title: scRNA-seq of mus musclus: E12.5 embryo male lung, CKO

city: shenzhen

first: Jiang

last: Yamei

address: longfei

country: China

institute: The Chinese University of Hong Kong-Shenzhen

description: Library name: scRNA_CKO

data_processing:
FASTQ files were run through CellRanger (v7.1.0) software with default parameters for de-multiplexing, aligning reads with STAR software to mm10, and counting unique molecular identifiers (UMIs). As input files of the Seurat R package (v4.4.0), the filtered gene expression matrices were then used for downstream analyses.
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix

source_name: lung

extract_protocol:
Single-cell transcriptomic libraries were constructed using Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics, PN-1000121) according to the manufacturer’s protocol. Briefly, after dissociation, whole lung cells were collected and resuspended to form cell suspension, and the cell concentration was adjusted to 1000 cells/μL (viability ≥ 85%). Ap proximately 5000 cells were captured in droplets, and then lysed to release total RNA. RNA was barcoded through reverse transcription from individual gel beads in emulsion. The cDNA was then amplified for the library construction. Prepared libraries were sequenced on the Illumina NovaSeq 6000. Each library produced at least 100 GB of raw data for downstream bioinformatics analysis.
Single-cell transcriptomic libraries were constructed using Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics, PN-1000121) according to the manufacturer’s protocol. Briefly, after dissociation, whole lung cells were collected and resuspended to form cell suspension, and the cell concentration was adjusted to 1000 cells/μL (viability ≥ 85%). Ap proximately 5000 cells were captured in droplets, and then lysed to release total RNA. RNA was barcoded through reverse transcription from individual gel beads in emulsion. The cDNA was then amplified for the library construction. Prepared libraries were sequenced on the Illumina NovaSeq 6000. Each library produced at least 100 GB of raw data for downstream bioinformatics analysis.

value: lung

value: lung epithelia cells

value: CKOL


title: G11_Plate 8B

status: Public on Oct 09 2025

type: SRA

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

description:
Library name: BSSE-QGF-131345
Smart-seq2

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Sequence reads were trimmed for quality control with trim_galore (v.0.6.5) and uniquely aligned to mouse reference genome (GRCm38) using kallisto pseudo-mode(v.0.46.1).
Transcript-level counts were converted into gene-level counts using tximport (v1.18.0) with mm10 Refseq
Assembly: UCSC, mm 10 (GRCm38)
Supplementary files format and content: TSV text file including a table of genes (rows) x cells (columns) showing counts  per single cell. Processed data file includes only samples that passed QC check.

molecule: total RNA

organism: Mus musculus

source_name: Dorsal Pancreas

extract_protocol:
Dorsal pancreatic tissue (E12.5) was dissected from Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS-sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to the Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

tag: tissue

value: Dorsal Pancreas

tag: developmental stage

tag: genotype


title: CARD11+/+ FO, Unstim, Rep 2

city: Baltimore

first: Joel

last: Pomerantz

address: 733 N. Broadway

department: Biological Chemistry

country: USA

institute: Johns Hopkins University School of Medicine

description: Library name: F2

library_source: transcriptomic

data_processing:
Raw reads of fastq format were cleaned by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data using Perl scripts.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: gene_count.xls tab-delimited xls file contains raw counts for each gene in each sample.
Supplementary files format and content: gene_fpkm.xls tab delimited xls file contains FPKM for each gene in each sample.

source_name: Follicular B cells

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini Kit with on-column DNase digestion according to the manufacturer’s instructions.
mRNA was purified from total RNA via polyA enrichment 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. Sequencing libraries were generated using NEBNext UltraRNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendation.

treatment_protocol: Follicular (FO) and Marginal Zone (MZ) B cells were harvested from the spleen using the Miltenyi MZ and FO B Cell Isolation Kit (Mouse) according to the manufacturer's instructions. Cells were either left unstimulated or treated for 24hrs with 4µg/mL anti-IgM.

tag: cell type

value: Follicular B cells

tag: treatment

value: Unstim


title: H11_Plate 8B

description:
Library name: BSSE-QGF-131346
Smart-seq2


title: CARD11+/+ FO, Unstim, Rep 1

description: Library name: F1


title: male zebra fish, 40 μg/L DBAN_3, day 56

city: Zhenjiang

first: Xinwei

last: Xu

state: Jiangsu

address: Xiangshan Street 301 Xuefu Road

department: School of Medicine

institute: Jiangsu University

description: Library name: M4_12_

data_processing:
FastQC software and R were used to evaluate the quality of the original sequencing data. Fastp software was used to filter some low-quality raw reads with adapters in the original sequencing sequence, and clean reads were used for subsequent analysis. Quality control first removes the sequencing primers, then removes the low-quality sequences at the end ( Q < 15 ), and finally removes the sequences with fragment length < 40 bp.
STAR software was used to compare the filtered reads with the reference database, and then Picard was used to count the results of STAR alignment. The distribution of each sample 's sequence in the coding region, untranslated region, intron and intergenic region was counted to evaluate the abnormal situation of the experimental library. RSeQC software was used to randomly sample all the sequences aligned to the reference genome, and the transcripts were expressed quantitatively with the sampled reads. For transcripts with different expression abundances, they were divided into 6 levels according to the RPKM value. The proportion of the error between the RPKM value obtained by sampling and the final RPKM value within 15 %.
Quantitative expression : Stringtie 's analysis process was used to quantify the expression of known genes and transcripts, and the gene level was normalized. Differential expression analysis : Deseq2 software was used to analyze the differentially expressed genes between the case group and the blank control group. Gene Ontology ( GO ) and Kyoto Encyclopedia of Genes and Genomes ( KEGG ) enrichment analysis of significantly different genes : GO and KEGG enrichment analysis of significantly different genes was performed using the R package cluster Profiler.
Assembly: rassf2b, foxq2, gpx7, syncrip, gpr182, etc.
Supplementary files format and content: raw reads count for each gene.

molecule: polyA RNA

organism: Danio rerio

source_name: brain tissue

growth_protocol: The fish room was maintained at a constant temperature (28 ± 0.5) °C, with a light cycle of 14 hours: 10 hours. The aquaculture water was filtered water with continuous aeration and sea salt added to adjust the conductivity to 500-530 μS/cm. Zebrafish are fed live plumpy shrimp twice daily.

extract_protocol:
The total RNA was extracted by TruSeq RNA sample Preparation kit V2, and mRNA was sorted. The mRNA with poly (A) structure was specifically bound by magnetic beads with oligo-dT.
The purified mRNA was synthesized into cDNA under the action of reverse transcriptase and polymerized into double-stranded cDNA. The double-stranded cDNA end repair reaction was performed, and the 3 ' end plus ' A ' buffer reaction system was added. The illumina sequencing adaptor was connected to both ends of the DNA by T4 DNA ligase to construct an RNA library.

treatment_protocol: Female and male zebrafish were categorized in the experiment, with a blank control group, 1.6, 8, 40, 200, and 1000 μg/L, 5 different doses of DBAN exposure groups, respectively. The exposure time was 56 days. During this period, the cycle of changing half of the exposure solution every day for the first two days and all of the exposure solution on the third day was carried out. The brain tissue of female zebrafish exposed to 0, 40 and 200 μg/L DBAN, and male zebrafish exposed to 0 and 40 μg/L DBAN was taken for RNA-seq after 56 days of exposure.

value: brain tissue

tag: Sex

value: male

value: 40 μg/L DBAN, day56


title: BS_lib2_Col_rep1

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

library_source: genomic

data_processing:
Reads were trimmed for low quality sequences and adapter contamination using TrimGalore (Babraham Institute) and mapped to the TAIR10 genome with Bismark. Bismark was also used to obtain the methylation percentages for each cytosine and to generate the per-position DNA methylation tracks.
Assembly: TAIR10
Supplementary files format and content: BED-like files containing six fields: chromosome, start, end (0-based end exclusive, same as BED), number of reads overlapping this position with an unmethylated cytosine, number of reads overlapping this position with a methylated cytosine, and the resulting % methylation, equal to 100*(# methyl / (# methyl + # unmethyl)). The three sequence contexts CG, CHG and CHH are in separate files. Each position in the file should correspond to a cytosine in the respective context in the TAIR10 genome sequence.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: mature pollen

growth_protocol: Plants were grown on soil in greenhouse under long-day conditions (16h light / 8h dark)

extract_protocol:
Pollen extraction was performed following protocol in Ichino et al. 2022. Briefly, ~500 uL of open flowers were harvested into 1.7 mL epp tubes, then 700 uL of Galbraith buffer (45 mM MgCl2, 30 mM C6H5Na3O7.2H2O [Trisodium citrate dihydrate], 20 mM MOPS, 0.1% [v/v] Triton X-100, pH 7, 5 l per ml of 14.3M Beta-mercaptoethanol [CAS-60-24-2, Fisher Scientific]) was added and samples were vortexed at max strength 2 min at 4C to release pollen from anthers. The suspension was filtered with an 80 um nylon mesh into a new 1.5 ml tube. The procedure was repeated one more time with the same flowers to increase the yield of pollen. The two aliquots of filtered pollen suspension were combined and centrifuged for 5 min at 500 g, 4°C. The pollen pellet was frozen in liquid nitrogen and stored at -80C. DNA extraction from pollen pellets was performed with the cetyl trimethylammonium bromide (CTAB) method and treated with RNase A (Qiagen).
40-100 ng of DNA per sample were sheared with the Covaris S2 instrument to an average fragment size of 200bp (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Treatment Time = 120 seconds). The sheared DNA was used as input for BS-seq library preparation using the Nugen Ultralow Methyl-Seq kit, following manufacturer’s instructions except for the bisulfite conversion, which was done with the EpiTect Bisulfite Kit (Qiagen, 59104) instead of the TrueMethyl oxBS. The bisulfite conversion reaction in the thermocycler was performed twice (overnight) to increase the efficiency. Final libraries were sequenced on Novaseq 6000 machines.

value: mature pollen

tag: ecotype

value: sln


title: A12_Plate 8B

description:
Library name: BSSE-QGF-131347
Smart-seq2


title: C12_Plate 8B

description:
Library name: BSSE-QGF-131349
Smart-seq2


title: MMR24

type: genomic

city: Toronto

first: Uri

last: Tabori

state: Ontario

address: 170 Elizabeth St

department: Haematology/Oncology

country: Canada

institute: Sick Kids

description:
Methylation data from brain tumor sample.
201492570127_R04C01

hyb_protocol: Illumina protocol.

scan_protocol: Signal was read with the iScan or NextSeq 550 systems (Illumina).

data_processing:
Methylation data from Illumina Infinium HumanMethylation450 and MethylationEPIC BeadChips were combined and preprocessed with normal-exponential out-of-band background (Noob) correction using the minfi (v.1.50.0) package in R.
Beta values normalized with minfi using the preprocessNoob method and a beta offset of 0.

label: cy3, cy5

organism: Homo sapiens

source_name: Primary MMRD Glioma

label_protocol: Illumina protocol.

extract_protocol: DNA was extracted from tumour and blood samples using different kits as appropriate for the sample type and format: Qiagen DNeasy Blood & Tissue Kit (Cat No./ID96504) for frozen tissue, and MasterPure Complete DNA and RNA Purification Kit (Epicentre #MC85200) for formalin fixed paraffin embedded tissue.

value: Primary MMRD Glioma

tag: subgroup


title: scRNA-seq of mus musclus: E12.5 embryo male lung

description: Library name: scRNA_ARC

data_processing:
We used the FASTQ files from both snATAC and snRNA as input files for CellRanger ARC (v2.0.2) to achieve mm10 mouse genome aligning, real cells identifying, cell barcode demultiplexing and molecular counting for both ATAC and GEX (Gene Expression). We employed the resulting files (filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and per_barcode_metrics.csv), as input files for the creation of a new Seurat object using the R packages Seurat (v4.4.0) and Signac (v1.13.0).
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix
Supplementary files format and content: fragment files

extract_protocol:
Single cell multiomics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) according to the manufacturer’s protocol. Briefly, after dissociation, cells (epithelia cells: whole lung cells= 1:10) were collected and resuspended in chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing Transposase. The Transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library
Single cell multiomics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) according to the manufacturer’s protocol. Briefly, after dissociation, cells (epithelia cells: whole lung cells= 1:10) were collected and resuspended in chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing Transposase. The Transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library

value: whole lung cells

value: WT


title: MMR22

description:
Methylation data from brain tumor sample.
206522880071_R01C01


title: male zebra fish, 40 μg/L DBAN_2, day 56

description: Library name: M4_9_


title: B12_Plate 8B

description:
Library name: BSSE-QGF-131348
Smart-seq2


title: MMR5

description:
Methylation data from brain tumor sample.
200992300002_R05C01


title: male zebra fish, 40 μg/L DBAN_1, day 56

description: Library name: M4_6_1_


title: D12_Plate 8B

description:
Library name: BSSE-QGF-131350
Smart-seq2


title: MMR6

description:
Methylation data from brain tumor sample.
204234720085_R03C01


title: Liver 3_KO

city: Guangzhou

first: Kai

last: Yan

state: Guangdong

address: No. 106, Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People's Hospital

data_processing:
Clean sequencing data were compared with STAR (Version 2.10.a)
Clean sequencing data obtained through the RPKM matching method and collated as Log2 values in R (Version 4.0.5)
Heat-map, gene-set enrichment analysis was followed-up analyzed based on the expression of target genes with Pheatmap (Version 1.0.12).
Assembly: mm10
Supplementary files format and content: Matrix table with raw clonotype counts, types and other details for samples

source_name: Liver

extract_protocol:
Livers tissues from wild type and Akr1d1-knockout mice with established tumors derived from Hepa 1-6 cells were collected and lysed with Trizol reagent.
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB,USA, Catalog #:E7530L)

value: Liver

value: Hepa1-6-induced HCC model


title: E12_Plate 8B

description:
Library name: BSSE-QGF-131351
Smart-seq2


title: Liver 2_KO


title: male zebra fish, control_2, day 56

description: Library name: M1_4_1_

value: 0 μg/L DBAN, day56


title: MMR2

description:
Methylation data from brain tumor sample.
200992300002_R02C01


title: male zebra fish, control_3, day 56

description: Library name: M1_7_


title: Liver 1_KO


title: F12_Plate 8B

description:
Library name: BSSE-QGF-131352
Smart-seq2


title: Liver 3_WT


title: VITAL01_SS2

city: San Francisco

first: Diana

middle: Matthew

last: Laird

state: CA

address: 35 Medical Center Way RM913D

institute: University of California

description:
Library name: Sample 2
SmartSeq2

data_processing:
Sequencing and Demultiplexing: 10X libraries were pooled and sequenced on NovaSeq S2 flow cells. Smart-seq2 libraries were pooled equimolar in sets of 4 to 16 384-well plates and sequenced on NextSeq 2000 P3 and NovaSeq S4 flow cells using the following cycling parameters:  Read 1: 100 cycles, Index 1: 12 cycles, Index 2: 12 cycles, Read 2: 100 cycles. The target read depth was 1–2 million paired-end reads per sample for Smart-seq2 libraries and 20,000 reads per cell for 10X 3’ GEX libraries. Raw BCL files were converted to FASTQ format and demultiplexed using Illumina’s bcl2fastq software (v2.20.0.422). For 10X Genomics libraries, FASTQ files were further processed and demultiplexed using CellRanger (v7.0.1).
Alignment and Gene Quantification: 10X Genomics data were aligned using CellRanger (v7.0.1) with the GRCh38 (human) reference genome. Gene counts were generated using HTSeq-count (v2.0.5) with stranded="no" and mode="intersection-nonempty".  Human reads were aligned to Gencode Reference v41 (GRCh38) using STAR (v2.7.11b). Gene counts were produced using HTSeq (v2.0.5) with stranded="false" and mode="intersection-nonempty".
Analysis: Samples were integrated usinf harmony and analysed using Seurat's standard workflow.
Assembly: Human: GRCh38
Supplementary files format and content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post SoupX ambient RNA removal but pre Seurat filtration.

source_name: Ovary

extract_protocol:
Human tissue was procured as previously described (159). Briefly, donated ovaries were procured at various hospital locations in Northern California through collaboration with Donor Network West (DNW, San Ramon, CA, USA). DNW is a not-for-profit, federally mandated organ procurement organization (OPO) for Northern California. Recovered ovaries were considered for research only after obtaining records of first-person authorization (i.e., donor’s consent during DMV registrations) and/or consent from the family members of the donor. Ovaries were processed consistently across all donors. Each ovary was collected and transported in University of Wisconsin (UW) solution on ice to preserve cell viability. A private courier service was used to keep the time between ovary procurement and initial tissue preparation as short as possible. The research protocol was approved by the DNW’s internal ethics committee (Research project STAN-19-104) and the medical advisory board, as well as by the Institutional Review Board at Stanford University which determined that this project does not meet the definition of human subject research as defined in federal regulations 45 CFR 46.102 or 21 CFR 50.3.  Ovaries were gently chopped using a razor blade and then transferred to a Conical tube with 2 mg/mL collagenase type IV (Gibco, 17104019) in DMEM (Gibco, 11960044). Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5min. The supernatant was aspirated and 0.25 % trypsin-EDTA (Gibco, 25200056) was added. Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5 min. The supernatant was aspirated, and the tissue was quenched with 10% FBS (Gibco, 10438026) in DMEM. Using a P1000, tissue was gently triturated to generate a single cell suspension. The cell suspension was filtered using a reversible 37µm sieve (STEMCELL Technologies, 27215). The sieve was rinsed with quench buffer (<37µm filtered flow through) and then flipped and placed in a new tube for rinsing with quench buffer (>37µm unfiltered mature oocyte pool hand-picked for SmartSeq2).
Smart-seq2 Library Preparation: Single oocytes were handpicked using an EZ-Grip pipette with a 125 μm EZ-Tip, briefly washed in 0.04% BSA-PBS, and transferred into individual wells containing lysis buffer master mix. Lysed oocytes were snap-frozen on dry ice and stored at −80°C for further processing by the Genomics Platform at the Chan Zuckerberg Biohub SF.   Reverse transcription (RT) and complementary DNA (cDNA) synthesis were performed in 96-well plates using the Smart-seq2 protocol. To preserve RNA integrity, 2–4 lysis plates were thawed on ice and processed in a pre-PCR laboratory. RT master mix (6 μL per well in 96-well plates; 0.6 μL per well in 384-well plates) was prepared using the following components: 0.06 μL 1M MgCl₂, 2 μL 5× First-Strand Buffer (Takara Bio, 639538), 2 μL 5M Betaine, 0.5 μL 100 mM DTT, 0.1 μL 100 μM TSO (Exiqon, 5′-AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG-3′), 0.25 μL RRI, 1 μL SmartScribe Reverse Transcriptase (Takara Bio, 639538), and 0.09 μL water. The RT master mix was dispensed into each well using an SPT Labtech Dragonfly Discovery liquid handler. Plates were sealed with a clear microseal, centrifuged at 1,000 rcf for 1 min, and incubated in a thermal cycler (Applied Biosystems ProFlex or Bio-Rad C1000 Touch Thermal Cycler**) under the following conditions: 42°C for 90 min, followed by 70°C for 5 min.  SmartSeq2 library construction: Second-strand synthesis and cDNA amplification were performed by adding 15 μL of cDNA master mix per 96-well plate (1.5 μL per 384-well plate), containing 12.5 μL KAPA HiFi HotStart ReadyMix 2X (Kapa Biosystems, KK2602), 0.25 μL 10 μM IS PCR primer (IDT, 5′-AAGCAGTGGTATCAACGCAGAGT-3′), 0.113 μL Lambda Exonuclease (NEB, M0262L), and 2.14 μL water. The cDNA master mix was dispensed using an SPT Labtech Dragonfly Discovery, and the plates were sealed, centrifuged at 1,000 rcf for 1 min, and subjected to the following cycling conditions: 37°C for 30 min; 95°C for 3 min; 21 cycles of 98°C for 20 s, 67°C for 15 s, 72°C for 4 min; followed by a final extension at 72°C for 5 min.   cDNA quantity was spot-checked using a Quant-iT dsDNA High Sensitivity Kit (Thermo Fisher, Q33120) and fluorescence was measured using a SpectraMax M5 microplate reader (Molecular Devices). cDNA quality was assessed on an Agilent 5300 Fragment Analyzer. High-concentration cDNA samples were diluted 1:10 with nuclease-free water for optimal enzymatic fragmentation.   Library preparation was performed using Illumina’s Nextera XT DNA Library Prep Kit (FC-131-1096), miniaturized for 384-well plates using an SPT Labtech Firefly liquid handler. Briefly, 0.4 μL cDNA (<1 ng) was stamped into each well of a 384-well plate, followed by 1.4 μL of tagmentation master mix (0.2 μL Tagment DNA buffer (TD) and 1.2 μL Amplicon Tagment Mix (ATM)). The plates were sealed, centrifuged at 2,000 rcf for 1 min, and incubated at 55°C for 5 min. Tagmentation was stopped by adding 0.4 μL of Neutralize Tagment Buffer (NT), followed by centrifugation at 2,000 rcf for 5 min.   Index PCR was performed by adding 1.2 μL of Nextera PCR Master Mix (NPM) and 0.8 μL of Nextera index adapters (0.4 μL of 5 μM i5 indexing primer, 0.4 μL of 5 μM i7 indexing primer, IDT). The thermal cycling program consisted of: 72°C for 3 min; 95°C for 30 s; 12 cycles of 95°C for 10 s, 55°C for 30 s, 72°C for 30 s; followed by a final extension at 72°C for 5 min.   Barcoded libraries were pooled using an SPT Labtech Mosquito LV, purified with two consecutive 0.7× AMPure XP bead clean-ups (Beckman Coulter, A63881), and eluted in 30 μL of nuclease-free water. Library fragment size was analyzed on an Agilent 4150 Tapestation System with D5000 ScreenTape (5067-5588) and quantified via qPCR (Bio-Rad CFX96 RT System) using the KAPA Library Quantification Kit (Kapa Biosystems, KK4923).  10X Genomics Library Preparation: Filtered cell suspensions were counted and adjusted to 1,000 cells/μL in 0.04% BSA (Research Products International, A30075) in 1X PBS. Library preparation was performed by the UCSF Genomics CoLabs using the 10X Genomics Chromium Next GEM Single Cell 3’ Kit with dual indexing, following the manufacturer’s protocol.

value: Ovary

value: Oocytes

value: Wildtype

tag: batch


title: MMR23

description:
Methylation data from brain tumor sample.
201492570127_R03C01


title: scRNA-seq of mus musclus: E12.5 embryo male lung, CTRL

description: Library name: scRNA_CTRL

value: lung

value: lung epithelia cells

value: CTRL


title: male zebra fish, control_1, day 56

description: Library name: M1_1_

value: brain tissue


title: VITAL01_10X

description:
Library name: Sample 1
10X Genomics

value: Whole Organ


title: G12_Plate 8B

description:
Library name: BSSE-QGF-131353
Smart-seq2

value: Dorsal Pancreas


title: 293T MDA Dam treated NAME-seq rep2

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
SNPs information at AT positions are generated by GATK (4.1.7.0)
Assembly: NC_000913.3; CP023448.1; Creinhardtii_281_v5.0; hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: BED, SNP information to filter 6mA
Library strategy: Methyl-seq

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 500-800 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was subjected to nitrite treatment. The treated DNA was used to construct sequencing library by customed protocol.

tag: cell line

value: human embryonic kidney cells

value: Wild-type


title: H12_Plate 8B

description:
Library name: BSSE-QGF-131354
Smart-seq2


title: female zebra fish, 200 μg/L DBAN_3, day 56

description: Library name: F5_3_1_

value: female

value: 200 μg/L DBAN, day56


title: 7dpf -28.5_Sox10:BFP>dsRed, dsRed+, trunk, multiome, snATAC

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

description: 10x Genomics, Multiome

library_source: genomic single cell

data_processing:
The count matrices of both multiome and snATACseq data were analyzed by R (v4.1.3) package Seurat (v4.3.0) and Signac (v1.6.0). For snRNAseq, Cellranger matrices for 7 dpf EWSR1::FLI1+ and 7 dpf control trunk were merged (merge, Seurat-methods) and then filterered based on nFeature_RNA >200, nFeature_RNA < 2500, and  nCount_RNA <2000. Matricies were then normalized (NormalizeData) and scaled for the top 2000 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 20 principal components (RunPCA) using variable features. The data were then subjected to neighbor finding (FindNeighbors) and clustering (FindClusters, resolution = 0.4) with input from the first through twentieth LSIs. For snATACseq datasets, Cellranger (10x Genomics) 7 dpf EWSR::FLI11+ and 7 dpf control trunk aggregated matrices were filtered for peak_region_fragments < 8000, pct_reads_in_peaks > 45, blacklist_ratio < 0.7, blacklist_ratio > 0.3, nucleosome_signal <1, nucleosome_signal > 0.2, and TSS.enrichment > 0.2. They were then normalized using RunTFIDF and RunSVD functions. The neighbor finding, clustering, and visualization were performed (RunUMAP, FindNeighbors, FindClusters, algorithm = 3 for FindClusters with resolution = 0.8) with input of the second to thirtieth LSIs. For snRNAseq (Fig. 7), tumor and control datasets were merged (merge, Seurat-methods), matrices were normalized (NormalizeData) and scaled for the top 500 variable genes (FindVariableFeatures, method = “vst” and ScaleData). The scaled matrices were dimensionally reduced to 15 principal components (RunPCA) based on JackStrawPlot and ElbowPlot.
Assembly: GRCz11
Supplementary files format and content: Count matricies in H5 file format; fragments files (cellranger output); bigWig files correspond to the snATAC samples.

source_name: trunk

growth_protocol: The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments (10885). Zebrafish embryos (Danio rerio) were raised in embryo media at 28.5°C. For adults, in the institute vivarium according to Protocol 10885.

extract_protocol:
Trunks from converted -28.5Sox10:Cre; actab2:loxP-BFP-STOP-loxP-DsRed (Sox10>DsRed) or -28.5Sox10:Cre;actab2:loxP-BFP-STOP-loxP-DsRed; Ubi:loxP-DsRed-STOP-loxP-GFP-2A-EF1 (Sox10>GFP-2A-EF1) fish at 7 dpf were cut posterior to ear and excluding swim bladder at all stages, cut into multiple pieces,  and placed in cold 1x PBS. Tumors from Sox10>GFP-2A-EF1 or normal tissue from control fish were dissected from young adult fish, cut into multiple pieces, and placed in cold 1x PBS. 1x PBS was then removed and replaced with pre-warmed Accumax. Samples were placed on a nutator at 30-32 °F, followed by mechanical dissociation by pipetting every 10 min (Innovative Cell Technologies Inc, AM105) for 1.5-2 hours. Cells were pelleted (200 × g, 10 min, 4 °C), supernatant was removed (leaving roughly 200 µL) and replaced with 1 mL of cold Hank’s Buffer solution (0.25% BSA, 10mM HEPES, 1x HBBS). Cells were vortexed to resuspend and pelleted again (376 × g, 5 min, 4 °C), supernatant removed (leaving roughly 100 µL) and replaced with 100 µL of cold 1x PBS per 24 trunk reaction. Pellets were resuspended by vortexing and filtered through 40 µm strainers (Corning, 431750). Cells derived from fish at  7 dpf were resuspended, placed on ice and fluorescence-activated cell sorted (FACS) for DsRed (control) or GFP (EWSR1::FLI1+). All samples were subjected to nuclei isolation according to manufacturer’s instructions (10x Genomics, protocol CG000169, “Low Cell Input Nuclei Isolation”).
Multiome and snATACseq libraries were prepared using 10x Genomics Chromium Next GEM  Single Cell Multiome ATAC + Gene Expression or Chromium Next GEM Single Cell ATAC v2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq. Sequenced data was aligned using Cellranger-arc v2.0.2, Cellranger-atac v2.0.0, Cellranger v6.0.2  or Cellranger-arc v8.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.

value: various

value: trunk

tag: age

value: 7 dpf

tag: strain

value: tubingen/WIK


title: 7dpf -28.5_Sox10:BFP>dsRed, dsRed+, trunk, multiome, snRNA

description: 10x Genomics, Multiome


title: Liver 1_WT

value: Liver

value: WT

value: Hepa1-6-induced HCC model


title: 293T MDA Dam treated NAME-seq rep1


title: female zebra fish, 200 μg/L DBAN_2, day 56

description: Library name: F5_2_1_


title: female zebra fish, 200 μg/L DBAN_1, day 56

description: Library name: F5_1_1_


title: 293T Dam-treated 6mA-DIP-seq

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
6mA peaks were called using macs2 (2.2.7.1)
Assembly: hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: bigwig, sequencing coverage visualization at genome browser

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 500-800 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was subjected to nitrite treatment. The treated DNA was used to construct sequencing library by customed protocol.
Methyl-seq


title: Protein_LNP, HTO

first: Roberto

last: Spreafico

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

description: Mixed Mouse5, Mouse6

data_processing:
scRNA-seq data were processed with CellRanger v6.1.2, using a single call to the count function for both GEX and HTO together. A custom reference genome was created by adding the RBD mRNA sequence to the GRCm38 mouse genome.
Each sample refers to a treatment and is a mixture of cells from two independent animals. Cells from individual animals were barcoded with HTOs. HTO counts are provided in the Cell Ranger output and allow demultiplexing individual animals.
Assembly: Custom reference genome with RBD mRNA sequence added to the GRCm38 mouse genome
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Lymph Node

extract_protocol:
Single cell suspensions were incubated with 1 μg ml−1 anti-CD16/32 in PBS supplemented with 0.5% BSA and 2 mM EDTA (PBE) for 5 min at room temperature and then stained for cell surface markers at 4 °C for 20 min in PBS. For single-cell transcriptomic analysis, stained cells were further incubated with DNA-barcoded anti-biotin and sample hashtag (anti-MHC-I) antibodies (BioLegend) for 20 minutes in PBE, washed three times with PBE, and bulk-sorted.
Sorted DCs were collected into a microfuge tube with 300 μl PBS supplemented with 0.4% BSA. After the sort, tubes were topped with PBS 0.4% BSA, centrifuged and the buffer was carefully reduced by removing the volume with a pipette to a final volume of 40 μl. Cells were counted for viability and immediately submitted to library preparation. The scRNA-seq library was prepared using the 10X Genomics Single Cell Chromium 5' system, according to the manufacturer’s instructions, at the Genomics Core of Rockefeller University and was sequenced on an Illumina NovaSeq SP flowcell to a minimum sequencing depth of 30,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.

treatment_protocol: 3×10^5CD40lgSrtA/YCD4-Cre OT-II CD4+T cellswere transferred intoCd40G5/G5recipient mice 18-hours prior to immunization. 22- hours post-immunization, Biotin-LPETG was injected intraperitoneally (i.p.) (100μl of 20 mM solution in PBS) six times 20 min apart, and then inguinal and popliteal lymph nodes were harvested 20 min after the last injection.

value: Lymph Node

tag: transferred cells

value: Dendritic Cells

tag: library type

value: HTO


title: Protein_LNP, GEX

description: Mixed Mouse5, Mouse6

value: GEX


title: 293T 6mA-DIP-seq


title: Protein_Addavax, HTO

description: Mixed Mouse3, Mouse4


title: HepG2 mtDNA DIP-NAME-seq rep2

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
6mA peaks were called using macs2 (2.2.7.1)
Assembly: hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: bigwig, sequencing coverage visualization at genome browser
Library strategy: Methyl-seq

value: human liver cancer cell line


title: female zebra fish, 40 μg/L DBAN_3, day 56

description: Library name: F4_6_1_

value: brain tissue

value: 40 μg/L DBAN, day56


title: female zebra fish, 40 μg/L DBAN_2, day 56

description: Library name: F4_3_


title: Protein_Addavax, GEX

description: Mixed Mouse3, Mouse4


title: 293T Input

value: human embryonic kidney cells

value: Wild-type


title: BS_lib1_Col_rep1

value: mature pollen

value: wild-type


title: female zebra fish, 40 μg/L DBAN_1, day 56

description: Library name: F4_2_1_

value: female


title: 293T Dam-treated DIP-NAME-seq


title: Liver 2_WT


title: K562 TASOR-KO SYSY-6mA-DIP-seq

value: lymphoblast cells


title: HepG2 mtDNA MDA NAME-seq


title: HepG2 mtDNA DIP-NAME-seq rep1


title: female zebra fish, control_3, day 56

description: Library name: F1_3_1_

value: 0 μg/L DBAN, day56


title: mRNA-LNP, HTO

description: Mixed Mouse1, Mouse2


title: female zebra fish, control_2, day 56

description: Library name: F1_2_1_


title: MTrPs participant [M7]

city: Jinan

first: Mingjian

last: Liu

address: Wenhua Xi Road 107

institute: Qilu Hospital of Shandong University

data_processing:
fastp software was used to filter the sequences.
The software used for sequence alignment was Hisat2. Its alignment algorithm is called the spliced maping algorithm.
Stringtie software was used to compare and count the fragments in each gene region, and then the Taylorimean of M values (TMM) algorithm was used to normalize, and finally the FPKM value of each gene was calculated.
Assembly: human GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide.

value: Skeletal muscle

tag: disease

value: MTrPs participant


title: mRNA-LNP, GEX

description: Mixed Mouse1, Mouse2


title: K562 PCR SYSY-6mA-DIP-seq


title: 293T DIP-NAME-seq


title: MTrPs participant [M6]


title: MMR20

description:
Methylation data from brain tumor sample.
200123460086_R06C02

value: Primary MMRD Glioma


title: K562 PCR CST-6mA-DIP-seq


title: female zebra fish, control_1, day 56

description: Library name: F1_1_1_


title: MTrPs participant [M5]


title: K562 WT SYSY-6mA-DIP-seq


title: MMR14

description:
Methylation data from brain tumor sample.
200123460086_R02C02


title: Adult_Tumor_FLAG_CUT&RUN_rep2

description:
Library name: Sample 7
Tumors_CUT&RUN.bigwig

data_processing:
For CUT& RUN, sequencing read quality was examined using FastQC. Trimming of low-quality reads and clipping of sequencing adapters were done using the FASTQ Quality Trimmer (Galaxy Version 1.1.5). Reads were aligned to the zebrafish genome (GRCz11) using Bowtie2 (Galaxy Version 2.5.0) using default settings. Bam files was were filtered with Filter SAM or BAM (Galaxy Version 1.8) and sorted SortSam (Galaxy Version 2.18.2.1). Duplicate reads were removed using RmDup (Galaxy Version 2.0.1). The individual bam files corresponding to biological replicates were merged using the MergeSamFiles (Galaxy Version 2.18.2.1) command. CUT&RUN peaks were called using MACS2 (Galaxy Version 2.2.7.1) with the callpeak command (--nomodel, --extsize 150, --shift 0) and a q-value threshold of <1e-05 for all Input_embryos, FLAG_embryos, Input_tumor, and FLAG_tumor files.
Assembly: GRCz11
Supplementary files format and content: Bigwig files
Library strategy: CUT&RUN

source_name: tumor

extract_protocol:
Embryos at 24hpf or tumors positive for GFP-2A-EF1 were dissected, cut into multiple pieces, and placed in pre-warmed Accumax at 30-32°C (Millipore Sigma, A7089), followed by mechanical dissociation by pipetting every 10 min for 1-1.5 hr. Cells were pelleted (200 × g, 10 min, 4 °C), and supernatant was removed and replaced with 1 mL of cold Hank’s Buffer solution (0.25% BSA, 10mM HEPES, 1x HBBS). Cells were resuspended by pipetting up and down and pelleted again (376 × g, 5 min, 4 °C), and supernatant was removed and replaced with 1ml of 1x PBS. Pellets were resuspended and filtered through 40 um strainers (Corning, 431750). Cell number was assessed by automated cell counter. Cells were fixed in 1%PFA for 2 min. 100,000-200,000 cells per sample were aliquoted and pelleted for processing using CUT&RUN Assay Kit #86652 according to the manufacturer’s protocol.
Smaples were proccessed by Novogene. The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

value: tumor

tag: tissue type

value: various

value: WIK


title: MMR13

description:
Methylation data from brain tumor sample.
200123460086_R01C01


title: MTrPs participant [M4]


title: K562 WT CST-6mA-DIP-seq


title: MTrPs participant [M3]


title: K562 Input


title: MMR11

description:
Methylation data from brain tumor sample.
200123460086_R05C01


title: MMR9

description:
Methylation data from brain tumor sample.
200123460086_R05C02


title: Adult_Tumor_FLAG_CUT&RUN_rep1

description:
Library name: Sample 5
Tumors_CUT&RUN.bigwig


title: 24hpf_Embryo_Input_CUT&RUN_rep2

description:
Library name: Sample 4
Embryos_CUT&RUN.bigwig

value: trunk


title: MTrPs participant [M2]


title: K562 TASOR-KO DIP-NAME-seq


title: MTrPs participant [M1]


title: MMR21

description:
Methylation data from brain tumor sample.
200123460086_R06C01


title: K562 WT DIP-NAME-seq


title: 24hpf_Embryo_FLAG_CUT&RUN_rep2

description:
Library name: Sample 3
Embryos_CUT&RUN.bigwig


title: Ecoli 0% native NAME-seq

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3) and customed python scripts
SNPs information at AT positions are generated by GATK (4.1.7.0)
Assembly: NC_000913.3; CP023448.1; Creinhardtii_281_v5.0; hg38
Supplementary files format and content: Comma-separated values, base content after nitrite treatment
Supplementary files format and content: BED, SNP information to filter 6mA

organism: Escherichia coli

value: Bacteria


title: Ecoli 12.5% native NAME-seq


title: Adult_Tumor_Input_CUT&RUN_rep2

description:
Library name: Sample 8
Tumors_CUT&RUN.bigwig


title: HCT116 EcoGII-24h DIP-NAME-seq

value: human colon cancer cell line

value: 1uM Shield-1 for 24 hours


title: Healthy participant [C5]

value: Healthy participant


title: K562 TASOR-KO CST-6mA-DIP-seq

value: Wild-type


title: 24hpf_Embryo_Input_CUT&RUN_rep1

description:
Library name: Sample 2
Embryos_CUT&RUN.bigwig


title: 24hpf_Embryo_FLAG_CUT&RUN_rep1

description:
Library name: Sample 1
Embryos_CUT&RUN.bigwig


title: Ecoli 25% native NAME-seq


title: Healthy participant [C4]


title: HCT116 EcoGII-0h DIP-NAME-seq


title: HCT116 WT DIP-NAME-seq


title: Healthy participant [C3]


title: K562 TASOR KO untreated

value: Lymphoblast cells

value: TASOR KO


title: Healthy participant [C2]


title: Ecoli 50% native NAME-seq


title: Adult_Tumor_Input_CUT&RUN_rep1

description:
Library name: Sample 6
Tumors_CUT&RUN.bigwig


title: DRB_4su_10m_cDNA_longread_rep1

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

description:
Library name: DRB_4su_10m_cDNA_longread_rep1
cDNA long read sequencing of K562 cells treated with 100uM DRB, followed by metabolic labeling for 10m with 1mM 4sU. Enriched 4sU RNA was ribodepleted, followed by polyI tailing, strand switching RT and PCR. Then sequenced using cDNA library prep following manufacture's intructions

data_processing:
Reads were mapped with minimap2 following their recommended settings depending on the sequenced library (RNA or cDNA)
Assembly: GRCh38
Supplementary files format and content: rRNA reads were removed from fastq files using SortMeRNA and the remaining reads were mapped to GRCh38.95 using minimap2/2.24 with the following paramters: -ax splice -uf -k14. Uniquely aligned reads whose 5’ end overlapped an annotated AFEs and 3’ end did not overlap an annotated PAS peak were used for downstream analysis since they likely represent complete molecules that had not yet finished transcription

source_name: blood

growth_protocol: K562 cells passage 10-12 were grown in RMPI medium supplemented with

extract_protocol:
Treated cells were transferred to low-bind tubes, spin down 2 minutes at 1000rcf, followed by Trizol/Chloroform extraction. Then, the aqueous phase was cleanup using the zymo-clean up kit.
We enriched labeled RNA using MTSEA biotin-XX pulldown, followed by RNAseH-based ribosomal RNA depletion. Then, we did a polyI tailing and direct RNA nanopore library prep. For cDNA libraries, polyI tailing was followed by strand-switching RT and PCR, followed by cdna library prep following manufacture's instructions.

treatment_protocol: cells were treated with DRB 100uM for 3 hours. During the last 5 minnutes of DRB, 4su was added to a final concentration of 1mM. After PBS wash, cells were resuspended in 4su 1mM for a 10m labeling.

value: blood

value: lymphobast

value: DRB 3h; 4su 10 minutes


title: Ecoli 100% native NAME-seq


title: DRB_4su_10m_directRNA_longread_rep2

description:
Library name: DRB_4su_10m_directRNA_longread_rep2
direct RNA of K562 cells treated with 100uM DRB, followed by metabolic labeling for 10m with 1mM 4sU. Enriched 4sU RNA was ribodepleted, followed by polyI tailing and then sequenced using direct RNA nanopore long read technology. Replicate 2


title: Healthy participant [C1]

value: Skeletal muscle


title: K562 WT untreated


title: Ecoli NAME-seq


title: DRB_4su_10m_directRNA_longread_rep1

description:
Library name: DRB_4su_10m_directRNA_longread_rep1
direct RNA of K562 cells treated with 100uM DRB, followed by metabolic labeling for 10m with 1mM 4sU. Enriched 4sU RNA was ribodepleted, followed by polyI tailing and then sequenced using direct RNA nanopore long read technology. Replicate 1


title: HPJP26 NAME-seq

organism: Helicobacter pylori


title: DS25, CD19 CAR-T cells, Butyrate

status: Public on Oct 08 2025

city: Madrid

last: Garcia-Vicente

address: Avd Cordoba s/n

department: Translational Hematology

country: Spain

institute: Instituto de Investigacion Hospital 12 de Octubre

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 from within Local Run Manager (Illumina).
Sequencing quality was evaluated via FastQC (v0.12.1)
Sequence trimming was performed with BBDuk BBMap (v39.01)
Sequences were mapped to the human genome using STAR (v2.7.11a)
Mapped reads were quantified by featureCounts (v.2.0.6) from the Subread package
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited files including raw counts for each Sample
Supplementary files format and content: tab-delimited files including normalized counts (DESeq2) for each Sample

source_name: T cell

growth_protocol: After transduction, CAR-T cells were grown in X-VIVO 15 (Lonza, Basel), supplemented with 10% of human AB serum (Merck) and 250 UI/mL hIL-2 (Miltenyi Biotec) at 1.5*10^6 cells/ml.

extract_protocol:
After butyrate stimulation CAR-T cells and their respective controls without stimulation, were collected and RNA were extracted using AllPrep DNA/RNA Mini Kit (cat. 80204, Qiagen)
Total RNA samples (500ng; RQS/RIN average 9.7, range 9.2-10) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.  {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

treatment_protocol: CAR-T cells were stimulated with sodium butyrate ( Merck), dissolved in culture medium, or control medium.

value: T cell

value: CD19 CAR-T

value: Butyrate


title: DS25, CD19 CAR-T cells, Control

value: Control


title: DS24, CD19 CAR-T cells, Butyrate


title: DS22, CD19 CAR-T cells, Butyrate


title: DS22, CD19 CAR-T cells, Control


title: DS21, CD19 CAR-T cells, Butyrate


title: RH30_DMSO_rep4

city: Cold Spring Harbor

first: Patrick

middle: Joseph

last: Cunniff

state: NY

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description:
Library name: RH30_DMSO_rep4
CB6644_nonPDAC_RNAseq_TPM.txt

data_processing:
For RNA-seq, fastq files were pseudo-aligned using Kallisto (single-end mode) in bootstrap mode (100) pseudo-alignment was performed using the NCBI_hg38_p12 transcriptome resulting TPM per transcripts were collapsed into gene level TPM values
Assembly: hg38
Supplementary files format and content: Text files containing transcriptome wide expression levels combined by cell line for RNA-seq.

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) based on the manufacturer’s instructions.

value: human alveolar rhabdomyosarcoma cell line

value: parental

value: 24h DMSO


title: DS21, CD19 CAR-T cells, Control


title: RH30_DMSO_rep3

description:
Library name: RH30_DMSO_rep3
CB6644_nonPDAC_RNAseq_TPM.txt


title: RH30_DMSO_rep2

description:
Library name: RH30_DMSO_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: RH30_CB6644_rep1

description:
Library name: RH30_CB6644_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: RH30_CB6644_rep3

description:
Library name: RH30_CB6644_rep3
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_DMSO_rep3

description:
Library name: H1048_DMSO_rep3
CB6644_nonPDAC_RNAseq_TPM.txt

value: human small cell lung cancer (P subtype (Tuft cell-like)) cell line


title: RH30_CB6644_rep2

description:
Library name: RH30_CB6644_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: RH30_DMSO_rep1

description:
Library name: RH30_DMSO_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_DMSO_rep4

description:
Library name: H1048_DMSO_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: DS24, CD19 CAR-T cells, Control


title: A375_DMSO_rep3

description:
Library name: A375_DMSO_rep3
CB6644_nonPDAC_RNAseq_TPM.txt

value: human melanoma cell line


title: A375_DMSO_rep4

description:
Library name: A375_DMSO_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_CB6644_rep2

description:
Library name: H1048_CB6644_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_CB6644_rep4

description:
Library name: H1048_CB6644_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_CB6644_rep1

description:
Library name: H1048_CB6644_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_DMSO_rep2

description:
Library name: H1048_DMSO_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_DMSO_rep1

description:
Library name: H1048_DMSO_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: A375_CB6644_rep1

description:
Library name: A375_CB6644_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: A375_CB6644_rep2

description:
Library name: A375_CB6644_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_DMSO_rep3

description:
Library name: T84_DMSO_rep3
CB6644_nonPDAC_RNAseq_TPM.txt

value: human colorectal cancer cell line


title: A375_CB6644_rep4

description:
Library name: A375_CB6644_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_DMSO_rep1

description:
Library name: T84_DMSO_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: A375_DMSO_rep1

description:
Library name: A375_DMSO_rep1
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_DMSO_rep4

description:
Library name: T84_DMSO_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_CB6644_rep4

description:
Library name: T84_CB6644_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: A375_CB6644_rep3

description:
Library name: A375_CB6644_rep3
CB6644_nonPDAC_RNAseq_TPM.txt


title: H1048_CB6644_rep3

description:
Library name: H1048_CB6644_rep3
CB6644_nonPDAC_RNAseq_TPM.txt


title: RH30_CB6644_rep4

description:
Library name: RH30_CB6644_rep4
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_DMSO_rep2

description:
Library name: T84_DMSO_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_CB6644_rep2

description:
Library name: T84_CB6644_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: T84_CB6644_rep3

description:
Library name: T84_CB6644_rep3
CB6644_nonPDAC_RNAseq_TPM.txt


title: A375_DMSO_rep2

description:
Library name: A375_DMSO_rep2
CB6644_nonPDAC_RNAseq_TPM.txt


title: RUVBL1_AsPC1_dTAG_KLF5_rep3.2

description:
Library name: RUVBL1_AsPC1_dTAG_KLF5_rep3.2
ChIP antibody: RUVBL1, Bethyl, A304-716A (RRID:AB_2620911)

data_processing:
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
Assembly: hg38
Supplementary files format and content: Bigwig files for ChIP-Seq.

extract_protocol:
For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies.
ChIP-seq ibraries were constructed using Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions.

value: human pancreatic cancer cell line

value: 4h dTAGv1


title: RUVBL1_AsPC1_dTAG_KLF5_rep3.1

description:
Library name: RUVBL1_AsPC1_dTAG_KLF5_rep3.1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)


title: RUVBL1_AsPC1_NEG_KLF5_rep3.1

description:
Library name: RUVBL1_AsPC1_NEG_KLF5_rep3.1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)

value: 4h dTAG-NEG


title: CRISPR_TF_SERPINB5_High

description:
Library name: CRISPR_TF_SERPINB5_High
FACS Antibody Serpin B5 (C-8): sc-271694 BULK
CRISPR_TF_Screen_Counts.txt

data_processing:
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
Assembly: hg38
Supplementary files format and content: Mageck count files for CRISPR libraries.
Library strategy: CRISPR Screen

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI with 10% FBS supplemented with pen-strep.

extract_protocol:
For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

treatment_protocol: Cas9-expressing cells were infected with human DNA Binding Domain-Focused (Addgene #123334) or genome-wide Brunello (Addgene #73178) sgRNA library-encoding suspension for a 20-30% infection percentage. Media was changed at 48-hours, and antibiotic selection was added for 72-hours. Cells were collected 8 days after infection.


title: RUVBL1_AsPC1_NEG_KLF5_rep3.2

description:
Library name: RUVBL1_AsPC1_NEG_KLF5_rep3.2
ChIP antibody: RUVBL1, Bethyl, A304-716A (RRID:AB_2620911)


title: CRISPR_TF_SERPINB5_Low

description:
Library name: CRISPR_TF_SERPINB5_Low
FACS Antibody Serpin B5 (C-8): sc-271694 LOW
CRISPR_TF_Screen_Counts.txt


title: CRISPR_TF_SERPINB5_Bulk

description:
Library name: CRISPR_TF_SERPINB5_Bulk
FACS Antibody Serpin B5 (C-8): sc-271694 BULK
CRISPR_TF_Screen_Counts.txt


title: MEC1_Stuffer 2

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

institute: IDIBAPS

description:
Library name: EPI0001242
2 × 50 bp, >40 million paired-reads

data_processing:
Quality control of fastq files was performed using fastqc-0.11.9
rRNA reads were identified using sortmerna-4.3.2
Non rRNA reads were trimmed using trimmomatic-0.39
Transcript abundance was quantified using kallisto-0.46.1
Assembly: hg38 release-100
Supplementary files format and content: tsv files: for each sample there is one tsv file containing the abundance estimates from kallisto tool

source_name: Peripheral Blood

extract_protocol:
RNA was extracted with Trizol reagent (ThermoFisher).
Total RNA strand-specific RNA libraries were prepared using 200 ng of total RNA with the Stranded RNA Prep Ligation kit with RiboZero Plus (Illumina) following manufacturer’s recommendations

value: Peripheral Blood

value: CLL cell line

value: WT

value: Cells transduced with control lentiviral vector (day 6 after infection)


title: MEC1_LEF1 FL overexpression 2

description:
Library name: EPI0001240
2 × 50 bp, >40 million paired-reads

value: LEF1-FL ov

value: Cells transduced with LEF1-FL ov lentiviral vector (day 6 after infection)


title: MEC1_LEF1 FL overexpression 1

description:
Library name: EPI0001239
2 × 50 bp, >40 million paired-reads


title: HG3_LEF1 Isoform 5 overexpression 1

description:
Library name: EPI0001389
2 × 50 bp, >40 million paired-reads

value: LEF1-I5 ov

value: Cells transduced with LEF1-I5 ov lentiviral vector (day 6 after infection)


title: MEC1_LEF1 Isoform 6 overexpression 1

description:
Library name: EPI0001395
2 × 50 bp, >40 million paired-reads

value: LEF1-I6 ov

value: Cells transduced with LEF1-I6 ov lentiviral vector (day 6 after infection)


title: MEC1_LEF1 Isoform 5 overexpression 1

description:
Library name: EPI0001393
2 × 50 bp, >40 million paired-reads


title: HG3_LEF1 FL overexpression 2

description:
Library name: EPI0001236
2 × 50 bp, >40 million paired-reads


title: HG3_LEF1 Isoform 6 overexpression 2

description:
Library name: EPI0001392
2 × 50 bp, >40 million paired-reads


title: MEC1_LEF1 Isoform 6 overexpression 2

description:
Library name: EPI0001396
2 × 50 bp, >40 million paired-reads


title: HG3_LEF1 Isoform 5 overexpression 2

description:
Library name: EPI0001390
2 × 50 bp, >40 million paired-reads


title: MEC1_Stuffer 1

description:
Library name: EPI0001241
2 × 50 bp, >40 million paired-reads


title: U-CLL6_g2 LEF1

description:
Library name: EPI0001387
2 × 50 bp, >40 million paired-reads

value: CLL

value: Cryopreserved cells from patient

value: LEF1 knockdown

value: Electroporated cells with LEF1 sgRNA#2 (4 days after CRISPR)


title: HG3_LEF1 Isoform 6 overexpression 1

description:
Library name: EPI0001391
2 × 50 bp, >40 million paired-reads


title: HG3_LEF1 FL overexpression 1

description:
Library name: EPI0001235
2 × 50 bp, >40 million paired-reads


title: T84_CB6644_rep1

description:
Library name: T84_CB6644_rep1
CB6644_nonPDAC_RNAseq_TPM.txt

value: human colorectal cancer cell line

value: parental


title: U-CLL6_g1 LEF1

description:
Library name: EPI0001386
2 × 50 bp, >40 million paired-reads

value: Electroporated cells with LEF1 sgRNA#1 (4 days after CRISPR)


title: HG3_Stuffer 2

description:
Library name: EPI0001238
2 × 50 bp, >40 million paired-reads

value: Peripheral Blood


title: HG3_Stuffer 1

description:
Library name: EPI0001237
2 × 50 bp, >40 million paired-reads

value: CLL cell line


title: U-CLL6_NTC

description:
Library name: EPI0001388
2 × 50 bp, >40 million paired-reads

value: WT

value: Electroporated cells with NTC sgRNA (4 days after CRISPR)


title: U-CLL2_g2 LEF1

description:
Library name: EPI0000851
2 × 50 bp, >40 million paired-reads


title: U-CLL2_g1 LEF1

description:
Library name: EPI0000850
2 × 50 bp, >40 million paired-reads


title: U-CLL1_g1 LEF1

description:
Library name: EPI0000841
2 × 50 bp, >40 million paired-reads


title: U-CLL2_NTC

description:
Library name: EPI0000852
2 × 50 bp, >40 million paired-reads


title: U-CLL1_g2 LEF1

description:
Library name: EPI0000842
2 × 50 bp, >40 million paired-reads


title: U-CLL1_NTC

description:
Library name: EPI0000843
2 × 50 bp, >40 million paired-reads


title: MEC1_LEF1 Isoform 5 overexpression 2

description:
Library name: EPI0001394
2 × 50 bp, >40 million paired-reads


title: M-CLL9_NTC

description:
Library name: EPI0000840
2 × 50 bp, >40 million paired-reads


title: M-CLL5_g2 LEF1

description:
Library name: EPI0000845
2 × 50 bp, >40 million paired-reads


title: M-CLL5_NTC

description:
Library name: EPI0000846
2 × 50 bp, >40 million paired-reads


title: M-CLL10_NTC

description:
Library name: EPI0000849
2 × 50 bp, >40 million paired-reads


title: U-CLL1_Day 6

description:
Library name: EPI0000837
2 × 50 bp, >40 million paired-reads

value: Stimulated (day 6 in culture MM1 cells)


title: U-CLL2_Day 6

description:
Library name: EPI0000835
2 × 50 bp, >40 million paired-reads


title: U-CLL2_Day 0

description:
Library name: EPI0000834
2 × 50 bp, >40 million paired-reads

value: Unstimulated (day 0, from crotube)


title: U-CLL12_Day 6

description:
Library name: EPI0000833
2 × 50 bp, >40 million paired-reads


title: M-CLL10_g2 LEF1

description:
Library name: EPI0000848
2 × 50 bp, >40 million paired-reads


title: M-CLL10_g1 LEF1

description:
Library name: EPI0000847
2 × 50 bp, >40 million paired-reads


title: M-CLL4_Day 6

description:
Library name: EPI0000676
2 × 50 bp, >40 million paired-reads


title: M-CLL5_g1 LEF1

description:
Library name: EPI0000844
2 × 50 bp, >40 million paired-reads


title: M-CLL9_Day 0

description:
Library name: EPI0000670
2 × 50 bp, >40 million paired-reads


title: M-CLL5_Day 6

description:
Library name: EPI0000674
2 × 50 bp, >40 million paired-reads


title: M-CLL9_Day 6

description:
Library name: EPI0000671
2 × 50 bp, >40 million paired-reads


title: U-CLL12_Day 0

description:
Library name: EPI0000832
2 × 50 bp, >40 million paired-reads


title: M-CLL3_Day 0

description:
Library name: EPI0000677
2 × 50 bp, >40 million paired-reads


title: M-CLL4_Day 0

description:
Library name: EPI0000675
2 × 50 bp, >40 million paired-reads


title: U-CLL1_Day 0

description:
Library name: EPI0000836
2 × 50 bp, >40 million paired-reads


title: Input_AsPC1_forDiffBind_CB6644_rep7

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep7
Input

data_processing:
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For SLAM-seq, single end 100 base pair sequencing reads were mapped to hg38 3’UTR exons, filtered, TC snps identified, and reads counted using the slamdunk package with default settings (Herzog et al. 2017). Counted TC converted transcript reads were compiled for each gene in each sample by summing reads mapping to different 3’UTR exons for a given gene.
For RNA-seq, fastq files were pseudo-aligned using Kallisto (single-end mode) in bootstrap mode (100) pseudo-alignment was performed using the NCBI_hg38_p12 transcriptome resulting TPM per transcripts were collapsed into gene level TPM values
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
Assembly: hg38
Supplementary files format and content: Text files containing transcriptome wide expression levels combined by cell line for RNA-seq and SLAM-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation. SLAM-seq experiments were performed using the SLAM-seq Explorer Kit Anabolic Kinetic Module (Lexogen) following manufacturer instructions.
RNA-seq and ChIP-seq ibraries were constructed using Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

value: human pancreatic cancer cell line


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep7.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep7.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep7.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep7.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: M-CLL9_g1 LEF1

description:
Library name: EPI0000838
2 × 50 bp, >40 million paired-reads


title: Input_AsPC1_forDiffBind_CB6644_rep6

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep6
Input


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep6.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep6.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep6.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep6.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: M-CLL9_g2 LEF1

description:
Library name: EPI0000839
2 × 50 bp, >40 million paired-reads


title: Input_AsPC1_forDiffBind_CB6644_rep5

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep5
Input


title: U-CLL11_Day 6

description:
Library name: EPI0000831
2 × 50 bp, >40 million paired-reads


title: U-CLL11_Day 0

description:
Library name: EPI0000830
2 × 50 bp, >40 million paired-reads


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep5.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep5.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: M-CLL3_Day 6

description:
Library name: EPI0000678
2 × 50 bp, >40 million paired-reads


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep5.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep5.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep4.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep4.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep3.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep3.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_forDiffBind_CB6644_rep1

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep1
Input


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep1.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep1.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_forDiffBind_CB6644_rep4

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep4
Input


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep1.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep1.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_forDiffBind_CB6644_rep3

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep3
Input


title: Input_AsPC1_forDiffBind_CB6644_rep2

description:
Library name: Input_AsPC1_forDiffBind_CB6644_rep2
Input


title: M-CLL5_Day 0

description:
Library name: EPI0000673
2 × 50 bp, >40 million paired-reads


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep3.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep3.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep2.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep2.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_DMSO_rep1.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_DMSO_rep1.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep4.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep4.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_forDiffBind_DMSO_rep2

description:
Library name: Input_AsPC1_forDiffBind_DMSO_rep2
Input


title: H3K27ac_AsPC1_forDiffBind_CB6644_rep2.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_CB6644_rep2.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_DMSO_rep1.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_DMSO_rep1.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_DMSO_rep2.1

description:
Library name: H3K27ac_AsPC1_forDiffBind_DMSO_rep2.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_forDiffBind_DMSO_rep2.2

description:
Library name: H3K27ac_AsPC1_forDiffBind_DMSO_rep2.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: KLF5_BxPC3_dTAG_KLF5

description:
Library name: KLF5_BxPC3_dTAG_KLF5
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)

value: 4h dTAGv1


title: Input_BxPC3_dTAG_KLF5

description:
Library name: Input_BxPC3_dTAG_KLF5
Input


title: RUVBL1_BxPC3_NEG_KLF5

description:
Library name: RUVBL1_BxPC3_NEG_KLF5
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)

value: 4h dTAG-NEG


title: RUVBL1_BxPC3_dTAG_KLF5

description:
Library name: RUVBL1_BxPC3_dTAG_KLF5
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)


title: KLF5_BxPC3_NEG_KLF5

description:
Library name: KLF5_BxPC3_NEG_KLF5
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: Input_BxPC3_NEG_KLF5

description:
Library name: Input_BxPC3_NEG_KLF5
Input


title: KLF5_AsPC1_NEG_KLF5_rep3

description:
Library name: KLF5_AsPC1_NEG_KLF5_rep3
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: H3K27ac_BxPC3_NEG_KLF5

description:
Library name: H3K27ac_BxPC3_NEG_KLF5
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_AsPC1_dTAG_NEG_rep2

description:
Library name: Input_AsPC1_dTAG_NEG_rep2
Input


title: KLF5_AsPC1_NEG_KLF5_rep2

description:
Library name: KLF5_AsPC1_NEG_KLF5_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: H3K27ac_AsPC1_NEG_KLF5_rep2

description:
Library name: H3K27ac_AsPC1_NEG_KLF5_rep2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_forDiffBind_DMSO_rep1

description:
Library name: Input_AsPC1_forDiffBind_DMSO_rep1
Input


title: RUVBL1_AsPC1_NEG_KLF5_rep2

description:
Library name: RUVBL1_AsPC1_NEG_KLF5_rep2
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)


title: KLF5_AsPC1_dTAG_KLF5_rep2

description:
Library name: KLF5_AsPC1_dTAG_KLF5_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: RUVBL1_AsPC1_dTAG_KLF5_rep2

description:
Library name: RUVBL1_AsPC1_dTAG_KLF5_rep2
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)


title: KLF5_AsPC1_dTAG_KLF5_rep3

description:
Library name: KLF5_AsPC1_dTAG_KLF5_rep3
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: H3K27ac_AsPC1_dTAG_KLF5_rep3

description:
Library name: H3K27ac_AsPC1_dTAG_KLF5_rep3
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: RUVBL1_AsPC1_dTAG_KLF5_rep1

description:
Library name: RUVBL1_AsPC1_dTAG_KLF5_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZJ4490454A)


title: H3K27ac_BxPC3_dTAG_KLF5

description:
Library name: H3K27ac_BxPC3_dTAG_KLF5
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: H3K27ac_AsPC1_NEG_KLF5_rep3

description:
Library name: H3K27ac_AsPC1_NEG_KLF5_rep3
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_dTAG_KLF5_rep2

description:
Library name: H3K27ac_AsPC1_dTAG_KLF5_rep2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_dTAG_KLF5_rep1

description:
Library name: Input_AsPC1_dTAG_KLF5_rep1
Input


title: RUVBL1_AsPC1_NEG_KLF5_rep1

description:
Library name: RUVBL1_AsPC1_NEG_KLF5_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZJ4490454A)


title: H3K27ac_AsPC1_NEG_KLF5_rep1

description:
Library name: H3K27ac_AsPC1_NEG_KLF5_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_dTAG_KLF5_rep1

description:
Library name: H3K27ac_AsPC1_dTAG_KLF5_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: H3K27ac_AsPC1_DMSO_12h_rep1

description:
Library name: H3K27ac_AsPC1_DMSO_12h_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_DMSO_12h_rep1

description:
Library name: Input_AsPC1_DMSO_12h_rep1
Input


title: KLF5_AsPC1_DMSO_12h_rep1

description:
Library name: KLF5_AsPC1_DMSO_12h_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)


title: RUVBL2_AsPC1_CB6644_12h_rep1

description:
Library name: RUVBL2_AsPC1_CB6644_12h_rep1
ChIP antibody: RUVBL2, ABclonal, A12564 (Lot: 0010460101)

value: 12h DMSO


title: Input_AsPC1_dTAG_NEG_rep3

description:
Library name: Input_AsPC1_dTAG_NEG_rep3
Input


title: RUVBL1_AsPC1_CB6644_12h_rep1

description:
Library name: RUVBL1_AsPC1_CB6644_12h_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: Input_AsPC1_CB6644_12h_rep1

description:
Library name: Input_AsPC1_CB6644_12h_rep1
Input


title: H3K27ac_AsPC1_CB6644_12h_rep1

description:
Library name: H3K27ac_AsPC1_CB6644_12h_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: Input_AsPC1_NEG_KLF5_rep1

description:
Library name: Input_AsPC1_NEG_KLF5_rep1
Input


title: KLF5_AsPC1_NEG_KLF5_rep1

description:
Library name: KLF5_AsPC1_NEG_KLF5_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_AsPC1_DMSO_3h_rep2

description:
Library name: KLF5_AsPC1_DMSO_3h_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)

value: 3h DMSO


title: RUVBL1_AsPC1_DMSO_3h

description:
Library name: RUVBL1_AsPC1_DMSO_3h
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: Input_AsPC1_DMSO_3h

description:
Library name: Input_AsPC1_DMSO_3h
Input


title: KLF5_AsPC1_dTAG_KLF5_rep1

description:
Library name: KLF5_AsPC1_dTAG_KLF5_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_AsPC1_CB6644_3h_rep1

description:
Library name: KLF5_AsPC1_CB6644_3h_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)


title: Input_AsPC1_CB6644_3h

description:
Library name: Input_AsPC1_CB6644_3h
Input


title: H3K27ac_AsPC1_DMSO_3h

description:
Library name: H3K27ac_AsPC1_DMSO_3h
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: RUVBL1_AsPC1_DMSO_12h_rep1

description:
Library name: RUVBL1_AsPC1_DMSO_12h_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: RUVBL1_BxPC3_RUVBL12_overlap_rep1

description:
Library name: RUVBL1_BxPC3_RUVBL12_overlap_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: H3K27ac_AsPC1_CB6644_3h

description:
Library name: H3K27ac_AsPC1_CB6644_3h
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: 1035079-1)


title: KLF5_BxPC3_RUVBL12_overlap

description:
Library name: KLF5_BxPC3_RUVBL12_overlap
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_AsPC1_RUVBL12_overlap_rep2

description:
Library name: KLF5_AsPC1_RUVBL12_overlap_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: Input_BxPC3_RUVBL12_overlap

description:
Library name: Input_BxPC3_RUVBL12_overlap
Input


title: RUVBL2_AsPC1_RUVBL12_overlap

description:
Library name: RUVBL2_AsPC1_RUVBL12_overlap
ChIP antibody: RUVBL2, ABclonal, A12564 (Lot: 0010460101)


title: KLF5_AsPC1_RUVBL12_overlap_rep1

description:
Library name: KLF5_AsPC1_RUVBL12_overlap_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_AsPC1_CB6644_12h_rep1

description:
Library name: KLF5_AsPC1_CB6644_12h_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)


title: Input_AsPC1_RUVBL12_overlap

description:
Library name: Input_AsPC1_RUVBL12_overlap
Input


title: KLF5_AsPC1_DMSO_3h_rep1

description:
Library name: KLF5_AsPC1_DMSO_3h_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)


title: RUVBL2_AsPC1_DMSO_12h_rep1

description:
Library name: RUVBL2_AsPC1_DMSO_12h_rep1
ChIP antibody: RUVBL2, ABclonal, A12564 (Lot: 0010460101)


title: H3K27ac_AsPC1_RUVBL12_overlap

description:
Library name: H3K27ac_AsPC1_RUVBL12_overlap
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: KLF5_AsPC1_NEG_KLF5_for_INO80_rep2

description:
Library name: KLF5_AsPC1_NEG_KLF5_for_INO80_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: RUVBL1_AsPC1_CB6644_3h

description:
Library name: RUVBL1_AsPC1_CB6644_3h
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: H3K27ac_BxPC3_RUVBL12_overlap

description:
Library name: H3K27ac_BxPC3_RUVBL12_overlap
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: KLF5_AsPC1_CB6644_3h_rep2

description:
Library name: KLF5_AsPC1_CB6644_3h_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-7)


title: RUVBL1_AsPC1_RUVBL12_overlap_rep2

description:
Library name: RUVBL1_AsPC1_RUVBL12_overlap_rep2
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZJ4490454A)


title: Input_AsPC1_NEG_KLF5_for_INO80

description:
Library name: Input_AsPC1_NEG_KLF5_for_INO80
Input


title: INO80_AsPC1_NEG_KLF5_for_INO80

description:
Library name: INO80_AsPC1_NEG_KLF5_for_INO80
ChIP antibody: INO80, ProteinTech, 18810-1-AP (Lot: 00129808)


title: KLF5_AsPC1_dTAG_KLF5_for_INO80_rep2

description:
Library name: KLF5_AsPC1_dTAG_KLF5_for_INO80_rep2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: RUVBL1_BxPC3_RUVBL12_overlap_rep2

description:
Library name: RUVBL1_BxPC3_RUVBL12_overlap_rep2
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZA4162137)


title: Input_AsPC1_dTAG_KLF5_for_INO80

description:
Library name: Input_AsPC1_dTAG_KLF5_for_INO80
Input


title: KLF5_AsPC1_dTAG_KLF5_for_INO80_rep1

description:
Library name: KLF5_AsPC1_dTAG_KLF5_for_INO80_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: RUVBL1_AsPC1_RUVBL12_overlap_rep1

description:
Library name: RUVBL1_AsPC1_RUVBL12_overlap_rep1
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: ZJ4490454A)


title: KLF5_AsPC1_NEG_KLF5_for_INO80_rep1

description:
Library name: KLF5_AsPC1_NEG_KLF5_for_INO80_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: INO80_AsPC1_dTAG_KLF5_for_INO80

description:
Library name: INO80_AsPC1_dTAG_KLF5_for_INO80
ChIP antibody: INO80, ProteinTech, 18810-1-AP (Lot: 00129808)


title: INO80_AsPC1_DMSO_12h_rep2

description:
Library name: INO80_AsPC1_DMSO_12h_rep2
ChIP antibody: INO80, ProteinTech, 18810-1-AP (Lot: 00129808)


title: H3K27ac_AsPC1_DMSO_12h_rep2

description:
Library name: H3K27ac_AsPC1_DMSO_12h_rep2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_AsPC1_CB6644_12h_rep2

description:
Library name: Input_AsPC1_CB6644_12h_rep2
Input


title: RUVBL1_AsPC1_CB6644_12h_rep2

description:
Library name: RUVBL1_AsPC1_CB6644_12h_rep2
ChIP antibody: RUVBL1, Invitrogen, PA5-29278 (Lot: AC4660180)


title: Input_AsPC1_DMSO_12h_rep2

description:
Library name: Input_AsPC1_DMSO_12h_rep2
Input


title: INO80_AsPC1_CB6644_12h_rep2

description:
Library name: INO80_AsPC1_CB6644_12h_rep2
ChIP antibody: INO80, ProteinTech, 18810-1-AP (Lot: 00129808)


title: p63_T3M4_KLF5_p63_overlap

description:
Library name: p63_T3M4_KLF5_p63_overlap
ChIP antibody: p63-alpha, CST, D2K8X (Lot 3 (39692S))

value: 6h DMSO


title: H3K27ac_AsPC1_CB6644_12h_rep2

description:
Library name: H3K27ac_AsPC1_CB6644_12h_rep2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_T3M4_KLF5_p63_overlap

description:
Library name: Input_T3M4_KLF5_p63_overlap
Input


title: H3K27ac_T3M4_KLF5_p63_overlap

description:
Library name: H3K27ac_T3M4_KLF5_p63_overlap
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: KLF5_AsPC1_KLF5_HNF4A_overlap

description:
Library name: KLF5_AsPC1_KLF5_HNF4A_overlap
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: HNF4A_AsPC1_KLF5_HNF4A_overlap

description:
Library name: HNF4A_AsPC1_KLF5_HNF4A_overlap
ChIP antibody: HNF4A, Abcam, ab181604 (Lot: 1084221-8)


title: Input_AsPC1_KLF5_HNF4A_overlap

description:
Library name: Input_AsPC1_KLF5_HNF4A_overlap
Input


title: KLF5_T3M4_KLF5_p63_overlap

description:
Library name: KLF5_T3M4_KLF5_p63_overlap
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_T3M4_NEG_rep1

description:
Library name: KLF5_T3M4_NEG_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_T3M4_rep1.2

description:
Library name: KLF5_T3M4_rep1.2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: Input_T3M4_rep1

description:
Library name: Input_T3M4_rep1
Input


title: H3K27ac_T3M4_rep1

description:
Library name: H3K27ac_T3M4_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: KLF5_T3M4_rep1.1

description:
Library name: KLF5_T3M4_rep1.1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: RUVBL1_AsPC1_DMSO_12h_rep2

description: Library name: RUVBL1_AsPC1_DMSO_12h_rep2


title: H3K27ac_T3M4_dTAG_rep1.1

description:
Library name: H3K27ac_T3M4_dTAG_rep1.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: H3K27ac_T3M4_dTAG_rep1.2

description:
Library name: H3K27ac_T3M4_dTAG_rep1.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_T3M4_NEG_rep1

description:
Library name: Input_T3M4_NEG_rep1
Input


title: H3K27ac_T3M4_NEG_rep1.2

description:
Library name: H3K27ac_T3M4_NEG_rep1.2
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_HPAFII_rep1

description:
Library name: Input_HPAFII_rep1
Input

source_name: HPAFII

value: HPAFII


title: KLF5_HPAFII_rep1.2

description:
Library name: KLF5_HPAFII_rep1.2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: Input_T3M4_dTAG_rep1

description:
Library name: Input_T3M4_dTAG_rep1
Input


title: H3K27ac_T3M4_NEG_rep1.1

description:
Library name: H3K27ac_T3M4_NEG_rep1.1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: KLF5_BxPC3_rep1.2

description:
Library name: KLF5_BxPC3_rep1.2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_HPAFII_rep1.1

description:
Library name: KLF5_HPAFII_rep1.1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: KLF5_BxPC3_rep1.1

description:
Library name: KLF5_BxPC3_rep1.1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: H3K27ac_BxPC3_rep1

description:
Library name: H3K27ac_BxPC3_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: H3K27ac_HPAFII_rep1

description:
Library name: H3K27ac_HPAFII_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_AsPC1_rep1

description:
Library name: Input_AsPC1_rep1
Input


title: KLF5_AsPC1_rep1.1

description:
Library name: KLF5_AsPC1_rep1.1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: H3K27ac_AsPC1_rep1

description:
Library name: H3K27ac_AsPC1_rep1
ChIP antibody: H3K27ac, Abcam, ab4729 (Lot: GKR3216173-1)


title: Input_BxPC3_rep1

description:
Library name: Input_BxPC3_rep1
Input


title: SUIT2_sgRosa_rep4

description: Library name: STUI2_sgRosa_rep4

value: sgRosa


title: SUIT2_sgRosa_rep2

description: Library name: STUI2_sgRosa_rep2


title: SUIT2_sgRosa_rep1

description: Library name: STUI2_sgRosa_rep1


title: SUIT2_sgKLF5_rep4

description: Library name: SUIT2_sgKLF5_rep4


title: KLF5_T3M4_dTAG_rep1

description:
Library name: KLF5_T3M4_dTAG_rep1
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: SUIT2_sgKLF5_rep2

description: Library name: SUIT2_sgKLF5_rep2


title: SUIT2_sgKLF5_rep3

description: Library name: SUIT2_sgKLF5_rep3


title: SUIT2_sgKLF5_rep1

description: Library name: SUIT2_sgKLF5_rep1


title: T3M4_sgRUVBL2_rep2.4

description: Library name: T3M4_sgRUVBL2_rep2.4


title: T3M4_sgRUVBL2_rep2.3

description: Library name: T3M4_sgRUVBL2_rep2.3


title: T3M4_sgRUVBL2_rep2.2

description: Library name: T3M4_sgRUVBL2_rep2.2


title: T3M4_sgRUVBL1_rep2.3

description: Library name: T3M4_sgRUVBL1_rep2.3


title: T3M4_sgRUVBL1_rep2.2

description: Library name: T3M4_sgRUVBL1_rep2.2


title: T3M4_sgRUVBL1_rep2.1

description: Library name: T3M4_sgRUVBL1_rep2.1


title: T3M4_sgRpa3_rep2.1

description: Library name: T3M4_sgRpa3_rep2.1


title: T3M4_sgRosa_rep2.4

description: Library name: T3M4_sgRosa_rep2.4


title: T3M4_sgRosa_rep2.3

description: Library name: T3M4_sgRosa_rep2.3


title: KLF5_AsPC1_rep1.2

description:
Library name: KLF5_AsPC1_rep1.2
ChIP antibody: KLF5, Abcam, ab137676 (Lot: 1056810-1)


title: T3M4_sgRosa_rep2.2

description: Library name: T3M4_sgRosa_rep2.2


title: T3M4_sgRosa_rep2.1

description: Library name: T3M4_sgRosa_rep2.1


title: T3M4_sgRpa3_rep2.2

description: Library name: T3M4_sgRpa3_rep2.2


title: T3M4_sgKLF5_rep2.4

description: Library name: T3M4_sgKLF5_rep2.4


title: T3M4_sgKLF5_rep2.3

description: Library name: T3M4_sgKLF5_rep2.3


title: SUIT2_sgRosa_rep3

description: Library name: STUI2_sgRosa_rep3


title: T3M4_sgKLF5_rep2.1

description: Library name: T3M4_sgKLF5_rep2.1


title: T3M4_sgCDK1_rep2.1

description: Library name: T3M4_sgCDK1_rep2.1


title: T3M4_sgKLF5_rep2.2

description: Library name: T3M4_sgKLF5_rep2.2


title: CFPAC1_sgRUVBL2_rep1.2

description: Library name: CFPAC1_sgRUVBL2_rep1.2


title: T3M4_sgCDK1_rep2.2

description: Library name: T3M4_sgCDK1_rep2.2


title: CFPAC1_sgRUVBL2_rep1.1

description: Library name: CFPAC1_sgRUVBL2_rep1.1


title: CFPAC1_sgRUVBL1_rep1.4

description: Library name: CFPAC1_sgRUVBL1_rep1.4


title: CFPAC1_sgRUVBL1_rep1.2

description: Library name: CFPAC1_sgRUVBL1_rep1.2


title: CFPAC1_sgRUVBL1_rep1.1

description: Library name: CFPAC1_sgRUVBL1_rep1.1


title: CFPAC1_sgRpa3_rep1.2

description: Library name: CFPAC1_sgRpa3_rep1.2


title: CFPAC1_sgRpa3_rep1.1

description: Library name: CFPAC1_sgRpa3_rep1.1


title: CFPAC1_sgRUVBL1_rep1.3

description: Library name: CFPAC1_sgRUVBL1_rep1.3


title: CFPAC1_sgRosa_rep1.4

description: Library name: CFPAC1_sgRosa_rep1.4


title: CFPAC1_sgRosa_rep1.3

description: Library name: CFPAC1_sgRosa_rep1.3


title: CFPAC1_sgRosa_rep1.2

description: Library name: CFPAC1_sgRosa_rep1.2


title: CFPAC1_sgRosa_rep1.1

description: Library name: CFPAC1_sgRosa_rep1.1


title: T3M4_sgRUVBL2_rep2.1

description: Library name: T3M4_sgRUVBL2_rep2.1


title: CFPAC1_sgKLF5_rep1.2

description: Library name: CFPAC1_sgKLF5_rep1.2


title: CFPAC1_sgKLF5_rep1.3

description: Library name: CFPAC1_sgKLF5_rep1.3


title: CFPAC1_sgKLF5_rep1.1

description: Library name: CFPAC1_sgKLF5_rep1.1


title: CFPAC1_sgCDK1_rep1.2

description: Library name: CFPAC1_sgCDK1_rep1.2


title: CFPAC1_sgCDK1_rep1.1

description: Library name: CFPAC1_sgCDK1_rep1.1


title: BxPC3_sgRUVBL1_rep2.1

description: Library name: BxPC3_sgRUVBL1_rep2.1


title: BxPC3_sgRUVBL2_rep2.3

description: Library name: BxPC3_sgRUVBL2_rep2.3


title: BxPC3_sgRUVBL2_rep2.2

description: Library name: BxPC3_sgRUVBL2_rep2.2


title: BxPC3_sgRUVBL2_rep2.1

description: Library name: BxPC3_sgRUVBL2_rep2.1


title: BxPC3_sgRUVBL1_rep2.3

description: Library name: BxPC3_sgRUVBL1_rep2.3


title: BxPC3_sgRUVBL1_rep2.4

description: Library name: BxPC3_sgRUVBL1_rep2.4


title: BxPC3_sgRpa3_rep2.2

description: Library name: BxPC3_sgRpa3_rep2.2


title: BxPC3_sgRpa3_rep2.1

description: Library name: BxPC3_sgRpa3_rep2.1


title: BxPC3_sgRosa_rep2.4

description: Library name: BxPC3_sgRosa_rep2.4


title: BxPC3_sgRosa_rep2.2

description: Library name: BxPC3_sgRosa_rep2.2


title: BxPC3_sgRosa_rep2.1

description: Library name: BxPC3_sgRosa_rep2.1


title: BxPC3_sgKLF5_rep2.4

description: Library name: BxPC3_sgKLF5_rep2.4


title: BxPC3_sgKLF5_rep2.1

description: Library name: BxPC3_sgKLF5_rep2.1


title: BxPC3_sgCDK1_rep2.2

description: Library name: BxPC3_sgCDK1_rep2.2


title: BxPC3_sgKLF5_rep2.2

description: Library name: BxPC3_sgKLF5_rep2.2


title: BxPC3_sgCDK1_rep2.1

description: Library name: BxPC3_sgCDK1_rep2.1


title: AsPC1_sgRUVBL1_rep3.1

description: Library name: AsPC1_sgRUVBL1_rep3.1


title: AsPC1_sgRUVBL2_rep3.4

description: Library name: AsPC1_sgRUVBL2_rep3.4


title: AsPC1_sgRUVBL2_rep3.3

description: Library name: AsPC1_sgRUVBL2_rep3.3


title: AsPC1_sgRUVBL2_rep3.2

description: Library name: AsPC1_sgRUVBL2_rep3.2


title: AsPC1_sgRUVBL1_rep3.4

description: Library name: AsPC1_sgRUVBL1_rep3.4


title: AsPC1_sgRUVBL2_rep3.1

description: Library name: AsPC1_sgRUVBL2_rep3.1


title: AsPC1_sgRUVBL1_rep3.3

description: Library name: AsPC1_sgRUVBL1_rep3.3


title: AsPC1_sgRosa_rep3.4

description: Library name: AsPC1_sgRosa_rep3.4


title: AsPC1_sgRpa3_rep3.1

description: Library name: AsPC1_sgRpa3_rep3.1


title: AsPC1_sgRpa3_rep3.2

description: Library name: AsPC1_sgRpa3_rep3.2


title: AsPC1_sgRosa_rep3.3

description: Library name: AsPC1_sgRosa_rep3.3


title: AsPC1_sgRosa_rep3.2

description: Library name: AsPC1_sgRosa_rep3.2


title: BxPC3_sgRUVBL1_rep2.2

description: Library name: BxPC3_sgRUVBL1_rep2.2


title: AsPC1_sgRosa_rep3.1

description: Library name: AsPC1_sgRosa_rep3.1


title: AsPC1_sgKLF5_rep3.2

description: Library name: AsPC1_sgKLF5_rep3.2


title: BxPC3_sgRosa_rep2.3

description: Library name: BxPC3_sgRosa_rep2.3


title: AsPC1_sgKLF5_rep3.3

description: Library name: AsPC1_sgKLF5_rep3.3


title: AsPC1_sgKLF5_rep3.1

description: Library name: AsPC1_sgKLF5_rep3.1


title: AsPC1_sgRUVBL1_rep3.2

description: Library name: AsPC1_sgRUVBL1_rep3.2


title: BxPC3_sgKLF5_rep2.3

description: Library name: BxPC3_sgKLF5_rep2.3


title: AsPC1_sgCDK1_rep3.2

description: Library name: AsPC1_sgCDK1_rep3.2


title: T3M4_sgRpa3_rep1.2

description: Library name: T3M4_sgRpa3_rep1.2


title: T3M4_sgRosa_rep1.2

description: Library name: T3M4_sgRosa_rep1.2


title: AsPC1_sgCDK1_rep3.1

description: Library name: AsPC1_sgCDK1_rep3.1


title: T3M4_sgRpa3_rep1.1

description: Library name: T3M4_sgRpa3_rep1.1


title: T3M4_sgRosa_rep1.1

description: Library name: T3M4_sgRosa_rep1.1


title: T3M4_EV_CB6644_rep3

description: Library name: T3M4_EV_CB6644_rep3

value: Lv-Empty


title: T3M4_EV_DMSO

description: Library name: T3M4_EV_DMSO

value: 24h DMSO


title: T3M4_EV_CB6644_rep1

description: Library name: T3M4_EV_CB6644_rep1


title: T3M4_dF109_DMSO

description: Library name: T3M4_dF109_DMSO


title: T3M4_EV_CB6644_rep2

description: Library name: T3M4_EV_CB6644_rep2


title: T3M4_dF109_CB6644_rep2

description: Library name: T3M4_dF109_CB6644_rep2


title: T3M4_dF109_CB6644_rep3

description: Library name: T3M4_dF109_CB6644_rep3


title: T3M4_dF109_CB6644_rep1

description: Library name: T3M4_dF109_CB6644_rep1


title: T3M4_A62T_DMSO

description: Library name: T3M4_A62T_DMSO


title: T3M4_A62T_CB6644_rep2

description: Library name: T3M4_A62T_CB6644_rep2


title: T3M4_A62T_CB6644_rep1

description: Library name: T3M4_A62T_CB6644_rep1


title: T3M4_sgKLF5_rep1.2

description: Library name: T3M4_sgKLF5_rep1.2


title: AsPC1_sgKLF5_rep3.4

description: Library name: AsPC1_sgKLF5_rep3.4


title: T3M4_sgKLF5_rep1.4

description: Library name: T3M4_sgKLF5_rep1.4


title: T3M4_sgKLF5_rep1.1

description: Library name: T3M4_sgKLF5_rep1.1


title: T3M4_sgKLF5_rep1.3

description: Library name: T3M4_sgKLF5_rep1.3


title: AsPC1_sgRosa_rep2.3

description: Library name: AsPC1_sgRosa_rep2.3


title: AsPC1_sgRUVBL1_rep2.2

description: Library name: AsPC1_sgRUVBL1_rep2.2


title: AsPC1_sgRUVBL1_rep2.4

description: Library name: AsPC1_sgRUVBL1_rep2.4


title: AsPC1_sgRUVBL1_rep2.3

description: Library name: AsPC1_sgRUVBL1_rep2.3


title: AsPC1_sgSERPINB5_rep2.1

description: Library name: AsPC1_sgSERPINB5_rep2.1


title: AsPC1_sgRUVBL1_rep2.1

description: Library name: AsPC1_sgRUVBL1_rep2.1


title: AsPC1_sgSERPINB5_rep2.3

description: Library name: AsPC1_sgSERPINB5_rep2.3


title: AsPC1_sgSERPINB5_rep2.2

description: Library name: AsPC1_sgSERPINB5_rep2.2


title: AsPC1_sgSERPINB5_rep2.4

description: Library name: AsPC1_sgSERPINB5_rep2.4


title: AsPC1_sgKLF5_rep1.5

description: Library name: AsPC1_sgKLF5_rep1.5


title: AsPC1_sgRosa_rep2.2

description: Library name: AsPC1_sgRosa_rep2.2


title: AsPC1_sgKLF5_rep1.6

description: Library name: AsPC1_sgKLF5_rep1.6


title: AsPC1_sgRosa_rep2.1

description: Library name: AsPC1_sgRosa_rep2.1


title: AsPC1_sgKLF5_rep1.4

description: Library name: AsPC1_sgKLF5_rep1.4


title: BxPC3_sgRpa3_rep1.2

description: Library name: BxPC3_sgRpa3_rep1.2


title: AsPC1_sgKLF5_rep1.3

description: Library name: AsPC1_sgKLF5_rep1.3


title: AsPC1_sgKLF5_rep1.1

description: Library name: AsPC1_sgKLF5_rep1.1


title: AsPC1_sgRosa_rep1.2

description: Library name: AsPC1_sgRosa_rep1.2


title: AsPC1_sgKLF5_rep1.2

description: Library name: AsPC1_sgKLF5_rep1.2


title: BxPC3_sgRpa3_rep1.1

description: Library name: BxPC3_sgRpa3_rep1.1


title: AsPC1_sgRosa_rep1.1

description: Library name: AsPC1_sgRosa_rep1.1


title: T3M4_A62T_CB6644_rep3

description: Library name: T3M4_A62T_CB6644_rep3


title: BxPC3_sgRosa_rep1.1

description: Library name: BxPC3_sgRosa_rep1.1


title: BxPC3_sgKLF5_rep1.3

description: Library name: BxPC3_sgKLF5_rep1.3


title: BxPC3_sgKLF5_rep1.1

description: Library name: BxPC3_sgKLF5_rep1.1


title: BxPC3_sgKLF5_rep1.2

description: Library name: BxPC3_sgKLF5_rep1.2


title: BxPC3_sgKLF5_rep1.4

description: Library name: BxPC3_sgKLF5_rep1.4


title: BxPC3_sgRosa_rep1.2

description: Library name: BxPC3_sgRosa_rep1.2


title: AsPC1_sgRosa_rep2.4

description: Library name: AsPC1_sgRosa_rep2.4


title: AsPC1_EV_CB6644_rep2

description: Library name: AsPC1_EV_CB6644_rep2


title: AsPC1_dF109_DMSO

description: Library name: AsPC1_dF109_DMSO


title: AsPC1_dF109_CB6644_rep3

description: Library name: AsPC1_dF109_CB6644_rep3


title: AsPC1_A62T_CB6644_rep2

description: Library name: AsPC1_A62T_CB6644_rep2


title: AsPC1_A62T_CB6644_rep1

description: Library name: AsPC1_A62T_CB6644_rep1


title: AsPC1_dF109_CB6644_rep2

description: Library name: AsPC1_dF109_CB6644_rep2


title: AsPC1_dF109_CB6644_rep1

description: Library name: AsPC1_dF109_CB6644_rep1


title: AsPC1_A62T_DMSO

description: Library name: AsPC1_A62T_DMSO


title: AsPC1_sgCHD4_rep2

description: Library name: AsPC1_sgCHD4_rep2


title: AsPC1_sgCHD4_rep1

description: Library name: AsPC1_sgCHD4_rep1


title: AsPC1_EV_DMSO

description: Library name: AsPC1_EV_DMSO