sample1_HTO

data_processing:
single cells were annotated by their respective CAR transcripts with cellranger-7.0.0.
Assembly: human reference GRCh38-2024-A incl. transcript of CAR constructs
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: isolated from bone marrow

extract_protocol: samples were prepared according to the Chromium next GEM Single Cell 3’ v3.1 with dual index

value: isolated from bone marrow

value: primary human T cells

value: JCAR017 and JCAR021

value: day 30


title: RKO_ArgRestricted_rep4

city: Pittsburgh

first: Parham

last: Habibzadeh

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh Medical Center

description: Library name: Restricted4

data_processing:
Adapters trimmed (Cutadapt), filtered for mature tRNAs.
Aligned to human tRNA reference (Bowtie2).
Counts aggregated to isoacceptor level then differential expression performed (DESeq2).
Assembly: hg38 (GRCh38)
Supplementary files format and content: raw read counts per tRNA isoacceptor

source_name: Large intestine

growth_protocol: DEME, 10%dFBS

extract_protocol:
Trizol-Chloroform
YAMAT tRNAseq, with illumina truseq small RNAseq protocol for tRNAs

treatment_protocol: with 400uM or 12.5uM of arginine in the media

value: Large intestine

value: RKO

value: Colon Carcinoma


title: RKO_ArgRestricted_rep3

description: Library name: Restricted3


title: RKO_ArgRestricted_rep1

description: Library name: Restricted1


title: RKO_ArgFed_rep4

description: Library name: Feed4


title: RKO_ArgFed_rep3

description: Library name: Feed3


title: Sample 2(Lane2) HashTagOligos

description: Library name: Sample2_HTO


title: RKO_ArgRestricted_rep2

description: Library name: Restricted2


title: Sample 1(Lane1) Gene expression

description: Library name: Sample1_GEX


title: RKO_ArgFed_rep1

description: Library name: Feed1


title: V4618

first: Christina

last: Thapa

state: Illinois

address: 1001 University Place

department: Center for Psychiatric Genetics (CPG)

institute: Endeavor Health

description: Library name: V4618

data_processing:
Trimmomatic was used to trim adapters and low quality reads and read ends. Then, both Spliced Transcripts Alignment to a Reference (STAR) and Burrows-Wheeler Aligner (BWA) was used for alignment resulting in gene expression counts tables and bam files, respectively. Final processed counts is provided.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values

source_name: iPS Cells

extract_protocol:
Cells were lysed with 800ul of Buffer RLT Plus (QIAGEN #1053393). Cell lysates were processed using RNeasy Plus Mini Kit (QIAGEN #74134) to extract purified RNA.
Library was constructed by Novogene using Illumina NovaSeq X.

value: iPS Cells

value: iPSC

tag: Sex

value: Male

tag: lof target_gene

tag: ancestry

value: EA


title: CW20107

description: Library name: CW20107

value: Female

value: Negative Control


title: V4642

description: Library name: V4642


title: RKO_ArgFed_rep2

description: Library name: Feed2


title: V4624

description: Library name: V4624


title: V4603

description: Library name: V4603


title: V4621

description: Library name: V4621


title: V4605

description: Library name: V4605


title: V4613

description: Library name: V4613


title: V4601

description: Library name: V4601


title: V4596

description: Library name: V4596


title: RUES2 nociceptor protocol DIV60 biol rep 1

description:
Library name: JB017
Samples multiplexed  in each lane, targeted number of paired-end 75bp reads/sample.

value: hESC-derived neurons

value: sensory neuron'


title: V4579

description: Library name: V4579


title: V4610

description: Library name: V4610


title: V4588

description: Library name: V4588


title: V4573

description: Library name: V4573


title: V4480

description: Library name: V4480


title: V4572

description: Library name: V4572


title: V4474

description: Library name: V4474


title: Sample 2(Lane2) Gene Expression

description: Library name: Sample2_GEX


title: V4483

description: Library name: V4483


title: V4598

description: Library name: V4598


title: V4475

description: Library name: V4475


title: V4484

description: Library name: V4484

value: DSCAM


title: V4481

description: Library name: V4481


title: V4458

description: Library name: V4458


title: V4469

description: Library name: V4469


title: V4614

description: Library name: V4614


title: V4454

description: Library name: V4454


title: V4449

description: Library name: V4449


title: V4471

description: Library name: V4471


title: V4447

description: Library name: V4447


title: V4434

description: Library name: V4434


title: V4438

description: Library name: V4438


title: V4424

description: Library name: V4424


title: V4440

description: Library name: V4440

value: TRIO


title: V4441

description: Library name: V4441


title: V4431

description: Library name: V4431


title: V4442

description: Library name: V4442


title: V4383

description: Library name: V4383


title: V4436

description: Library name: V4436


title: V4452

description: Library name: V4452


title: V4472

description: Library name: V4472


title: V4396

description: Library name: V4396


title: V4394

description: Library name: V4394


title: V4410

description: Library name: V4410


title: V4366

description: Library name: V4366


title: V4363

description: Library name: V4363


title: V4357

description: Library name: V4357


title: V4364

description: Library name: V4364


title: V4355

description: Library name: V4355


title: V4353

description: Library name: V4353


title: V4332

description: Library name: V4332


title: V4404

description: Library name: V4404

value: NIPBL


title: V4342

description: Library name: V4342


title: V4345

description: Library name: V4345


title: V4334

description: Library name: V4334


title: V4341

description: Library name: V4341


title: V4380

description: Library name: V4380


title: V4330

description: Library name: V4330


title: V4326

description: Library name: V4326

value: AA


title: V4323

description: Library name: V4323


title: V4317

description: Library name: V4317


title: V4290

description: Library name: V4290


title: V4312

description: Library name: V4312


title: V4321

description: Library name: V4321


title: V4303

description: Library name: V4303


title: V4308

description: Library name: V4308


title: V4266

description: Library name: V4266


title: V4301

description: Library name: V4301


title: V4271

description: Library name: V4271


title: V4259

description: Library name: V4259


title: V4253

description: Library name: V4253


title: V4300

description: Library name: V4300


title: V4270

description: Library name: V4270


title: V4239

description: Library name: V4239


title: V4251

description: Library name: V4251


title: V4221

description: Library name: V4221


title: V4245

description: Library name: V4245


title: V4267

description: Library name: V4267


title: V4225

description: Library name: V4225


title: V4207

description: Library name: V4207


title: V4217

description: Library name: V4217


title: V4213

description: Library name: V4213


title: V4200

description: Library name: V4200


title: V4193

description: Library name: V4193


title: V4191

description: Library name: V4191


title: V4220

description: Library name: V4220


title: V4232

description: Library name: V4232


title: V4186

description: Library name: V4186


title: V4184

description: Library name: V4184


title: V4174

description: Library name: V4174


title: V4166

description: Library name: V4166


title: V4179

description: Library name: V4179


title: V4159

description: Library name: V4159


title: V4172

description: Library name: V4172


title: V4170

description: Library name: V4170


title: V4158

description: Library name: V4158


title: V4246

description: Library name: V4246


title: V4161

description: Library name: V4161


title: V4194

description: Library name: V4194


title: V4229

description: Library name: V4229


title: V4147

description: Library name: V4147


title: V4130

description: Library name: V4130


title: V4140

description: Library name: V4140


title: V4131

description: Library name: V4131


title: V4133

description: Library name: V4133


title: V4124

description: Library name: V4124


title: V4141

description: Library name: V4141


title: V4178

description: Library name: V4178


title: V4101

description: Library name: V4101


title: V4119

description: Library name: V4119


title: V4103

description: Library name: V4103


title: V4098

description: Library name: V4098


title: V4094

description: Library name: V4094


title: V4093

description: Library name: V4093


title: V4095

description: Library name: V4095


title: V4089

description: Library name: V4089


title: V4078

description: Library name: V4078


title: V4088

description: Library name: V4088


title: V4075

description: Library name: V4075


title: V4116

description: Library name: V4116


title: V4061

description: Library name: V4061


title: V4059

description: Library name: V4059


title: V4066

description: Library name: V4066


title: V4054

description: Library name: V4054


title: V4064

description: Library name: V4064


title: V4049

description: Library name: V4049


title: V4069

description: Library name: V4069


title: V4043

description: Library name: V4043


title: V4005

description: Library name: V4005


title: V4032

description: Library name: V4032


title: V4016

description: Library name: V4016


title: V3595

description: Library name: V3595


title: V4031

description: Library name: V4031


title: V4107

description: Library name: V4107


title: V3581

description: Library name: V3581


title: V4008

description: Library name: V4008


title: V3585

description: Library name: V3585


title: V3588

description: Library name: V3588


title: V4037

description: Library name: V4037


title: V3583

description: Library name: V3583


title: V4006

description: Library name: V4006


title: V4053

description: Library name: V4053


title: PARCB9, ST, Rep2

city: Los Angeles

first: Evan

middle: Robert

last: Abt

state: CA

address: 650 Charles E. Young Drive, South

department: Molecular and Medical Pharmacology

institute: University of California Los Angeles

description:
Library name: Sample 14
P9-1-ST

data_processing:
To quantify sgRNA abundance from FASTQ files, we used the count_spacers.py script developed by Dr. Feng Zhang's group, as published in Joung et al. 2018. Counts were then processed using the MAGeCK pipeline.
Assembly: hg38
Supplementary files format and content: merged_spacer_counts.txt: tab-deliminated text file of guide counts
Supplementary files format and content: merged_spacer_counts_mageck_test.gene_summary.txt: tab-deliminated text file of MAGeCK output
Library strategy: CRISPR Screen

source_name: Prostate

extract_protocol:
Genomic DNA from the initial and endpoint cells was isolated using QIAamp DNA Blood Midi Kit (Qiagen, 51183).
sgRNA libraries were constructed following a published protocol (Joung J et al., Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening, Nat Protoc., 2017.). In addition, the complete library plasmid was also used as a template to build a sequencing library to estimate the sgRNA distribution in the lentiviral vectors.

value: Prostate

value: Transformed prostate basal cells

value: Starting timepoint


title: PARCB9, 2W, Rep2

description:
Library name: Sample 17
P9-1-2W

value: Two weeks timepoint


title: V4033

description: Library name: V4033


title: V4030

description: Library name: V4030


title: V3578

description: Library name: V3578


title: PARCB3, 2W, Rep3

description:
Library name: Sample 12
P3-4-2W


title: PARCB9, ST, Rep1

description:
Library name: Sample 13
P9-0-ST


title: PARCB9, 2W, Rep3

description:
Library name: Sample 18
P9-3-2W


title: PARCB9, 2W, Rep1

description:
Library name: Sample 16
P9-0-2W


title: V3579

description: Library name: V3579


title: V3571

description: Library name: V3571

value: PTEN


title: V3565

description: Library name: V3565

value: iPS Cells


title: PARCB3, 2W, Rep2

description:
Library name: Sample 11
P3-3-2W


title: V3561

description: Library name: V3561

value: iPSC


title: PARCB9, ST, Rep3

description:
Library name: Sample 15
P9-3-ST


title: V3554

description: Library name: V3554


title: V3564

description: Library name: V3564


title: V3543

description: Library name: V3543

value: RORB


title: PARCB3, 2W, Rep1

description:
Library name: Sample 10
P3-0-2W


title: V3540

description: Library name: V3540

value: EA


title: V3559

description: Library name: V3559

value: Female


title: V3535

description: Library name: V3535


title: PARCB3, ST, Rep3

description:
Library name: Sample 9
P3-4-ST


title: PARCB1, 2W, Rep1

description:
Library name: Sample 4
P1-0-2W


title: PARCB3, ST, Rep2

description:
Library name: Sample 8
P3-3-ST


title: PARCB1, ST, Rep3

description:
Library name: Sample 3
P1-5-ST


title: V3542

description: Library name: V3542


title: V3568

description: Library name: V3568


title: PARCB1, 2W, Rep3

description:
Library name: Sample 6
P1-5-2W


title: V3452

description: Library name: V3452


title: PARCB3, ST, Rep1

description:
Library name: Sample 7
P3-0-ST


title: Mab treated with DMSO, Rep2

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

description: Library name: Mab_DMSO_Rep_2_S94

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5).
The sequencing reads were analyzed using the commercially licensed CLC Genomics Suite
Assembly: M. abscessus  ATCC 19977 (GCA_000069185.1)
Supplementary files format and content: Dataset_1.xlsx contains CPM and FC values.

organism: Mycobacteroides abscessus ATCC 19977

source_name: Bacterial Cell

growth_protocol: Mab cultures were cultured for 24 hours in T25 standing flasks in a 37C incubator (without 5% CO2).

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: For Mab, cultures were treated with at 5X the MIC with the compounds, 53 uM MSU-43085, and 19 uM MSU-45683 or an equivalent volume of DMSO, for 24 hours.

value: Bacterial Cell

value: Mab treated with DMSO


title: V3546

description: Library name: V3546


title: V3262

description: Library name: V3262


title: V3271

description: Library name: V3271

value: Male


title: V3528

description: Library name: V3528


title: PARCB1, ST, Rep2

description:
Library name: Sample 2
P1-2-ST


title: Mab treated with MSU-45683, Rep2

description: Library name: MSU45683_B_S100

value: Mab treated with MSU-45683


title: V3519

description: Library name: V3519

value: SPAST


title: PARCB1, ST, Rep1

description:
Library name: Sample 1
P1-0-ST


title: PARCB1, 2W, Rep2

description:
Library name: Sample 5
P1-2-2W


title: Mab treated with MSU-45683, Rep1

description: Library name: MSU45683_A_S99


title: V3533

description: Library name: V3533

value: Negative Control


title: V3517

description: Library name: V3517


title: Mab treated with MSU-43085, Rep2

description: Library name: MSU43085_B_S98

value: Mab treated with MSU-43085


title: whole larvae, ra-2

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

state: --- Select a state ---

address: Stocker Road

institute: University of Exeter

description: Library name: LS5

data_processing:
Trinity Assembly r20131110
RSEM Gene quantification and differential expression
Assembly: Trinity Assembly r20131110
Supplementary files format and content: Trinity.fasta
Supplementary files format and content: gene quantification (Sample_LS2.genes.results)

organism: Magallana gigas

source_name: whole larvae

growth_protocol: C. gigas larvae were cultured in artificial sea water at 22'C for 9 hours.

extract_protocol:
Trizol
Scriptseq v2

treatment_protocol: C. gigas larvae were treated with 1uM all trans retionic acid or Ro-41-5232

value: whole larvae

value: retiniic acid


title: whole larvae, ra-1

description: Library name: LS4


title: V3272

description: Library name: V3272


title: Mab treated with DMSO, Rep1

description: Library name: Mab_DMSO_Rep_1_S93


title: V3442

description: Library name: V3442

value: SKI


title: Mab treated with MSU-43085, Rep1

description: Library name: MSU43085_A_S97


title: V3242

description: Library name: V3242


title: V3440

description: Library name: V3440

value: POGZ


title: whole larvae, ro-3

description: Library name: LS9


title: V3219

description: Library name: V3219


title: cells under Th17 polarlization condition and treated with AZD1208 sample2

city: 深圳市

first: su

last: zepeng

address: 深南中路3025号

institute: 中山大学附属第八医院（深圳福田）

data_processing:
The sequencing was performed by the Beijing Genomics Institute using the BGISEQ500 platform. After the removal of splice contamination, low-quality reads and reads with a high content of unknown base N using SOAPnuke (v1.5.2), the remaining clean reads were mapped to GCF_000001405.38_GRCh38.p12 using HISAT (v2.0.4) and aligned to the reference coding gene set using Bowtie (v2.2.5).
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: PRKM value for each sample

source_name: PBMCs

growth_protocol: 1640 Medium+10%FBS

extract_protocol:
Total RNA was extracted using Trizol (AG)
The procession of the PolyA+ RNA fraction was performed and the cDNA library was constructed.

value: PBMCs

value: Naive CD4+ T cells

value: lymphocyte

value: wild type


title: V3252

description: Library name: V3252

value: iPS Cells

value: iPSC

value: EA


title: whole larvae, ro-2

description: Library name: LS8


title: cells under Th17 polarlization condition and treated with AZD1208 sample1

institute: 中山大学附属第八医院（深圳福田）


title: V3259

description: Library name: V3259


title: whole larvae, ro-1

description: Library name: LS7


title: whole larvae, ra-3

description: Library name: LS6


title: V3261

description: Library name: V3261


title: V3266

description: Library name: V3266


title: whole larvae, control-1

description: Library name: LS1


title: whole larvae, control-3

description: Library name: LS3


title: cells under Th17 polarlization condition and treated with AZD1208 sample3

institute: 中山大学附属第八医院（深圳福田）


title: V3224

description: Library name: V3224


title: cells under Th17 polarlization condition sample1

institute: 中山大学附属第八医院（深圳福田）

value: under Th17 polarlization condition


title: V3237

description: Library name: V3237

value: Male


title: Naïve CD4+ T cells sample4

institute: 中山大学附属第八医院（深圳福田）

value: negative control


title: V3200

description: Library name: V3200


title: V3193

description: Library name: V3193


title: V3211

description: Library name: V3211

value: DSCAM


title: V3255

description: Library name: V3255


title: V3212

description: Library name: V3212


title: V3233

description: Library name: V3233


title: V3225

description: Library name: V3225


title: cells under Th17 polarlization condition and treated with AZD1208 sample4

institute: 中山大学附属第八医院（深圳福田）


title: V3214

description: Library name: V3214


title: cells under Th17 polarlization condition sample4

institute: 中山大学附属第八医院（深圳福田）


title: V3210

description: Library name: V3210


title: V3208

description: Library name: V3208


title: V3180

description: Library name: V3180

value: Female


title: cells under Th17 polarlization condition sample3

institute: 中山大学附属第八医院（深圳福田）


title: V3185

description: Library name: V3185


title: V3179

description: Library name: V3179


title: Naïve CD4+ T cells sample2

institute: 中山大学附属第八医院（深圳福田）


title: cells under Th17 polarlization condition sample2

institute: 中山大学附属第八医院（深圳福田）


title: Veg Post770CU_rep_C

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

description: Library name: Sample 21

data_processing:
reads quality-check using FastQC
alignments were performed with STAR
read counts with Multicovbed  bamcov function in bedtools version 2.30.1
Differential expression analysis usign NOISeq package
Assembly: Prunus persica NCBIv2.51
Supplementary files format and content: counts_veg2021.csv
Supplementary files format and content: counts_veg2022.csv
Supplementary files format and content: counts_flower2022.csv

organism: Prunus persica

source_name: Vegetative bud

extract_protocol:
RNeasy Plant Mini Kit for RNA Extraction
Illumina TruSeq Stranded mRNA Library

value: Vegetative bud

tag: cultivar

value: Fantasia


title: Veg Post770CU_rep_B

description: Library name: Sample 20


title: V3196

description: Library name: V3196

tag: cell line

value: Negative Control


title: Naïve CD4+ T cells sample1

institute: 中山大学附属第八医院（深圳福田）

tag: cell type


title: V3145

description: Library name: V3145

value: AA


title: Flor Post770CU_rep_B

description: Library name: Sample 25

source_name: Flower bud

value: Flower bud


title: Veg Post770CU_rep_A

description: Library name: Sample 19


title: Naïve CD4+ T cells sample3

institute: 中山大学附属第八医院（深圳福田）

value: PBMCs

tag: genotype


title: V3178

description: Library name: V3178

tag: tissue


title: Flor Post770CU_rep_A

description: Library name: Sample 24


title: V3163

description: Library name: V3163

tag: batch


title: Flor Pre0CU_rep_A

description: Library name: Sample 22


title: Veg 475CU_rep_2B

description: Library name: Sample 17


title: V3168

description: Library name: V3168


title: Flor Pre0CU_rep_B

description: Library name: Sample 23


title: V3143

description: Library name: V3143


title: Veg 475CU_rep_2C

description: Library name: Sample 18


title: V3155

description: Library name: V3155


title: V3175

description: Library name: V3175


title: whole larvae, control-2

description: Library name: LS2

value: whole larvae


title: V3132

description: Library name: V3132


title: Veg 200CU_rep_B

description: Library name: Sample 14


title: Veg Pre0CU_rep_B

description: Library name: Sample 11


title: Veg Pre0CU_rep_C

description: Library name: Sample 12


title: V3137

description: Library name: V3137


title: Veg 200CU_rep_C

description: Library name: Sample 15


title: V3134

description: Library name: V3134


title: Veg 200CU_rep_A

description: Library name: Sample 13


title: V3159

description: Library name: V3159


title: V3128

description: Library name: V3128


title: V3121

description: Library name: V3121


title: V3126

description: Library name: V3126


title: Veg 475CU_rep_1B

description: Library name: Sample 5


title: V3107

description: Library name: V3107


title: Veg 770CU_rep_A

description: Library name: Sample 7


title: Veg Pre0CU_rep_A

description: Library name: Sample 10


title: Veg 770CU_rep_C

description: Library name: Sample 9


title: V3123

description: Library name: V3123


title: Veg 770CU_rep_B

description: Library name: Sample 8


title: Veg 475CU_rep_1A

description: Library name: Sample 4


title: Veg 475CU_rep_2A

description: Library name: Sample 16


title: V3100

description: Library name: V3100


title: ss2-3

city: wuhan

first: lang

last: tian

state: hubei

address: 1 Shizishan Street, Hongshan District

institute: huazhong agricultural university

description: Library name: Sample 6

data_processing:
Filter out unqualified sequences from the raw data using Cutadapt to obtain Clean data.
Alignment to the reference genome was performed using Hisat2.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value
Differentially expressed genes (DEGs) Analysis Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Assembly: Sscrofa11.1
Supplementary files format and content: txt file includes FPKM values for each sample

organism: Sus scrofa

source_name: Trachea

extract_protocol:
RNA was harvested using  Trizol reagent. 5.0 ug of total RNA was used for the construction of sequencing libraries
total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.

value: Trachea

value: NPTr

value: Tracheal epithelial cells


title: V3116

city: Evanston

description: Library name: V3116

value: iPS Cells

value: iPSC


title: V3101

description: Library name: V3101


title: V3091

description: Library name: V3091

value: NIPBL


title: V3098

description: Library name: V3098


title: Veg 475CU_rep_1C

description: Library name: Sample 6


title: V3093

description: Library name: V3093


title: V3095

description: Library name: V3095


title: ss2-2

description: Library name: Sample 5


title: V3088

description: Library name: V3088


title: Veg 0CU_rep_C

description: Library name: Sample 3


title: Veg 0CU_rep_B

description: Library name: Sample 2


title: Mock3

description: Library name: Sample 3


title: V3090

description: Library name: V3090


title: Veg 0CU_rep_A

description: Library name: Sample 1


title: anti-ARID1A, Trp53-/-; sgPten gastric organoid, rep2

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description: Library name: CUTTag_ARID1A_TP2

data_processing:
CUT&Tag assays were conducted on chromatin isolated from TP and TPA gastric organoids using antibodies against ARID1A or control IgG. The Illumina NovaSeq X plus platform was employed to perform sequencing. Following quality control by the fastp standard workflow, the Bowtie2 software was utilized to construct an index for the mouse genome (mm10) and align paired-end clean data of 150 bp length using the options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700". The SAMtools program was utilized to convert sam files to sorted bam files. Picard's MarkDuplicates tool was used to remove duplicates with the option "REMOVE_DUPLICATES=true". Normalized bw files were generated using deepTools with the option "bamCoverage -bs=25 --normalizeUsing BPM" for further visualization in the Integrated Genome Viewer. Peak calling was performed using the MACS2 software with the option "macs2 callpeak --broad -q 1e-5 -f BAMPE -g mm --keep-dup all". ChIPseeker was employed to identify the genomic distribution of the peaks, with the TSS region "tssRegion" set as (-3000, 3000) for annotation. The "narrowPeak" files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential modification were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig files and peak files(except for IgG samples)
Library strategy: CUT&Tag

source_name: gastric organoid

extract_protocol:
We analyzed gastric organoids with two engineered genotypes: Trp53−/−; Pten−/− (TP) and Trp53−/−; Pten−/−; Arid1a−/− (TPA). sgRNAs targeting Pten and Arid1a were introduced into Trp53−/−; Cas9-EGFP gastric organoids to generate the corresponding genotypes. TP organoids served as the control group, and an IgG control was included to account for nonspecific background binding. Organoids from each group were collected for downstream CUT&Tag-seq library preparation and comparative differential binding analyses.
TP and TPA organoids were used for ARID1A CUT&Tag. The chromatin was combined with ChiTag™ 2.0 Transposome, then fragmented using Tagmentation Buffer for 1 h at 37 °C. ChIP DNA was purified using DNA Clean Beads and amplified using the PCR system from this kit. PCR conditions were as follows: 72 °C for 3 min, 98 °C for 30 s, followed by 10–25 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, then 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads. The purified ChIP DNA was used for library preparation.

value: gastric organoid

value: Trp53-/-; sgPten

value: ARID1A (Cell Signaling Technology, Cat# 12354)


title: V3089

description: Library name: V3089

value: Female


title: V3127

description: Library name: V3127

value: DSCAM

value: EA


title: V3071

description: Library name: V3071


title: V3087

description: Library name: V3087

value: Negative Control


title: V3086

description: Library name: V3086

value: AA


title: anti-ARID1A, Trp53-/-; sgPten gastric organoid, rep1

description: Library name: CUTTag_ARID1A_TP1


title: V3051

description: Library name: V3051


title: ss2-1

description: Library name: Sample 4


title: V3073

description: Library name: V3073


title: Mock2

description: Library name: Sample 2


title: V3085

description: Library name: V3085


title: Trp53-/-; sgPten; sgArid1a gastric organoid, rep2

description: Library name: ATAC_TPA_rep2

data_processing:
To remove adapters from the 150 bp paired-end raw data, NGmerge was employed with the option "NGmerge -a -v -n 20". Bowtie2 software was used to construct an index for the mouse genome (mm10), followed by alignments using the option "--very-sensitive -X2000 -x mm10". Duplicates were removed using Picard's MarkDuplicates tool. Mitochondrial genome contamination was eliminated using SAMtools and awk commands, resulting in bam files. Normalized bw files were generated using deepTools with the option "bamCoverage -bs=1 --normalizeUsing BPM" for subsequent visualization in the Integrated Genome Viewer (IGV). The macs3 “macs3 hmmratac” standard workflow was utilized for peak calling in ATAC-seq. The genomic distribution of accessibility sites was determined using ChIPseeker with the option "annotatePeak", and the TSS region "tssRegion" was set as (-3000, 3000). The peak files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential accessibility were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig files and peak files

extract_protocol:
Gastric TP and TPA organoids (5×10^4 cells/each group) were harvested and resuspended in 1 mL ice-cold PBS, followed by centrifugation at 500 g for 5 min. The supernatant was removed, and the pellet was gently resuspended in 50 μL lysis buffer. Tubes were placed on ice for 5 min, then 950 μL wash buffer was added. The mixture was gently pipetted (blown) 5 times and centrifuged at 500 g for 5 min at 4 °C. The sediment was collected for downstream reactions.
ATAC-seq libraries were constructed using a Chromatin Profile Kit (Novoprotein, Cat. N248-01A). The sediment was resuspended in 40 μL fragmented mixture and transferred to PCR tubes for incubation at 37 °C for 30 min. The reaction was stopped by adding 10 μL stop buffer and incubating at 55 °C for 5 min. DNA extraction beads were used to purify the fragments. Transposed DNA fragments were amplified using the PCR system provided in the kit with the following conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 9–18 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, and a final extension at 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads.The Illumina X plus platform was utilized to sequence the library.

value: Trp53-/-; sgPten; sgArid1a


title: V3049

description: Library name: V3049


title: Mock1

description: Library name: Sample 1


title: Trp53-/-; sgPten; sgArid1a gastric organoid, rep1

description: Library name: ATAC_TPA_rep1


title: anti-ARID1A, Trp53-/-; sgPten; sgArid1a gastric organoid, rep1

description: Library name: CUTTag_ARID1A_TPA_1


title: IgG, Trp53-/-; sgPten, sgArid1a

description: Library name: CUTTag_IgG_2


title: V3056

description: Library name: V3056


title: Trp53-/-; sgPten; sgArid1a gastric organoid, rep3

description: Library name: ATAC_TPA_rep3


title: V3048

description: Library name: V3048


title: CoCl2_M_IP

city: yangling

first: Jian

last: Sun

address: xinong road

institute: Northwest Agriculture & Forestry University

description: Library name: CoCl2_M_IP

data_processing:
Basecalls were performed using bcl2fastq v20.1 for Novaseg output.
ChlP-seq reads were trimmed from 3" end until the final base had a quality score > 30, usingTrimmomatic vO.33, dis carding reads left w ith < 20 bp.
ChlP-seq reads w ere aligned to the NCBI HZGC01 genome using Bowtie version 2.4.2. Only uniguely mapping reads w ith at most two mismatches were retained.
To create ChiP-seq coverage plots, the locations of the mapped ChiP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per milion.rpm) and reformatted in the bigwig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off g-value <=0.01. bigWig files were generated using the genomicRanges R package. Score represents thenormalized coverage of DNA fragments at a given genomic coordinate. Narrow Peak files were generated using MACs v2.2.7.1 with default settings.
Assembly: HZGC01
Supplementary files format and content: bigwig

organism: Ctenopharyngodon idella

source_name: Adipose tissue

extract_protocol:
1× 107 cells were fixed with 1% formaldehyde (Sigma-Aldrich, cat. no. F8775) for 10 min at room temperature, followed by quenching with 125 mM glycine for 5 min. After lysis, cell nuclei were pelleted by centrifugation at 1000 rpm for 5 min at 4°. The chromatin was fragmented through sonication to achieve an average DNA fragment size of 200–500 base pairs.
ChIP DNA libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB). End repair/A-tailing, adaptor ligation, and USER enzyme treatment were performed according to the manufacturer’s instructions. Libraries were amplified by 8–10 PCR cycles, size-selected, and purified using AMPure XP beads. Library quality was assessed by Qubit and high-sensitivity DNA chip analysis.

value: Adipose tissue

value: Primary Cells

value: preadipocyte


title: Control_M_Input

description: Library name: Control_M_Input


title: V3042

description: Library name: V3042


title: Trp53-/-; sgPten gastric organoid, rep3

description: Library name: ATAC_TP_rep3


title: Ube2fΔIEC mice-1, male, 8 weeks old, untreated with DSS

city: Hangzhou

first: Zhijian

last: Li

address: Kaixuan street number 86

institute: Zhejiang university

description: Library name: KO_1

data_processing:
AcDNAlibrary constructed by technology from the pooled RNA from < colon epithelium > samples of <mouse > was sequenced run with Illumina NovaseqTM X Plus sequence platform. Using the Illumina paired-end RNA seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the < mouse > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: LC-P20250115035_genes_expression.xlsx includes FPK values for each Sample

source_name: Colon

growth_protocol: Normal drinking.

extract_protocol:
Colon epithelial cells were collected from Ube2fflox and Ube2fΔIEC mice. Colons were collected, opened longitudinally, and flushed with cold PBS. The tissue was cut into ~2 mm pieces and incubated in 5 mM EDTA-PBS at 37 °C for 30 min. Following the incubation, the fluid containing cells and residual tissues were filtered through a 40-μm cell strainer and centrifuged at 300 × g for 5 min. Samples were digested with trizol to extract total RNA.
Total RNA was extracted using Trizol reagent (ThermoFisher, 15596018) following the manufacturer’s procedure.The total RNA quantity and purity were analysis of Thermo Fisher Qubit3.0 (ThermoFisher, Q33216) and Agilent 5300 Fragment Analyzer (Agilent, CA, USA, M5311AA), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

treatment_protocol: Mice were untreated with any drugs.

value: Colon

value: no

value: epithelial cells

value: KO