title: HCT116, pooled virus infection, 4dpi, biol rep2, targeted

description:
Library name: HCT116-pool-targeted-2
multiplexed single cell libraries


title: Input nucleoplasm RNA 60hr embryo rep3

status: Public on Jan 12 2026

type: SRA

city: Knoxville

first: Maxim

last: Zagoskin

state: TN

address: 1311 Cumberland Avenue

department: BCMB

country: USA

institute: University of Tennessee Knoxville

description:
Library name: INPUT_60hr_nucleoplasm_rep3
Small RNA sequencing library prepared from Ascaris suum.

library_source: other

data_processing:
Adapter trimming and length filtering of raw sequencing reads were performed using FASTX-Toolkit (v0.0.14). Reads were separated into small RNA (18–30 nt) and longer RNA fragment (31–150 nt) fractions.
Small RNA reads were mapped using Bowtie allowing one mismatch to Ascaris suum reference databases including rRNAs, tRNAs, mitochondrial genome, miRNAs, repetitive elements, and annotated transcripts. RNA fragments (31–150 nt) were mapped using Bowtie2 against the same reference databases.
Reads mapping to rRNAs and reads without genomic matches were excluded. Expression levels were quantified as counts per million mapped reads (CPM). Reads were classified as sense or antisense relative to annotated transcripts and assigned to intronic or intergenic regions as appropriate.
ChIP-seq reads were aligned to the reference genome using Bowtie2. Duplicate reads were removed prior to peak calling. Enriched regions were identified using MACS3 (v3.0.1) with default parameters and a significance threshold of q < 0.05.
Biological replicates were combined using MSPC to generate reproducible consensus peak sets based on statistical significance. Genome browser tracks were generated in BigWig format for visualization.
Assembly: Ascaris suum reference genome (v37)
Supplementary files format and content: Processed data include genome-wide coverage tracks in BigWig (.bw) format representing normalized read coverage derived from merged biological replicates. Additional processed files include peak coordinates in BED format for ChIP-seq experiments. BigWig files are intended for visualization in genome browsers such as UCSC.
Supplementary files format and content: Raw sequencing data (FASTQ files) are available through the Sequence Read Archive (SRA) and linked to individual GEO Sample (GSM) records. Processed files provided at the Series level correspond to merged biological replicates.

molecule: other

organism: Ascaris suum

source_name: embryo

growth_protocol: Ascaris suum embryos were obtained and staged as previously described. Embryos were collected at defined developmental time points corresponding to programmed DNA elimination (PDE) stages and maintained under standard laboratory conditions prior to subcellular fractionation, immunoprecipitation, or chromatin immunoprecipitation.

extract_protocol:
Subcellular fractionation was performed to isolate cytoplasmic, nuclear, and chromatin-associated fractions from Ascaris suum embryos. Argonaute-containing ribonucleoprotein complexes were immunoprecipitated using specific antibodies. For DuoRIP-seq, RNase-assisted co-immunoprecipitation was performed to recover Argonaute-bound small RNAs (18–30 nt) and protected target RNA fragments (18–150 nt). For ChIP-seq, embryos were cross-linked with formaldehyde, chromatin was isolated, and DNA was sheared to ~300–800 bp prior to immunoprecipitation with AsWAGO-specific antibodies.
RNA recovered from immunoprecipitated complexes was used for library preparation with the Lexogen Small RNA-Seq Kit (catalog #052), which enables simultaneous capture of Argonaute-bound small RNAs and their associated target RNA fragments without size selection. Libraries were prepared using a 5′-end independent strategy to capture RNAs with non-canonical 5′ ends. ChIP-seq libraries were prepared from purified immunoprecipitated DNA as previously described. Sequencing was performed as paired-end (2 × 150 bp) on an Illumina NovaSeq 6000 platform.

tag: tissue

value: embryo


title: HEK293 APEX2 ELAVL1 nucleolar lysate rep3

city: Bethesda

first: Markus

last: Hafner

state: Maryland

address: 50 South Drive

institute: NIAMS/NIH

description: Library name: ELAVL1_NIK3x_rep3

library_source: transcriptomic

data_processing:
Illumina Nextseq2000 and NextSeq500 platform was used for sequencing
Basecalling was done using bcl2fastq V2.20.0
The reads were aligned to the hg38 genome and peak was called using PCLIPtools v0.7.2
normalized reads and clusters were combined in a tsv file
Assembly: hg38
Supplementary files format and content: PCLIPtools output conaining read depth and T-to-C mismatch information

molecule: total RNA

organism: Homo sapiens

source_name: KIDNEY

growth_protocol: APEX2 compatible HEK293 cell lines were cultured in DMEM media supplemented with 10% Fetal Bovine Serum, 1% Penicillin-Streptomycin, 100 μg/ml of Hygromycin B and 5 μg/ml of Blastacidin. While HEK293 cells were cultured in complete media without Hygromycin and Blasticidin.

extract_protocol:
Cells were lysed into total lysates and clarified by centrifugation. In the case of YBX1 and ELAVL1: first biotinylated proteins were enriched by immunoprecipitation with anti-biotin antibody and eluted by 2% acetic acid. Eluted lysates were neutralized by NaOH. Then YBX1 and ELAVL1 was enriched by immunoprecipitation with anti-YBX1 and anti-ELAVL1, respectively.  After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed. In the case of AGO2: first FLAG-AGO2 was immpunoprecipitated, eluted with FLAG-peptide. After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised and eluted. anti-biotin was immunoprecipitated on the eluted material followed by proteinase K treatment, RNA extraction and 5' end labelling with T4 RNA ligase. Following small RNA cDNA library preparation was performed.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 16 h before cell harvesting, cells were treated with 4-thiouridine (4SU) at a final concentration of 100 μM for all cell lines and additional 2 μg/ml of doxycycline for APEX2 cell lines. Just before harvesting, APEX2 cells biotinylated and washed with quenching solution. HEK293 cells were washed with 1x PBS. The cells were then crosslinked with 312 nm UV-light for 5 min and collect the cells immediately.

value: KIDNEY

tag: cell line

tag: genotype

value: APEX2 expression

tag: treatment

value: Doxycycline, biotinylation, 4SU, and 312 nm UV light


title: HEK293 APEX2 ELAVL1 nucleolar lysate rep2

description: Library name: ELAVL1_NIK3x_rep2


title: CD4T, WT H3K27ac rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

library_source: genomic

data_processing:
sequnced using Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g mm (--broad for H3K4me1,H3K27me3 ChIP-seq peak calling and -q 0.001 for H3K27ac ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: CD4 T cells prepared from CreER or CreER;Ctcffl/fl mice were culutred under the presence of anti-CD3ε and anti-CD28 for 6 days with chaning medium every 2 days. For the deletion of CTCF allele, 4-OH tamoxifen is added only on the first day of culture.

extract_protocol:
ChIP-seq was performed using the protocol from Schmidl et al., 2015 with small modifications. Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform.

treatment_protocol: CD4 T cells were stimulated with Il-2 at the concentration of 100U/ml every 2 days.

tag: cell type

value: T cells

tag: age

value: 10 weeks old

tag: strain

value: CreER

tag: chip antibody

value: H3K27ac (Abcam #ab4729)


title: RKO-et, pooled virus infection, 4dpi, biol rep2, targeted

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description:
Library name: RKO-pool-targeted-2
multiplexed single cell libraries

library_source: transcriptomic single cell

data_processing:
scRNAseq libraries were demultiplexed by transgene barcodes, as given in the feature_references.csv file
Assembly: GRCh38
Supplementary files format and content: h5 file (output of cell ranger for each sample)
Supplementary files format and content: h5ad file (anndata object containing all samples)

molecule: polyA RNA

source_name: RKO-et

growth_protocol: Caco2-et, HT-29-et, RKO-et, SW480-et, HCT116 were cultured in Dubecco´s Modified Eagle´s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) (PanBiotech),1 % stable L-glutamine (PanBiotech), and 1 % penicillin/streptomycin (PanBiotech) at 37 °C and 5 % CO2 and according Puromycin concentration.

extract_protocol:
For single cell RNA sequencing, cells were harvested using TrypLE, resuspended in PBS, filtered through 30 µm  filters, facs sorted into PBS+1% FBS and directly processed into a library.
Gene expression (GEX) libraries were created from 10000-30000 cells, which were sorted using FACSAria (BD Bioscience) and processed right after sorting following the standard Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics), following standard dual-index protocols and the Chromium-X controller (10xGenomics). Libraries were sequenced on the Nova Seq X Plus 25B with 150 PE (Illumina, Inc.) Barcode-targeted libraries were generated from amplified cDNA used for GEX libraries. PCR was performed with a primer (5′-GTGGTGTTAATTAACCTAGAGGGC-3′) carrying a specific handle and partial Read One primer to amplify the 10 bp viral barcode. Each 100 µL reaction included 100 ng cDNA, primers, and KAPA HiFi mix, with cycling: 95 °C (3 min), 5 cycles of 98 °C (20 s), 67 °C (60 s), 72 °C (60 s), and a final 72 °C (5 min). PCR products were size-selected with SPRIselect beads (0.6X/1.2X) per 10X Genomics protocol. For index PCR, 30 µL of cleaned product underwent 14 cycles, followed by standard indexing and clean-up. Final product size (~360 bp) was confirmed via TapeStation (Agilent). Sequcing was performed as for GEX libraries.

treatment_protocol: CRC cells at 50% confluency were infected using viral supernatant and 8 µg/mL Polybrene (Santa Cruz Biotechnology) at a maximum MOI of 0.2. HCT116 cells were pre-treated with Ecotropic Receptor Booster (Takara Bio) as per the manufacturer’s instructions before infection. After 20 hours of viral exposure, the medium was replaced. All cells used for single-cell datasets were collected 4 days post-infection (dpi).

value: RKO-et

value: colorectal cancer

value: virus pool

tag: batch


title: Input nucleoplasm RNA 60hr embryo rep1

description:
Library name: INPUT_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: CD4T, WT H3K27ac rep1


title: HEK293 APEX2 ELAVL1 cytoplasmic lysate rep2

description: Library name: ELAVL1_NES_rep2


title: SW480-et, pooled virus infection, 4dpi, biol rep2, GEX

description:
Library name: SW480-pool-GEX-2
multiplexed single cell libraries


title: Input cytoplasm RNA 60hr embryo rep1

description:
Library name: INPUT_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: Input chromatin RNA 60hr embryo rep4

description:
Library name: INPUT_60hr_chromatin_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: HT-29-et, pooled virus infection, 4dpi, biol rep2, targeted

description:
Library name: HT-29-pool-targeted-2
multiplexed single cell libraries


title: HEK293 APEX2 ELAVL1 nucleolar lysate rep1

description: Library name: ELAVL1_NIK3x_rep1


title: HEK293 APEX2 ELAVL1 cytoplasmic lysate rep1

description: Library name: ELAVL1_NES_rep1


title: Input chromatin RNA 60hr embryo rep2

description:
Library name: INPUT_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: HEK293 APEX2 ELAVL1nuclear lysate rep3

description: Library name: ELAVL1_H2B_rep3


title: CD4T, WT CTCF rep2

value: CTCF (CST #2899)


title: CD4T, WT H3K27me3 rep1

value: H3K27me3 (Abcam #ab6002)


title: RKO-et, pooled virus infection, 4dpi, biol rep2, GEX

description:
Library name: RKO-pool-GEX-2
multiplexed single cell libraries


title: CD4T, KO SMC1A rep2

value: CreER;Ctcf fl/fl

value: SMC1 (Bethyl #A300-055A)


title: Caco-2-et, pooled virus infection, 4dpi, biol rep2, targeted

description:
Library name: Caco-2-pool-targeted-2
multiplexed single cell libraries


title: HEK293 APEX2 ELAVL1 nuclear lysate rep1

description: Library name: ELAVL1_H2B_rep1


title: CD4T, KO STAT5 rep2


title: HT-29-et, pooled virus infection, 4dpi, biol rep2, GEX

description:
Library name: HT-29-pool-GEX-2
multiplexed single cell libraries


title: HEK293 APEX2 ELAVL1 nuclear lysate rep2

description: Library name: ELAVL1_H2B_rep2


title: IgG IP total RNA 64hr embryo rep1

description:
Library name: IGG_64hr_total_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: Caco-2-et, pooled virus infection, 4dpi, biol rep2, GEX

description:
Library name: Caco-2-pool-GEX-2
multiplexed single cell libraries


title: Input chromatin RNA 60hr embryo rep3

description:
Library name: INPUT_60hr_chromatin_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: HCT116, pooled virus infection, 4dpi, biol rep1, targeted

description:
Library name: HCT116-pool-targeted-1
multiplexed single cell libraries

source_name: HCT 116

value: HCT 116


title: CD4T, KO RPB1-S5P rep1

value: Phospho-Rpb1 CTD (Ser5) (CST #13523)


title: CD4T, KO H3K27me3 rep1


title: SW480-et, pooled virus infection, 4dpi, biol rep2, targeted

description:
Library name: SW480-pool-targeted-2
multiplexed single cell libraries


title: Rep2_Input

city: Baltimore

first: Taeyoung

last: Hwang

state: MD

address: 855 N. Wolfe St, 3rd floor, Suite 300

institute: Lieber Institute for Brain Development

description: Library name: Rep2_Input

data_processing:
Sequencing reads were assigned to the designed oligonucleotides based on barcode sequence matching. Barcode sequences were extracted from the provided oligo pool FASTA file as the 10-nucleotide segment immediately upstream of the final 17 nucleotides. When sequencing reads extended beyond the barcode region (as in our dataset), reads were assigned to a given oligonucleotide if they contained no more than two mismatches relative to the corresponding designed target sequence. The designed target sequences were obtained from the oligo pool FASTA file by removing the first 16 nucleotides and the final 27 nucleotides of each oligonucleotide.
Assembly: Not applicable, using custom sequences
Supplementary files format and content: Comma-separated file include sequencing read counts for oligonucleotides and samples.

growth_protocol: HEK293T cells cultured in DMEM plus 10% FBS, 1% Penicillin-streptomycin, and 1% GlutaMAX supplement (Gibco) were passaged onto 15-cm dishes.

extract_protocol:
For the reverse cross-linking reaction, lysates were mixed with 33 μL of reverse crosslinking buffer (3X PBS, 6% N-Lauroylsarcosine, 30 mM EDTA, 15 mM DTT), 10 μL of Proteinase K (Ambion), and 1 μL of RNaseOUT (Invitrogen) and incubated at 42C for 1 hour then 55C for 1 hour. TRIzol (Invitrogen) and chloroform, followed by RNeasy Plus Mini Kit (Qiagen), were used to isolate RNAs.
Sequencing libraries were generated using customized primers that anneal to the universal priming sites on the oligos and attach Illumina-compatible sequencing adapters: reverse primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), forward primer (caagcagaagacggcatacgagatCGTGATgtgactggagttcagacgtgtgctcttccgatctACTGGCCGCTTCACTG, CGTGAT is a Illumina truseq index and can be variable).
Amplicon sequencing was performed with a single-end run.

treatment_protocol: Oligo pools were transfected into HEK293T cells using X-tremeGENE HP DNA Transfection Reagent (Roche) according to manufacturer’s instruction. Cells were harvested 48 hours post-transfection by scraping, collected by centrifugation at 500 x g for 5 minutes at 4C, and washed once with cold PBS. Cells were cross-linked in cold PBS resuspension (~5 million cells/mL) with 0.1% formaldehyde for 10 minutes on a nutator at room temperature. To cease the reaction, glycine was added to cells with a final concentration of 125 mM followed by incubation for 5 minutes on a nutator at room temperature. Cross-linked cells were centrifuged at 500 x g for 5 minutes at 4C. Cross-linked cell pellets were washed twice with PBS including cOmplete Protease Inhibitor Cocktail (Roche), flash-frozen and stored at -80C until use.

value: Input


title: Input chromatin RNA 60hr embryo rep1

description:
Library name: INPUT_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.

value: embryo


title: IgG IP nucleoplm RNA 60hr embryo rep2

description:
Library name: IGG_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: Rep3_Input

description: Library name: Rep3_Input


title: Rep3_PUM2

description: Library name: Rep3_PUM2


title: CD4T, KO CTCF rep2


title: IgG IP nucleoplm RNA 60hr embryo rep4

description:
Library name: IGG_60hr_nucleoplasm_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: IgG IP nucleoplm RNA 60hr embryo rep3

description:
Library name: IGG_60hr_nucleoplasm_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: HCT116, pooled virus infection, 4dpi, biol rep1, GEX

description:
Library name: HCT116-pool-GEX-1
multiplexed single cell libraries


title: Rep1_PUM2

description: Library name: Rep1_PUM2


title: CD4T, KO H3K4me3 rep2

value: H3K4me3 (Millipore #04-745)


title: CD4T, KO H3K27ac rep2


title: IgG IP nucleoplm RNA 60hr embryo rep1

description:
Library name: IGG_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: GCB2 scRNA-seq

city: Nanjing

first: jingjing

last: chen

address: 101 Longmian Road

country: China

institute: Nanjing Medical University

description: single cell 3' RNA

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters
Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively
Genome_build: mm10
Supplementary_files_format_and_content: txt files include raw counts for each cells

source_name: Germinal center B cells

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3.

value: Germinal center B cells from spleens


title: SW480-et, pooled virus infection, 4dpi, biol rep1, targeted

description:
Library name: SW480-pool-targeted-1
multiplexed single cell libraries


title: HEK293 APEX2 AGO2 cytoplasmic lysate biol rep1

description: Library name: AGO2_NES_rep1

value: KIDNEY

value: APEX2 expression

value: Doxycycline, biotinylation, 4SU, and 312 nm UV light


title: IgG IP chromatin RNA 60hr embryo rep4

description:
Library name: IGG_60hr_chromatin_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: Rep2_PUM2

description: Library name: Rep2_PUM2


title: HT-29-et, pooled virus infection, 4dpi, biol rep1, GEX

description:
Library name: HT-29-pool-GEX-1
multiplexed single cell libraries


title: Rep1_Input

description: Library name: Rep1_Input


title: IgG IP chromatin RNA 60hr embryo rep3

description:
Library name: IGG_60hr_chromatin_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: SW480-et, pooled virus infection, 4dpi, biol rep1, GEX

description:
Library name: SW480-pool-GEX-1
multiplexed single cell libraries


title: RKO-et, pooled virus infection, 4dpi, biol rep1, GEX

description:
Library name: RKO-pool-GEX-1
multiplexed single cell libraries


title: GCB1 scRNA-seq

description: single cell 3' RNA


title: RKO-et, pooled virus infection, 4dpi, biol rep1, targeted

description:
Library name: RKO-pool-targeted-1
multiplexed single cell libraries


title: IgG IP cytoplm RNA 60hr embryo rep1

description:
Library name: IGG_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: HT-29-et, pooled virus infection, 4dpi, biol rep1, targeted

description:
Library name: HT-29-pool-targeted-1
multiplexed single cell libraries


title: HEK293 APEX2 AGO2 nuclear lysate biol rep2

description: Library name: AGO2_H2B_rep2


title: HEK293 APEX2 AGO2 nuclear lysate biol rep1

description: Library name: AGO2_H2B_rep1


title: IgG IP chromatin RNA 60hr embryo rep1

description:
Library name: IGG_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: IgG IP chromatin RNA 60hr embryo rep2

description:
Library name: IGG_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: Caco-2-et, pooled virus infection, 4dpi, biol rep1, targeted

description:
Library name: Caco-2-pool-targeted-1
multiplexed single cell libraries


title: HEK293 APEX2 AGO2 cytoplasmic lysate biol rep2

description: Library name: AGO2_NES_rep2


title: Caco-2-et, pooled virus infection, 4dpi, biol rep1, GEX

description:
Library name: Caco-2-pool-GEX-1
multiplexed single cell libraries


title: female, central brain dissection, 5-day-old, replicate 2

city: Oxford

first: Aaron

middle: Munro

last: Allen

address: Tinsley Building, Mansfield Road

department: DPAG

country: United Kingdom

institute: University of Oxford

description:
Library name: FemaleBrainRep2
10x Genomics Chromium 3' v2

data_processing:
The fastq files were aligned to the r6.30 transcriptome release and included all transcript types. Digital expression matrices were generated using salmon-alevin tool for all the droplets per sample (v1.7.0, Srivastava et al., 2019). To identify cell-containing droplets, we used the "emptyDrops" function from the DropletUtils package (Lun et al., 2019).
Assembly: BDGP6.30
Supplementary files format and content: Tab-sparated value files and matrix files

organism: Drosophila melanogaster

source_name: central brain dissection

growth_protocol: Flies were raised at 25°C on standard cornmeal-agar food in an incubator with a 12:12 light/dark cycle. Virgin males and females were collected and stored individually. Flies were aged 5 days post-eclosion at 25°C prior to dissection.

extract_protocol:
2 replicates each of 20 male and 20 female central brains were individually dissected, removing optic lobes, in toxin-supplemented ice-cold calcium- and magnesium-free DPBS (GibcoTM, + 50 mM D(−)-2-Amino-5-phosphonovaleric acid, 20 mM 6,7-dinitroquinoxaline-2,3-dione and 0.1 mM tetrodotoxin). Each replicate was then washed in 1 mL ice-cold toxin-supplemented Schneider’s medium (tSM: GibcoTM + toxins, as above). Brains were then incubated for 30 minutes in 0.5 mL of tSM containing 1 mg/mL papain (Sigma-Aldrich) and 1 mg/mL collagenase I (Sigma-Aldrich). Brains were washed once more with tSM and subsequently triturated with flame-rounded 200 mL pipette tips. Dissociated brains were resuspended into 1 mL PBS + 0.01% BSA and filtered through a 10 µm CellTrics strainer (Sysmex, 04-0042-2314).
Libraries were made using the Chromium Single Cell 3' v2 kit from 10x Genomics. Cells were loaded in accordance with 10x Genomics documentation. The samples were sequenced with 8 lanes of Illumina HiSeq4000 by the Oxford Genomics Centre.

value: central brain dissection

value: +/w*; {UAS-Stinger}, {13XLexAop2-IVS-tdTomato.nls}/+; dsx[GAL4]/+

tag: Sex

value: female

value: 5-day-old adult


title: male, central brain dissection, 5-day-old, replicate 1

description:
Library name: MaleBrainRep1
10x Genomics Chromium 3' v2

value: male


title: scRNA-seq_ATRXKO_ery

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

description:
Library name: scRNA-seq_sample 2
Smart-seq2 scRNA-seq of d13 ATRX KO erythroid cells

data_processing:
For scRNA-seq analysis, demultiplexed FASTQ files were trimmed for polyA tails using TrimGalore; files from different lanes were merged using samtools and aligned to hg19 genome using STAR. Gene counts for each cell were obtained with FeatureCounts and normalised by dividing total library size of the cell and multiplying by the mean library size across all processed cells. Genes with normalised counts <1 were considered non-detected and their expression values were set to 0. The normalized counts were further applied with log2 normalisation. QC filtering was performed to retain cells with >3000 reads; <10% mitochondrial reads, and >70% mapped reads per cell. Highly variable genes were identified by fitting a LOESS model of log2(mean expression) versus coefficient of variation for each gene. Genes with a coefficient of variation above the fitted model and log2(mean expression) ≥ 0 were selected as HVGs. Dimensionality reduction was performed by PCA (20 dimensions) and t-SNE (‘Rtsne’ package, with “perplexity = 10, max_iter = 500”) using HVGs, and plotted using ‘‘ggplot2’’ package in R. Differentially expressed genes were identified using a non-parametric Wilcoxon test and expressing cell frequency was computed using Fisher′s exact tests on log2-normalized counts for genes expressed in ≥5 cells. Significant genes were defined by an adjusted p value (false discovery rate (FDR) <0.05) and an absolute log2 fold change (|log2FC| > 0.5). P values were combined using Fisher’s method, and adjusted p-values were calculated using the Benjamini & Hochberg FDR procedure. Violin plots from selected genes were generated using ‘‘ggplot2’’ package in R. GSEA was conducted using ClusterProfiler R package. Differentially expressed gene set was compared with the gene list from org.Hs.eg.db from the Bioconductor package for GO analysis with settings ont = "BP", pAdjustMethod = "fdr". For cell cycle analysis, a Seurat object was created using the original count table. Cell cycle scores were computed and used to assign cell cycle stages. Fisher’s test was used to examine cell cycle difference between groups.
Assembly: hg19
Supplementary files format and content: csv countmatrix file for raw counts

source_name: Erythroid cells differentiated from CD34+ HSCs

growth_protocol: CD34+ cells were differentiated along the erythroid lineage using a previously described three-phase liquid culture system (Scott, C. et al. 2020).

extract_protocol:
Single live nucleated cells were sorted into each well of a cold 384-well PCR plate (FrameStar 4titude, Cat No 4ti-0384/C) containing lysis buffer with barcoded Oligo(dT)-tailed oligonucleotides as described in Rodriguez-Meira et al., 2019. The sorted plates can be stored at -80°C for up to 3 month before library processing.
Retrotranscription and PCR steps were performed on the sorted plates. Briefly, proteinase in the lysis buffer was heat-inactivated at 72°C for 15 min, during which retrotranscription mix was prepared by mixing SMARTScribe retrotranscriptase (Clontech, Cat No 639537), RNase inhibitor (TaKara, Cat No 2313A), and template-switching oligo TSO-LNA (sequence: AAGCAGTGGTATCAACGCAGAGTACATrGrG+G, RNase-free HPLC purified). The RT mix was dispensed into each well after heat inactivation and first-strand cDNA was synthesised. Afterwards, the cDNA was amplified by SeqAMP (Clontech, Cat No 638509) using 21 PCR cycles. Amplified products from each plate were pooled, bead-purified, tagmented, and indexed using Tn5 enzyme (Illumina Nextera XT Kit, Cat No FC-131-1096) to construct libraries. The libraries were purified with AMPure beads, assessed on TapeStation System (Agilent), quantified using the NEBNext Library Quant Kit (NEB, Cat No E7630L), and sequenced on a NextSeq platform with 75 bp single-end reads using the NextSeq 500/550 High-output 75 Cycle Kit (Illumina, Cat No 20024906).

value: ATRX knockout


title: H3S10p IP total nuclei RNA 65hr embryo rep1

description:
Library name: H3S10p_65hr_totalLN_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: Input_ChIP-seq_HUDEP-2_d8

description:
Library name: Sample 10
ChIP-seq input control of differention day 8 HUDEP-2 cells

data_processing:
ChIP-seq data quality was assessed by FASTQC. Data was analysed using a customised in-house pipeline (script: https://github.com/Hughes-Genome-Group/NGseqBasic/releases). Paired-end reads were aligned to the hg19 genome using bowtie 2. Output BAM files were sorted and indexed using Samtools, normalised to RPKM using Deeptools (--normalizeUsingRPKM), and converted to BigWig files for visualisation in the USCS genome browser. Peaking Calling was done using LanceOtron (Hentges LD et al, 2022).
Assembly: hg19
Supplementary files format and content: bigWig files

source_name: HUDEP-2 WT

growth_protocol: Differentiation of HUDEP-2 cells used a two-phase liquid culture system, requiring a base media consisted of IMDM supplemented with 3% Human AB plasma, 10 μg/mL human insulin, 3 U/mL heparin, 3 U/mL EPO, 200 μg/mL holo-transferrin, 2% (v/v) FBS and 1x P/S. From day 0 to day 6, 1 ng/mL IL3, 50 ng/mL SCF, and 2 μg/mL doxycycline were added to the base media. After 6 days, media was changed to the second phase, where only 300 μg/mL holo-transferrin supplemented.

extract_protocol:
ATRX ChIP-seq was carried out on 50x10^6 cells following the optimised protocol described in Truch et al., 2018. Briefly, cells were double-fixed with firstly 2mM ethylene glycol bis succinimidyl succinate (EGS, Sigma, Cat No E3257) for 45 min and then 1% formaldehyde solution for 20 min at room temperature. The cross-linking was quenched with 125 mM glycine (Sigma-Aldrich, Cat No G7126). After cells lysis, the chromatin was fragmented using Covaris ME220 ultrasonicator followed by pre-clearing with Protein A/G Dynabeads (Invitrogen, Cat No 10001D, 10003D) before taking input controls and immunoprecipitation with 15 μg ATRX antibody (Abcam, Cat No ab97508). After sequential washes at 4°C, samples were eluted, de-crosslinked and proteinase K treated. DNA was precipitated using phenol/chloroform extraction and ethanol precipitation with GlycoBlue (15 mg/mL) (Thermo Scientific, Cat No AM9516) prior to dissolving in 20 μL of ultrapure water.
Purified DNA was quantified using the Qubit dsDNA HS assay (Invitrogen, Cat No Q32854) and indexed using NEBNext Ultra II DNA library prep kit (NEB, Cat No E7645L). Libraries were quantified, and sequenced on an Illumina NextSeq machine with paired-end reads.

value: HUDEP-2 WT

value: Differentiated erythroid progenitor cells

value: Wild type


title: CD4T, KO H3K27ac rep1

value: T cells

value: 10 weeks old

value: CreER;Ctcf fl/fl

value: H3K27ac (Abcam #ab4729)


title: GLO1AKR1A1ADKO 5

city: Mannheim

first: Shu

last: Li

address: Neckarpromenade

institute: ECAS

description: Library name: GLO1AKR1A1ADKO5

data_processing:
Raw sequence data with adapter sequences or low-quality sequences was filtered.
Filtered reads were aligned to the Zebrafish reference genome (GRCz11)
Raw counts levels were quantified using FeatureCounts (v2.0.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit(QIAGEN), 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library.

value: larvae

value: GLO1/AKR1A1A DKO

value: No


title: scRNA-seq_AAVS1_ery

description:
Library name: scRNA-seq_sample 1
Smart-seq2 scRNA-seq of d13 AAVS1 erythroid cells

value: Erythroid cells differentiated from CD34+ HSCs

value: AAVS1 control


title: H3S10p IP total RNA 65hr embryo rep1

description:
Library name: H3S10p_65hr_total_rep1
Small RNA sequencing library prepared from Ascaris suum.

value: embryo


title: female, central brain dissection, 5-day-old, replicate 1

description:
Library name: FemaleBrainRep1
10x Genomics Chromium 3' v2

value: central brain dissection

value: +/w*; {UAS-Stinger}, {13XLexAop2-IVS-tdTomato.nls}/+; dsx[GAL4]/+

value: female


title: H3S10p IP total RNA 65hr embryo rep2

description:
Library name: H3S10p_65hr_total_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: AsCSR-1 IP cytoplasm RNA 64hr embryo rep2

description:
Library name: CSR1_64hr_cytoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: GLO1AKR1A1ADKO 4

description: Library name: GLO1AKR1A1ADKO4


title: AsCSR-1 IP nuclei RNA 64hr embryo rep1

description:
Library name: CSR1_64hr_nuclei_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: ATRX-ChIP-seq_HUDEP-2_d8

description:
Library name: Sample 9
ATRX ChIP-seq of differention day 8 HUDEP-2 cells


title: GBM_091713

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the genes using htseq-count

source_name: patient derived glioblastoma tissue sample

extract_protocol:
Total RNA was isolated from glioblastoma samples collected from glioblastoma patients. RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

value: glioblastoma tumor


title: GLO1AKR1A1ADKO 6

description: Library name: GLO1AKR1A1ADKO6


title: male, central brain dissection, 5-day-old, replicate 2

description:
Library name: MaleBrainRep2
10x Genomics Chromium 3' v2

value: male

value: 5-day-old adult


title: ATRX-ChIP-seq_HUDEP-2_d6

description:
Library name: Sample 7
ATRX ChIP-seq of differention day 6 HUDEP-2 cells

value: HUDEP-2 WT

value: Differentiated erythroid progenitor cells

value: Wild type


title: GLO1AKR1A1ADKO 1

description: Library name: GLO1AKR1A1ADKO1


title: GLO1KO 6

description: Library name: GLO1KO6


title: GBM_110413

treatment_protocol: Total RNA was isolated from glioblastoma samples collected from glioblastoma patients


title: GBM_072512


title: GBM_020315


title: Input_ChIP-seq_HUDEP-2_d6

description:
Library name: Sample 8
ChIP-seq input control of differention day 6 HUDEP-2 cells


title: GLO1AKR1A1ADKO 2

description: Library name: GLO1AKR1A1ADKO2


title: GBM_081313


title: GBM_111813


title: AsCSR-1 IP nucleoplasm RNA 60hr embryo rep2

description:
Library name: CSR1_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: AsCSR-1 IP chromatin RNA 60hr embryo rep2

description:
Library name: CSR1_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: GLO1KO 5

description: Library name: GLO1KO5


title: GBM_071917


title: Input_ChIP-seq_HUDEP-2_d2

description:
Library name: Sample 4
ChIP-seq input control of differention day 2 HUDEP-2 cells


title: GLO1KO 4

description: Library name: GLO1KO4


title: AsCSR-1 IP cytoplasm RNA 60hr embryo rep1

description:
Library name: CSR1_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: ATRX-ChIP-seq_HUDEP-2_d2

description:
Library name: Sample 3
ATRX ChIP-seq of differention day 2 HUDEP-2 cells


title: AsCSR-1 IP nucleoplasm RNA 60hr embryo rep1

description:
Library name: CSR1_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: A.64ra.Stbl

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
Library name: A.64ra.Stbl
Poly-A bulk RNA-seq

data_processing:
Sequenced reads were processed and aligned to the rat reference genome (Rnor_6), for scRNA seq using 10x Genomics Cell Ranger (version 6.1.2), and for bulk RNA-seq using CFCE Viper pipeline
Assembly: Rnor_6
Supplementary files format and content: Filter matrix h5 and count matrix
Supplementary files format and content: counts.tab

organism: Rattus norvegicus

source_name: Tumor

extract_protocol:
Tissue digestion was performed using 2 mg/mL collagenase type IV (Worthington, LS004189) in DMEM/F12 (Thermo Fisher Scientific, MT10090CV) with constant stirring at 37°C for 1–2 hours.
For single-cell RNA sequencing (scRNAseq) of whole mammary glands, viable cells were resuspended in PBS containing 0.04% BSA at a concentration of 1,000 cells/μL. A total of 10,000 cells were loaded onto a 10x Genomics Chromium instrument (10x Genomics) following the manufacturer's protocol. scRNAseq libraries were constructed using the Chromium Next GEM Single Cell 5’ HT v2 kit (10x Genomics). Quality control of the amplified cDNA and final sequencing libraries was conducted using the Bioanalyzer High Sensitivity DNA Kit (Agilent). The pooled libraries were sequenced on an Illumina NovaSeq S4 platform. Bulk RNA was extracted and subjected to poly(A) enrichment to select for mRNA. Enriched RNA was reverse transcribed into cDNA, barcoded, and dual-indexed with i5 and i7 adapters before sequencing.

value: Tumor


title: AsCSR-1 IP chromatin RNA 60hr embryo rep1

description:
Library name: CSR1_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: GBM_012814


title: P1A.5.Grw

description:
Library name: P1A.5.Grw
Poly-A bulk RNA-seq


title: ATRX-ChIP-seq_HUDEP-2_d4

description:
Library name: Sample 5
ATRX ChIP-seq of differention day 4 HUDEP-2 cells


title: GLO1AKR1A1ADKO 3

description: Library name: GLO1AKR1A1ADKO3


title: AKR1A1AKO 5

description: Library name: AKR1A1AKO5


title: GBM_012015


title: AKR1A1AKO 4

description: Library name: AKR1A1AKO4


title: GBM_040815


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + control miRNA (+DOX) rep 3

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: Library name: Clone2_DOX_Scr_1

data_processing:
The FASTQ files were analyzed and quality-checked using FastQC v0.11.9 18.
Reads were mapped against the human reference genome (build hg38) using the STAR (v2.6.1d) spliced alignment algorithm 19 with parameters --twopassMode basic and --quantMode GeneCounts and otherwise default parameters.
STAR output files containing the number of reads mapping to each gene were combined and rows for summary statistics have been removed. Additional processed data files are available as supplementary files for the associated journal article.
Assembly: hg38
count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains counts of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis with the statistics package "Fitnoise". gene.csv lists the genomic locations of the genes that were used. Locations are 1-based.
Supplementary files format and content: counts of reads aligning to each gene in each sample

growth_protocol: The MDA-MB-231 (ATCC: HTB-26) immortalised human breast cancer cell line was obtained from American Type Culture Collection (ATCC, Rockville, MD) and used to generate ZEB-expressing stable cell lines. All MDA-MB-231 derived cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (Invitrogen). Cells were sub-cultured every 2–3 days, using 0.2% Trypsin/1× PBS to dissociate cells during passaging. All cell lines tested negative for mycoplasma.

extract_protocol:
Total RNA was harvested 72 hrs post transfection using TRIzol (Invitrogen), following standard manufacturers protocol.
High quality RNA samples (in biological duplicate from parental, endogZEB and oexZEB cells + 5nM negative control or miR-200c-3p miRNA mimic (genepharma)) were DNAse treated according to manufacturers protocol (#AM1907, TURBO DNA-freeTM Kit) prior to library preparation. Total RNA was treated with RNAseH and strand-specific libraries were prepared and sequenced using a single-end 75 cycle high output kit on an Illumina NextSeq500 at the ACRF Cancer Genomics Facility.

treatment_protocol:
To generate cell lines with inducible ZEB1 and ZEB2 expression, pENTR2B-ZEB2 (HsCD00829572, Centre for Personalized Diagnostics, DNASU) was recombined with pInducer21 using LR Clonase to produce pInducer21-ZEB2-GFP 15,16. GFP is independently encoded within the same vector as ZEB2 and is driven by the same promoter though is not a fusion protein. pInducer20-ZEB1 was previously generated by PCR and restriction enzyme cloning 17. Plasmids were transformed into competent E. coli cells, purified by QIAfilter Plasmid Midi Kit (#12243, Qiagen) and sanger sequenced for insert verification. For lentivirus production, HEK293T cells were plated at 2 × 106 cells in T25 flasks. The following day, cells were transfected with pLP1, pLP2, pLP-VSVG, pTAT (1µg of each) and 4µg of either pInducer20-ZEB1 or pInducer21-ZEB2-GFP. DNA was mixed in 500µl opti-MEM (Invitrogen) and transfected in combination with 12µl Lipofectamine-2000 (Invitrogen). Transfection reagent was removed 6hrs post transfection and viral supernatant of either pInducer20-ZEB1 and pInducer21-ZEB2-GFP was collected after 72hrs. MDA-MB-231 cells were seeded at 2 × 10^5 cells in T25 flasks. The following day, cells were co-transduced with viral supernatant of pInducer20-ZEB1 and pInducer21-ZEB2-GFP (1:8 each) in the presence of polybrene (4mg/ml). Polyclonal or single cell selection was done using 1.0mg/ml of G418, followed by cell sorting for GFP expression (encoded on pInducer21-ZEB2 vector).
For cell sorting, MDA-MB-231_ZEB1/2 cells were washed twice with warm washing buffer (1× PBS + 10 mM EDTA) followed by short incubation with 3 mM EDTA in 1× PBS. Semi-detached cells were treated with TrypLE followed by dilution in 1× PBS + 10 mM EDTA. Cells were centrifuged at 350×g for 5 min, washed with 1× PBS + 10 mM EDTA and resuspended in sorting buffer (ice cold 1× PBS, 5 mM EDTA, 1% FCS and 25 mM HEPES; pH 7.0). Cells were then filtered using a 30µm Filcon sterile filter (BD Biosciences) and sorted by GFP fluorescence intensity compared to control cells (parental MDA-MB-231, no colour). Single cells separated in 96-well plates were grown in conditioned media before transferring into larger 6-well plates. Flow Cytometry sorting was performed on the MoFlo Astrios EQ High Speed Cell Sorter using Summit Software version: 6.3.1 (Beckman Coulter, Miami, FL, USA) utilising the 488 nm (150 mW) laser line and 100 micron nozzle at 30 PSI. Laser and light filter usage are displayed on plot axes. No forward scatter masks were used. Flow cytometry data was analysed using the Apple Macintosh-version of FCS express 6 (De Novo Software, Los Angeles, CA, USA). Single clones and pools were selected for strength of ZEB1 and ZEB2 induction by qPCR and western blotting, ensuring endogenous-like and supraphysiological levels of expression following miR-200c transfection.
Transfection Cells were seeded at 2 × 105 cells per well in 6-well plates and treated with or without 0.5µg/mL Doxycycline (DOX) to induce expression of ZEB1 and ZEB2. The following day, cells were transfected with 5nM miR-200c mimic (GenePharma) or 5nM negative control RNA, using optiMEM (Invitrogen) and Lipofectamine RNAiMAX (Invitrogen) as per manufacturers protocol. Media was replaced 6hrs post transfection. DOX was replenished in fresh media every 48hrs.

value: breast

value: WT with dox-inducible ZEB1 and ZEB2

value: DOX treatment

value: control (scrambled; scr) miRNA transfection

tag: replicate

value: replicate 3


title: Input_ChIP-seq_HUDEP-2_d4

description:
Library name: Sample 6
ChIP-seq input control of differention day 4 HUDEP-2 cells


title: Input_ChIP-seq_HUDEP-2_undiff_d0

description:
Library name: Sample 2
ChIP-seq input control of undifferentiated HUDEP-2 cells

value: Erythroid progenitor cells


title: ATRX-ChIP-seq_HUDEP-2_undiff_d0

description:
Library name: Sample 1
ATRX ChIP-seq of undifferentiated HUDEP-2 cells


title: GBM_062816


title: GLO1KO 2

description: Library name: GLO1KO2

value: larvae

value: No


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + control miRNA (+DOX) rep 1

description: Library name: Clone2_DOX_Scr_3

value: replicate 1


title: GBM_080409


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + miR-200 (+DOX) rep 3

description: Library name: Clone2_DOX_200c_1

value: miR-200c transfection


title: GBM_040313

value: glioblastoma tumor


title: GBM_092208


title: A.59.Stbl

description:
Library name: A.59.Stbl
Poly-A bulk RNA-seq


title: P1A.5rsu.Stbl

description:
Library name: P1A.5rsu.Stbl
Poly-A bulk RNA-seq


title: GBM_061615


title: GLO1KO 3

description: Library name: GLO1KO3


title: P1.57lsu.Stbl

description:
Library name: P1.57lsu.Stbl
Poly-A bulk RNA-seq


title: P1.57.Stbl

description:
Library name: P1.57.Stbl
Poly-A bulk RNA-seq


title: A.64.Grw

description:
Library name: A.64.Grw
Poly-A bulk RNA-seq


title: MDA-MB-231 cells + miR-200 (+DOX) rep 3

description: Library name: Parental_DOX_200c_1

value: WT


title: A.53ma.Grw

description:
Library name: A.53ma.Grw
Poly-A bulk RNA-seq


title: AKR1A1AKO 3

description: Library name: AKR1A1AKO3


title: GLO1KO 1

description: Library name: GLO1KO1


title: AKR1A1AKO 2

description: Library name: AKR1A1AKO2


title: GBM_031417


title: A.53.Stbl

description:
Library name: A.53.Stbl
Poly-A bulk RNA-seq


title: MDA-MB-231 cells + control miRNA (+DOX) rep 3

description: Library name: Parental_DOX_Scr_1


title: GBM_022315


title: AKR1A1AKO 1

description: Library name: AKR1A1AKO1


title: MDA-MB-231 cells + miR-200 (+DOX) rep 1

description: Library name: Parental_DOX_200c_3


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + miR-200 (+DOX) rep 1

description: Library name: Clone2_DOX_200c_3


title: WT 6

description: Library name: WT6


title: P1A.51.Stbl

description:
Library name: P1A.51.Stbl
Poly-A bulk RNA-seq


title: WT 4

description: Library name: WT4


title: Vh.36rsu.Stbl

description:
Library name: Vh.36rsu.Stbl
Poly-A bulk RNA-seq

value: Vehicle


title: MDA-MB-231 cells + control miRNA (+DOX) rep 1

description: Library name: Parental_DOX_Scr_3


title: TNBC4T1-Saline-Tumor in Lung, sample 2

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

description: Library name: T26

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Assembly: mm39
Supplementary files format and content: The processed data file was saved in text format, which contains gene ENSEMBL ID, sample names, gene symbol, gene location, gene length, gene biotype and gene description.

extract_protocol:
Total RNA was extracted from the harvested tumour cells using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). Bulk RNA sequencing with cDNA library construction were performed at Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

value: Triple-negative breast cancer

value: PBS control


title: Vh.36.Grw

description:
Library name: Vh.36.Grw
Poly-A bulk RNA-seq


title: WT 1

description: Library name: WT1


title: MDA-MB-231 cells + control miRNA rep 1

description: Library name: Parental_NO-DOX_Scr_3


title: TNBC4T1-Saline-Tumor in Lung, sample 1

description: Library name: T25


title: P1.35.Grw

description:
Library name: P1.35.Grw
Poly-A bulk RNA-seq


title: WT 2

description: Library name: WT2


title: WT 5

description: Library name: WT5


title: P1A.42.Stbl

description:
Library name: P1A.42.Stbl
Poly-A bulk RNA-seq


title: TNBC4T1-cmLumi-Olap-Tumor in Lung, sample 2

description: Library name: T30

value: cmLumi-Olap


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + miR-200 (+DOX) rep 3

description: Library name: Pool_DOX_200c_1


title: TNBC4T1-cmLumi-Olap-Tumor in Lung, sample 1

description: Library name: T29


title: MDA-MB-231 cells + control miRNA rep 3

description: Library name: Parental_NO-DOX_Scr_1


title: GBM_021114


title: WT 3

description: Library name: WT3


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + miR-200 (+DOX) rep 1

description: Library name: Pool_DOX_200c_3


title: siCT_3

city: Cambridge

first: Veronica

last: Dezi

address: Tennis Ct Rd

department: MRC Toxicology Unit

institute: University of Cambridge

data_processing:
Salmon pseudoalignment
Assembly: GRCh38 (release 109)
Supplementary files format and content: .sh file generated with Salmon

source_name: epithelium

growth_protocol: MCF10A cells were cultured at 37°C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM)/F12 (1:1) supplemented with horse serum (5%), recombinant human epidermal growth factor (20 ng/ml, Peprotech), recombinant human insulin (10 µg/ml, Sigma-Aldrich), hydrocortisone (500 ng/ml, Sigma-Aldrich), and cholera toxin (10 ng/ml, Sigma-Aldrich).

extract_protocol:
RNA was extracted with RNeasy Mini Kit (QIAGEN) and RNA integrity was assessed using the Agilent 4150 TapeStation (Agilent).
Libraries were prepared according to TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat (Illumina Inc.) system. Paired-end sequencing was performed using Illumina NextSeq500 High Output 150-cycle (2x75bp) sequencing (Illumina Inc.).

treatment_protocol: Cells were reverse-transfected for 48h with 10nM siRNA, growth media replaced 6 hours post-transfection

value: epithelium

value: breast epithelial cells

value: siRNA-mediated KD


title: Vh.3ra.Stbl

description:
Library name: Vh.3ra.Stbl
Poly-A bulk RNA-seq

value: Tumor


title: siCT_2


title: CD4T, WT Tofacitinib untreat RNA rep3

data_processing:
sequnced using Illumina Hiseq X ten platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.6.0a with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: RSEM output files including raw counts, FPKM, TPM values
Supplementary files format and content: normalized bigwig

growth_protocol: CD4 T cells prepared from CreER or CreER;Ctcffl/fl mice were culutred under the presence of anti-CD3ε and anti-CD28 for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.

extract_protocol:
RNA was extracted from cells based on chloroform-phenol/guanidine. Total RNA prepared with rRNA depletion and PolyA RNA was isolated by oligo dT beads.
cDNA is amplified through 8-11 cycles of PCR amplification using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were paired-end sequenced on Illumina HiSeq X ten platform.

treatment_protocol: CD4 T cells were stimulated with IL-2 at the concentration of 100U/ml every 2 days.

value: T cells

value: 10 weeks old

value: CreER


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + control miRNA (+DOX) rep 3

description: Library name: Pool_DOX_Scr_1

value: breast

value: WT with dox-inducible ZEB1 and ZEB2

value: DOX treatment

value: control (scrambled; scr) miRNA transfection

value: replicate 3


title: ISLET1_4C_NT_HH25

city: São Paulo

first: Irene

last: Yan

state: São Paulo

address: Av Prof Lineu Prestes

country: Brazil

institute: University of Sao Paulo

description:
Library name: NT_1_2_NEB_4c_lib_WIN21
HH25 neural tube

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal6 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Assembly: galGal6
Supplementary files format and content: bigwigs
Library strategy: 4C-Seq

organism: Gallus gallus

source_name: neural tube

growth_protocol: HH25 chicken embryo neural tubes were obtained from fertilized eggs and dissected in Ringers solution

extract_protocol:
Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 50bp reads on an Illumina NextSeq1000 instrument.

value: neural tube

tag: developmental stage

tag: axis

value: truncal


title: Vh.34.Vh

description:
Library name: Vh.34.Vh
Poly-A bulk RNA-seq

value: Vehicle


title: CD4T, WT Tofacitinib treat RNA rep2


title: siPDCD4_2

value: WT


title: siPDCD4_3


title: siCT_1


title: CD4T, WT RNA rep4


title: T0TnA

city: Kennedy Space Center

first: Aubrie

middle: E.

last: O'Rourke

state: Florida

address: Kennedy Space Center

institute: National Aeronautics and Space

description: Library name: T0TnA_R1_001.fastq.gz

data_processing:
For Tn-Seq analysis, read 1 (P5) raw sequencing reads for all libraries were trimmed for the following transposon specific sequence: GGTGCATCAGGCGGATGAACGCGCGGCCGC using Cutadapt (version 5.1). Any reads that did not contain the sequence were discarded. Surviving reads were mapped to the reference genome (B. contaminans, strain B17-01563-1, GCF_022533485.1_ASM2253348v1_genomic.fna) using bowtie2 (version 2.5.4). The “local” option was used which allows bowtie to trim reads according to any detected trends in the 5’ region of the read for better alignment. This process allows for any Tn5 mosaic ends that were not trimmed by Cutadapt to be removed during the alignment step. The featureCounts tool (Subreads package, version 2.1.1) was used to compile all mapped read counts by gene feature. The resulting counts table was processed to keep genes with nonzero counts for all the triplicates in the T0 control. The counts table was fed into the DESeq2 program in RStudio (RStudio version 2024.09.1+394) to arrive at log2FoldChange values with associated adjusted p-values across the mutated genes for the relevant comparisons between treatment groups. Outputs from DESeq2 for each of the mutated genes were multiplied by -1 to obtain a relative gene fitness measurement for the wildtype of B. contaminans. Gene Ontology (GO) term enrichment was determined using ShinyGO 0.8. Differences and commonalities in relative gene fitness among the experimental treatment groups were visualized using upSet and volcano plots. The antiSMASH tool was used to identify secondary metabolites from the B. contaminans reference genome. The genes with the most significant fitness contributions and from related operons were visualized using the “pheatmap” tool in RStudio. Samtools was used to convert the sam file output from bowtie2 to a bam file, the bam file was sorted and Samtools “coverage” feature was used to find a corresponding coverage for each Tn-Seq library and the initial input Tn-Seq mutant pool across the four chromosomes of the reference genome. The TPP tool of the TRANSIT program [42] was used to establish Tn5 insertion counts for each library.
Assembly: B. contaminans, strain B17-01563-1, GCF_022533485.1_ASM2253348v1_genomic.fna
Supplementary files format and content: processed_data.xlsx

organism: Burkholderia contaminans

source_name: microbe

growth_protocol: The B. contaminans Tn-Seq library was revived by slightly thawing the freezer stock and pipetting 100 mL of Tn-Seq library into 3 mL of TSB containing 50 mg/mL kanamycin and incubated at 35°C with shaking at 200 rpm for 16 hours. Three separate Tn-Seq starter cultures were prepared to serve as timepoint 0 (T0) and to inoculate the seed films as the three biological replicates (TnA, TnB, and TnC) of the experiment. Cells which were not used for the experiment were retained as T0 for Tn-Seq sequencing.  At harvest, shoot and root tissues were separated and placed into 50 mL Falcon tubes with 10 mL of 50 mg/mL kanamycin in TSB media and allowed to grow for 16 hours at 35°C with shaking at 200 rpm to select for the transposed B. contaminans Tn-Seq library. Plant material was removed from the Falcon tube, the bacterial culture was pelleted by centrifugation at 3000 rpm for 5 min, and media decanted. Three cell pellets were obtained for scenarios a, b roots, b shoots, c roots, c shoots, and timepoint 0 for a total of 18 cell pellets for DNA extraction.

extract_protocol:
Plant material was removed from the Falcon tube, the bacterial culture was pelleted by centrifugation at 3000 rpm for 5 min, and media decanted. Three cell pellets were obtained for scenarios a, b roots, b shoots, c roots, c shoots, and timepoint 0 for a total of 18 cell pellets for DNA extraction. 19 Pellets of DNA were extracted using the DNeasy Powerlyzer PowerSoil kit
Sequencing library preparation of samples for the Tn-Seq experiment followed the protocol used in Ganesan et al. 2021 with modifications. The NEBNext® Ultra™ II DNA Library Prep Kit for Illumina was used but at half reaction volumes. Specifically, 400 ng of input DNA in 13 mL was processed for each of the 19 samples. To the DNA for each sample, 3.5 mL NEBNext Ultra II FS Reaction Buffer and 1 mL of NEBNext Ultra II FS Enzyme Mix was added. This mixture was incubated for 15 minutes at 37°C and then 30 minutes at 65°C to fragment the DNA and terminate the fragmentase activity. Next, 15 mL of NEBNext Ultra II Ligation Master Mix, 0.5 mL of NEBNext Ligation Enhancer, and 1.25 mL of NEBNext Adaptor for Illumina was added to this mixture and incubated for 15 minutes at 20°C. 1.5 mL USER® Enzyme was added to this mixture and incubated at 37°C for 15 minutes with heated lid set to ≥ 47°C. This 37.75 ml reaction volume was brought to 100 ml using 0.1X TE and size selected with SPRI Ampure magnetic beads with right side selection of 0.3X and a left side selection of 0.15X. The size selected fragments concentrated into 7.5 mL were PCR amplified using 2.5 mL of a forward primer specific for the transposon that also harbored a 5’ biotin label, 2.5 mL of a P7 barcoded sequencing primer NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 and 2), and 12.5 mL of NEBNext Ultra II Q5 Master Mix. The thermocycler denature, anneal and extension times were an initial 98°C for 30 seconds, then ten rounds of 98°C for 10 seconds, 65°C for 30 seconds, and 72°C for 30 seconds, with a final extension of 72°C for 2 minutes. This reaction was cleaned up by 0.9X left side selection with SPRI Ampure magnetic beads. 12.5 mL of the biotin tagged product was hybridized to streptavidin magnetic beads to select for reads harboring the transposon primer. The beads were washed with 1X binding and wash buffer to remove any products harboring the biotinylated transposon-specific DNA fragments. A second PCR was carried out using the hybridized biotinylated transposon-streptavidin beads in 7.5 mL of 0.1X TE, 2.5 mL of a forward primer that included the P5 adapter sequence followed by a random hexamer sequence and the transposon specific primer sequence, 2.5 mL of the corresponding P7 barcoded sequencing primer NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 and 2 ) used in the first PCR reaction for the respective sample, and 12.5 mL of NEBNext Ultra II Q5 Master Mix. Each library was quantified using the Qubit DNA High Sensitivity (HS) kit and the Agilent Bioanalyzer DNA HS kit. The 19 barcode sequencing reads were pooled to achieve a 20 nM sample in 40 mL and shipped to Azenta GeneWiz for sequencing on the Illumina Nextseq platform.

treatment_protocol: Magenta vessels were placed into a controlled-environment chamber set to 50% RH and ambient CO2. At seven days after initiation, vessels were thinned to one plant per vessel and 10 µL of 103 CFU/mL FOL culture was applied to the corner opposite to the established plant in the fungal control and experimental treatment vessels. Plants were grown for 28 days total before they were photographed and harvested.

value: microbe

value: Veggie isolate

value: bacterial

value: Cells from TSB used to start the experiment


title: T0TnC

description: Library name: T0TnC_R1_001.fastq.gz


title: P1.33n.Stbl

description:
Library name: P1.33n.Stbl
Poly-A bulk RNA-seq

value: Tumor


title: P1.33.Grw

description:
Library name: P1.33.Grw
Poly-A bulk RNA-seq


title: P1.25.Grw

description:
Library name: P1.25.Grw
Poly-A bulk RNA-seq


title: FLAG-SCRT2_NT_HH25

description:
Library name: NT_HH25_eletrop_SCRT2_R1_S19_L001_R1_001_galGal6
HH25 neural tube

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal6 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Assembly: galGal6
Supplementary files format and content: bigwigs
Library strategy: CUT&RUN


title: T0TnB

description: Library name: T0TnB_R1_001.fastq.gz


title: CD4T, WT Tofacitinib treat RNA rep1

value: T cells


title: P1A.24.Grw

description:
Library name: P1A.24.Grw
Poly-A bulk RNA-seq


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + control miRNA (+DOX) rep 1

description: Library name: Pool_DOX_Scr_3

value: replicate 1


title: CD4T, WT Tofacitinib treat RNA rep3

value: 10 weeks old

value: CreER


title: A.23.Grw

description:
Library name: A.23.Grw
Poly-A bulk RNA-seq


title: NT_HH25_ATAC

description:
Library name: NT_HH25_Sample2_S2_R1_001_galGal6
HH25 neural tube

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal6 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Assembly: galGal6
Supplementary files format and content: bigwigs


title: CD4T, WT Tofacitinib untreat RNA rep1


title: H3K27ac_NT_HH25

description:
Library name: K27ac_NT_HH25_S9_R1_001_galGal6
HH25 neural tube


title: CD4T, WT RNA rep3


title: CD4T, WT Tofacitinib untreat RNA rep2


title: CD4T, WT RNA rep2


title: V.20.Grw

description:
Library name: V.20.Grw
Poly-A bulk RNA-seq


title: IgG_1

data_processing:
Raw fastq file was demultiplexed using iCount
Demultiplexed samples were mapped to the human genome (ensembl release 88) using iCount
BAM files used to generate BED files with identified and quantified cross-linked sites using iCount
BED files used to generate new BED file with subset of significantly cross-linked sites using iCount
Assembly: ensembl release 88
Supplementary files format and content: peak files with significant cross-linked sites

extract_protocol:
iCLIP performed according to bioRxiv 2021.08.27.457890
iCLIP performed according to bioRxiv 2021.08.27.457890

value: epithelium

value: breast epithelial cells


title: IgG_2

treatment_protocol: iCLIP performed according to bioRxiv 2021.08.27.457890


title: ShootTnA

description: Library name: ShootTnA_R1_001.fastq.gz

source_name: microbe from plant shoot

value: microbe from plant shoot

value: Shoot from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed is applied


title: CD4T, WT RNA rep1


title: ShootTnC

description: Library name: ShootTnC_R1_001.fastq.gz


title: CD4T, KO Tofacitinib untreat RNA rep3

value: CreER;Ctcf fl/fl


title: PDCD4_2


title: Vh.2.Stbl

description:
Library name: Vh.2.Stbl
Poly-A bulk RNA-seq


title: RootTnB

description: Library name: RootTnB_R1_001.fastq.gz

source_name: microbe from plant root

value: microbe from plant root

value: Root from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed is applied


title: RootTnA

description: Library name: RootTnA_R1_001.fastq.gz


title: CD4T, KO Tofacitinib treat RNA rep2


title: siPDCD4_1

value: WT

value: siRNA-mediated KD


title: Fv18

description:
Library name: Fv18
10X Genomics 5'HTv2

source_name: Mammary gland

value: Mammary gland

value: Fulvestrant


title: WT1_n2

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

data_processing:
QC: FastQC ( v0.11.2 )
Filters: PRINSEQ-lite ( 0.20.4 )
Mapping & QC: STAR ( 2.4.1d ), samtools ( 0.1.19 )
Counting: HTSeq-count ( 0.8.0 )
Pseudo-mapping for transcripts : Kallisto (v0.43.1)
Assembly: EnsEMBL Human GRCh37.87
Supplementary files format and content: Raw genes counts of each sample (.txt)
Supplementary files format and content: Raw transcripts counts of each sample (.tsv)

extract_protocol:
Medium was remove and 350µl RLTplus was add, Sample were extracted on QUIACUBE following the Rneasy Plus Micro kit protocole (Qiagen)
For each sample, 100 ng of total RNA was used to perform the QuantSeq 3' mRNA-Seq Library Prep Kit for Ion Torren resulting in NGS libraries which originate from the 3' end of polyadenylated RNA. The libraries were PCR amplified and barcoded in 13 cycles and were quantified using Agilent High Sensitivity DNA kit. 100 pM of the 10 libraries were combined, emulsion PCR and enrichment were performed on the Ion OT2 system Instrument using the Ion PI Hi-Q OT2 200 kit (Thermo Fisher Scientific). Samples were loaded on an Ion PI v3 Chip and sequenced on the Ion Proton System using Ion PI Hi-Q sequencing 200 kit chemistry (200 bp read length; Thermo Fisher.

value: hiPSC-derived myotubes


title: WT1_n1


title: CD4T, KO Tofacitinib untreat RNA rep1


title: CD4T, KO Tofacitinib untreat RNA rep2


title: NSTnC

description: Library name: NSTnC_R1_001.fastq.gz

source_name: microbe on seed film control

value: microbe on seed film control

value: Veggie isolate

value: bacterial

value: NoSeed


title: P1A.19.Grw

description:
Library name: P1A.19.Grw
Poly-A bulk RNA-seq

value: Tumor


title: PDFv54

description:
Library name: PDFv54
10X Genomics 5'HTv2


title: RootTnC

description: Library name: RootTnC_R1_001.fastq.gz


title: PDFv39

description:
Library name: PDFv39
10X Genomics 5'HTv2


title: NSTnA

description: Library name: NSTnA_R1_001.fastq.gz


title: input

description: Library name: s1_34_R1.fastq.gz

value: microbe

value: Tn-Seq input library


title: WT3_n2


title: ShootTnB

description: Library name: ShootTnB_R1_001.fastq.gz

value: microbe from plant shoot


title: Fv44

description:
Library name: Fv44
10X Genomics 5'HTv2


title: Kidney, Obese+enalapril 2

first: Michael

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

institute: Charité - Universitätsmedizin Berlin

description:
10x Genomics
RK83_2

data_processing:
Raw fastq files were aligned to the ENSEMBL rn6 genome and quantified with CellRanger v7.0.1. Seurat v4.3.0 was used for data quality control, preprocessing, and dimensional reduction. In short, for every sample, a separate gene-cell data matrix was generated and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >50 were excluded. Remaining barcodes of high-quality nuclei were log-normalized and the top 3000 highly variable genes were identified with the vst method. After data scaling, linear dimension reduction was performed using principal component analysis (PCA). A shared nearest neighbor network was created based on Euclidian distances between cells in multidimensional PC space using the first 15 dimensions before clustering using FindClusters and dimension reduction using RunUMAP functions, respectively.
Doublet-like cells were identified using DoubletFinder v2.0. Assuming no ground truth to facilitate an unbiased approach, pK was identified using paramSweep_v3 function with PCs=1:15. Homotypic doublet proportion was estimated with function modelHomotypic using above clustering information. Finally, function doubletFinder_v3 was run with pN=0.25, pK and nExp as identified by the functions above and Uniform Manifold Approximation and Projections (UMAPs) were manually inspected for singlet/doublet status.
After determining high quality ambient RNA-corrected singlet barcodes for every sample individually using SoupX v1.5.2, 10X filtered output matrices of all 11 samples were subset to singlet barcodes, as determined above, before merging of Seurat objects. The Seurat preprocessing pipeline was then rerun on the merged object (normalization, identification of highly variable genes, scaling, linear dimension reduction), regressing out nCount_RNA during scaling. Then, harmony v0.1.0 was used to correct for potential batch effects. The first 15 harmony-corrected principal components were used for nearest neighbor network creation, clustering, and dimension reduction. A clustering resolution of 1.3 was chosen to best reflect separate cell identities without artificial over-clustering.
Assembly: rn6
Supplementary files format and content: Counts matrix RDS object
Supplementary files format and content: metadata CSV table

source_name: kidney

extract_protocol:
Rats were perfused with chilled 1x PBS via the left ventricle prior to euthanasia. Single cells were isolated using a previously established protocol. In short, rat kidneys were digested using Miltenyi multi tissue dissociation kit 1 (130-110-2011). Debris was removed using Miltenyi debris removal solution (130-109-398), dead cells were removed using Miltenyi dead cell removal kit (130-090-101). Cell number and viability were analyzed using a Countess AutoCounter (Invitrogen, C10227).
10,000 cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM chip G Single-Cell Kit (10X Genomics, PN-1000120) to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, PN-1000121). The cDNA and library were made using the Chromium Next GEM Single-Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262) according to the manufacturer’s protocol. Quality control for the libraries was performed using Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Libraries were sequenced on an Illumina Novaseq 6000 system with 2 × 150 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index and 91 bp Read2 for transcript.

treatment_protocol: 12 weeks old male ZSF1 lean and ZSF1 obese rats were obtained from Charles River. The animals were housed in a temperature (22-24 °C) and humidity-controlled environment with a light/dark cycle. Access to water and high energy rodent chow 5008 was provided ad libitum. The protocol was approved by the Institutional Animal Care and Use Committee at the University of Pennsylvania. ZSF1 obese rats were randomly divided into 2 groups (vehicle, enalapril) and compared to ZSF1 lean rats as controls. Vehicle or enalapril was dissolved in drinking water and water consumption was measured daily to calculate the daily dose per rat and to compare intended and observed dose. Enalapril concentration was adjusted every week based on body mass (individual) and water intake (cage average).

value: kidney

tag: phenotype

value: Obese

value: enalapril


title: FolShootTnB

description: Library name: FolShootTnB_R1_001.fastq.gz

value: Shoot from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed for additional FOL challenge


title: WT2_n3

value: WT


title: Kidney, Obese+enalapril 1

description:
10x Genomics
RK83_0


title: Kidney, Obese 4

description:
10x Genomics
RK91_1


title: CD4T, KO Tofacitinib treat RNA rep3

value: T cells

value: 10 weeks old

value: CreER;Ctcf fl/fl


title: WT2_n2

value: hiPSC-derived myotubes


title: CD4T, KO Tofacitinib treat RNA rep1


title: PDFv63

description:
Library name: PDFv63
10X Genomics 5'HTv2

value: Mammary gland


title: CD4T, KO RNA rep3


title: CD4T, KO RNA rep1


title: Kidney, Obese 3

description:
10x Genomics
RK91_0


title: CD4T, WT PRO rep4

data_processing:
sequnced using Illumina HiSeq X ten platform
Raw PRO-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
peaks were called using homer v2.2.7.1 with the following setting: -style groseq
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: Peak, CPM normalized bigwig
Library strategy: PRO-seq

extract_protocol:
PRO-seq was performed using the protocol from Mahat et al., 2016 with small modifications. Permeabilized cells were incubated in polymerase run-on reactions with ribonucleotide triphosphate (NTP) substrates.
cDNA is amplified through 15–17 cycles of PCR amplification with Illumina TRU-seq multiplexing primers. Libraries were paired-end sequenced on Illumina HiSeq X ten platform.

value: CreER


title: WT3_n3


title: WT3_n1


title: CD4T, WT PRO rep3


title: WT1_n3


title: CD4T, WT PRO rep2


title: PDCD4_1

value: epithelium

value: breast epithelial cells


title: NSTnB

description: Library name: NSTnB_R1_001.fastq.gz

value: microbe on seed film control

value: Veggie isolate

value: bacterial

value: NoSeed


title: CD4T, KO RNA rep4


title: FolRootTnA

description: Library name: FolRootTnA_R1_001.fastq.gz

value: microbe from plant root

value: Root from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed for additional FOL challenge


title: LGMD R2_KO1_n2

source_name: LGMD R2 nonsense 1

value: LGMD R2 nonsense 1


title: FolShootTnA

description: Library name: FolShootTnA_R1_001.fastq.gz

value: microbe from plant shoot

value: Shoot from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed for additional FOL challenge


title: CD4T, KO PRO rep3

value: T cells


title: FolShootTnC

description: Library name: FolShootTnC_R1_001.fastq.gz


title: LGMD R2_KO1_n1


title: FolRootTnC

description: Library name: FolRootTnC_R1_001.fastq.gz


title: Kidney, Obese+enalapril 3

description:
10x Genomics
RK92_1

value: kidney

value: Obese

value: enalapril


title: LGMD R2_KO1_n3

value: hiPSC-derived myotubes


title: Kidney, Obese 1

description:
10x Genomics
RK88_0


title: LGMD R2_KO2_n2

source_name: LGMD R2 nonsense 2

value: LGMD R2 nonsense 2


title: WT2_n1

value: WT


title: Maxiprep

description: Library name: Maxiprep

data_processing:
Sequencing reads were assigned to the designed oligonucleotides based on barcode sequence matching. Barcode sequences were extracted from the provided oligo pool FASTA file as the 10-nucleotide segment immediately upstream of the final 17 nucleotides. When sequencing reads extended beyond the barcode region (as in our dataset), reads were assigned to a given oligonucleotide if they contained no more than two mismatches relative to the corresponding designed target sequence. The designed target sequences were obtained from the oligo pool FASTA file by removing the first 16 nucleotides and the final 27 nucleotides of each oligonucleotide.
Assembly: Not applicable, using custom sequences
Supplementary files format and content: Comma-separated file include sequencing read counts for oligonucleotides and samples.

source_name: Plasmid DNA

extract_protocol:
For the reverse cross-linking reaction, lysates were mixed with 33 μL of reverse crosslinking buffer (3X PBS, 6% N-Lauroylsarcosine, 30 mM EDTA, 15 mM DTT), 10 μL of Proteinase K (Ambion), and 1 μL of RNaseOUT (Invitrogen) and incubated at 42C for 1 hour then 55C for 1 hour. TRIzol (Invitrogen) and chloroform, followed by RNeasy Plus Mini Kit (Qiagen), were used to isolate RNAs.
Sequencing libraries were generated using customized primers that anneal to the universal priming sites on the oligos and attach Illumina-compatible sequencing adapters: reverse primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), forward primer (caagcagaagacggcatacgagatCGTGATgtgactggagttcagacgtgtgctcttccgatctACTGGCCGCTTCACTG, CGTGAT is a Illumina truseq index and can be variable).
Amplicon sequencing was performed with a single-end run.

value: Plasmid DNA


title: Fv17

description:
Library name: Fv17
10X Genomics 5'HTv2

value: Mammary gland

value: Fulvestrant


title: old, glia, replicate 6

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

description: Library name: Sample 18

data_processing:
Data was analysed using an in-house built pipeline
Raw reads were processed and demultiplexed using bcl2fastq (v2.20.2).
Quality control of raw sequencing data was done using FastQC (v0.11.5).
Reads were aligned to the mouse (mm10) genome with the STAR aligner (v2.5.2b)
feature Counts (v1.5.1) was used to generate read counts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: C57/B6, male, 16 months, brain, hippocampus, CA1

extract_protocol:
RNA was isolated using Tri reagent (Sigma), followed by purification with the RNA Clean & Concentrator-5 kit (Zymo)
Libraries were generated from 300 ng RNA with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara)

value: old

value: glia


title: Kidney, Lean 1

description:
10x Genomics
RK100_0

value: Lean


title: Kidney, Lean 4

description:
10x Genomics
RK42_2


title: LGMD R2_KO2_n1


title: FolRootTnB

description: Library name: FolRootTnB_R1_001.fastq.gz

value: microbe from plant root

value: Veggie isolate

value: bacterial

value: Root from tomato where B. contaminans Tn-Seq library (108 CFU/mL) plus seed for additional FOL challenge


title: LGMD R2_MIS1_n3

source_name: LGMD R2 missense 1

value: LGMD R2 missense 1


title: CD4T, WT RPB1-S5P rep2

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

data_processing:
sequnced using Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g mm (--broad for H3K4me1,H3K27me3 ChIP-seq peak calling and -q 0.001 for H3K27ac ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

extract_protocol:
ChIP-seq was performed using the protocol from Schmidl et al., 2015 with small modifications. Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform.

value: T cells

value: 10 weeks old

value: CreER

value: Phospho-Rpb1 CTD (Ser5) (CST #13523)


title: CD4T, KO RNA rep2

value: CreER;Ctcf fl/fl


title: lin-15B mutant treated with cco-1 RNAi rep#1

city: 杭州

first: hongyun

last: tang

state: 浙江省 — Zhejiang Sheng

address: 墩余路600号

department: School of Life Sciences

institute: Westlake University

description: Library name: lin-15B(jef48) cco-1 RNAi a

data_processing:
data processing step Raw RNA-seq reads were filtered using SOAPnuke (v1.5.6) to remove adapter contamination, reads with >5% Ns, and low-quality reads (quality <15 in >20% bases), generating clean data.
Clean reads were mapped to the reference genome (WBcel235) using HISAT2 (v2.1.0) and to the reference gene set using Bowtie2 (v2.3.4.3).
Gene expression was quantified with RSEM (v1.3.1) and clustered heatmaps were generated using pheatmap (v1.0.8).
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text file RNAseq_raw_and_normalized_counts_all_genes including raw and normalized read counts for all genes in each sample.

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: C. elegans strains were maintained on NGM plates seeded with E. coli OP50 at 20°C under standard laboratory conditions

extract_protocol:
Total RNA was extracted from L4-stage C. elegans using TRIzol reagent according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA using standard BGI mRNA library construction protocols, including mRNA enrichment, fragmentation, cDNA synthesis, end repair, adapter ligation, PCR amplification, and quality control. Sequencing was performed on the BGISEQ platform using DNA nanoball (DNB) technology.

treatment_protocol: Synchronized L1 larvae were cultured on IPTG-NGM plates seeded with RNAi bacteria (EV or cco-1 RNAi) at 20°C until the L4 stage.

value: Whole organism

value: cco-1 RNAi


title: LGMD R2_KO2_n3

value: hiPSC-derived myotubes

value: LGMD R2 nonsense 2


title: old, glia, replicate 4

description: Library name: Sample 16

value: old


title: Kidney, Lean 3

description:
10x Genomics
RK42_1

value: kidney


title: CD4T, WT PRO rep1

institute: Yonsei University College of Medicine


title: Kidney, Obese 2

description:
10x Genomics
RK88_1

value: Obese


title: CD4T, KO H3K27me3 rep2

value: H3K27me3 (Abcam #ab6002)


title: CD4T, WT STAT5 rep1


title: CD4T, KO PRO rep2


title: lin-15B mutant treated with cco-1 RNAi rep#2

description: Library name: lin-15B(jef48) cco-1 RNAi b


title: Kidney, Lean 2

description:
10x Genomics
RK100_2

value: Lean


title: old, glia, replicate 3

description: Library name: Sample 15

value: glia


title: LGMD R2_MIS1_n2


title: CD4T, WT ATAC rep1

data_processing:
sequnced using Illumina HiSeq X ten platform
Raw ATAC-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bowtie2 v2.3.5.1 with the following setting: --end-to-end --very-sensitive
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
filtered reads were shifted and reads in Nucleome-free regions extracted using deeptools alignmentSieve with the following setting: --maxFragmentLength 100 --ATACshift
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g mm
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: narrowPeak, CPM normalized bigwig

extract_protocol:
ATAC-seq was performed using the protocol from Corces et al., 2015 with small modifications. Nuclear pellets at 5x10^4 were permeabilized and tagmented by Tn5 enzyme.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq X ten platform.


title: CD4T, KO PRO rep1


title: old, glia, replicate 5

description: Library name: Sample 17


title: young, neurons, replicate 5

description: Library name: Sample 11

source_name: C57/B6, male, 3 months, brain, hippocampus, CA1

value: young

value: neurons


title: young, neurons, replicate 6

description: Library name: Sample 12


title: CD4T, KO ATAC rep2

value: T cells


title: lin-15B mutant treated with EV rep#2

description: Library name: lin-15B(jef48) Ev b

value: EV control


title: LGMD R2_MIS1_n1

value: LGMD R2 missense 1


title: CD4T, KO ATAC rep1

value: 10 weeks old


title: CD4T, KO RPB1-S5P rep2

value: CreER;Ctcf fl/fl

value: Phospho-Rpb1 CTD (Ser5) (CST #13523)


title: CD4T, WT SMC1A rep1

value: CreER

value: SMC1 (Bethyl #A300-055A)


title: ePCR

first: Taeyoung

last: Hwang

address: 855 N. Wolfe St, 3rd floor, Suite 300

description: Library name: ePCR

source_name: PCR amplicon

value: PCR amplicon


title: lin-15B mutant treated with EV rep#1

description: Library name: lin-15B(jef48) Ev a

value: Whole organism


title: old, glia, replicate 1

description: Library name: Sample 13

value: old


title: CD4T, WT H3K4me3 rep1

value: H3K4me3 (Millipore #04-745)


title: old, glia, replicate 2

description: Library name: Sample 14


title: CD4T, WT H3K27me3 rep2

value: H3K27me3 (Abcam #ab6002)


title: atfs-1 mutant treated with cco-1 RNAi rep#1

description: Library name: atfs-1(gk3094) cco-1 RNAi a

value: cco-1 RNAi


title: atfs-1 mutant treated with EV rep#2

description: Library name: atfs-1(gk3094) Ev b


title: CD4T, KO STAT5 rep1


title: CD4T, WT CTCF rep1

value: CTCF (CST #2899)


title: young, neurons, replicate 4

description: Library name: Sample 10

value: young


title: atfs-1 mutant treated with cco-1 RNAi rep#2

description: Library name: atfs-1(gk3094) cco-1 RNAi b


title: pT3 mA3 2-N

first: Duowei

last: Wang

state: JIANGSU

address: Longmian Road 639

institute: China Pharmaceutical University

data_processing:
Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US)."
Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: DEN-induced Hepatocarcinoma in pT3-mA3 group

growth_protocol: HCC in age-matched male mice were induced by DEN injection.

extract_protocol:
Tumor tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: relatively normal tissue from pT3-mouse APOBEC3B plasmid injected mice

tag: tumor stage

value: 8 months after DEN treatment


title: young, neurons, replicate 1

description: Library name: Sample 7

value: neurons


title: CD4T, WT ATAC rep2

value: T cells


title: CD4T, WT H3K4me1 rep2

value: 10 weeks old

value: H3K27ac (Abcam #ab4729)


title: atfs-1 mutant treated with EV rep#1

description: Library name: atfs-1(gk3094) Ev a

value: EV control


title: pT3 mA3 2-T

treatment_protocol: HCC in age-matched male mice were induced by DEN injection.

value: tumor tissue from pT3-mouse APOBEC3B plasmid injected mice


title: N2 treated with cco-1 RNAi rep#2

description: Library name: N2 cco-1 RNAi b

value: WT


title: young, glia, replicate 5

description: Library name: Sample 5

value: glia


title: N2 treated with cco-1 RNAi rep#1

description: Library name: N2 cco-1 RNAi a

value: Whole organism


title: CD4T, WT H3K4me1 rep1

value: CreER


title: young, neurons, replicate 3

description: Library name: Sample 9


title: young, neurons, replicate 2

description: Library name: Sample 8


title: CD4T, KO H3K4me3 rep1

value: CreER;Ctcf fl/fl

value: H3K4me3 (Millipore #04-745)


title: N2 treated with EV rep#2

description: Library name: N2 Ev b


title: pT3 mA3 1-T

value: tumor tissue  from pT3-mouse APOBEC3B plasmid injected mice


title: pT3 mA3 1-N


title: young, glia, replicate 4

description: Library name: Sample 4


title: CD4T, KO H3K4me1 rep1


title: CD4T, KO H3K4me1 rep2


title: young, glia, replicate 3

description: Library name: Sample 3


title: N2 treated with EV rep#1

description: Library name: N2 Ev a


title: young, glia, replicate 6

description: Library name: Sample 6


title: 48 hpf olig2 multiome, ATAC

city: Aurora

first: Kim

last: Arena

state: CO

address: RC1S 12801 E 17th Ave

institute: University of Colorado Anschutz

description:
Library name: 48 hpf ATAC
10X Genomics multiomic, ATAC-seq
oligegfp_48hpf_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Fastq sequencing files from 10X Genomics multiomic single-nuclei RNA-seq and ATAC-seq were processed through Cell Ranger ARC with a zebrafish GRCz11 library. A Seurat Object was craeted form the matrix.h5 and fragments.tsv.gz files, annotated with GRCz11.v99.EnsDb, and ATAC peaks corrected by calling with macs2 and filtered to exclude cells with gene count <750, total ATAC counts <300, percent mitochondrial gene expression >10%, nucleosome expression >2, or TSS enrichment <1.
Assembly: GRCz11
Supplementary files format and content: h5 files are Hierarchical Data Formats files of cellranger_arc count matrix output
Supplementary files format and content: tsv.gz files are gzipped tab delimited bed files of atac fragments
Supplementary files format and content: RDS files are R files containing Seurat Object

source_name: spinal cord

extract_protocol:
Spinal cord cells were extracted from the trunks of wildtype zebrafish larvae expressing the olig2:egfp transgene at 36 and 48 hpf. Cells were sorted for EGFP prior to nuclei isolation. Single-cell sequencing was performed using the Chromium Next Gen Single Cell Multiome ATAC and Gene Expression Library and Gel Bead Kit (10X Genomics) and the Chromium X.
Libraries were sequenced on an Illumina Novaseq 6000

value: spinal cord

value: wildtype


title: CD4T, KO SMC1A rep1

city: Seoul

value: SMC1 (Bethyl #A300-055A)


title: pT3 vector 9-T

source_name: DEN-induced Hepatocarcinoma in pT3-vector group

value: tumor tissue  from pT3-vector plasmid injected mice

value: 8 months after DEN treatment


title: pT3 vector 1-T


title: M20_3

status: Public on Jan 11 2026

description: Library name: Sample 22

data_processing:
VIPER pipeline (https://github.com/hanfeisun/viper-rnaseq/blob/master/cfce/README_CFCE.md) was used for alignment, assembly and gene counting.
Assembly: rn6
Supplementary files format and content: csv files including raw counts for each gene and each sample

source_name: mammary tumor

extract_protocol:
A piece of tumors were cut and grinded. Then RNA was harvested using RNeasy Micro Kit. 3000 ng RNA of each sample was submitted for the construction of sequencing libraries by GENEWIZ.
Libraries preparation with poly(A) selection and 150-bp paired-end sequencing on an Illumina HiSeq platform were performed by GENEWIZ (USA; www.GENEWIZ.com).

value: mammary tumor


title: 48 hpf olig2 multiome, RNA

description:
Library name: 48 hpf GEX
10X Genomics multiomic, RNA-seq
oligegfp_48hpf_filtered_feature_bc_matrix.h5


title: 36 hpf olig2 multiome, ATAC

description:
Library name: 36 hpf ATAC
10X Genomics multiomic, ATAC-seq
oligegfp_36hpf_filtered_feature_bc_matrix.h5


title: CD4T, KO CTCF rep1

value: T cells

value: 10 weeks old

value: CTCF (CST #2899)


title: young, glia, replicate 2

description: Library name: Sample 2

value: young


title: young, glia, replicate 1

description: Library name: Sample 1


title: M20_1

description: Library name: Sample 20


title: 36 hpf olig2 multiome, RNA

description:
Library name: 36 hpf GEX
10X Genomics multiomic, RNA-seq
oligegfp_36hpf_filtered_feature_bc_matrix.h5


title: M12_3

description: Library name: Sample 19


title: M3_5

description: Library name: Sample 12


title: M20_2

description: Library name: Sample 21


title: M12_1

description: Library name: Sample 17


title: M3_7

description: Library name: Sample 14


title: M3_3

description: Library name: Sample 10


title: M3_8

description: Library name: Sample 15


title: CD4T, Input


title: pT3 vector 1-N

value: relatively normal tissue from pT3-vector plasmid injected mice


title: M3_4

description: Library name: Sample 11


title: M20_4

description: Library name: Sample 23


title: M12_2

description: Library name: Sample 18


title: M1_8

description: Library name: Sample 7


title: M6_2

description: Library name: Sample 16


title: M1_7

description: Library name: Sample 6


title: EXP-1

city: nantong

first: wen

last: li

address: qixiu road 19

institute: Nantong University

description:
Library name: SAMPLE 4
EXP-1

data_processing:
RNA-Seq
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Unmapped reads were collected to identify the circRNA utilizing ACFS
Assembly: Rnor 6.0
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus


title: NC-3

description:
Library name: SAMPLE 3
NC-3


title: M20_2 [exome-seq]

description: Library name: Sample 23

data_processing:
Somatic mutation calling was performed using the nf-core/sarek pipeline (v3.4.1) with Singularity. Raw sequencing reads were aligned to rat Rnor_6.0 reference genome. Following GATK Best Practices, GATK4 was used for duplicate marking, and Strelka2 was applied for variant calling using matched normal liver tissue as control. High-confidence variants were annotated with Ensembl VEP v107 and converted to Mutation Annotation Format (MAF) using vcf2maf (https://github.com/mskcc/vcf2maf).
Assembly: Rnor_6.0
Supplementary files format and content: vcf files including the mutations for each sample

extract_protocol:
A piece of tumors were cut and grinded. Then genomic DNA was harvested using AllPrep DNA/RNA/Protein Mini Kit.
Whole-exome sequencing libraries were prepared using the Agilent SureSelectXT Target Enrichment System following the manufacturer’s protocol. DNA from the liver of an untreated healthy rat served as a normal control. Briefly, 3 µg of genomic DNA extracted from rat tumors was sheared to the desired fragment size using ultrasonication, followed by end-repair, A-tailing, and adapter ligation. The adapter-ligated DNA was hybridized to biotinylated RNA baits targeting exome regions, and captured DNA fragments were enriched using streptavidin-coated magnetic beads. After PCR amplification, the final libraries were quantified, assessed for quality using a Bioanalyzer, and sequenced on an Illumina platform to generate paired-end reads.


title: pT3 vector 9-N


title: M1_6

description: Library name: Sample 5


title: M1_5

description: Library name: Sample 4