title: Tumor, mteth.IL15.IL21_good response, #12 FBC

description: 10X Genomics

value: GPC2-CAR T w/ mteth.IL15.IL21


title: mip6d, memory, time 20, rep 1

status: Public on Jun 17 2025

type: SRA

city: València

first: Joan

last: Serrano Quílez

state: València

address: Jaume Roig, 11

country: Spain

institute: CSIC

library_source: transcriptomic

data_processing:
RNAseq data were obtained after Illumina sequencing and fastq files were obtained from Macrogen server
The quality of the raw sequencing data was checked by fastQC and trimmomatic program was used to withdraw the adapter sequences and the bases with a low base quality from the ends.
bases of reads which had a window size lower than 4 and a mean quality lower than 15 and the reads shorter than 36 bp were also trimmed.
Trimmed reads were mapped using sacCer3 as a reference genome with HISAT2, splice-aware aligner, and StringTie
Assembly: sacCer3
Supplementary files format and content: tab-delimited text containing raw reads for each sample
Supplementary files format and content: tab-delimited text containing TMM-normalised reads for each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: For all samples, yeast cells were growth until exponential phase (O.D.600 = 0.7) in rich medium (YPD).

extract_protocol:
A 10 mL aliquote is collected from each culture, washed twice with pure water and celular pellet was then frozen in liquid nitrogen. Total RNA was extracted with hot acid phenol protocol.
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: A cell culture was split into two flasks. One of them (memory) was exposed to a first 20 min heat shock and, after a 60 min recovery phase at optimal conditions, to a second 20 min heat shock. In the meantime, the other flask (no memory) was only exposed to a single 20 min heat shock. The heat shocks were performed by adding media at 51 ºC.

tag: cell line

tag: genotype

tag: memory

value: Yes

tag: time


title: SKN-1t[DNDD] transgenic rep1

city: Seattle

first: Nicolas

last: Lehrbach

state: WA

address: 1100 Fairview Ave. N, Seattle, WA 98109-102.

country: USA

institute: Fred Hutchinson Cancer Center

data_processing:
STAR v2.7.7a(https://pubmed.ncbi.nlm.nih.gov/23104886/) with 2-pass mapping was used to align paired-end reads to WBcel235 genome assembly and quantify gene-level counts based on ENSEMBL gene annotation v52. FastQC 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RNA-SeQC 2.3.4 (https://pubmed.ncbi.nlm.nih.gov/22539670/) were used to check read QC metrics.
Assembly: WBcel235
Supplementary files format and content: plain text containing gene-by-sample count matrix

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: For each sample/genotype, animals were bleach synchronized and hatched overnight rotating in M9 at 20°C. ~2000 synchronized L1 larvae were plated onto 9cm NGM plates. The animals were then allowed to grow to L4 stage before collection. Animals were washed 3x with M9 before resuspending the worm pellet in 1mL of TRIzol reagent (product #) and then stored at -80°C.

extract_protocol:
TriZol
TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA)

tag: tissue

value: whole animal

value: unc-119(ed3) III; mgTi41(SKN-1t[DNDD])

tag: treatment

value: synchronized L4 stage animals

tag: strain


title: Tumor, mteth.IL15.IL21_good response, #12

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.0.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.0.1 (STAR 2.7.2a). Sequenced reads were aligned to a custom human and mouse reference sequence containing CAR T. Sequenced reads were also aligned to the Total Seq C antibody Streptavidin and cell hashes HTO1, HTO2, and HTO3.
Assembly: GRCh38_mm10
Supplementary files format and content: feature_bc_matrix.h5

organism:
Homo sapiens
Mus musculus

source_name: Tumor

extract_protocol: Freshly collected spleens or tumors were processed using Papain Dissociation System (Worthington Biochemical Corporation) according to manufacturer's protocol. In brief, each specimen were minced in the papain solution containing DNase and incubated in 37 degrees in a CO2 incubator for 30 minutes. The cloudy supernatant was collected, and was layered on top of Earle's Balanced Salt Solution containing 10% of albumin-ovomucoid inhibitor. The samples were centrifuged, and the pelleted cells were resuspended in PBS. Tumor #83 and #93 were submitted for scRNA-seq as is. All the other samples were incubated with the hIL-15 PE-conjugated antibody, and given TotalSeq™-C0951 PE Streptavidin. Spleen samples were also hashtagged as follows. Splenocyte #12: TotalSeq-C0251, barcode seq. GTCAACTCTTTAGCG; #17: TotalSeq-C0252, barcode seq. TGATGGCCTATTGGG; #18: TotalSeq-C0253, barcode seq. TTCCGCCTCTCTTTG; Splenocyte #83: TotalSeq-C0251, barcode seq. GTCAACTCTTTAGCG; #93; TotalSeq-C0252, barcode seq. TGATGGCCTATTGGG; #87; TotalSeq-C0253, barcode seq. TTCCGCCTCTCTTTG. #12, #17, and #18 were combined into one sample, and #83, #93, and #87 were combined into one sample.

value: Tumor

tag: cell type

value: Neuroblastoma

value: ffLuc +, GFP +


title: SKN-1t[NDNN] transgenic rep1

value: unc-119(ed3) III; mgTi42(SKN-1t[NDNN])


title: mip6d, memory, time 15, rep 1


title: TRIM28 LKO CR ad 26

city: lexington

first: ka wing

last: Fong

state: KY

address: 760 press ave

institute: University of Kentucky

description: Library name: TRIM28 LKO CR ad 26

library_source: genomic

data_processing:
Paired-end sequencing reads were trimmed using Trimmomatic(v0.39) to remove adapters and low quality bases. Trimmed reads were mapped to the human reference genome assembly GRCh37 (hg19) using Bowtie2 (v2.3.5.1), allowing fragments up to 2kb to be aligned.
The alignment result was further filtered by SAMtools to remove reads unmapped, not primary alignment, reads failing platform, reads mapped to mitochondria, reads mapped to ENCODE blacklisted genomic regions and multi-mapped reads.
PCR duplicates were removed using Picard(v2.26.8). Peaks were called by MACS2(v2.2.7.1). The coverage track bigwig files were generated with bin size 10 and were normalized by reads per genome coverage using deeptools (v3.5.1).
Assembly: GRCH37
Supplementary files format and content: bigwig
Supplementary files format and content: narrowpeak file
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: LNCaP and C4-2B cells were grown in RPMI + 10% FBS and 1% PS.

extract_protocol:
For CUT&RUN assay, 0.5x10^6  cells bound to Concanavalin A-coated beads were incubated with indicated primary antibodies and secondary antibody.  pA-MNase was used to digest chromatin/DNA bound by the antibodies-protein complex in CUT&RUN, followed by Proteinase K digestion and PCI extraction. For ATAC-seq, 50,000 cells were collected, then washed once by 1×PBS and tagmented in 1×TD buffer with 2.5 μl Tn5, 0.01% digitonin, and 0.3×PBS. The reactions were incubated at 37 °C for 30 min in a thermomixer with 300 rpm mixing. The tagmented DNA was purified using the DNA Clean & Concentrator-5 kit.
CUT&RUN libraries were prepared from 15-20ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 160-320bp (CUT&RUN) in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). All CUT&RUN Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000. ATAC-seq Libraries were amplified and adapter dimers and primer dimers were cleaned up.

treatment_protocol: LNCaP and C4-2B cells were infected by lentivirial supernatent containing shTRIM28, shRb, lenti-HAF TRIM28-WT and S473A for 4 days before being harvested for CUT&RUN assay.

value: Human prostate cancer cells

tag: chip antibody


title: SKN-1t[NNNN] transgenic rep1

value: unc-119(ed3) III; mgTi21(SKN-1t[NNNN])


title: TRIM28 WT rep2

description: Library name: TRIM28 WT rep2


title: mip6d, memory, time 0, rep 1


title: Spleen, combined and hashtagged, #12, #17, #18 FBC

description: 10X Genomics

source_name: Spleen

value: Spleen

value: Splenocytes

value: GPC2-CAR T w/ mteth.IL15.IL21 or NFAT.mteth.IL15.IL21


title: allSamples8

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

description:
Library name: Sample8
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4

data_processing:
FASTQ files were processed using split-pipe (v1.4.0, Parse Biosciences) to generate cell-by-gene count matrices aligned to the mm39 mouse reference genome.
Assembly: mm39
Supplementary files format and content: Normalized counts across all conditions and annotated cell types (.txt)

molecule: nuclear RNA

organism: Mus musculus

source_name: Pancreatic islets

growth_protocol: Hand picked islets were cultured in RPMI-1640 with 10% FBS and 2 mM glutamate/1mM Na-pyruvate, penicillin/streptomycin, beta-mercaptoethanol

extract_protocol:
Nuclei were extracted from ~100 primary islets, stained with DAPI and FACS sorted.
Isolated nuclei were fixed using Evercode Nuclei Fixation v3 (Parse) and barcoded using Evercode WT v3 (Parse) according to manufacturer's instructions.

treatment_protocol: In the treated condition, islets were exposed to Exendin-4 (10nM) for 16 hours

value: Pancreatic islets

value: Endocrine pancreas


title: LN shRb shTRIM28 E2F1 rep1

description: Library name: LN shRb shTRIM28 E2F1 rep1

source_name: LNCaP

value: LNCaP

value: E2F-1 Antibody #3742


title: Spleen, combined and hashtagged, #12, #17, #18

description: 10X Genomics


title: LN shRb shTRIM28 E2F1rep 2

description: Library name: LN shRb shTRIM28 E2F1rep 2


title: allSamples7

description:
Library name: Sample7
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: Tumor, NFAT.mteth.IL15.IL21_good response, #17 FBC

description: 10X Genomics

value: GPC2-CAR T w/ NFAT.mteth.IL15.IL21


title: 5 dpf hematopoietic zebrafish cells, session 2

city: Paris

first: Lea

last: Torcq

address: 25 Rue du docteur Roux

country: France

institute: Institut Pasteur

description: Library name: marsseq_2

data_processing:
Raw reads were converted to fastq files using bcl2fastq package (2.20.0). Reads were demultiplexed and mapped to the Lawson Lab curated genome [(Lawson et al., 2020), v4.3.2] using the MARS-seq pipeline scripts (Keren-Shaul et al., 2019)
Assembly: zebrafish genome (Lawson lab version 4.3.2).
Supplementary files format and content: Tab-separated value files

organism: Danio rerio

source_name: sorted hematopoietic cells

extract_protocol:
Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources (Bresciani et al., 2018; Manoli and Driever, 2012; Samsa et al., 2016). All steps were performed with cooled solutions (4°C), and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly, 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine, at a final concentration of 640 µg/ml. Larvae (between 20 and 30 whole larvae or 60-80 dissected segments per tube) were washed twice in PBS before centrifugation (300 x g for 1 min @4°C) and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium (Life Technologies, Cat#: 12605-010) for 10 min on ice, with gentle pipetting every 3 mins, first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g, before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium (Genlantis, Cat#: T200100). Ultimately, samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow-through was transferred to a FACS tube and kept on ice until sorting (within the hour). Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples, gating was done on SSC-A vs. FSC-A to collect cells, then on FSC-W vs. FSC-A to keep only singlets and on APC-A to remove dead cells marked by Draq7 (Thermofisher, Cat#: D15106).
Cells were sorted in 384 wells plates (28 plates, in 2 independent sessions of 14 plates each) and the transcriptomic library was prepared according to the MARS-seq protocol 2.0 (Keren-Shaul et al. 2019). Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 (75 cycles) (Illumina). Raw reads were converted to fastq files using bcl2fastq package (2.20.0). Reads were demultiplexed and mapped to the Lawson Lab curated genome [(Lawson et al., 2020), v4.3.2] using the MARS-seq pipeline scripts (Keren-Shaul et al., 2019). Briefly, a first step of reverse transcription (RT) (SuperScript III, Thermo Fisher, Cat#: 18080085) was conducted to barcode the transcripts with unique cell and UMI barcodes. After RT, primers were removed with an exonuclease (ExoI NEB, Cat#: M0293L), and the barcoded cDNAs for each single cell in a half-plate were pooled together for the next steps. cDNA was converted to dsDNA (Second Strand synthesis kit, NEB, Cat#: E611L) and linearly amplified by in vitro transcription (HiScribe T7 High Yield RNA Synthesis Kit, NEB, Cat#: E2040S). The dsDNA was degraded (TURBO DNase Fisher, Cat#: 10646175) and the amplified RNA fragmented for sequencing (Fisher, Cat#: 10426914). A pool barcode with Illumina adapters for each half-plate was added by RNA-DNA ligation before a second RT step (AffinityScript Multiple Temperature reverse transcriptase, Agilent, Cat#: 600109). Final amplification by PCR was performed (KAPA HiFi HotStart ReadyMix, Roche Diagnostics, Cat#: 7958935001). The resulting libraries were controlled by qPCR amplification of housekeeping genes (ef1a and ß-actin), DNA quality control using a TapeStation, Agilent) and DNA concentration using the Qubit dsDNA high-sensitivity assay.

value: sorted hematopoietic cells


title: LN shRb E2F1 rep1

description: Library name: LN shRb E2F1 rep1

value: shRb


title: LN shRb E2F1 rep2

description: Library name: LN shRb E2F1 rep2


title: ERAP1 hetero type, Intestine

city: Swon

first: Hye-Myung

last: Ryu

address: 206, World cup-ro

department: Microbiolgy

country: South Korea

institute: Ajou Hospital

description: Library name: ERAP1 HT

data_processing:
Sequencing reads were aligned to the GENCODE GRCm38 v23 transcript reference using Bowtie2, and gene expression levels were quantified using RSEM. Expression values were normalized using the trimmed mean of M values (TMM) method
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: intestine

extract_protocol:
RNA was harvested usig Trizol. 1ug of total RNA was used for the construction of sequencing library.
RNA libraries for RNA-Seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

value: intestine

value: Hetero type


title: LN shTRIM28 E2F1 rep2

description: Library name: LN shTRIM28 E2F1 rep2


title: allSamples5

description:
Library name: Sample5
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: 5 dpf hematopoietic zebrafish cells, session 1

description: Library name: marsseq_1


title: ERAP1 wild type, Intestine

description: Library name: ERAP1 WT

value: Wild type


title: allSamples4

description:
Library name: Sample4
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: control (non-transgenic) rep1

value: whole animal

value: synchronized L4 stage animals


title: allSamples3

description:
Library name: Sample3
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: LN LKO E2F1 rep2

description: Library name: LN LKO E2F1 rep2

value: Human prostate cancer cells

value: LKO


title: allSamples2

description:
Library name: Sample2
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: LN LKO E2F1 rep1

description: Library name: LN LKO E2F1 rep1


title: allSamples1

description:
Library name: Sample1
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4


title: 5' RNA expression

city: New York

first: Stylianos

last: Bournazos

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: 10x Genomics

data_processing:
The following steps were derived from Seurat vignette. First, the filtered counting matrices of the samples were loaded into Seurat object. The features detected in less than five cells were removed. The proportion of mitochondrial genes oriented UMI counts (percent.mt) was also estimated. Then, the Seurat object was subjected to log normalization (Seurat::NormalizeData) and variable features identification (Seurat::FindVariableFeatures). After this step, amount 2000 variable features were identified by vst method. To merge the Seurat objects for all samples, the CCA-based workflow was applied. After merging all samples, the cells with the following criteria were removed: (i) too few genes detected (nFeature_RNA < 200); (ii) potential doublets (nCount_RNA > 99% quantile of UMI counts); (iii) potential cell debris (percent.mt > 10%). After removing low quality cells, a principal component analysis was performed (Seurat::RunPCA). The PCs used was determined by an Elbow plot (Seurat::ElbowPlot). In this case, we decided to use the first 15 PCs for the following steps, including identify neighbors (Seurat::FindNeighbors), made UMAP projection (Seurat::RunUMAP). Finally, the clusters were identified by using Louvain clustering with resolution as 0.5 (Seurat::FindClusters). The UMAP projection and clustering information were extracted and imported into Loupe Browser for more customized visualization.
Assembly: mm9; hg18
Supplementary files format and content: RDS files

source_name: Lung

extract_protocol:
Mice were euthanized and lungs were perfused by injection of PBS containing 10 U/ml heparin into the right cardiac ventricle. Lungs were excised and homogenized using the gentleMACS dissociator (mouse lung dissociation kit, Miltenyi), according to the manufacturer’s recommendations.
Single cells (pooled from individual mice) were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs) using Chromium Controller (10X Genomics) following manufacture’s protocol. Chromium Single Cell 5’ Library & Gel Bead (PN1000014), Single Cell V(D)J Enrichment Kit, Mouse T Cell (PN1000071), and Single Cell 5' Feature Barcode (PN1000080) kits were used to prepare single cell 5’ RNA, single cell TCR, and single cell surface protein (SCP) libraries following manufacture’s protocol. The quality and quantity of the libraries were assessed with Agilent TapeStation (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).

value: Lung

value: NK cells, T cells

value: C57Bl/6 FcR humanized (Smith et al. PNAS 2012; PMID:22474370)

value: H1N1 infection (PR8; 0.5 mLD50; i.n.)


title: genomic DNA from SKOV3ip1 bulk tumors Azacytidine plus B20 treated-2

type: genomic

city: Houston

first: Emine

last: Bayraktar

address: 1881 East Road

institute: MD Anderson Cancer Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Bulk SKOV3ip1 tumors

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: Bulk tumor

tag: disease state

value: tumor

value: Azacytidine plus B20 treated


title: allSamples6

description:
Library name: Sample6
Round1 plate. A1-A8: WT_CON, A9-B4: WT_FSK, B5-B12: WT_Ex-4, C1-C8: Med14S983A_CON, C9-D4: Med14S983A_FSK, D5-D12: Med14S983A_Ex-4

value: Pancreatic islets

value: Endocrine pancreas


title: DU PI3KCAAX + 4-OHT rep 3

status: Public on Jun 16 2025

type: RNA

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

hyb_protocol: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3)

label: biotin

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice  infected with PI3KCAAX plasmid treated with 4-OHT for 15 days

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix)

growth_protocol: All cells were grown in DMEM (Dulbecco's Modified Eagle Medium) supplemented with 10% fetal bovine serum, 1% L-glutamine, penicillin (10 mg/ml) and streptomycin (100 mg/ml). All cell lines were maintained at 37 °C in a humidified 5% CO2 atmosphere. In all cases, cells were dissociated using TripLE™ Express (cat. no. 12604013, GIBCO).

extract_protocol: Total RNAs from DU, DU R-Ras2G23V and DU-PI3KCAAX cells were isolated using the RNAeasy Mini Kit (Catalog No. 74104, Qiagen)

treatment_protocol: DU, DU R-Ras2G23V and DU-PI3KCAAX cells were treated or not with 4-OHT during 15 days, rinsed with PBS and processed for RNA extraction according to the kit's instructions.

value: MEFs from embryonic day 13.5 embryos and immortalized by standard methods

value: Cells infected with lentiviral particles obtained with pLVX-IRES-Hyg PI3KCAAX plasmid. Selected with hygromycyn (800 ug/ml) and then treated with 4-OHT ( 0,6 uM)


title: genomic DNA from SKOV3ip1 bulk tumors  B20 treated-2

value: B20 treated


title: single cell surface protein

description: 10x Genomics


title: LN shTRIM28 E2F1 rep1

description: Library name: LN shTRIM28 E2F1 rep1

value: LNCaP

value: E2F-1 Antibody #3742


title: single cell TCR

description: 10x Genomics


title: genomic DNA from SKOV3ip1 bulk tumors B20 treated-1


title: DU RRAS2G23V + 4-OHT  rep 1

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice  infected with RRAS2G23V plasmid treated with 4-OHT for 15 days

value: Cells infected with lentiviral particles obtained with pLVX-IRES-Hyg RRAS2G23V plasmid. Selected with hygromycyn (800 ug/ml) and then treated with 4-OHT ( 0,6 uM)


title: DU RRAS2G23V + 4-OHT  rep 3


title: DU PI3KCAAX + 4-OHT rep 1


title: DU PI3KCAAX rep 1

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice infected with PI3KCAAX plasmid

value: Cells infected with lentiviral particles obtained with pLVX-IRES-Hyg PI3KCAAX plasmid. Selected with hygromycyn (800 ug/ml)


title: DU PI3KCAAX + 4-OHT rep 2


title: DU PI3KCAAX rep 2


title: DU PI3KCAAX rep 3

value: Cells infected with lentiviral particles obtained with pLVX-IRES-Hyg PI3KCAAX plasmid.Selected with hygromycyn (800 ug/ml)


title: genomic DNA from SKOV3ip1 bulk tumors Azacytidine treated-2

value: Azacytidine treated


title: genomic DNA from SKOV3ip1 bulk tumors Azacytidine plus B20 treated-1


title: DU RRAS2G23V rep 1

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice infected with RRAS2G23V plasmid

value: Cells infected with lentiviral particles obtained with pLVX-IRES-Hyg RRAS2G23V plasmid. Selected with hygromycyn (800 ug/ml).


title: DU rep 3

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice (DU)

value: Control cells


title: DU + 4-OHT  rep 3

source_name: MEFs from H-Ras−/−;N-Ras−/−;K-Raslox/lox mice treated with 4-OHT for 10 days

value: 0,6 uM treatment with 4-OHT


title: DU RRAS2G23V + 4-OHT  rep 2


title: DU RRAS2G23V rep 3


title: DU + 4-OHT  rep 2


title: B20-treated SKOV3ip1 tumors, biol repl 1

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Quality check and probe level processing of the Ilumina microarray data were further made with R bioconductor package. The data were normalized using quantile normalization with IlluminaGUI in R. All bioconductor packages are available at http://bioconductor.org and all computation was performed under R environment (http://www.r-project.org).
quantile normalized

label_protocol: cRNAwas labeled 1ug of RNA using the Illumina® RNA amplification kit (Ambion/ Life Technologies), followed by hybridization the labeled cRNA to HumanHT-12 Expression BeadChips ( Illumina), following the manufacturer's instructions.

extract_protocol: RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN).

value: Nude mice

tag: age

value: 6-8 weeks

value: Bulk tumor tissue


title: Azacytidine-treated SKOV3ip1 tumors, biol repl 2

description: replicate 2


title: Azacytidine+B20-treated SKOV3ip1 tumors, biol repl 3

description: replicate 3


title: Azacytidine+B20-treated SKOV3ip1 tumors, biol repl 2

description: replicate 2


title: Azacytidine+B20-treated SKOV3ip1 tumors, biol repl 1

description: replicate 1


title: B20-treated SKOV3ip1 tumors, biol repl 3

description: replicate 3


title: B20-treated SKOV3ip1 tumors, biol repl 2

description: replicate 2


title: Azacytidine-treated SKOV3ip1 tumors, biol repl 1

description: replicate 1


title: DU rep 2


title: DU RRAS2G23V rep 2


title: DU + 4-OHT  rep 1


title: Azacytidine-treated SKOV3ip1 tumors, biol repl 3

description: replicate 3


title: genomic DNA from SKOV3ip1 bulk tumors control IgG treated-2

description: Control 113_3_9829118079_R02C01

value: Female

value: Bulk tumor

value: tumor

value: control IgG treated


title: genomic DNA from SKOV3ip1 bulk tumors Azacytidine treated-1


title: trnE-mutant-1, scRNA-seq

city: Hangzhou

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

country: China

institute: Westlake University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellanger software 7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Kidneys were harvested and minced into approximately 1 mm3 cubes. Enzymatic dissociation was performed in a 5 mL digestion buffer at 37 °C for 30 minutes. The digestion buffer contained 0.25 mg/mL of Liberase TM Research Grade enzyme (Roche, USA) and 50 µg/mL DNase I (New England Biolabs, USA). The reaction was deactivated by adding 10% fetal bovine serum (FBS). The resulting cell suspension was passed through a 70 μm cell strainer (Bioland, China), and cells were collected by centrifugation at 400 × g for 5 minutes at 4 °C. The cell pellet was treated with 3 mL red blood cell (RBC) lysis buffer (Invitrogen, USA) for 1 minute on ice, followed by another centrifugation at 400 × g for 5 minutes at 4 °C. Subsequent washes were performed with chilled 1x phosphate-buffered saline (PBS), and the cells were filtered through a 40 μm cell strainer (Bioland, China). The cells were then centrifuged at 400 × g at 4 °C for 5 minutes and resuspended in 500 µl pre-chilled 1x PBS with 2% BSA. Viability dye eBioscience™ Fixable Viability Dye eFluor™ 780 (ThermoFisher, #65-0865-14) was used to stain viable single cells for 15 minutes, followed by two washes with pre-chilled PBS. Viable single cells were sorted using a BD FACSAria Fusion flow cytometer (BD Biosciences)
Single-cell suspensions with greater than 80% viability were submitted to Novogene Biotechnology Co., Ltd (Beijing, China). Each sample, consisting of approximately ten thousand cells, was loaded onto the Chromium Single Cell Controller (10X Genomics) for cell encapsulation into gel beads in emulsion (GEMs). Subsequent steps involved cDNA library construction using the Chromium Single Cell 3' Reagent Kits, GEMs breakdown, barcoded cDNA purification and amplification, fragmentation, A-tailing, adaptor ligation, and PCR amplification for sample indexing and scRNA-Seq library enrichment.

value: Kidney

value: 79% mutation load mouse


title: Ectodermal cells (H1), 70 mM EtOH 2

city: Helsinki

first: Nina

last: Kaminen-Ahola

address: Haartmaninkatu 8

department: Department of Medical and Clinical Genetics

country: Finland

institute: University of Helsinki

description: Ectodermal cells (H1), 70 mM EtOH, EPIC1

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

scan_protocol: Arrays were scanned using iScan system and standard recommended Illumina scanner settings.

data_processing:
The raw DNAm dataset was pre-processed, quality-controlled, and filtered with ChAMP R package using the minfi method. Data was filtered using detection P-values and bead count values with default thresholds. Probes were normalized with noob in minfi R package, and BMIQ in wateRmelon R package. Following normalization, probes located in sex chromosomes and probes binding to polymorphic and off-target sites were filtered.
Average Beta

label: Cy3 and Cy5

label_protocol: The Infinium MethylationEPIC array uses direct hybridization without labeled nucleotides. After hybridization, labeled nucleotides were arred during primer extension step.

growth_protocol: hESCs were differentiated into the three germ layers by using the STEMdiff Trilineage Differentiation kit (Stemcell Technologies). Differentiation was performed according to the manufacturer’s instructions, and the medium was changed daily. Endodermal and mesodermal cells were collected after five days and ectodermal cells after seven days.

extract_protocol: DNA were extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The medium was supplemented with EtOH (≥ 99.5 p-%) at a final concentration of 20 mM or 70 mM. Exposure was started at the same time as the differentiation (day 1). The exposure durations were four days (96 h) for endodermal and mesodermal cells, and six days (144h) for ectodermal cells.

value: ectodermal cells

value: 70 mM EtOH


title: Control IgG-treated SKOV3ip1 tumors, biol repl 3

description: replicate 3


title: Ectodermal cells (H1), 70 mM EtOH 1


title: Ectodermal cells (H1), 70 mM EtOH 3


title: Control IgG-treated SKOV3ip1 tumors, biol repl 1

description: replicate 1


title: Ectodermal cells (H1), Control 3

description: Ectodermal cells (H1), Control, EPIC1

value: control


title: WT-1, scRNA-seq

description: 10x Genomics

value: wild-type mouse


title: Ectodermal cells (H1), 70 mM EtOH 4


title: trnE-mutant-2, scRNA-seq

description: 10x Genomics

value: 76% mutation load mouse


title: WT-2, scRNA-seq

description: 10x Genomics


title: Ectodermal cells (H1), Control 2

description: Ectodermal cells (H1), Control, EPIC1


title: DU rep 1

value: MEFs from embryonic day 13.5 embryos and immortalized by standard methods


title: Mesodermal cells (H1), 70 mM EtOH 4

description: Mesodermal cells (H1), 70 mM EtOH, EPIC1

value: mesodermal cells


title: genomic DNA from SKOV3ip1 bulk tumors control IgG treated-1

description: Control 113_1_9829118079_R01C01


title: Ectodermal cells (H1), Control 1

description: Ectodermal cells (H1), Control, EPIC1


title: Control IgG-treated SKOV3ip1 tumors, biol repl 2

description: replicate 2


title: Mesodermal cells (H1), 70 mM EtOH 3


title: Mesodermal cells (H1), Control 3

description: Mesodermal cells (H1), Control, EPIC1


title: Mesodermal cells (H1), Control 1

description: Mesodermal cells (H1), Control, EPIC1


title: Endodermal cells (H1), 70 mM EtOH 3

description: Endodermal cells (H1), 70 mM EtOH, EPIC1

value: endodermal cells


title: Endodermal cells (H1), 70 mM EtOH 4


title: Ectodermal cells (H1), Control 4

description: Ectodermal cells (H1), Control, EPIC1


title: Mesodermal cells (H1), Control 4

description: Mesodermal cells (H1), Control, EPIC1


title: Mesodermal cells (H1), 70 mM EtOH 2


title: Mesodermal cells (H1), 70 mM EtOH 1


title: Mesodermal cells (H1), Control 2

description: Mesodermal cells (H1), Control, EPIC1


title: Endodermal cells (H1), 70 mM EtOH 2


title: Endodermal cells (H1), 70 mM EtOH 1


title: Endodermal cells (H1), Control 4

description: Endodermal cells (H1), Control, EPIC1


title: Endodermal cells (H1), Control 1

description: Endodermal cells (H1), Control, EPIC1


title: Endodermal cells (H1), Control 3

description: Endodermal cells (H1), Control, EPIC1


title: TRE3G (IGHG3) c17 +Dox rep2

city: Freiburg im Breisgau

first: Maximilian

middle: Christian

last: von der Linde

address: Stefan-Meier-Straße 17

department: Institute for Medical Bioinformatics and Systems Medicine (IBSM)

country: Germany

institute: University Medical Center Freiburg

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Assembly: NCBI HG38
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

source_name: Ramos

growth_protocol: see Methods

extract_protocol:
cells were harvested and gen.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

treatment_protocol: see Methods

value: Ramos

value: Burkitt's Lymphoma

value: with Dox


title: TRE3G (IGHG3) c9 +Dox rep2


title: D3 +Dox rep3


title: TRE3G (IGHG3) c17 -Dox rep2

value: no Dox


title: TRE3G (IGHG3) c9 -Dox rep1


title: D3 -Dox rep2


title: TRE3G (IGHG3) c17 +Dox rep1


title: D3 +Dox rep2


title: TRE3G (IGHG3) c17 -Dox rep1


title: D3 -Dox rep3


title: TRE3G (IGHG3) c9 +Dox rep1


title: D3 -Dox rep1


title: D3 +Dox rep1


title: 601c-SB

city: West Haven

first: Kazushi

last: Suzuki

state: CT

address: 850 West Campus Drive

department: Genetics

institute: Yale University

description: insertion site mapping

data_processing:
Though paired-end files were retrieved from Miseq, only the forward reads were used for analysis; thus, only R1 files were included. FASTQ files from prepared samples were first processed for quality q>26 using BBDuk. Then, non-integrated AAV was removed with Cutadapt using a sequence unique to the AAV ITR. Next, transposon arms were trimmed out and only sequences that were trimmed were kept. After trimming 10 bases from the 5p end, reads were trimmed to a length of 30 bases and then mapped to the GRCh38 human genome using the hisat2 function. Resulting .sam files were filtered with samtools for q>=30.
.sam files were converted to .bam files using samtools view, and .bam files were converted to .bed files using bamtoBed. .bed files were renamed with the .txt extension.
Assembly: grch38
Supplementary files format and content: .txt files contain genomic coordinates of detected insertion sites of the Sleeping Beauty transposon CAR transgene in T cells of two different human donors (0286 and 601c).
Library strategy: insertion site mapping

source_name: CD4 T cell

extract_protocol:
Genomic DNA from untreated and CAR-T cells was extracted using QIAGEN's Blood Mini Kit.
First, gDNA was fragmented using NEB Ultra II FS Enzyme Mix. Then, Splinkerette adaptors were annealed by heating to 98C for 10 min and then cooling to room temp. Annealed Splinkerette adaptors were ligated to fragmented DNA using NEBNext Ultra II Ligation Master Mix. Library fragments were size selected for an approximate insert size of 200-350bp using NEBNext Sample purification beads. A two step PCR was then performed: the first PCR to amplify integrated transposon sequences (18 cycles) and the 2nd PCR to attach sequencing indeces (12 cycles). The libraries for each sample were quantified by qPCR, diluted to 2nM, and then pooled for sequencing by Miseq.

value: MAJESTIC (SB005 AAV, SB100x mRNA)

value: CD4 T cell

tag: purity

value: Unsorted for CAR

tag: car percentage

tag: donor

tag: condition

value: in vitro CAR-Ts

tag: day stimulated_after_electroporation

tag: day collected_after_electroporation


title: 0286-SB

description: insertion site mapping

source_name: CD8 T cell

value: CD8 T cell


title: 601c-WT

description: insertion site mapping

value: untreated


title: AAV-GFP_QUADRICEPS_Rep4

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.4.2a).
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats. Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.1.5.0)
Assembly: mm10
Supplementary files format and content: The excel table including CPM, and raw counts

source_name: Bulk quadriceps

growth_protocol: 12 to 14 weeks old male mice were used

extract_protocol:
Total RNAs were extracted from nitrogen frozen bulk livers or quadriceps tissues using QIAzol lysis reagent (Qiagen, #79306). RNA cleanup and DNAse treatment were performed using the RNeasy cleanup kit (Qiagen, #74204) and DNaseI
Standard Ion Total RNA-Seq kit v2 protocol

treatment_protocol: Animals were subjected to sham surgery or 70% partial hepatectomy. On day3 post-surgery, animals were euthanized, then livers and quadriceps were collected to extract total RNA for subsequent RNA0sequencing experiment. 3 sham control animals and 5 partial hepatectomy animals were used.

value: Bulk quadriceps

tag: genotype

tag: days post-aav_infection

value: Day 7


title: AAV-GFP_QUADRICEPS_Rep2

tag: tissue


title: AAV-Yap1S5A_QUADRICEPS_Rep4


title: AAV-GFP_QUADRICEPS_Rep3


title: AAV-Yap1S5A_QUADRICEPS_Rep3


title: Endodermal cells (H1), Control 2

description: Endodermal cells (H1), Control, EPIC1

tag: cell line

tag: treatment

value: control


title: AAV-Yap1S5A_QUADRICEPS_Rep1


title: AAV-Yap1S5A_QUADRICEPS_Rep2


title: AAV-GFP_LIVER_Rep4

source_name: Bulk Liver

value: Bulk Liver


title: AAV-GFP_LIVER_Rep3


title: AAV-GFP_LIVER_Rep2


title: AAV-Yap1S5A_LIVER_Rep3


title: AAV-Yap1S5A_LIVER_Rep1


title: AAV-Yap1S5A_LIVER_Rep4


title: AAV-Yap1S5A_LIVER_Rep2


title: Liver, Rat 80

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

description: Library name: index35-80-Chemical-Ozone000ppm_S14.fastq

data_processing:
Partek Flow NGS analysis software (Build 11.0.24.0102) was used to demultiplex data, trim adapters, and remove low quality bases.
Processed reads were aligned using STAR 2.6.1d to rn6 (Ensembl release 104 v2). One sample from the male ozone offspring group was identified as an extreme outlier in the principal component analysis and was removed from the study.
Differentially expressed genes (DEGs) were determined using DESeq2 following median ratio normalization and statistical significance was set at Storey q-value < 0.05.
Assembly: rn6
Supplementary files format and content: tab-delimited text file contains normalized values for each sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was isolated from liver using the Direct-Zol RNA Miniprep kit (Zymo Research) and concentrations were determined by Qubit (ThermoFisher Scientific).
RNA quality was determined using Bioanalyzer (Beckman Coulter, Inc.), with RIN values > 7. Hepatic RNA samples were processed on Apollo324 for polyA selection prior to library preparation, which was performed using the PrepX mRNA library prep kit for Illumina (Takara Bio USA, Inc.). Sample products were measured for quality and quantity using the Bioanalyzer High Sensitivity DNA chips, with final pooled libraries quantified using the Qubit High Sensitivity kit.

treatment_protocol: A subset of rats was exposed to episodic exposures which included 3 exposures on the first week and 2 exposures on the second. Exposures occurred for 4 hours from 0700-1100 in Rochester-style Hinners chambers. Ozone was generated via a silent arc discharge generator (OREC) and transferred to the chambers using a mass flow controller. Control rats were exposed to filtered air. Temperature and humidity in each chamber were controlled throughout the final exposure and remained between 21 – 23◦C and 41 – 43%, respectively. he average ozone concentration for each chamber was 0.000 ± 0.000 ppm, 0.401 ± 0.001 ppm, and 0.798 ± 0.001 ppm.

value: Liver

tag: Sex

value: Male

value: Maternal Ozone


title: Liver, Rat 79

description: Library name: index33-79-Chemical-Ozone000ppm_S17.fastq


title: Liver, Rat 77

description: Library name: index32-77-Chemical0-0Ozone0000ppm_S11.fastq


title: Liver, Rat 76

description: Library name: index31-76-Chemical-Ozone000ppm_S9.fastq


title: Liver, Rat 57

description: Library name: index22-57-Chemical0-0Ozone0000ppm_S3.fastq

value: Female


title: Liver, Rat 59

description: Library name: index24-59-Chemical0-0Ozone0000ppm_S12.fastq


title: AAV-GFP_QUADRICEPS_Rep1


title: 0286-WT

description: insertion site mapping

tag: cell type


title: Liver, Rat 52

description: Library name: index19-52-Chemical-Ozone000ppm_S19.fastq


title: Liver, Rat 55

description: Library name: index20-55-Chemical0-0Ozone0000ppm_S7.fastq


title: Liver, Rat 51

description: Library name: index18-51-Chemical0-0Ozone0000ppm_S1.fastq


title: Liver, Rat 56

description: Library name: index21-56-Chemical0-0Ozone0000ppm_S24.fastq


title: Liver, Rat 32

description: Library name: index8-32-Chemical0-0Ozone0000ppm_S17.fastq

value: Maternal Air


title: Liver, Rat 29

description: Library name: index7-29-Chemical-Ozone000ppm_S20.fastq


title: Liver, Rat 28

description: Library name: index6-28-Chemical-Ozone000ppm_S18.fastq


title: Liver, Rat 34

description: Library name: index10-34-Chemical-Ozone000ppm_S11.fastq


title: Liver, Rat 33

description: Library name: index9-33-Chemical0-0Ozone0000ppm_S5.fastq


title: Liver, Rat 27

description: Library name: index5-27-Chemical0-0Ozone0000ppm_S19.fastq


title: Liver, Rat 12

description: Library name: index45-12-Chemical-Ozone000ppm_S12.fastq


title: Liver, Rat 6

description: Library name: index23-6-Chemical-Ozone000ppm_S23.fastq


title: AAV-GFP_LIVER_Rep1


title: Liver, Rat 4

description: Library name: index12-04-Chemical0-0Ozone0000ppm_S18.fastq


title: Liver, Rat 10

description: Library name: index34-10-Chemical-Ozone000ppm_S2.fastq


title: Liver, Rat 11

description: Library name: index44-11-Chemical-Ozone000ppm_S22.fastq


title: Liver, Rat 83

description: Library name: index36-83-Chemical-Ozone000ppm_S4.fastq


title: Liver, Rat 2

description: Library name: index1-2-Chemical-Ozone000ppm_S6.fastq


title: 5L

first: Maria

last: Vecherkovskaya

address: 101 Avenue of Americas 3rd floor

institute: Human Microbiology Institute

description: Library name: Experiment

data_processing:
All reads from the sequencing experiment were mapped to the reference human genome (GRCh38) using STAR (v2) Duplicate reads were removed using Picard tools (v1.126) (http://broadinstitute.github.io/picard/). Reads-per-million-normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4) [81]. Read count tables were generated using HTSeq (v0.6.0) and normalized based on library size factors using DEseq2, after which differential gene-expression analysis was performed. Transcripts with an adjusted p value of <0.05 and a log2 fold-change value of ±1.0 (2-fold) were considered significantly DEGs. All downstream statistical analyses and plot generations were performed using R (v3.1.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Experiment

extract_protocol:
The cells were harvested via centrifugation at 300 ´ g for 15 min and resuspended in phosphate-buffered saline (PBS). RNA was extracted from leukocytes using the RNeasy Mini Kit (Qiagen, Germantown, Maryland, USA).
RNA quality was assessed spectrophotometrically at 230, 260, and 280 nm with a Promega GloMax Discover Microplate Reader (Promega, Madison, WI, USA). Ribodepletion was performed using the Ribo-Zero Magnetic Gold Kit (Epicenter, Madison, Wisconsin, USA). Transcriptome sequencing libraries were prepared from RNA using the TruSeq Stranded Total RNA Library Prep Kit

value: leukocytes


title: NCI-H146-shKLF9-2

city: Guangzhou

first: Wei

state: 广东Guangdong

address: Zhongshandadao West 55

department: Institute of Brain Science and Rehabilitation Medicine

institute: South China Normal University

description: Library name: Sample8

data_processing:
mRNA profiles were generated by deep sequencing using novaseq 6000 sequencing platform. The reads were mapped to the human reference genome (GRCh38) by STAR software (Version 2.5.1), annotation from GENCODE version vM21 was used. Differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values and counts for each Sample.

source_name: lung

growth_protocol: NCI-H1688 and NCI-H146 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and Pen/Strep antibiotic at 37 °C in a balanced air humidified incubator with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94℃ for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3µl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X)Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Human SCLC cells (NCI-H1688 and NCI-H146) were cultured under standard conditions, and the cells were infected with shRNA lentivirus and screened with appropriate concentrations of puromycin for 2 weeks to obtain stably transfected cell lines. Total RNA from each treatment group was collected and subjected to RNA sequence analysis. Biological replicates and analyses were performed.

value: lung

value: epithelial cell

value: KLF9 knockdown

value: cells were infected with shRNA KLF9 lentivirus and screened with appropriate concentrations of puromycin for 2 weeks


title: 1L

description: Library name: Control

source_name: Control


title: NCI-H146-shKLF9-1

description: Library name: Sample7


title: NCI-H1688-shKLF9-2

description: Library name: Sample4


title: NCI-H146-shcontrol-2

description: Library name: Sample5

value: WT

value: cells were infected with shRNA control lentivirus and screened with appropriate concentrations of puromycin for 2 weeks


title: NCI-H1688-shcontrol-1

description: Library name: Sample1


title: NCI-H1688-shcontrol-2

description: Library name: Sample2


title: ALI, TNFa, donor 2

city: Lübeck

first: Yamil

middle: Abdala

last: Maluje

state: Schleswig- Holstein

address: Ratzeburger Allee 160

department: Institute of Experimental Dermatology

institute: University of Luebeck

description: Library name: C250124002_scR

data_processing:
Sequencing reads were mapped to Homo Sapiens GRCh38 using ‘kallisto’ (v.0.46.1) and ‘bustools’ (v.0.46.1)
The output-filtered gene expression matrices were analyzed in ‘R’ (v4.2.1) with the ‘DropletUtils’ (v1.8.0) and ‘Seurat’ (v4.3) packages and integrated using Harmony
Assembly: Homo Sapiens GRCh38
Supplementary files format and content: Seurat object (.rds)

source_name: nasal epithelial cells

extract_protocol:
Singleron standard processing protocol
Singleron standard library construction protocol

value: nasal epithelial cells

value: human primary nasal

value: male

value: TNFa


title: ALI, TNFa_TGFb, donor 1

description: Library name: C250107004_scR

value: female

value: TNFa + TGFb


title: ALI, TNFa_TGFb, donor 2

description: Library name: C250124004_scR


title: ALI, TGFb, donor 2

description: Library name: C250124003_scR

value: TGFb


title: ALI, TGFb, donor 1

description: Library name: C250107003_scR


title: ALI, PBS, donor 2

description: Library name: C250124001_scR

value: PBS


title: ALI, PBS, donor 1

description: Library name: C250107001_scR


title: ALI, TNFa, donor 1

description: Library name: C250107002_scR


title: YCLO-6 Control RNA_seq

city: Seoul

first: KIM

last: JINSU

address: 50-1 Yonsei-ro, Seodaemun-gu, Seoul, Korea

department: Internal Medicine

institute: Yonsei University College of Medicine

description: Library name: YCLO-6 RNA_seq

data_processing:
RNA-seq: Adapter trimming and quality filtering were performed using cutadapt (v2.8) to remove low-quality reads (shorter than 50 bp or with a Phred score < 20). Filtered reads were aligned to the reference genome using STAR (v2.7.1a) with the -quantMode TranscriptomeSAM option for transcriptome quantification. Gene expression levels were estimated using RSEM (v1.3.1) with the --strandedness and --estimate-rspd options for accurate transcript quantification. Differential gene expression analysis was conducted using the TCC (v1.26.0) R package, applying robust normalization with DESeq2 or edgeR methods.
Assembly: The genome assembly used for  RNA-seq analyses was the UCSC hg19 human reference genome.
Supplementary files format and content: RNA-seq: Processed data includes FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million) normalized expression matrices, as well as differential expression analysis results in tab-delimited text files (e.g., .tsv). Quality control reports from fastQC are also included to verify sequencing quality.

extract_protocol:
RNA were extracted from conditionally reprogrammed cells (CRCs) organoids using the QIAamp DNA Mini Kit (QIAGEN) and oligo(dT) magnetic beads, respectively. RNA was isolated through mRNA purification and fragmentation, followed by reverse transcription into double-stranded cDNA using random hexamer priming.
RNA (RNA-seq) Library Preparation: mRNA molecules were purified from total RNA using oligo(dT) magnetic beads and subsequently fragmented. Single-stranded cDNA was synthesized using random hexamer priming, followed by second-strand synthesis to generate double-stranded cDNA. This cDNA was then processed through end repair, A-tailing, adapter ligation, and PCR amplification. Quality assessment was conducted using the Agilent 2100 BioAnalyzer, and the final libraries were quantified using the KAPA Library Quantification Kit.

value: Patient-derived Organoid


title: YCLO-2 Control RNA_seq

description: Library name: YCLO-2 RNA_seq


title: YCLO-4 Control RNA_seq

description: Library name: YCLO-4 RNA_seq


title: YCLO-7 Control RNA_seq

description: Library name: YCLO-7 RNA_seq


title: YCLO-1 Control RNA_seq

description: Library name: YCLO-1 RNA_seq


title: MDA-MB-231, shHMGA2-2-1

city: Tianjin

first: Lu

last: Qiao

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin City

institute: Tianjin Medical University

description:
Library name: Sample 5
S231-2671-1

data_processing:
Data filtering steps
The alignment of short reads was performed using Hisat2(v2.2.1) software, with default parameters
Gene expression calculation was performed using Htseq software (V 0.6.1).
Assembly: GRCh38.p13
Supplementary files format and content: File includes count and FPKM values for each sample.

extract_protocol:
The nucleic acid mass ≥1.5 μg. The sample is clear and colorless, without viscosity or any dissolved substances.
Total RNA quality detection, mRNA capture, mRNA disruption and synthesis of double-stranded cDNA, end repair, add A and joints, fragment sorting, PCR amplification, library quality inspection.


title: MDA-MB-231, shHMGA2-1-2

description:
Library name: Sample 4
231-SH2-C9-2


title: MDA-MB-231, shNC-1

description:
Library name: Sample 1
231-WT-1


title: MDA-MB-231, shNC-2

description:
Library name: Sample 2
231-WT-2


title: MDA-MB-231, shHMGA2-2-2

description:
Library name: Sample 6
S231-2671-2


title: NCI-H1688-shKLF9-1

last: Zhang

description: Library name: Sample3


title: NCI-H146-shcontrol-3

description: Library name: Sample6


title: 12, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 90 min chase

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

address: 25 William St

department: CBE

institute: Princeton University

description: Library name: Sample 127

data_processing:
5eU-seq pipeline v1.0.0 was used for data processing (https://doi.org/10.5281/zenodo.14908465). Briefly, sequencing reads were trimmed with Trimmomatic v0.39 to remove adaptor sequences and bases containing low quality scores. Trimmed reads were then aligned to the rDNA genome (GenBank: U13369.1) using STAR (2.7.11a).
rRNA cleavage metrics to calculate the "fraction cleaved" metric were calculated with custom scripts in the 5eU-seq pipeline to generate ‘allJunctions3_parsed.txt’. 2’-O-Methylation scores (scoreC) were also calculated with custom scripts to generate ‘human_all_2methylPositions.csv’. These files were further processed to match the site names used in the publication to generate 'allJunctions3_renamed.txt'. The 2'-O-Me sites were updated to add the established names from the numeric methylPositions and classified as located on the 18S or 28S region to generate 'human_all_2methylPositions_renamed.csv'.
Assembly: rDNA genome (GenBank: U13369.1)
Supplementary files format and content: rRNA cleavage metrics and 2'-O-Methylation scores provided in comman separated value (CSV) fomat

growth_protocol: MCF10A cells were cultured in a humidified chamber at 37 °C with 5% CO2 and 1% streptomycin and penicillin (GIBCO, 15140122). DMEM/F12 medium (Thermo Scientific, 11320082) supplied with 5% horse serum (Sigma, H1138), 20 ng/mL EGF (Novoprotein, C029), 10 ng/mL insulin (Sigma, 91077C), 1 µg/mL hydrocortisone (Sigma, H0888) was used.

extract_protocol:
RNA isolation was performed with Qiagen RNeasy Mini kits followed by DNAse digestion (TURBO DNase, Invitrogen, AM2238) to remove genomic DNA. RNA concentrations were measured with Qubit RNA BR (Fisher Scientific, Q10211) and RNA integrity was analyzed on Agilent RNA High Sensitivity (HS) Tapestation. Total RNA (10-15 µg) isolated after 5eU-pulse chase was click-reacted with biotin picolyl azide (Click chemistry tools, 1167-25) as described in Bhat, P., et al., Nature. 2024 with the following modifications. Capture of biotinylated RNA was performed using 20uL Dynabeads MyOne Streptavidin C1 beads (Invitrogen, 65002) after click chemistry. Captures and washes were performed as previously described except for a modification to the 3 x 5 min washes of captured material, which were changed to 75° C in No Salt Urea buffer (4M Urea, 10mM HEPES, pH 7.5, 10mM EDTA, 0.5% Triton X-100, 0.2% SDS, 0.1% Na-DOC). We found that 3 rounds of sequential captures (as described by Bhat et al, 202432) as well an optimized protocol introduced here performing washes at high temperature and in a buffer lacking salt were essential to reduce background of highly abundant mature rRNA.
Captured RNA was used for library construction as previously described in Banerjee, A., et al. Cell. 2020.

treatment_protocol: Cells were seeded for 5eU pulse chase labeling such that their confluence was ~50-60% at the time of harvesting. Cells were pulse labeled with 5eU (Jena Biosciences; CLK-N002-10) for 15 minutes at 37 °C with 5% CO2. Cells were then removed from the incubator and quickly washed twice with 1x DPBS to remove 5eU from the cells. Cells were then chased with media containing 10 mM Uridine (Sigma, U6381) to outcompete the leftover 5eU in cells over different chase time points. Cells were returned to the 37 °C incubator immediately upon chase or any other media exchanges, and all solutions were kept at 37 °C using a heat block to minimize temperature-induced changes to the cells, which could impact RNA transcription and processing. After the given chase time, cells were harvested in 1x Buffer RLT (QIAGEN, 79216) and frozen at -80° C for RNA isolation.

value: Breast epithelial cells

tag: time

value: 15min 5eU pulse, 90 min chase


title: 08, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 123

value: 15min 5eU pulse, 15 min chase


title: 13, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 120 min chase

description: Library name: Sample 128

value: 15min 5eU pulse, 120 min chase


title: 11, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 126

value: 15min 5eU pulse, 60 min chase


title: 07, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 122

value: 15min 5eU pulse, 0 min chase


title: 05, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 120


title: 04, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 119


title: 03, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 118

value: 15min 5eU pulse, 30 min chase


title: 08, MCF10A, U3b, TREATED-U3_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 115


title: 01, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 116


title: 07, MCF10A, U3b, TREATED-U3_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 114


title: 02, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 117


title: 05, MCF10A, U3b, TREATED-U3_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 112


title: 06, MCF10A, U3b, TREATED-U3_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 113


title: MDA-MB-231, shHMGA2-1-1

description:
Library name: Sample 3
231-SH2-C9-1


title: 03, MCF10A, U3b, CONTROL-SCR_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 110


title: 02, MCF10A, U3b, CONTROL-SCR_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 109


title: 04, MCF10A, U3b, CONTROL-SCR_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 111


title: 18, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 107


title: 16, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 105


title: 13, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 102


title: 15, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 104


title: 14, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 103


title: 17, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 106


title: 09, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 124


title: 01, MCF10A, U3b, CONTROL-SCR_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 108


title: 12, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 101


title: 06, MCF10A, U8, CONTROL-SCR_ASO, 15min 5eU pulse, 120 min chase

description: Library name: Sample 121


title: 11, MCF10A, U3a, TREATED-U3_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 100


title: 10, MCF10A, U8, TREATED-U8_ASO, 15min 5eU pulse, 45 min chase

description: Library name: Sample 125

value: 15min 5eU pulse, 45 min chase


title: 09, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 98


title: 10, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 99


title: 08, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 97


title: 05, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 94


title: 04, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 93


title: 01, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 90


title: 03, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 92


title: 02, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 91


title: 16, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 89


title: 15, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 88


title: 14, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 87


title: 13, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 86


title: 11, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 20 min chase

description: Library name: Sample 84

value: 15min 5eU pulse, 20 min chase


title: 12, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 85


title: 08, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 81


title: 09, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 82


title: 03, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 20 min chase

description: Library name: Sample 76


title: 05, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 78


title: 07, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 80


title: 01, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 74


title: 02, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 75


title: 04, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 77


title: 06, MCF10A, RPL5, CONTROL-SCR_shRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 79


title: 18, MCF10A, MCF10A, none, 15min 5eU pulse, 240 min chase

description: Library name: Sample 73

value: 15min 5eU pulse, 240 min chase


title: 07, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 60 min chase

description: Library name: Sample 96


title: 06, MCF10A, U3a, CONTROL-SCR_ASO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 95


title: 15, MCF10A, MCF10A, none, 15min 5eU pulse, 120 min chase

description: Library name: Sample 70


title: 16, MCF10A, MCF10A, none, 15min 5eU pulse, 120 min chase

description: Library name: Sample 71


title: 12, MCF10A, MCF10A, none, 15min 5eU pulse, 75 min chase

description: Library name: Sample 67

value: 15min 5eU pulse, 75 min chase


title: 14, MCF10A, MCF10A, none, 15min 5eU pulse, 90 min chase

description: Library name: Sample 69


title: 17, MCF10A, MCF10A, none, 15min 5eU pulse, 240 min chase

description: Library name: Sample 72


title: 13, MCF10A, MCF10A, none, 15min 5eU pulse, 90 min chase

description: Library name: Sample 68


title: 10, MCF10A, MCF10A, none, 15min 5eU pulse, 60 min chase

description: Library name: Sample 65


title: 08, MCF10A, MCF10A, none, 15min 5eU pulse, 45 min chase

description: Library name: Sample 63


title: 09, MCF10A, MCF10A, none, 15min 5eU pulse, 60 min chase

description: Library name: Sample 64


title: 06, MCF10A, MCF10A, none, 15min 5eU pulse, 30 min chase

description: Library name: Sample 61


title: 05, MCF10A, MCF10A, none, 15min 5eU pulse, 30 min chase

description: Library name: Sample 60


title: 04, MCF10A, MCF10A, none, 15min 5eU pulse, 15 min chase

description: Library name: Sample 59


title: 10, MCF10A, RPL5, TREATED-RPL5_shRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 83


title: 02, MCF10A, MCF10A, none, 15min 5eU pulse, 0 min chase

description: Library name: Sample 57


title: 03, MCF10A, MCF10A, none, 15min 5eU pulse, 15 min chase

description: Library name: Sample 58


title: 01, MCF10A, MCF10A, none, 15min 5eU pulse, 0 min chase

description: Library name: Sample 56


title: 24, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 90 min chase

description: Library name: Sample 55

value: TREATED-FVP


title: 23, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 90 min chase

description: Library name: Sample 54


title: 21, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 70 min chase

description: Library name: Sample 52

value: 15min 5eU pulse, 70 min chase


title: 22, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 70 min chase

description: Library name: Sample 53


title: 20, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 45 min chase

description: Library name: Sample 51


title: 19, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 45 min chase

description: Library name: Sample 50


title: 18, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 30 min chase

description: Library name: Sample 49


title: 17, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 30 min chase

description: Library name: Sample 48


title: 14, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 0 min chase

description: Library name: Sample 45


title: 11, MCF10A, MCF10A, none, 15min 5eU pulse, 75 min chase

description: Library name: Sample 66


title: 13, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 0 min chase

description: Library name: Sample 44


title: 15, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 15 min chase

description: Library name: Sample 46


title: 11, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 42

value: CONTROL-DMSO


title: 12, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 90 min chase

description: Library name: Sample 43


title: 08, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 45 min chase

description: Library name: Sample 39


title: 07, MCF10A, MCF10A, none, 15min 5eU pulse, 45 min chase

description: Library name: Sample 62


title: 09, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 70 min chase

description: Library name: Sample 40


title: 07, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 45 min chase

description: Library name: Sample 38


title: 06, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 37


title: 04, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 35


title: 02, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 33


title: 03, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 15 min chase

description: Library name: Sample 34


title: 28, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 28


title: 29, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 29


title: 31, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 31


title: 05, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 30 min chase

description: Library name: Sample 36


title: 01, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 0 min chase

description: Library name: Sample 32


title: 16, MCF10A, FVP, TREATED-FVP, 15min 5eU pulse, 15 min chase

description: Library name: Sample 47


title: 26, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 75 min chase

description: Library name: Sample 26


title: 25, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 25


title: 23, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 23


title: 22, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 22


title: 24, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 24


title: 27, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 75 min chase

description: Library name: Sample 27


title: 21, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 21


title: 20, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 20


title: 10, MCF10A, FVP, CONTROL-DMSO, 15min 5eU pulse, 70 min chase

description: Library name: Sample 41


title: 16, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 16


title: 19, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 19


title: 18, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 18


title: 14, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 14


title: 15, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 15


title: 17, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 17


title: 12, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 12


title: 13, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 90 min chase

description: Library name: Sample 13


title: 11, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 75 min chase

description: Library name: Sample 11


title: 10, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 10


title: 08, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 8


title: 09, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 60 min chase

description: Library name: Sample 9


title: 07, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 45 min chase

description: Library name: Sample 7


title: 05, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 5


title: 06, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 30 min chase

description: Library name: Sample 6


title: 04, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 4


title: 30, MCF10A, FBL, TREATED-FBL_siRNA, 15min 5eU pulse, 120 min chase

description: Library name: Sample 30


title: 02, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 2


title: 03, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 15 min chase

description: Library name: Sample 3


title: 01, MCF10A, FBL, CONTROL-SCR_siRNA, 15min 5eU pulse, 0 min chase

description: Library name: Sample 1


title: PDAC04

city: Baltimore

first: Neeha

last: Zaidi

address: 1650 Orleans Street

institute: Johns Hopkins

description:
Library name: Pt4-PDAC04
Selected region of pancreatic ductal adenocarcinoma

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics)
Quality check and filtering with Seurat
Normalization using SCTransform in Seurat
Dimensional reduction using PCA in Seurat
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: spatial barcodes
Supplementary files format and content: features.tsv: genes
Supplementary files format and content: matrix.mtx: sequencing counts
Supplementary files format and content: aligned_fiducials.jpg: capture field aligned to fiducial spots
Supplementary files format and content: detected_tissue_image.jpg: visium spots capturing tissue
Supplementary files format and content: scalefactors_json.json: scaling factors from imaging to spots
Supplementary files format and content: tissue_hires_image.png: high-resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-resolution image of tissue
Supplementary files format and content: tissue_position_list.csv: table of spatial barcode coordinates
Supplementary files format and content: tissue_positions_list_cellular_compositions.xlsx: Cellular deconvolution of spot composition using the CODA tissue image classification tool
Library strategy: Spatial Transcriptomics

source_name: Resected pancreas

extract_protocol:
Visium FFPE Spatial Gene Expression
Libraries were constructed using the Visium FFPE Spatial Gene Expression Reagent Kits (10x Genomics)

value: PanIN and chronic pancreatitis in association with pancreatic ductal adenocarcinoma (PDAC)

value: pancreas

value: treatment naïve


title: CP05A

description:
Library name: Pt5-CP05A
Selected region of chronic pancreatitis


title: NRL05

description:
Library name: Pt5-NRL05
Selected region of non-neoplastic (normal) pancreas tissue


title: PDAC03

description:
Library name: Pt3-PDAC03
Selected region of pancreatic ductal adenocarcinoma


title: PDAC05

description:
Library name: Pt5-PDAC05
Selected region of pancreatic ductal adenocarcinoma


title: NRL01

description:
Library name: Pt1-NRL01
Selected region of non-neoplastic (normal) pancreas tissue


title: PDAC01

description:
Library name: Pt1-PDAC01
Selected region of pancreatic ductal adenocarcinoma


title: CP03

description:
Library name: Pt3-CP03
Selected region of chronic pancreatitis


title: NRL02

description:
Library name: Pt2-NRL02
Selected region of non-neoplastic (normal) pancreas tissue


title: NRL03

description:
Library name: Pt3-NRL03
Selected region of non-neoplastic (normal) pancreas tissue


title: CP01

description:
Library name: Pt1-CP01
Selected region of chronic pancreatitis


title: PDAC02

description:
Library name: Pt2-PDAC02
Selected region of pancreatic ductal adenocarcinoma


title: PANIN01

description:
Library name: Pt1-PANIN01
Selected region of pancreatic intraductal neoplasm


title: IGHG1TRE3G c12 rep4 (5h Dox + 10h IAA)

description:
Library name: IGHG1TRE3G_c12_rep4_(5h_Dox)
PE150

data_processing:
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: NCBI HG38
Supplementary files format and content: Tab separated matrix showing normalized interaction counts
Library strategy: Tri-C

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

value: Ramos

value: Burkitt's Lymphoma


title: IGHG1TRE3G c12 rep4 (0h Dox)

description:
Library name: IGHG1TRE3G_c12_rep4_(0h_Dox)
PE150

value: no Dox


title: IGHG1TRE3G c12 rep4 (5h Dox)

description:
Library name: IGHG1TRE3G_c12_rep4_(5h_Dox+10h_IAA)
PE150


title: IGHG1TRE3G c12 rep3 (5h Dox + 10h IAA)

description:
Library name: IGHG1TRE3G_c12_rep3_(5h_Dox)
PE150


title: IGHG1TRE3G c12 rep2 (5h Dox + 10h IAA)

description:
Library name: IGHG1TRE3G_c12_rep2_(5h_Dox)
PE150


title: IGHG1TRE3G c12 rep2 (5h Dox)

description:
Library name: IGHG1TRE3G_c12_rep2_(5h_Dox+10h_IAA)
PE150


title: HCT116 wild type

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description: Library name: HCT116 wild type

data_processing:
Acquired DNA libraries were sequenced by the Illumina NovaSeq 6000 platform at Vanderbilt Technologies for Advanced Genomics core laboratory.
Sequencing reads were aligned to the human reference genome GRCh38 using Bowtie2. Peaks for each sample were called by MACS2 with a q value cutoff of 0.01 and the corresponding input as the control. Peaks were annotated using Homer (http://homer.ucsd.edu/homer/) and assigned to their closest genes.
Enriched motifs were identified by the Homer command findMotifsGenome with the default region size and the motif length (-size 200 and length 8, 10, 12).
Assembly: GRCh38/gh38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: HCT116 human colon cancer cells were cultured in McCoy's 5A media with 10% FBS, 1X penicilin/Streptomycin at 37°C at 5% CO2..

extract_protocol:
To perform protein:protein crosslinking, disuccinimidyl glutarate (DSG) was added to the cell suspension at final concentration of 2 mM and incubated for 30 min at room temperature. Then fresh formaldehyde was added to the cell suspension at final concentration of 1% and incubated for 10 min at room temperature. Glycine was added to final concentration of 0.125 M to quench the reaction..Cells were resuspended at 1x107/ml in sonication buffer and sonicated for 25-30 sec with Diagenode One sonicator (Diagenode) in a 50 μl Bioruptor® One soinication Chip to achieve DNA fragments in the size range of 200-700bp.
After chromatin immunoprecipitation, Illumina sequencing adapters were added on bead-bound DNA fragments via tagmetation using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina). Then bead- bound DNA fragments were extracted by reversing the crosslink and proteinase K digestion. DNA fragments were purified with AMPure XP beads (Beckman Coulter). qPCR was performed first with KAPA HiFi HotStart Ready Mix and a pair of Nextera custom primers to determine the optimal PCR cycles for the DNA library preparation for each immunoprecipitation. The final enriched DNA library for each immunoprecipitation was created by PCR with KAPA HiFi HotStart Ready Mix and Nextera custom primers using the optimal PCR cycles determined by qPCR. The Enriched DNA library was purified with AMPure XP beads, and size-selection was performed by controlling the concentration of ethanol in the AMPure XP beads and DNA mixture.

value: Wild type

tag: chip antibody


title: IGHG1TRE3G c12 rep1 (5h Dox)

description:
Library name: IGHG1TRE3G_c12_rep1_(5h_Dox)
PE150


title: A549 cells, KPS64, 2hours

city: San Diego

first: Dwayne

last: Roach

address: 5500 Campanile Dr

department: Biology

institute: San Diego State University

description: Library name: 2h.KPS64

data_processing:
Quality control and adapter trimming was performed with Illumina’s bcl2fastq2 Conversion Software (v. 2.20)
Read quantification was performed with RSEM
Read counts were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm
Subsequent values were then converted to counts per million (cpm)
Differential expression analysis was performed using edgeR’s exact test (exactTest) functionality against treatment groups (dispersion was estimated as .04 as per the edgeR user manual)
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw and quantified counts for each sample
Supplementary files format and content: tab-delimited files includes sample name, genes, descriptions, log fold change, p values, false discovery rate, and normalized counts per million of the control and sample

source_name: Lung

growth_protocol: Lung epithelial cell line A549 was obtained from ATCC (cat#CCL-185) and cultured in in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (GIBCO, Germany) at 37°C in 5% CO2. A549 cells were seeded at 9×105 cells/well and grown for 24 h to a density of 1×106 cells/well in a 6-well tissue culture plate.

extract_protocol:
After 2 or 6 h, the culture supernatant was removed and cells were washed in triplicate with sterile dPBS. Total RNA was prepared from treated and untreated A549 cells using the RNeasy Kit (Qiagen, Hilden, Germany). The samples were stored at -80°C.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep following manufacturer's protocols

treatment_protocol: The cells were then incubated in serum-free DMEM for 2 or 6 h with 10µg/mL of PAK or P1A DNA. Untreated A549 cells were cultured under the same medium conditions and incubated with sterile dPBS for 2 h.

value: Lung

value: adenocarcinomic human alveolar basal epithelial cells

value: 10µg/mL KPS64 DNA

value: 2 hours


title: A549 cells, KPS64, 6hours

description: Library name: 6h.KPS64

value: 6 hours


title: IGHG1TRE3G c12 rep2 (0h Dox)

description:
Library name: IGHG1TRE3G_c12_rep2_(0h_Dox)
PE150


title: A549 cells, PAK_P1, 2hours

description: Library name: 2h.PAK_P1

value: 10µg/mL PAK_P1 DNA


title: BEAS-2B cells, DMSO control, replicate 2

city: Pittsburgh

first: Jason

middle: R

last: Kennerdell

state: PA

address: 100 Technology Drive

department: Aging Institute

institute: University of Pittsburgh

description: Library name: DMSO-replicate2

data_processing:
Alignment was performed using STAR (v2.7.3a). Reads mapping to ribosomal and mitochondrial genome were removed before perfoming alignment.
The raw read counts were estimated using HTSeq (v0.11.2).
Assembly: GRCh37/hg19
Supplementary files format and content: Counts of reads corresponding to each gene in each sample were prepared using HTSeq (v0.11.2), with the htseq-count method.

extract_protocol:
Total RNA was Purified using the RNeasy Plus Mini Kit (Qiagen).
Sequencing library was prepared from polyA selected RNA using the SMART-Seq v4 Ultra low Input RNA kit (Takara) at MedGenome.

treatment_protocol: Cells were treated for 18 hours in either vehicle control (DMSO) or 3µM BC18630.

value: DMSO


title: BEAS-2B cells, DMSO control, replicate 1

description: Library name: DMSO-replicate1


title: GD012

city: Miami

first: Mustafa

last: Tekin

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

description: Library name: Sample 9

data_processing:
STAR aligner
Assembly: mm10
Supplementary files format and content: raw_counts.txt is a matrix of raw count values for the RNAseq data

source_name: dermal

growth_protocol: Human dermal fibroblasts were maintained in DMEM media, supplemented with 10% fetal bovine serum (FBS), 1x penicillin, 1x streptomycin, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
total RNA was harvested using RNeasy mini plus kit (Qiagen)
Total RNA was prepped with the Nugen Universal Plus mRNA-Seq (M01442 v2) using 600ng via Qubit and 14 cycles PCR.  Libraries were sequenced on Illumina Novaseq X and >37M PE150 were generated per sample.

treatment_protocol: Human dermal fibroblasts were treated with DMEM without any supplement for 16 hours, in humidified atmosphere with 5% CO2 at 37C.

value: dermal

value: Human dermal fibroblast

value: DMEM(0) overnight


title: IGHG1TRE3G c12 rep3 (5h Dox)

description:
Library name: IGHG1TRE3G_c12_rep3_(5h_Dox+10h_IAA)
PE150


title: GD009

description: Library name: Sample 8


title: GD004

description: Library name: Sample 5


title: GD001

description: Library name: Sample 4

value: ADAMTSL2, 182G>A, 493G>A


title: BEAS-2B cells, 18630 treatment, 3µM, replicate 1

description: Library name: 18630-replicate1


title: IL1B+2DG_RNA-Seq_rep1

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

description: Library name: IL1B+2DG_rep1

data_processing:
RNA-seq FASTQ were mapped to hg38 using STAR with default parameters
The gene expression raw counts were quantified by HOMER’s  'analyzeRepeats' command with the option “-condenseGenes -count exons -noadj”.
Differential gene expression was calculated using the HOMER command “getDiffExpression.pl”. TPM (transcript per kilobase million) were quantified for all genes matching accession number to raw counts.
Differentially expressed genes were assessed with DESeq2 at p-adj (adjusted pvalue) < 0.05 and FC (fold change) > 2 where indicated. Genes with TPM < 4 in all conditions were removed from analysis.
Assembly: hg38
Supplementary files format and content: raw and TPM counts

source_name: brain

extract_protocol:
Total RNA was isolated from HoxB8 cells with RNeasy Plus micro (Qiagen, 74034) or Direct-zol RNA MicroPrep (Zymo Research, R2052) kits and stored at -80°C until RNA-seq library preparation.
RNA-seq libraries were prepared as previously described (Gosselin et al., Science 2017). Briefly, polyA mRNA was enriched by two successive rounds of incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94 °C for 9 min. cDNA was then synthesized with Superscript III (first-strand synthesis; Life Technologies kit 18080-044) and then DNA Polymerase I (second-strand synthesis; Enzymatics P7050L) with dUTP. Resulting cDNA libraries were prepared for sequencing by blunting/end repair, A-tailing, and barcoded adapter ligation (NEXTflex, Bioo Scientific/PerkinElmer) as previously described in Heinz et al77. The resulting RNA-seq libraries were digested by incubation with Uracil DNA Glycosylase for 30 min at 37°C. Libraries were PCR amplified for 12-16 cycles, size for 200–500 bp size range, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

value: brain

value: primary

value: primary astrocytes

value: control


title: BEAS-2B cells, DMSO control, replicate 3

description: Library name: DMSO-replicate3


title: BEAS-2B cells, 18630 treatment, 3µM, replicate 2

description: Library name: 18630-replicate2


title: GD018

description: Library name: Sample 11


title: GD006

description: Library name: Sample 6

value: ADAMTSL2, 542T>C, 707C>T


title: IL1B+2DG_RNA-Seq_rep2

description: Library name: IL1B+2DG_rep2


title: IGHG1TRE3G c12 rep3 (0h Dox)

description:
Library name: IGHG1TRE3G_c12_rep3_(0h_Dox)
PE150

value: Ramos

value: Burkitt's Lymphoma

value: no Dox


title: 2DG_RNA-Seq_rep2

description: Library name: 2DG_rep2


title: BEAS-2B cells, 18630 treatment, 3µM, replicate 3

description: Library name: 18630-replicate3


title: GD016E

description: Library name: Sample 2

value: WT


title: GD014E

description: Library name: Sample 1


title: GD008

description: Library name: Sample 7


title: 2DG_RNA-Seq_rep1

description: Library name: 2DG_rep1


title: GD017E

description: Library name: Sample 3


title: IGHG1TRE3G c12 rep1 (0h Dox)

description:
Library name: IGHG1TRE3G_c12_rep1_(0h_Dox)
PE150


title: IGHG1TRE3G c12 rep1 (5h Dox + 10h IAA)

description:
Library name: IGHG1TRE3G_c12_rep1_(5h_Dox+10h_IAA)
PE150


title: A549 cells, control, 2hours

description: Library name: 2h.untreated

value: Lung

value: adenocarcinomic human alveolar basal epithelial cells

value: dPBS

value: 2 hours


title: IL1B_RNA-Seq_rep2

description: Library name: IL1B_rep2


title: A549 cells, PAK_P1, 6hours

description: Library name: 6h.PAK_P1

value: 10µg/mL PAK_P1 DNA

value: 6 hours


title: IL1B_RNA-Seq_rep1

description: Library name: IL1B_rep1


title: Vehicle_RNA-Seq_rep2

description: Library name: Vehicle_rep2

value: Vehicle


title: GD007

description: Library name: Sample 10

value: dermal

value: Human dermal fibroblast

value: DMEM(0) overnight


title: Vehicle_RNA-Seq_rep1

description: Library name: Vehicle_rep1

value: brain

value: primary

value: primary astrocytes


title: 2DG_rep3

description: Library name: 2DG_rep3

data_processing:
ATAC-seq FASTQ files  were trimmed to 30 bp. ATAC-seq and ChIP-seq FASTQ were mapped to mm10 or hg38 using Bowtie 2 with default parameters.
After mapping, tag directories were created using the HOMER (Heinz et al., Mol Cell 2010) command 'makeTagDirectory'.
ATAC-seq experiments were performed in replicates with corresponding input experiments. Peaks were called with HOMER 's 'findPeaks'for each tag directory with relaxed peak finding parameters “-L 0 -C 0 -fdr 0.9”.
IDR was used to test for reproducibility between replicates, only peaks with an IDR < 0.05 were used for downstream analyses. Peak sets from all pairwise IDR comparisons were merged into a final set of peaks for further analysis.
To quantify the chromatin accessibility between conditions, raw and normalized tag counts at merged IDR peaks called by HOMER’s 'mergePeaks' were identified using HOMER’s 'annotatePeaks' with “-noadj,”  “-size 200". DESeq2 was used to identify differentially differential distal chromatin accessibility (p-adj. < 0.05 and FC >2 or <-2).
Assembly: hg38
Supplementary files format and content: annotated peaks with raw and normalzied counts

extract_protocol:
Cells were lysed in 50 µl lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 in water). Resulting nuclei were centrifuged at 500xg for 10 min.
Pelleted nuclei were resuspended in 50 μL transposase reaction mix (47.5 μL ATAC lysis bufferand 2.5 μL Tagment DNA TDE1 enzyme I (Illumina, 20034197)) and incubated at 37°C for 30 min. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research, D5205), eluted with 11 µL of elution buffer, and amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs, M0541) with the Nextera primer Ad1 (1.25 µM) and a unique barcoding primer Ad2 (1.25 µM) for 8-12 cycles. Resulting libraries were size selected by gel excision to 155–250 bp

value: control


title: IL1B+2DG_rep1

description: Library name: IL1B+2DG_rep1


title: 2DG_rep1

description: Library name: 2DG_rep1


title: 2DG_rep2

description: Library name: 2DG_rep2


title: IL1B+2DG_rep3

description: Library name: IL1B+2DG_rep3


title: IL1B_rep1

description: Library name: IL1B_rep1


title: Vehicle_rep2

description: Library name: Vehicle_rep2


title: IL1B+2DG_rep2

description: Library name: IL1B+2DG_rep2


title: IL1B_rep2

description: Library name: IL1B_rep2


title: Vehicle_rep1

description: Library name: Vehicle_rep1


title: BRCA1

city: Nanjing

first: Cong

last: Wang

address: 639, Longmi Avenue

institute: China Pharmaceutical University

description:
Library name: BRCA1_CHIP
The raw data are being made available for controlled access in dbDaP

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018)software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content ofthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to thereference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and presentsignificant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al.,2008) predicted method with default parameters. MACS2 scan all the genome with a specific windowsize and calculate the reads enrichment level. A particular number of windows were used as samples tobuild enrichment model and to predict fragment size. The following peak calling analysis was based onthis predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak callingsoftware to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for alldata sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment,significant level and peak summit number per peak were all displayed.
The interaction between transcript factor or chromatin histone modification and DNA were not random,while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect thedenovo sequence motif and the matched known motifs.
Assembly: hg18
Supplementary files format and content: bigWig

growth_protocol: DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
cells were firstly crosslinked with 1% paraformaldehyde. After addtion of glycine solution , cells were lysed with cell lysis buffer and nuclear lysis buffer.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by NovogeneCorporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illuminaplatform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: ovarian cancer

value: wt


title: IRN5 - Insulin Resistant Normoxia

city: Oxford

first: Ryan

middle: Daniel

last: Carter

address: Sherrington Building, Sherrington Rd

department: DPAG

country: United Kingdom

institute: University of Oxford

description:
Library name: IRN5
Column name in raw counts all_sample_deseq.csv: IRN5

data_processing:
Quality control was performed with FastQC, trimming with cutadapt to remove adaptors and low-quality sequences
Transcript quantification for hiPSC-CM was executed with Salmon using decoys and a gentrome indexed from the gencode v44 GRCh38
Gene level counts were summarised using tximport
Assembly: gencode v44 GRCh38
Supplementary files format and content: raw gene counts in csv format

growth_protocol: IMR90 human induced pluripotent stem cells (hiPSCs) were differentiated into hiPSC-derived cardiomyocytes (hiPSC-CMs) using a Wnt signaling modulation protocol. Cells were grown to confluency in TeSR-E8 media on Matrigel-coated plates, then differentiated over 15 days. Key steps included treatment with CHIR99021 (days 0-1), Wnt-C59 (day 3), and glucose-free media (days 11-13) for metabolic selection. From day 15, cells were maintained in RB+ media (RPMI with B27 complete).

extract_protocol:
Cells were washed in PBS, lysed using the RNAeasy kit QIAzol lysis agent, scraped, and homogenised using needles before being flash-frozen in liquid nitrogen. RNA was extracted from the lysates using the Qiagen RNeasy Mini kit following the manufacturer’s protocol.
Stranded paired 150-bp poly-A enrichment protocol by Novogene

treatment_protocol: Insulin resistance (IR) was induced in hiPSC-CMs or EHTs using a six-day protocol with two media types: glucose-free IR media (3 days) and glucose-enriched IR media (3 days), both containing palmitic acid, insulin, and supplements. Controls were cultured in maturation media. For some experiments, hiPSC-CMs were exposed to high palmitate media (0.4 mM palmitate) or hypoxia (2% O2 for 16 hours), with controls in normoxia (21% O2).

value: hiPSC cardiomyocytes

value: Insulin Resistant Normoxia


title: IRN3 - Insulin Resistant Normoxia

description:
Library name: IRN3
Column name in raw counts all_sample_deseq.csv: IRN3


title: IRN2 - Insulin Resistant Normoxia

description:
Library name: IRN2
Column name in raw counts all_sample_deseq.csv: IRN2


title: IRN1 - Insulin Resistant Normoxia

description:
Library name: IRN1
Column name in raw counts all_sample_deseq.csv: IRN1


title: IRH5 - Insulin Resistant Hypoxia

description:
Library name: IRH5
Column name in raw counts all_sample_deseq.csv: IRH5

value: Insulin Resistant Hypoxia