title: Female_Cocaine_1

status: Public on Aug 07 2023

description: snATAC-seq

data_processing:
snATAC-seq data was aligned to the mRatBN7.2/Rn7 reference assembly using cellranger-atac v2.1.0 and the procedure outlined by 10X Genomics.
Analysis of the cellranger-atac output was analyzed using Signac v1.9.068 and Seurat v4.3.063. Counts, fragments, and barcode information for each treatment group were loaded and combined into Seurat objects as outlined by the Stuart lab website (https://stuartlab.org/signac/).
Using Signac and Suerat functions, samples were merged into one object based on a common set of features and the standard Signac dimensionality reduction and clustering workflow was performed using 2:30 dimensions and a resolution value of 0.2. Data was then integrated with the snRNA-seq data from the same samples (available at GSE222418). Common anchors between the two were used to predict and label the cell types present in the snATAC-seq data.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger Arc outputs including  matrices for barcodes (.tsv), ATAC matrix (.mtx), and peak locations (.bed) are provided for each sample.

source_name: Sprague-Dawley

extract_protocol:
Flash-frozen NAc tissue was added to a tube containing 500µl lysis buffer (1mM Tris-HCl pH 7.4, 1mM NAc, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Igepal in nuclease free water, 0.001% Digitonin, 0.1% BSA), homogenized using a motorized homogenizer and RNase free pestle, and incubated on ice for 5 minutes. Samples were then pipette mixed 15x and incubated on ice for an additional 10 minutes. Following lysis, 4 samples from same sex and treatment were grouped into a single sample, and 2mL chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20) was added. Samples were then passed through 70µM and 40µM Scienceware Flowmi Cell Strainers. Samples were then centrifuged at 250 rcf for 5 min at 4°C. Supernatant was removed and the pellet was resuspended in 1mL of chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20). 100µL of sample was then stained with 7-aminoactinomycin D and used to set a representative gate for fluorescence activated cell sorting (FACs). This gate was then used to purify nuclei further. Following FACs, samples were spun at 250 rcf for 10 min at 4°C to remove any remaining debris. Samples were then loaded into individual wells of the Chromium NextGem Single Cell Chip using 4 of the 8 available wells.
FACS-sorted nuclei were subject to 10X GEM generation, transposase barcoding, and library construction using a Chromium Next GEM Single Cell ATAC Kit v2. Libraries were quantified and underwent sequencing on an Illumina sequencing platform (NextSeq 500) using a dual-indexed, paired-end strategy (Read 1N, 50 cycles; i7 index, 8 cycles; i5 index, 16 cycles; Read 2N, 50 cycles).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. Injections occured daily across 7 consecutive days. Tissue was harvested 1hr after the final (7th) injection, when rats were sacrificed, the brain was blocked into 1mm sections, abd the NAc was harvested and flash frozen. A total of 16 rats (8 male, 8 female, 4 per GEMwell) were used for this experiment.

tag: source

value: Nucleus accumbens

value: Cocaine

value: Female


title: RNA K1

type: SRA

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

country: USA

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Paired-end FASTQ files were analyzed using a custom bioinformatics pipeline built with Snakemake (v6.1.0). Read quality was assessed using FastQC before and after trimming with Trim_Galore! (v0.6.7). Splice-aware alignment to the mRatBn7.2/Rn7 reference assembly for cultured embryonic rat striatal neurons was performed using Ensembl gene transfer format (gtf) file (version 105) with STAR (v2.7.9a).
Binary alignment map (BAM) files were indexed with SAMtools (v1.13)
Gene-level counts were generated using the featureCounts function within the Rsubread package (v2.6.1) in R (v4.1.1)
QC metrics were collected and reviewed with MultiQC(v1.11).
Differential expression testing was conducted using DeSeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini-Hochberg method. DEGs were designated as those genes with an adjusted p-value < 0.05 and a |log2FoldChange| > 0.5.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Str_4h_KCl_count_matrix.txt contains RNA-seq count values for annotated gene for each sample

molecule: total RNA

organism: Rattus norvegicus

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to RNA-seq. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads) on an Illumina sequencing platform (NextSeq500).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 10mM) for 4 hours on DIV 11.

tag: strain

value: Sprague-Dawley

tag: age

value: Embryonic day 18, 11 DIV

value: Striatum

tag: treatment

value: KCl (10mM)


title: WT prostate 4

status: Public on Apr 28 2020

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

organism: Mus musculus

source_name: WT prostate

growth_protocol: 8-12 week old WT C57BL/6 male mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left seminal vesicle is used as a landmark and the anterior lobe of the prostate is pulled out. 50 μl of a plasmid mix (see table below) was injected into the right anterior lobe of the prostate using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two pulses of electrical current (60V) given for 35 ms lengths at 500 ms intervals were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole prostate tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

tag: tissue

value: normal prostate

tag: genotype

value: WT

value: non-treated


title: AML21-T

status: Public on Aug 28 2023

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

country: Switzerland

institute: Bern University Hospital

description: BM AML1/ETO positive LSPCs treated +rhIL-33

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software  and analyzed using ArrayStar software (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization.
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from the treated AML LSPCs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified AML1/ETO positive LSPCs were harvested and LSPCs treated w/o rhIL-33. Treated LSPCs were then harvested for the RNA extraction.

tag: population

value: AML1/ETO positive LSPCs

value: Bone marrow (BM) derived LSPCs


title: Male_Saline_1

description: snATAC-seq

library_source: genomic

molecule: genomic DNA

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

value: Saline

tag: Sex

value: Male


title: WT prostate 2


title: WT prostate 1


title: K2H

status: Public on Jul 28 2020

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore v0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore v0.4.5
Post-trimming QC with FastQC
Splice-aware alignment to Rn6 genome reference with star v2.6.0c.
Merging of BAM files and index generation with samtools v1.9
Identification of transcriptionally active putative enhancers (TAPEs) with custom processing in Seqmonk v 1.46.0
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of transcriptionally active putative enhancer (TAPE) expression estimates, in counts per kilobase per million mapped reads for each sample. Columns are TAPE_ID, chromosome, start, end, type, distance, sample values (several columns), TAPE center, nearest gene, and information related to nearest gene.

source_name: Hippocampal neuron culture

growth_protocol: Neurons were removed from cortical, hippocampal, or striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads; ~12.6-20.4 M reads/sample) on an Illumina sequencing platform (NextSeq500)

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 25mM) for 1hr on DIV 11. Media was removed and RNA was extracted.

value: Hippocampal neuron culture

value: 25mM KCl


title: Hep_Proliferating_1

status: Public on Apr 18 2020

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

growth_protocol: KP (KRASG12D,Tp53-/-) cells were grown in DMEM supplemented with 10% FBS and 100UI/ml penicillin/streptomycin.

extract_protocol:
Trizol RNA extraction protocol
Poly-A RNA-Seq / Paired-end 50

treatment_protocol: KP (KRASG12D,Tp53-/-) cells were treated for 8 days with either DMSO or the combination of MEK inhibitor (Trametinib) (25nM) and Cdk4/6 inhibitor (Palbociclib)  (500nM).After 8 days, the cells were harvested and subjected to RNAseq analysis. For the hydrodinamic tail vein injection experiments each mouse received 25ug of pT3-Caggs-NRASG12V-IRES-GFP plasmid and 5ug CMV-SB13 through hydrodynamic tail vein injection. Six days after, GFP-positive (NRASG12V overexpressing hepatocytes) and GFP-negative (untransduced hepatocytes) were isolated via low pressure fluorescence-activated cell sorting following liver perfusion and then were subjected to RNAseq analysis.

tag: model

value: Hydrodynamic tail vein injection of NRASG12V

tag: tissue source

value: Liver

tag: cell type

value: Sorted primary hepatocytes

tag: oncotype (sorted cells)

value: Untransduced hepatocytes (GFP-)

tag: experimental condition

value: Proliferating

tag: age/stage (upon sample collection)

value: 12 weeks old

tag: sample collection time point

value: 6 days after hydrodynamic tail vein injection


title: Hep_Proliferating_2


title: V2S

source_name: Striatal neuron culture

value: Sprague-Dawley

value: Embryonic day 18, 11 DIV

value: Striatal neuron culture

value: Vehicle


title: Hep_Senescence_2

value: NRASG12V overexpression (GFP+)

value: Senescent


title: Hep_Senescence_1


title: KP_Proliferating_1

value: lung

tag: cell line

value: KP

value: Murine Lung adenocarcinoma cell line (KrasG12D,Tp53-/-)

value: DMSO

value: After 8 days of treatment


title: KP_Proliferating_2


title: V1H

value: Hippocampal neuron culture


title: KP_Senescence_2

value: MEK inhibitor (Trametinib) (25nM) and Cdk4/6 inhibitor (Palbociclib) (500nM)


title: Plate2D_62

status: Public on Mar 30 2020

data_processing:
Adapter removal and removing reads shorter than 36bp using Bbduk
Align reads to reference genome mm9 using Kallisto and obtain read count tables
Genome_build: mm9
Supplementary_files_format_and_content: read count table

source_name: KPC1199EGFP Adherent cells at passage 9

growth_protocol: KPC1199-EGFP cells were thawed and passaged in DMEM supplemented with 10% Fetal Bovine Serum, 1% Pencillin/streptomycin

extract_protocol:
Trypsinzed to create suspension of adherent cells
Single cells were isolated and cDNA amplified on medium sized IFC from Fluidigm on the C1 system following the manufacturer's instructions. Library was constucted using nextera XT kit again following the guildlines from Fluidigm

treatment_protocol: No treatment

tag: strain background

value: Pancreatic cancer

tag: genotype/variation

value: EGFP expression


title: Plate2D_59


title: Plate2D_61


title: Plate2D_58


title: Plate2D_60


title: KP_Senescence_1


title: THP-1 macrophages, acLDL

status: Public on Apr 14 2020

type: RNA

first: Coen

last: van Solingen

state: NY

address: 435 E30th street SB 704

department: Medicine/Cardiology

institute: NYU Grossman School of Medicine

description: cholesterol loaded

data_processing:
provided data sheet from SABiosciences
CT-values, 2^deltadeltaCT

label: SYBR

growth_protocol: RPMI + FCS and PS

extract_protocol: RNA isolation by miRNA Isolation kit (SABiosciences)

treatment_protocol: loading: acLDL (37.5 ug/mL) for 24 hours. Depletion; 5 uM simvastatin for 24 hours

value: thp-1 macrophages

value: acLDL to load with cholesterol


title: THP-1 macrophages, statin

description: cholesterol depleted

value: statin to deplete cholesterol


title: 103_2_S2

status: Public on Jun 24 2020

description: Experiment 1

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore=0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore=0.4.5
Post-trimming QC with FastQC
Splice-aware alignment with star=2.6.0c. The genome utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Merging of BAM files and index generation with samtools=1.6
Count generation with bioconductor-rsubread=1.26.1 (R version: r-base=3.4.1). The GTF file utilized was: Rattus_norvegicus.Rnor_6.0.90.gtf
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of gene expression values (raw counts) for each gene in each sample. Genes are in rows, and columns contain the Ensembl ID, chromosome, start, end, and sample names.

molecule: polyA RNA

growth_protocol: Neurons were removed from striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at the UAB Helfin Genomics Core. Libraries were quantified and underwent sequencing (~25M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Neurons were treated as described with CRISPR sgRNAs and dCas9-VPR fusion lentiviruses on DIV 4. Media was removed and RNA was extracted on DIV 11.

tag: strain

value: Sprague-Dawley

value: Embryonic day 18, 11 DIV

value: Dopaplex


title: Plate2D_57


title: Plate2D_55


title: Plate2D_56


title: Plate2D_54


title: Plate2D_53


title: Plate2D_52


title: Plate2D_51


title: Plate2D_50


title: Plate2D_48


title: Plate2D_49


title: Plate2D_47


title: 103_6_S6

description: Experiment 1

value: Striatal neuron culture

tag: age


title: Plate2D_46


title: Plate2D_44


title: Plate2D_42


title: Plate2D_43


title: Plate2D_39


title: Plate2D_40


title: Plate2D_38


title: Plate2D_45


title: Plate2D_41


title: Plate2D_37


title: Plate2D_36


title: Plate2D_35


title: Plate2D_34


title: Plate2D_33


title: Plate2D_30


title: Plate2D_29


title: Plate2D_32


title: Plate2D_31


title: Plate2D_26


title: Plate2D_25


title: Plate2D_28


title: Plate2D_24


title: Plate2D_23


title: Plate2D_22


title: Plate2D_27


title: Plate2D_19


title: Plate2D_21


title: Plate2D_17


title: Plate2D_18


title: Plate2D_20


title: Plate2D_16


title: Plate2D_14


title: Plate2D_15


title: Plate2D_13


title: Plate2D_10


title: Plate2D_9


title: Plate2D_11


title: Plate2D_12


title: Plate2D_8


title: Plate2D_7


title: Plate2D_4


title: Plate2D_5


title: Plate2D_3


title: Plate2D_2


title: Mouse3_GFPSpleenMet_S48_clean

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to mm9 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome mm9 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: mm9
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

source_name: Mouse3_Spleen Metastasis

extract_protocol:
Primary tumors were dissociated using collagenase D and trypsin. They were treated with ACK lysis buffer to remove contaminating red blood cells. These dissociated cells were stained with EpCam, CD45 antibodies. Single cells were isolated by flow cytometry for GFP+, EpCAM+, GFP+EpCAM+ and CD45+ from primary tumors. GFP+ cells were isolated from various metastases
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor. Next they were processed for mRNA transcription for first strand synthesis using Oligo-dT primer and cDNA generated is amplified for 15 cycles following SMART-Seq2 PCR primers. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. resulting cDNA and gDNA fragments are quantified.  Following this, libraries for sequencing were prepared by subjecting the 1ug of gDNA and cDNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

treatment_protocol: 50000 KPC1199-EGFP cells in matrigel were injected orthotopically into the pancreas of 6-8 week old C57BL/6 male mice. Tumors were allowed to grow for 6-8 weeks before tumors were extracted.

value: male

tag: tumor type

value: Metastasis

value: Spleen

value: Tumor

tag: marker

value: GFP, Calcien Violet for Live/Dead

tag: molecule type

value: genomic DNA and mRNA


title: Mouse3_GFPSpleenMet_S47_clean

tag: tissue


title: Mouse3_GFPSpleenMet_S45_clean

tag: Sex


title: Plate2D_1


title: Mouse3_GFPSpleenMet_S42_clean


title: Mouse3_GFPSpleenMet_S43_clean


title: Mouse3_GFPSpleenMet_S41_clean


title: Mouse3_GFPSpleenMet_S40_clean


title: Mouse3_GFPSpleenMet_S36_clean


title: Mouse3_GFPSpleenMet_S35_clean


title: Mouse3_GFPSpleenMet_S34_clean


title: Mouse3_GFPSpleenMet_S33_clean


title: Mouse3_GFPSpleenMet_S32_clean


title: Mouse3_GFPSpleenMet_S31_clean


title: Mouse3_GFPSpleenMet_S28_clean


title: Mouse3_GFPSpleenMet_S29_clean


title: Mouse3_GFPSpleenMet_S26_clean


title: Mouse3_GFPSpleenMet_S25_clean


title: Mouse3_GFPPrimary_S40_clean

source_name: Mouse3_Primary Pancreatic Tumor

value: Primary

value: Pancreas


title: Mouse3_GFPPrimary_S41_clean


title: Mouse3_GFPPrimary_S38_clean


title: Mouse3_GFPPrimary_S39_clean


title: Mouse3_GFPPrimary_S37_clean


title: Mouse3_GFPPrimary_S36_clean


title: Mouse3_GFPPrimary_S32_clean


title: Mouse3_GFPPrimary_S30_clean


title: Mouse3_GFPPrimary_S31_clean


title: Mouse3_GFPPrimary_S28_clean


title: Mouse3_GFPPrimary_S29_clean


title: Mouse3_GFPPrimary_S27_clean


title: Mouse3_GFPPrimary_S25_clean


title: Mouse3_GFPPrimary_S21_clean


title: Mouse3_GFPPrimary_S19_clean


title: Mouse3_GFPPrimary_S18_clean


title: Mouse3_GFPPrimary_S17_clean


title: Mouse3_GFPPrimary_S16_clean


title: Mouse3_GFPPrimary_S20_clean


title: Mouse3_GFPPrimary_S15_clean


title: Mouse3_GFPPrimary_S10_clean


title: Mouse3_GFPPrimary_S09_clean


title: Mouse3_GFPPrimary_S08_clean


title: Mouse3_GFPPrimary_S05_clean


title: Mouse3_GFPPrimary_S06_clean


title: Mouse3_GFPPeritoneumMet_S96_clean

source_name: Mouse3_Peritoneum Metastasis

value: Peritoneum


title: Mouse3_GFPPrimary_S04_clean


title: Mouse3_GFPPeritoneumMet_S95_clean


title: Mouse3_GFPPeritoneumMet_S93_clean


title: Mouse3_GFPPeritoneumMet_S94_clean


title: Mouse3_GFPPeritoneumMet_S91_clean


title: Mouse3_GFPPrimary_S07_clean


title: Mouse3_GFPPeritoneumMet_S88_clean


title: Mouse3_GFPPeritoneumMet_S90_clean


title: Mouse3_GFPPeritoneumMet_S87_clean


title: Mouse3_GFPPeritoneumMet_S86_clean


title: Mouse3_GFPPeritoneumMet_S84_clean


title: Mouse3_GFPPeritoneumMet_S83_clean


title: Mouse3_GFPPeritoneumMet_S82_clean


title: Mouse3_GFPPeritoneumMet_S81_clean


title: Mouse3_GFPPeritoneumMet_S79_clean


title: Mouse3_GFPPeritoneumMet_S78_clean


title: Mouse3_GFPPeritoneumMet_S75_clean


title: Mouse3_GFPPeritoneumMet_S74_clean


title: Plate2D_6

value: Pancreatic cancer

value: EGFP expression


title: Mouse3_GFPPeritoneumMet_S76_clean


title: Mouse3_GFPPeritoneumMet_S73_clean


title: Mouse3_GFPLiverMet_S24_clean

source_name: Mouse3_Liver Metastasis

value: Liver


title: Mouse3_GFPSpleenMet_S46_clean


title: Mouse3_GFPSpleenMet_S44_clean


title: Mouse3_GFPLiverMet_S20_clean


title: Mouse3_GFPLiverMet_S18_clean


title: Mouse3_GFPLiverMet_S12_clean


title: Mouse3_GFPLiverMet_S11_clean


title: Mouse3_GFPSpleenMet_S30_clean


title: Mouse3_GFPLiverMet_S10_clean


title: Mouse3_GFPLiverMet_S09_clean


title: Mouse3_GFPLiverMet_S08_clean


title: Mouse3_GFPLiverMet_S06_clean


title: Mouse3_GFPLiverMet_S02_clean


title: Mouse3_GFPLiverMet_S01_clean


title: Mouse3_GFPPrimary_S35_clean


title: Mouse3_GFPPrimary_S26_clean


title: Mouse3_GFPKidneyMet_S70_clean

source_name: Mouse3_Kidney Metastasis

value: Kidney


title: Mouse3_GFPKidneyMet_S67_clean


title: Mouse3_GFPKidneyMet_S68_clean


title: Mouse3_GFPKidneyMet_S69_clean


title: Mouse3_GFPKidneyMet_S66_clean


title: Mouse3_GFPKidneyMet_S71_clean


title: Mouse3_GFPKidneyMet_S72_clean


title: Mouse3_GFPKidneyMet_S64_clean


title: Mouse3_GFPKidneyMet_S62_clean


title: Mouse3_GFPKidneyMet_S65_clean


title: Mouse3_GFPKidneyMet_S63_clean


title: Mouse3_GFPKidneyMet_S60_clean


title: Mouse3_GFPKidneyMet_S58_clean


title: Mouse3_GFPKidneyMet_S56_clean


title: Mouse3_GFPKidneyMet_S55_clean


title: Mouse3_GFPKidneyMet_S52_clean


title: Mouse3_GFPKidneyMet_S53_clean


title: Mouse3_GFPKidneyMet_S51_clean


title: Mouse3_GFPKidneyMet_S54_clean


title: Mouse3_GFPKidneyMet_S49_clean


title: Mouse3_GFPKidneyMet_S50_clean


title: Mouse3_GFPEpCamPrimary_S62_clean

value: GFP, EpCam, Calcien Violet for Live/Dead


title: Mouse3_GFPPeritoneumMet_S92_clean


title: Mouse3_GFPPeritoneumMet_S89_clean


title: Mouse3_GFPPeritoneumMet_S85_clean


title: Mouse3_GFPEpCamPrimary_S60_clean


title: Mouse3_GFPEpCamPrimary_S59_clean


title: Mouse3_GFPEpCamPrimary_S61_clean


title: Mouse3_GFPEpCamPrimary_S58_clean


title: Mouse3_GFPEpCamPrimary_S57_clean


title: Mouse3_GFPEpCamPrimary_S56_clean


title: Mouse3_GFPEpCamPrimary_S54_clean


title: Mouse3_GFPEpCamPrimary_S55_clean


title: Mouse3_GFPEpCamPrimary_S53_clean


title: Mouse3_GFPEpCamPrimary_S52_clean


title: Mouse3_EpCamPrimary_S50_clean

value: EpCam, Calcien Violet for Live/Dead


title: Mouse3_EpCamPrimary_S51_clean


title: Mouse3_EpCamPrimary_S49_clean


title: Mouse3_EpCamPrimary_S48_clean


title: Mouse3_EpCamPrimary_S45_clean


title: Mouse3_EpCamPrimary_S47_clean


title: Mouse3_EpCamPrimary_S46_clean


title: Mouse3_GFPPeritoneumMet_S77_clean


title: Mouse3_CD45Primary_S80_clean

value: Stromal

value: CD45, Calcien Violet for Live/Dead


title: Mouse3_EpCamPrimary_S42_clean

value: male


title: Mouse3_CD45Primary_S82_clean


title: Mouse3_CD45Primary_S81_clean


title: Mouse3_CD45Primary_S79_clean


title: Mouse3_CD45Primary_S77_clean


title: Mouse3_CD45Primary_S76_clean


title: Mouse3_GFPLiverMet_S21_clean

value: Metastasis


title: Mouse3_CD45Primary_S72_clean


title: Mouse3_CD45Primary_S73_clean


title: Mouse3_CD45Primary_S70_clean


title: Mouse3_CD45Primary_S69_clean


title: Mouse3_CD45Primary_S68_clean


title: Mouse3_CD45Primary_S71_clean


title: Mouse3_CD45Primary_S67_clean


title: Mouse3_CD45Primary_S66_clean


title: Mouse3_CD45Primary_S63_clean


title: Mouse3_CD45Primary_S65_clean


title: Mouse2_GFPSpleenMet_S29_clean

source_name: Mouse2_Spleen Metastasis

value: Spleen


title: Mouse2_GFPSpleenMet_S28_clean

value: Tumor


title: Mouse2_GFPSpleenMet_S27_clean

value: GFP, Calcien Violet for Live/Dead


title: Mouse2_GFPSpleenMet_S26_clean

value: genomic DNA and mRNA


title: Mouse2_GFPSpleenMet_S25_clean


title: Mouse2_GFPSpleenMet_S24_clean


title: Mouse2_GFPSpleenMet_S23_clean


title: Mouse2_GFPSpleenMet_S22_clean


title: Mouse2_GFPSpleenMet_S20_clean


title: Mouse2_GFPSpleenMet_S19_clean


title: Mouse2_GFPSpleenMet_S21_clean


title: Mouse2_GFPSpleenMet_S18_clean


title: Mouse2_GFPSpleenMet_S17_clean


title: Mouse2_GFPSpleenMet_S15_clean


title: Mouse2_GFPSpleenMet_S13_clean


title: Mouse2_GFPSpleenMet_S12_clean


title: Mouse2_GFPSpleenMet_S14_clean


title: Mouse2_GFPPrimary_S29_clean

source_name: Mouse2_Primary Pancreatic Tumor

value: Primary


title: Mouse2_GFPPrimary_S30_clean

value: Pancreas


title: Mouse2_GFPPrimary_S27_clean


title: Mouse2_GFPPrimary_S25_clean


title: Mouse2_GFPPrimary_S24_clean


title: Mouse2_GFPPrimary_S22_clean


title: Mouse2_GFPPrimary_S18_clean


title: Mouse2_GFPPrimary_S23_clean


title: Mouse2_GFPPrimary_S16_clean


title: Mouse2_GFPPrimary_S14_clean


title: Mouse2_GFPPrimary_S13_clean


title: Mouse2_GFPPrimary_S12_clean


title: Mouse2_GFPPrimary_S11_clean


title: Mouse2_GFPPrimary_S10_clean


title: Mouse2_GFPPrimary_S08_clean


title: Mouse2_GFPPrimary_S06_clean


title: Mouse2_GFPPrimary_S04_clean


title: Mouse2_GFPPrimary_S05_clean


title: Mouse2_GFPPrimary_S02_clean


title: Mouse2_GFPPrimary_S01_clean


title: Mouse2_GFPPrimaryBulk_S26_clean


title: Mouse2_GFPPeritoneumMet_S60_clean

source_name: Mouse2_Peritoneum Metastasis

value: Peritoneum


title: Mouse2_GFPPrimary_S03_clean


title: Mouse2_GFPPeritoneumMet_S59_clean


title: Mouse2_GFPPeritoneumMet_S58_clean


title: Mouse2_GFPPeritoneumMet_S57_clean


title: Mouse2_GFPPeritoneumMet_S56_clean


title: Mouse2_GFPPeritoneumMet_S55_clean


title: Mouse2_GFPPeritoneumMet_S53_clean


title: Mouse2_GFPPeritoneumMet_S54_clean


title: Mouse2_GFPPeritoneumMet_S50_clean


title: Mouse2_GFPPeritoneumMet_S51_clean


title: Mouse2_GFPPeritoneumMet_S49_clean


title: Mouse2_GFPPeritoneumMet_S48_clean


title: Mouse2_GFPPeritoneumMet_S47_clean


title: Mouse2_GFPPeritoneumMet_S46_clean


title: Mouse2_GFPPeritoneumMet_S44_clean


title: Mouse2_GFPPeritoneumMet_S43_clean


title: Mouse2_GFPPeritoneumMet_S42_clean


title: Mouse2_GFPPeritoneumMet_S41_clean


title: Mouse2_GFPPeritoneumMet_S40_clean


title: Mouse2_GFPPeritoneumMet_S39_clean


title: Mouse2_GFPPeritoneumMet_S38_clean


title: Mouse2_GFPPeritoneumMet_S37_clean


title: Mouse2_GFPPeritoneumMet_S36_clean


title: Mouse2_GFPLiverMet_S12_clean

source_name: Mouse2_Liver Metastasis


title: Mouse2_GFPLiverMet_S11_clean


title: Mouse2_GFPLiverMet_S10_clean


title: Mouse2_GFPLiverMet_S09_clean


title: Mouse2_GFPLiverMet_S08_clean


title: Mouse2_GFPLiverMet_S07_clean


title: Mouse2_GFPLiverMet_S06_clean


title: Mouse2_GFPLiverMet_S05_clean


title: Mouse2_GFPLiverMet_S04_clean


title: Mouse2_GFPLiverMet_S03_clean


title: Mouse2_GFPLiverMet_S02_clean


title: Mouse2_GFPLiverMet_S01_clean


title: Mouse2_GFPLiverMet_S13_clean


title: Mouse2_GFPLiverMet_S14_clean


title: Mouse2_GFPLiverMet_S15_clean


title: Mouse2_GFPLiverMet_S16_clean


title: Mouse2_GFPLiverMet_S17_clean


title: Mouse2_GFPLiverMet_S18_clean


title: Mouse2_GFPLiverMet_S20_clean


title: Mouse2_GFPLiverMet_S21_clean


title: Mouse2_GFPPeritoneumMet_S45_clean


title: Mouse2_GFPKidneyMet_S52_clean

source_name: Mouse2_Kidney Metastasis


title: Mouse2_GFPKidneyMet_S51_clean


title: Mouse2_GFPKidneyMet_S50_clean


title: Mouse2_GFPKidneyMet_S49_clean


title: Mouse2_GFPKidneyMet_S48_clean


title: Mouse2_GFPKidneyMet_S47_clean


title: Mouse2_GFPKidneyMet_S46_clean


title: Mouse2_GFPKidneyMet_S45_clean


title: Mouse2_GFPKidneyMet_S44_clean


title: Mouse2_GFPKidneyMet_S43_clean


title: Mouse2_GFPKidneyMet_S42_clean


title: Mouse2_GFPKidneyMet_S41_clean


title: Mouse2_GFPKidneyMet_S40_clean


title: Mouse2_GFPKidneyMet_S39_clean


title: Mouse2_GFPKidneyMet_S38_clean


title: Mouse2_GFPKidneyMet_S37_clean


title: Mouse2_GFPKidneyMet_S36_clean


title: Mouse2_GFPKidneyMet_S35_clean


title: Mouse2_GFPKidneyMet_S34_clean


title: Mouse2_GFPKidneyMet_S33_clean


title: Mouse2_GFPKidneyMet_S32_clean


title: Mouse2_GFPKidneyMet_S31_clean


title: Mouse2_GFPKidneyMet_S30_clean


title: Mouse2_GFPEpCamPrimary_S48_clean


title: Mouse2_GFPEpCamPrimary_S47_clean


title: Mouse2_GFPEpCamPrimary_S46_clean


title: Mouse2_GFPEpCamPrimary_S45_clean


title: Mouse2_GFPEpCamPrimary_S44_clean


title: Mouse2_GFPSpleenMet_S16_clean


title: Mouse2_GFPLiverMet_S19_clean


title: Mouse2_GFPPrimary_S31_clean


title: Mouse2_GFPSpleenMet_S11_clean


title: Mouse2_GFPPrimary_S32_clean


title: Mouse2_GFPSpleenMet_S10_clean


title: Mouse2_GFPEpCamPrimary_S43_clean


title: Mouse2_GFPEpCamPrimary_S42_clean


title: Mouse2_GFPEpCamPrimary_S15_clean


title: Mouse2_GFPPrimary_S28_clean


title: Mouse2_GFPEpCamPrimary_S14_clean


title: Mouse2_GFPEpCamPrimary_S13_clean


title: Mouse2_GFPPrimary_S21_clean


title: Mouse2_GFPPrimary_S17_clean


title: Mouse2_GFPPrimary_S20_clean


title: Mouse2_GFPPrimary_S19_clean


title: Mouse2_EpCamPrimary_S40_clean


title: Mouse2_EpCamPrimary_S41_clean


title: Mouse2_EpCamPrimary_S39_clean


title: Mouse2_GFPPrimary_S15_clean


title: Mouse2_EpCamPrimary_S35_clean


title: Mouse2_EpCamPrimary_S37_clean


title: Mouse2_EpCamPrimary_S38_clean


title: Mouse2_EpCamPrimary_S36_clean


title: Mouse2_EpCamPrimary_S34_clean


title: Mouse2_EpCamPrimary_S33_clean


title: Mouse2_CD45Primary_S34_clean


title: Mouse2_CD45Primary_S35_clean


title: Mouse2_CD45Primary_S33_clean


title: Mouse2_CD45Primary_S32_clean


title: Mouse2_GFPPrimary_S07_clean


title: Mouse2_CD45Primary_S31_clean


title: Mouse2_CD45Primary_S29_clean


title: Mouse2_CD45Primary_S27_clean


title: Mouse2_CD45Primary_S28_clean


title: Mouse2_CD45Primary_S25_clean


title: Mouse2_CD45Primary_S24_clean


title: Mouse2_CD45Primary_S22_clean


title: Mouse2_CD45Primary_S21_clean


title: Mouse2_CD45Primary_S23_clean


title: Mouse2_CD45Primary_S19_clean


title: HNRNPC, HNRNPC, Re-CLIP, HEK293T, Rep 2

status: Public on Jan 28 2025

city: Stanford

first: Luca

last: Ducoli

state: California

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: Re-CLIP protocol

data_processing:
Custom processing scripts available at https://github.com/lducoli/irCLIP-RNP/.
Assembly: Human GRCh38 Gencode release 39 and a custom chromosome made of repetitive elements
Supplementary files format and content: Tab separated text file of RT stops counts at genomic windows as determined by htseq-clip. Scaled bigwig files using scale factors estimated from window counts using DEWSeq.
Library strategy: CLIP-seq

growth_protocol: HEK293T and A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
For irCLIPv2, immunoprecipitation (IP) followed by 3'ligation. For Re-CLIP, 1st IP, 3' ligation, IP destruction and reconstitution, 2nd IP. Then, ligated RNPs were resolved on SDS-page, transferred to nitrocellulose, and RNA was recovered after protein K digestion using streptavidin beads.
On-beads 1st strand cDNA synthesis, 3’ cDNA-tailing, 2nd strand synthesis, and amplification.

treatment_protocol: UV cross-linked at 253nm on plates. Where specified, cells were treated with 50ng/mL recombinant human EGF for the given time.

value: Human embryonic kidney cell line


title: Mouse2_CD45Primary_S17_clean


title: Mouse2_CD45Primary_S16_clean


title: Mouse1_GFPNegativePrimaryBulk_S44_clean

source_name: Mouse1_Primary Pancreatic Tumor


title: Mouse2_CD45Primary_S18_clean


title: Mouse1_GFPPrimary_S56_clean


title: Mouse1_GFPPrimary_S54_clean


title: Mouse1_GFPPrimary_S55_clean


title: Mouse1_GFPPrimary_S53_clean


title: Mouse1_GFPPrimary_S52_clean


title: Mouse1_GFPPrimary_S51_clean


title: Mouse1_GFPPrimary_S50_clean


title: Mouse1_GFPPrimary_S49_clean


title: Mouse1_GFPPrimary_S48_clean


title: Mouse1_GFPPrimary_S47_clean


title: Mouse1_GFPPrimary_S46_clean


title: Mouse1_GFPPrimary_S45_clean


title: Mouse1_GFPPrimary_S44_clean


title: Mouse1_GFPPrimary_S42_clean


title: Mouse1_GFPPrimary_S43_clean


title: Mouse1_GFPPrimary_S41_clean


title: Mouse1_GFPPrimary_S40_clean


title: Mouse1_GFPPrimary_S38_clean


title: Mouse1_GFPPrimary_S35_clean


title: Mouse1_GFPPrimary_S37_clean


title: Mouse1_GFPPrimary_S36_clean


title: Mouse1_GFPPrimary_S30_clean


title: Mouse1_GFPPrimary_S34_clean


title: Mouse1_GFPPrimary_S31_clean


title: Mouse1_GFPPrimary_S33_clean


title: Mouse1_GFPPrimary_S29_clean


title: Mouse1_GFPPrimary_S25_clean


title: Mouse1_GFPPrimary_S26_clean


title: Mouse1_GFPPrimary_S28_clean


title: Mouse1_GFPPrimary_S23_clean


title: Mouse1_GFPPrimary_S22_clean


title: Mouse1_GFPPrimary_S21_clean


title: Mouse1_GFPPeritoneumMet_S53_clean

source_name: Mouse1_Peritoneum Metastasis


title: Mouse1_GFPPeritoneumMet_S50_clean


title: Mouse1_GFPPeritoneumMet_S51_clean


title: Mouse1_GFPPeritoneumMet_S49_clean


title: Mouse1_GFPPeritoneumMet_S45_clean


title: Mouse1_GFPPeritoneumMet_S44_clean


title: Mouse1_GFPPeritoneumMet_S42_clean


title: Mouse1_GFPPeritoneumMet_S41_clean


title: Mouse1_GFPPeritoneumMet_S38_clean


title: Mouse1_GFPPeritoneumMet_S37_clean


title: Mouse1_GFPPeritoneumMet_S36_clean


title: Mouse1_GFPPeritoneumMet_S35_clean


title: Mouse1_GFPPeritoneumMet_S34_clean


title: Mouse1_GFPPeritoneumMet_S32_clean


title: Mouse1_GFPPeritoneumMet_S30_clean


title: Mouse1_GFPPeritoneumMet_S29_clean


title: Mouse1_GFPPeritoneumMet_S28_clean


title: Mouse1_GFPPeritoneumMet_S26_clean


title: Mouse1_GFPPeritoneumMet_S25_clean


title: Mouse1_GFPPeritoneumMet_S24_clean


title: Mouse1_GFPPeritoneumMet_S23_clean


title: Mouse1_GFPPrimary_S24_clean


title: Mouse1_GFPPeritoneumMet_S22_clean


title: Mouse1_GFPPeritoneumMet_S21_clean


title: Mouse1_GFPPeritoneumMet_S54_clean


title: Mouse1_GFPPeritoneumMet_S19_clean


title: Mouse1_GFPPeritoneumMet_S18_clean


title: Mouse1_GFPPeritoneumMet_S17_clean


title: Mouse1_GFPPeritoneumMet_S16_clean


title: Mouse1_GFPPeritoneumMet_S15_clean


title: Mouse1_GFPPeritoneumMet_S14_clean


title: Mouse1_GFPPeritoneumMet_S13_clean


title: Mouse1_GFPNegativePeritoneumMetBulk_S55_clean


title: Mouse1_GFPPrimaryBulk_S57_clean


title: Mouse1_EpCamPrimary_S60_clean


title: Mouse1_EpCamPrimary_S59_clean


title: Mouse1_GFPPeritoneumMetBulk_S43_clean


title: Mouse1_EpCamPrimary_S08_clean


title: Mouse1_EpCamPrimary_S05_clean


title: Mouse1_EpCamPrimary_S04_clean


title: Mouse1_GFPPeritoneumMet_S20_clean


title: Mouse1_EpCamPrimary_S03_clean


title: Mouse1_EpCamPrimary_S02_clean


title: Mouse1_EpCamPrimary_S01_clean


title: Mouse1_GFPEpCamPrimary_S20_clean


title: Mouse2_CD45Primary_S30_clean


title: Mouse2_CD45Primary_S26_clean


title: Mouse1_GFPEpCamPrimary_S19_clean


title: Mouse2_CD45Primary_S20_clean


title: Mouse1_GFPEpCamPrimary_S18_clean


title: Mouse1_GFPEpCamPrimary_S17_clean


title: Mouse1_GFPEpCamPrimary_S15_clean


title: Mouse1_GFPEpCamPrimary_S16_clean


title: Mouse1_GFPEpCamPrimary_S14_clean


title: Mouse1_GFPEpCamPrimary_S12_clean


title: Mouse1_GFPEpCamPrimary_S13_clean


title: Mouse1_GFPPrimary_S39_clean


title: Mouse1_GFPEpCamPrimary_S11_clean


title: Mouse1_GFPEpCamPrimary_S09_clean


title: Mouse1_GFPEpCamPrimary_S10_clean


title: Mouse1_CD45Primary_S43_clean


title: Mouse1_GFPPrimary_S32_clean


title: Mouse1_GFPPrimary_S27_clean


title: Mouse1_CD45Primary_S42_clean


title: Mouse1_EpCamPrimary_S06_clean


title: Mouse1_CD45Primary_S41_clean


title: Mouse1_EpCamPrimary_S07_clean


title: Mouse1_CD45Primary_S40_clean


title: Mouse1_CD45Primary_S39_clean


title: Mouse1_CD45Primary_S37_clean


title: Mouse1_CD45Primary_S38_clean


title: Mouse1_GFPPeritoneumMet_S52_clean


title: Mouse1_CD45Primary_S36_clean


title: Mouse1_CD45Primary_S35_clean


title: Mouse1_CD45Primary_S34_clean


title: Mouse1_GFPPeritoneumMet_S48_clean


title: Mouse1_GFPPeritoneumMet_S47_clean


title: Mouse1_GFPPeritoneumMet_S46_clean


title: Mouse1_CD45Primary_S32_clean


title: Mouse1_CD45Primary_S31_clean


title: Mouse1_CD45Primary_S29_clean


title: Mouse1_CD45Primary_S30_clean


title: Mouse1_CD45Primary_S28_clean


title: Mouse1_CD45Primary_S27_clean


title: Mouse1_CD45Primary_S26_clean


title: Mouse1_GFPPeritoneumMet_S40_clean


title: Mouse1_CD45Primary_S23_clean


title: Mouse1_CD45Primary_S24_clean


title: Mouse1_CD45Primary_S25_clean


title: Mouse1_CD45Primary_S22_clean


title: Mouse1_CD45Primary_S21_clean


title: Mouse1_GFPPeritoneumMet_S39_clean


title: DNA_4N_4_S88

data_processing:
library strategy: scWGS for CNV analysis
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: mm9
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

extract_protocol:
Adherent cells were trypsinzed, counted and resuspended in NST-DAPI buffer. Cells were sorted on flow cytometer based on the DNA content to obtain single nuclei for scWGS
Single cells isolated into 10x Lysis and Fragmentation Buffer were processed for genomic DNA amplification using SeqXE kit from Sigma Aldrich. Manufacturer's instructions very followed for gDNA amplification. Library preparation was done by end repair, adenylation, adapter ligation and PCR steps.

value: Pancreatic cancer tumor cell line

tag: labelling for flow

value: EGFP expression

tag: molecule subtype

value: genomic DNA in nuclei


title: Mouse1_CD45PrimaryBulk_S33_clean

tag: cell type


title: DNA_4N_8_S92


title: DNA_4N_3_S87


title: DNA_4N_6_S90


title: DNA_4N_5_S89


title: DNA_4N_12_S96


title: DNA_4N_11_S95


title: DNA_4N_10_S94


title: DNA_2N+_Bulk_S84


title: DNA_4N_1_S85


title: DNA_2N+_8_S56


title: DNA_2N+_7_S55


title: DNA_2N+_6_S54


title: DNA_2N+_5_S53


title: DNA_2N+_4_S52


title: DNA_2N+_35_S83


title: DNA_2N+_33_S81


title: DNA_2N+_32_S80


title: DNA_2N+_34_S82


title: DNA_2N+_3_S51


title: DNA_2N+_30_S78


title: DNA_2N+_29_S77


title: DNA_2N+_25_S73


title: DNA_2N+_26_S74


title: DNA_2N+_24_S72


title: DNA_2N+_23_S71


title: DNA_2N+_20_S68


title: DNA_2N+_22_S70


title: DNA_2N+_21_S69


title: DNA_2N+_2_S50


title: DNA_2N+_18_S66


title: DNA_2N+_15_S63


title: DNA_2N+_17_S65


title: DNA_2N+_16_S64


title: DNA_2N+_14_S62


title: DNA_2N+_13_S61


title: DNA_2N+_12_S60


title: DNA_2N+_10_S58


title: DNA_2N+_1_S49


title: DNA_2N+_11_S59


title: DNA_2N_8_S08


title: DNA_2N_6_S06


title: DNA_2N_9_S09


title: DNA_2N_47_S48


title: DNA_2N_5_S05


title: DNA_2N_46_S47


title: DNA_2N_45_S46


title: DNA_2N_44_S45


title: DNA_2N_43_S44


title: DNA_2N_4_S04


title: DNA_2N_40_S41


title: DNA_2N_39_S40


title: DNA_2N_41_S42


title: DNA_2N_36_S36


title: DNA_2N_35_S35


title: DNA_2N_33_S33


title: DNA_2N_34_S34


title: DNA_2N_31_S31


title: DNA_2N_30_S30


title: DNA_2N_29_S29


title: DNA_2N_3_S03


title: DNA_2N_28_S28


title: DNA_2N_32_S32


title: DNA_2N_27_S27


title: DNA_2N_25_S25


title: DNA_2N_26_S26


title: DNA_2N_24_S24


title: DNA_2N_23_S23


title: DNA_2N_22_S22


title: DNA_2N_21_S21


title: DNA_4N_7_S91


title: DNA_2N_2_S02


title: DNA_2N_20_S20


title: DNA_4N_9_S93


title: DNA_2N_19_S19


title: DNA_4N_2_S86


title: DNA_2N_18_S18


title: DNA_2N+_9_S57


title: DNA_2N_16_S16


title: DNA_2N_17_S17


title: DNA_2N_14_S14


title: DNA_2N_15_S15


title: DNA_2N_13_S13


title: DNA_2N_12_S12


title: DNA_2N+_31_S79


title: DNA_2N_10_S10


title: DNA_2N_11_S11


title: DNA_2N+_28_S76


title: DNA_2N+_27_S75


title: E315A-RNA-3_clean

description:
315A-RNA-3_S15
Bulk RNA sequencing of RNA extracted from 315A cells.

data_processing:
Adapter removal and removing reads shorter than 36bp using Bbduk
Align reads to reference genome hg19 using Kallisto and obtain read count tables
Genome_build: hg19
Supplementary_files_format_and_content: read count table

source_name: 315A Diploid lymphoblastoid cell line

growth_protocol: Cells were cultured in respective media at 37C, 5% CO2

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen Rneasy kit. RNA was qunatified and then a reverse transcription step was done using Oligo dT primer and Clontech Reverse Transcriptase to generate cDNA. 2ug of cDNA was used for library preparation
2ug of cDNA was fragemented to 400bp using Covaris somicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

value: 315A Diploid lymphoblastoid cell line

tag: cell line source

value: Lymphoblastoid

value: Suspension cell line

tag: culture condition

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: DNA_2N_Bulk_S37


title: DNA_2N_1_S01


title: E315A-RNA-2_clean

description:
315A-RNA-2_S14
Bulk RNA sequencing of RNA extracted from 315A cells.


title: E315A-RNA-1_clean

description:
315A-RNA-1_S13
Bulk RNA sequencing of RNA extracted from 315A cells.


title: SKBR3-RNA-3_clean

description:
SKBR3-RNA-3_S24
Bulk RNA sequencing of RNA extracted from SKBR3 cells.

source_name: SKBR3 Her2 overexpresson breast cancer cell line

value: Breast

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: SKBR3-RNA-2_clean

description:
SKBR3-RNA-2_S23
Bulk RNA sequencing of RNA extracted from SKBR3 cells.

value: SKBR3 Her2 overexpresson breast cancer cell line


title: SKBR3-RNA-1_clean

description:
SKBR3-RNA-1_S22
Bulk RNA sequencing of RNA extracted from SKBR3 cells.


title: DNA_2N+_19_S67


title: BT549-RNA-3_clean

description:
BT549-RNA-3_S21
Bulk RNA sequencing of RNA extracted from BT549 cells.

source_name: BT549 Triple negative breast cancer cell line


title: BT549-RNA-1_clean

description:
BT549-RNA-1_S19
Bulk RNA sequencing of RNA extracted from BT549 cells.

value: BT549 Triple negative breast cancer cell line


title: BT549-RNA-2_clean

description:
BT549-RNA-2_S20
Bulk RNA sequencing of RNA extracted from BT549 cells.


title: A375-RNA-2_clean

description:
A375-RNA-2_S17
Bulk RNA sequencing of RNA extracted from A375 cells.

source_name: A375 Melanoma cancer cell line

value: A375 Melanoma cancer cell line

value: Skin


title: 315A_Cy13_S23

description:
315A_Cy13_S23
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to hg19 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome hg19 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: hg19
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

source_name: 315A_Diploid lymphoblastoid cell line

extract_protocol:
Cells were trypsinized, diluted to 1000cells/ml and handpicked as single cells in 10x Lysis buffer
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor were processed for mRNA transcription for first strand synthesis and cDNA amplification following SMART-Seq2 protocol. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. Libraries were made by end repair, Adenylation, Adapter ligation and PCR steps.

value: 315A_Diploid lymphoblastoid cell line

tag: culture type

tag: media

value: genomic DNA and mRNA


title: 315A_Cy13_S22

description:
315A_Cy13_S22
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt

tag: cell line


title: A375-RNA-1_clean

description:
A375-RNA-1_S16
Bulk RNA sequencing of RNA extracted from A375 cells.


title: 315A_Cy13_S21

description:
315A_Cy13_S21
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 315A_DNA

description:
315A_DNA_S24
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 315A_Cy13_S20

description:
315A_Cy13_S20
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 315A_Cy13_S19

description:
315A_Cy13_S19
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 315A_Cy13_S18

description:
315A_Cy13_S18
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: 315A_Cy13_S17

description:
315A_Cy13_S17
processed data file:
GTO_315A_scRNAseq.txt, Celllines_GTO_315A_bincount.txt


title: SKBR3_Cy0_S95

description:
SKBR3_0cycles_S95_S95
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

source_name: SKBR3_Her2 overexpresson breast cancer cell line


title: SKBR3_Cy0_S94

description:
SKBR3_0cycles_S94_S94
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line


title: SKBR3_Cy0_S93

description:
SKBR3_0cycles_S93_S93
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S92

description:
SKBR3_0cycles_S92_S92
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S91

description:
SKBR3_0cycles_S91_S91
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S90

description:
SKBR3_0cycles_S90_S90
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S89

description:
SKBR3_0cycles_S89_S89
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: DNA_2N_7_S07

source_name: KPC1199EGFP Adherent cells at passage 9

tag: strain background

value: Pancreatic cancer tumor cell line


title: SKBR3_Cy0_S88

description:
SKBR3_0cycles_S88_S88
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S87

description:
SKBR3_0cycles_S87_S87
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S86

description:
SKBR3_0cycles_S86_S86
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: A375-RNA-3_clean

description:
A375-RNA-3_S18
Bulk RNA sequencing of RNA extracted from A375 cells.


title: SKBR3_Cy0_S85

description:
SKBR3_0cycles_S85_S85
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S82

description:
SKBR3_0cycles_S82_S82
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S83

description:
SKBR3_0cycles_S83_S83
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S81

description:
SKBR3_0cycles_S81_S81
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S80

description:
SKBR3_0cycles_S80_S80
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S79

description:
SKBR3_0cycles_S79_S79
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S77

description:
SKBR3_0cycles_S77_S77
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S75

description:
SKBR3_0cycles_S75_S75
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S73

description:
SKBR3_0cycles_S73_S73
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S76

description:
SKBR3_0cycles_S76_S76
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_Cy0_S74

description:
SKBR3_0cycles_S74_S74
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: DNA_2N_42_S43

value: EGFP expression


title: SKBR3_Cy13_DNA

description:
SKBR3_DNA_S35
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S43

description:
SKBR3_Cy7_S43_S43
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S41

description:
SKBR3_Cy7_S41_S41
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: DNA_2N_38_S39

value: genomic DNA in nuclei


title: SKBR3_C1_Cy7_S40

description:
SKBR3_Cy7_S40_S40
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S39

description:
SKBR3_Cy7_S39_S39
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: DNA_2N_37_S38


title: SKBR3_C1_Cy7_S38

description:
SKBR3_Cy7_S38_S38
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy7_S37

description:
SKBR3_Cy7_S37_S37
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S17

description:
SKBR3_Cy17_S17_S57
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S14

description:
SKBR3_Cy17_S14_S54
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S11

description:
SKBR3_Cy17_S11_S51
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy15_S60

description:
SKBR3_Cy15_S60_S60
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S15

description:
SKBR3_Cy17_S15_S55
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy15_S59

description:
SKBR3_Cy15_S59_S59
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy15_S58

description:
SKBR3_Cy15_S58_S58
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy17_S12

description:
SKBR3_Cy17_S12_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy15_S56

description:
SKBR3_Cy15_S56_S56
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy15_S53

description:
SKBR3_Cy15_S53_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S56

description:
SKBR3_Cy13_S56_S56
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S55

description:
SKBR3_Cy13_S53_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S52

description:
SKBR3_Cy13_S52_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S51

description:
SKBR3_Cy13_S51_S51
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S38

description:
SKBR3_Cy13_S38_S38
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S34

description:
SKBR3_Cy13_S34_S34
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S35

description:
SKBR3_Cy13_S35_S35
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy13_S33

description:
SKBR3_Cy13_S33_S33
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S50

description:
SKBR3_Cy11_S50_S50
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S49

description:
SKBR3_Cy11_S49_S49
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S48

description:
SKBR3_Cy11_S48_S48
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S46

description:
SKBR3_Cy11_S46_S46
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S47

description:
SKBR3_Cy11_S47_S47
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: SKBR3_C1_Cy11_S45

description:
SKBR3_Cy11_S45_S45
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt


title: BT549_Cy13_DNA_S16

description:
BT549_DNA_S16
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

source_name: BT549_Triple negative breast cancer cell line


title: BT549_Cy13_S15

description:
B5549_Cy13_S9
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt

value: BT549_Triple negative breast cancer cell line


title: BT549_Cy13_S14

description:
B5549_Cy13_S15
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S13

description:
B5549_Cy13_S14
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S12

description:
B5549_Cy13_S13
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S11

description:
B5549_Cy13_S12
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S10

description:
B5549_Cy13_S11
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy13_S9

description:
B5549_Cy13_S10
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S67

description:
BT549_Cy11_S67_S67
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S66

description:
BT549_Cy11_S66_S66
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S69

description:
BT549_Cy11_S69_S69
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S64

description:
BT549_Cy11_S64_S64
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S61

description:
BT549_Cy11_S61_S61
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S56

description:
BT549_Cy11_S56_S56
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S58

description:
BT549_Cy11_S58_S58
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S55

description:
BT549_Cy11_S55_S55
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: BT549_Cy11_S54

description:
BT549_Cy11_S54_S54
processed data file:
GTO_BT549_scRNAseq.txt, Celllines_GTO_BT549_bincount.txt


title: A375_Cy13_S32

description:
A375_Cy13_S32
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

source_name: A375_Melanoma cancer cell line

value: A375_Melanoma cancer cell line


title: A375_Cy13_S31

description:
A375_Cy13_S31
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_DNA

description:
A375_DNA_S33
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S30

description:
A375_Cy13_S30
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S28

description:
A375_Cy13_S28
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S29

description:
A375_Cy13_S29
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S26

description:
A375_Cy13_S26
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S48

description:
A375_Cy11_S48_S48
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S27

description:
A375_Cy13_S27
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy13_S25

description:
A375_Cy13_S25
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S47

description:
A375_Cy11_S47_S47
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S44

description:
A375_Cy11_S44_S44
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S43

description:
A375_Cy11_S43_S43
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S40

description:
A375_Cy11_S40_S40
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S39

description:
A375_Cy11_S39_S39
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S37

description:
A375_Cy11_S37_S37
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S36

description:
A375_Cy11_S36_S36
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S35

description:
A375_Cy11_S35_S35
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S30

description:
A375_Cy11_S30_S30
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S29

description:
A375_Cy11_S29_S29
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S28

description:
A375_Cy11_S28_S28
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S27

description:
A375_Cy11_S27_S27
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S25

description:
A375_Cy11_S25_S25
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: E315A-DNA-3

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-3_S3

data_processing:
library strategy: bulk DNA sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: hg19
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen DNeasy blood and tissue kit.
2ug of DNA was fragmented to 400bp using Covaris sonicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

value: 315A Diploid lymphoblastoid cell line

value: Lymphoblastoid

value: Suspension cell line


title: E315A-DNA-2

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-2_S2

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: E315A-DNA-1

description:
single cell whole genome sequencing of 315A DNA
315A-DNA-1_S1


title: SKBR3-DNA-2

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-2_S11

value: Breast

value: Adherent cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: SKBR3-DNA-1

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-1_S10

value: SKBR3 Her2 overexpresson breast cancer cell line


title: BT549-DNA-1

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-1_S7

value: BT549 Triple negative breast cancer cell line


title: A375-DNA-3

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-3_S6

value: A375 Melanoma cancer cell line

value: Skin


title: A375-DNA-2

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-2_S5


title: A375-DNA-1

description:
single cell whole genome sequencing of A375 DNA
A375-DNA-1_S4


title: KP_T1_25

status: Public on Mar 18 2020

description:
KP_T1_IGO_10027_25_S25
KP LUAD cells (untransduced parental population).
SE-76

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a).
Genome-wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table.
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: FSR_RNAseq.featureCounts.cnt.csv: Comma-separated text file includes raw count values for each sample.

source_name: Murine KrasG12D/+;Trp53-/- (KP) lung adenocarcinoma (LUAD) cells

growth_protocol: All cells were maintained in a humidified incubator at 37°C with 5% CO2, and grown in DMEM supplemented with 10% FBS and 100 IU/ml penicillin/streptomycin. Cells sampled here were cultured for 120hrs post-transduction, at which point RNA was harvested.

extract_protocol:
RNeasy Mini Kit (Qiagen)
Poly-A RNA-Seq / Single-end 76

treatment_protocol: 1 million KP LUAD cells were seeded in 10cm plates and immediately transduced with retroviral supernatants and 8ug/mL polybrene. Cells were grown for 48hrs before purifying using fluorescence activated cell sorting (FACS). All transductions were done in triplicate. Following transduction, stable GFP+ populations were purified by FACS on a FACSAria (BD Biosciences). 120 hours post-transduction, total RNA was isolated using the RNeasy Mini Kit (Qiagen) following standard manufacturer protocols.

value: KP LUAD cells

tag: genotype/variation

tag: oncotype

tag: stably transduced

value: Untransduced parental population

tag: time point

value: 120 hours post-transduction

tag: sorting strategy

value: GFP+


title: R277K_E282K_B_23

description:
696_B_IGO_10027_23_S23
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate B.
SE-76

tag: replicate

value: B


title: AML21-U

description: BM AML1/ETO positive LSPCs untreated

source_name: AML1/ETO positive LSPCs untreated

tag: population

value: AML1/ETO positive LSPCs

tag: tissue

value: Bone marrow (BM) derived LSPCs


title: R277K_E282K_A_22

description:
696_A_IGO_10027_22_S22
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate A.
SE-76

value: A


title: R277K_E282K_C_24

description:
696_C_IGO_10027_24_S24
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate C.
SE-76

value: C


title: R277T_E284D_C_21

description:
691_C_IGO_10027_21_S21
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate C.
SE-76


title: AML24-U

description: BM AML1/ETO positive LSPCs untreated


title: R277T_E284D_B_20

description:
691_B_IGO_10027_20_S20
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate B.
SE-76


title: R277T_E284D_A_19

description:
691_A_IGO_10027_19_S19
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate A.
SE-76


title: E284D_C_18

description:
206_C_IGO_10027_18_S18
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate C.
SE-76


title: E284D_A_16

description:
206_A_IGO_10027_16_S16
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate A.
SE-76


title: E284D_B_17

description:
206_B_IGO_10027_17_S17
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate B.
SE-76


title: R277K_C_15

description:
51_C_IGO_10027_15_S15
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate C.
SE-76


title: R277T_C_12

description:
41_C_IGO_10027_12_S12
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate C.
SE-76


title: R277T_A_10

description:
41_A_IGO_10027_10_S10
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate A.
SE-76


title: E282K_C_9

description:
12_C_IGO_10027_9_S9
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate C.
SE-76


title: E282K_A_7

description:
12_A_IGO_10027_7_S7
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate A.
SE-76


title: WT_C_6

description:
WT_C_IGO_10027_6_S6
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate C.
SE-76


title: E282K_B_8

description:
12_B_IGO_10027_8_S8
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate B.
SE-76


title: SKBR3_C1_Cy15_S52

description:
SKBR3_Cy15_S52_S52
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: SKBR3_Her2 overexpresson breast cancer cell line

tag: molecule type

value: genomic DNA and mRNA


title: SKBR3_C1_Cy17_S13

description:
SKBR3_Cy17_S13_S53
processed data file:
GTO_SKBR3_scRNAseq.txt, Celllines_GTO_SKBR3_bincount.txt

value: Breast

value: Adherent cell line


title: WT_B_5

description:
WT_B_IGO_10027_5_S5
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate B.
SE-76


title: WT_A_4

description:
WT_A_IGO_10027_4_S4
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate A.
SE-76


title: E_C_3

description:
E_C_IGO_10027_3_S3
KP LUAD cells stably transduced with pMIG-Empty - Replicate C.
SE-76

value: pMIG-Empty


title: E_B_2

description:
E_B_IGO_10027_2_S2
KP LUAD cells stably transduced with pMIG-Empty - Replicate B.
SE-76


title: R277K_B_14

description:
51_B_IGO_10027_14_S14
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate B.
SE-76


title: R277K_A_13

description:
51_A_IGO_10027_13_S13
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate A.
SE-76


title: R277T_B_11

description:
41_B_IGO_10027_11_S11
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate B.
SE-76


title: E_A_1

description:
E_A_IGO_10027_1_S1
KP LUAD cells stably transduced with pMIG-Empty - Replicate A.
SE-76


title: D80 WT rep2

status: Public on Feb 24 2020

description: Adoptive transferred p14 T cells form spleen day 80 post immunisation

data_processing:
Primary data analysis was performed with the Illumina RTA v1.18.66.3.
The  sequence assembly and alignment was performed using the ArrayStar software v.13 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: p14 T cells

extract_protocol:
Total RNA was extracted from WT and KO p14 T cells of naïve, D6 and D80 immunized mice using the RNeasy Micro Kit (QIAGEN AG, Switzerland)
Libraries were generated from 10ng total RNA using the SmartSeq2 Kit (Takara Bio, Japan).

treatment_protocol: One day post adoptive transfer of  naïve WT and KO  p14 T cells, mice were immunized with LCMV-WE strain. P14 T cells were purified form spleen at  D6 or D80 post immunisation.

tag: strain

value: p14 T cells (spleen)

tag: age

value: post natal week 8

tag: genotype

value: wild type;p14


title: D80 WT rep1


title: D80 KO rep2


title: D80 KO rep1


title: D6 WT rep2

description: Adoptive transferred p14 T cells form spleen day 6 post immunisation


title: D6 WT rep1


title: D6 KO rep3


title: A375_Cy11_S45

description:
A375_Cy11_S45_S45
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: A375_Melanoma cancer cell line

tag: cell line source

value: Skin

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: A375_Cy11_S46

description:
A375_Cy11_S46_S46
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

tag: culture type


title: D6 KO rep2


title: D6 KO rep1


title: naïve WT rep2

description: Naive p14 T cells form spleen


title: naïve WT rep1

description: Naive p14 T cells form spleen


title: Mouse2_GFPPrimary_S09_clean

source_name: Mouse2_Primary Pancreatic Tumor

tag: Sex

value: male

tag: tumor type

value: Primary

value: Pancreas

tag: cell type

value: Tumor

tag: marker

value: GFP, Calcien Violet for Live/Dead


title: A375_Cy11_S41

description:
A375_Cy11_S41_S41
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

tag: cell line

tag: media


title: A375_Cy11_S42

description:
A375_Cy11_S42_S42
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: naïve KO rep1

description: Naive p14 T cells form spleen


title: naïve KO rep2

description: Naive p14 T cells form spleen


title: A375_Cy11_S32

description:
A375_Cy11_S32_S32
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S33

description:
A375_Cy11_S33_S33
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S34

description:
A375_Cy11_S34_S34
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: A375_Cy11_S38

description:
A375_Cy11_S38_S38
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt


title: Tumor cells, T/P 3

status: Public on Feb 03 2020

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: tumor cells from KPCmut transplant PDAC tumors

growth_protocol: To generate orthotopic PDAC tumors, 5x10e5 KrasG12D/+;Trp53R172H/wt (KPCmut) PDAC cells expressing luciferase and GFP (LUC-GFP) were orthotopically transplanted into the pancreas of 8-10 week old C57BL/6 female mice as described above. Mice were monitored for tumor development (5-8 days post-transplantation) by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum imager (PerkinElmer) before being randomized into various study cohorts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: PDAC-bearing mice were treated with vehicle or combined trametinib (1 mg/kg body weight), and palbociclib (100 mg/kg body weight) per os for 4 consecutive days followed by 3 days off treatment for 10 days before sacrifice.

value: tumor cells

tag: treatment

value: T/P


title: Tumor cells, T/P 2


title: Tumor cells, T/P 1


title: Tumor cells, T/P 4


title: Tumor cells, Vehicle 4

value: Vehicle


title: Tumor cells, Vehicle 3


title: Tumor cells, Vehicle 2


title: Tumor cells, Vehicle 1


title: non-infect

status: Public on Jan 13 2020

description: 7 days after infection (mock infection with spinnning and polybrene but no vrus added)

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38) or human transcriptome (hg19, GRCh37)
Supplementary_files_format_and_content: Tab-delimited text file includes rpkm normalized table for each sample

source_name: MLLAF9-NrasG12D mouse leukemia

growth_protocol: Cells were cultured with RPMI medium supplemented with 10% FBS (Gibco)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

value: no drug treatment, sample with intact pdxk


title: human-2 +

description: 7 days after infection with sgRNA (Linked to GFP) targeting human locus (as non-Pdxk inhibited control), sorted GFP +


title: human-2 -

description: 7 days after infection with sgRNA (Linked to GFP) targeting human locus (as non-Pdxk inhibited control), sorted GFP -


title: A375_Cy11_S26

description:
A375_Cy11_S26_S26
processed data file:
GTO_A375_scRNAseq.txt, Celllines_GTO_A375_bincount.txt

value: Adherent cell line

value: genomic DNA and mRNA


title: human-1 +


title: Pdxk-6 +

description: 7 days after infection with sgRNA (Linked to GFP) targeting mouse.Pdxk, sorted GFP +

value: no drug treatment, sample with pdxk knock-out


title: Pdxk-5 +


title: human-1 -


title: Pdxk-5 -

description: 7 days after infection with sgRNA (Linked to GFP) targeting mouse.Pdxk, sorted GFP -


title: Pdxk-4 -


title: Pdxk-3 +


title: Pdxk-4 +


title: Pdxk-6 -


title: Pdxk-3 -


title: Pdxk-2 +


title: Pdxk-2 -


title: Pdxk-1 -


title: Pdxk-1 +


title: Rosa26 + 2

description: 7 days after infection with sgRNA (Linked to GFP) targeting Rosa26 mouse locus (as non-Pdxk inhibited control), sorted GFP +


title: OMP_Day6_2

description: 6 day treatment

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file includes rpkm normalized table for each sample

source_name: Leukemic cell

growth_protocol: Nras(G12D)/MLL–AF9 cells were cultured in RPMI medium supplemented with 10 % Fetal Bovine Serum (FBS), L-glutamine, penicillin streptomycin, recombinant mouse SCF, IL-3, and IL-6.

extract_protocol:
Total RNA were extracted using RNeasy Mini Kit (Qiagen).
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

treatment_protocol: Nras(G12D)/MLL-AF9 cells were treated with 100 micro molar OMP for 6 days, while the same volume of PBS was used as vehicle.

value: Blood

value: OMP 100 micro molar


title: OMP_Day6_1

description: 6 day treatment


title: Vehicle_Day6_3

description: 6 day treatment


title: Vehicle_Day6_1

description: 6 day treatment


title: Rosa26 + 1


title: Rosa26 - 2

description: 7 days after infection with sgRNA (Linked to GFP) targeting Rosa26 mouse locus (as non-Pdxk inhibited control), sorted GFP -


title: Vehicle_Day6_2

description: 6 day treatment


title: OMP_Day6_3

description: 6 day treatment


title: empty +

description: 11 days after infection with sgRNA (Linked to GFP) vector with no payload sgRNA (as non-PDXK inhibited control), sorted GFP +

source_name: MOLM13 human leukemia line

value: no drug treatment, sample with intact PDXK


title: Rosa26 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse Rosa26 locus (as non-PDXK inhibited control), sorted GFP +


title: empty -

description: 11 days after infection with sgRNA (Linked to GFP) vector with no payload sgRNA (as non-PDXK inhibited control), sorted GFP -


title: Rosa26 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse Rosa26 locus (as non-PDXK inhibited control), sorted GFP -


title: hPDXK-aa230 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting human PDXK, sorted GFP +

value: no drug treatment, sample with PDXK knock-out


title: hPDXK-aa230 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting human PDXK, sorted GFP -


title: hPDXK-aa105 +


title: hPDXK-aa22 +


title: hPDXK-aa22 -


title: Cr8 +

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse chrom 8 locus (as non-PDXK inhibited control), sorted GFP +


title: hPDXK-aa15 -


title: Cr8 -

description: 11 days after infection with sgRNA (Linked to GFP) targeting mouse chrom 8 locus (as non-PDXK inhibited control), sorted GFP -


title: 10 days Cherry+ repl.3

status: Public on Aug 28 2019

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

data_processing:
The RSEM package (version 1.2.29) and Bowtie2 were used to aling reads to the mouse mm10 transcriptome, taken from known Gene reference table available at UCSC
The “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.12.4) within the R programming (version 3.3.1)
Genome_build: mm10 UCSC
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent UCSC mouse genes and columns represent individual samples.

extract_protocol:
Lungs were minced manually and then digested for 30 min at 37 degrees in a HBSS digestion solution containing DNase I (Sigma-Aldrich) and Liberase TM and TH (Roche Diagnostics). Samples were then washed, passed through a 100 um filter and incubated with Red Blood Cell Lysis buffer (Miltenyi Biotec) for 3-5 min. After a wash with MACS buffer (0.5% BSA and 250 mM EDTA in PBS), samples were passed through a 40 um filter and a 20 um strainer-capped flow cytometry tube to generate a single cell suspension to use for flow cytometric analysis or further purification. Samples were stained with a CD45 and a Ter119 antibody. Murine CD45-Ter119- cells were isolated via FACS.
Total RNA from sorted cell samples was isolated using the MagMax-96 Total RNA Isolation Kit (ThermoFIsher Scientific). The quality and concentration of total RNA for each sample was determined on Agilent 2100 Bioanalyzer using the Total RNA 6000 Pico Kit. RNA was amplified and libraries were prepared for sequencing using Illumina protocols.

treatment_protocol: Balb/c female mice 6-10 weeks old were injected intravenously with 4T1-labelling tumour cells and lungs were isolated at day 5 and day 10 after injection

value: Lung

value: CD45-Ter119- cells


title: 10 days Cherry+ repl.2


title: 10 days Cherry- repl.3


title: 10 days Cherry- repl.2


title: 10 days Cherry- repl.1


title: 5 days Cherry+ repl.1


title: 5 days Cherry+ repl.2


title: 5 days Cherry- repl.1


title: KPsh-1 on dox_aKG_rep_2

status: Public on May 10 2019

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: KPsh-1 on dox_aKG

growth_protocol: All conditions were passaged every 48 hours.  For KPsh cells analyzed off dox, cells were washed and grown without dox 8 days before collection. DMSO or dimethyl-alpha ketoglutarate were added where indicated for 72 hours.

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

treatment_protocol: Cells were treated with DMSO (vehicle) or dimethyl-alpha ketoglutarate for 72 hours.

value: Primary mouse PDAC cell line

tag: p53 shrna status

value: p53 shRNA ON

value: 4mM DMaKG


title: KPsh-1 off dox_DMSO_rep_2

source_name: KPsh-1 off dox_DMSO

value: p53 shRNA OFF

value: DMSO (vehicle)


title: 5 days Cherry- repl.2


title: KPsh-1 off dox_DMSO_rep_1


title: KL974_shRen_D7_2

status: Public on May 08 2019

description: KL974_GEPIR_shRen_DAY7_2_IGO_09439_2_S55

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: AML

extract_protocol:
Briefly, total RNA from 11B3fl/Trp53fl;shNf1;shMll3;Vav1-cre or Trp53fl/fl;shNf1;shMll3;Vav1-cre leukaemia cells (four lines per cohort), isolated from the bone marrow of moribund mice, was isolated by Trizol extraction (Life Technologies).
After ribogreen quantification (Life Technologies) and quality control on an Agilent BioAnalyzer, 500 ng of total RNA (RNA integrity number > 8) underwent polyA selection and Truseq library preparation according to instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2) with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50 bp/50 bp pairedend run, using the TruSeq SBS Kit v.3 (Illumina).

value: Bone marrow

value: shRen

tag: developmental stage


title: ChIP_Foxh1_KL974_shRen_D7_1

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to bigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: The cells were selected with puromycin and were then treated with doxycyclin for 7 days.

tag: disease state

value: AML

tag: time

tag: chip antibody

value: Foxh1 Abcam 49133


title: KL974_shp53_D7_1

tag: strain

tag: tissue


title: KL974_shFoxh1_1072_D7_2

description: KL974_GEPIR_shFoxh1_1072_DAY7_2_IGO_09439_8_S60

tag: genotype


title: KL974_shFoxh1_1072_D7_1

description: KL974_GEPIR_shFoxh1_1072_DAY7_1_IGO_09439_7_S59


title: p53R172H/-_rep2

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file containing quantified counts


title: p53R172H/-_rep1


title: p53-/-_rep4


title: p53-/-_rep3


title: Rosa26 - 1

value: no drug treatment, sample with intact pdxk


title: CD8-Adverse CD8_P9

status: Public on Apr 04 2019

description:
Gene expression data
Well-defined cell populations were FACS-purified from BM of newly diagnosed AML patients and also control subjects.

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label: biotin

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol: Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

tag: gender

value: M


title: CD8-Intermediate CD8_P7

value: F


title: KTPB17_IGO_11254_13_S13

status: Public on Sep 08 2022

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Pancreas tumor

growth_protocol: Mice undergo a survival surgery where the pancreas is exposed and 100.000 cells of the different genotypes are injected. Mice are then monitored and when they have overt disease assessed by palpation (~4 weeks after injection), the tumors are collected and a piece is flash frozen for total RNA extraction.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Mice were pre-treated with either IgG or anti-IFNAR1 antibodies (200 ug i.p. 3 times a week) starting one week before injection of cells and kept until the end of the experiment.

value: Pancreas tumor

value: Whole tissue

value: IFNAR1 antibody

value: KrasG12D; sgP53; dL


title: hPDXK-aa105 -

value: no drug treatment, sample with intact PDXK


title: CD8-Adverse CD8_P8


title: hPDXK-aa15 +

value: no drug treatment, sample with PDXK knock-out


title: 10 days Cherry+ repl.1

value: Lung

value: CD45-Ter119- cells


title: 5 days Cherry+ repl.3


title: CD8-Adverse CD8_P5


title: CD8-Adverse CD8_P6


title: 5 days Cherry- repl.3


title: KPsh-1 on dox_aKG_rep_1

value: Primary mouse PDAC cell line

value: p53 shRNA ON

value: 4mM DMaKG


title: CD8-Intermediate CD8_P4


title: CD8-Intermediate CD8_P33


title: CD8-Favorable CD8_P32


title: CD8-Favorable CD8_P31


title: KPsh-1 on dox_DMSO_rep_2

source_name: KPsh-1 on dox_DMSO

value: DMSO (vehicle)


title: Input_KL974_shRen_D7_2

value: AML

value: Bone marrow

value: shRen


title: KPsh-1 on dox_DMSO_rep_1


title: CD8-Adverse CD8_P3

value: M


title: CD8-Adverse CD8_P30

value: F


title: CD8-Intermediate CD8_P29


title: CD8-Intermediate CD8_P28


title: CD8-Intermediate CD8_P24


title: CD8-Intermediate CD8_P23


title: KL974_shRen_D7_1

description: KL974_GEPIR_shRen_DAY7_1_IGO_09439_1_S48


title: KL974_shp53_D7_2


title: CD8-Intermediate CD8_P22


title: CD8-Intermediate CD8_P21


title: CD8-Intermediate CD8_P18


title: CD8-Intermediate CD8_P20


title: CD8-Favorable CD8_P16


title: CD8-Adverse CD8_P19


title: CD8-Favorable CD8_P14


title: CD8-Favorable CD8_P15


title: CD8-Favorable CD8_P17


title: CD8-Adverse CD8_P2


title: CD8-Favorable CD8_P13


title: CD8-Favorable CD8_P12


title: p53-/-_rep2


title: p53-/-_rep1


title: CD8-Favorable CD8_P11


title: CD8-Adverse CD8_P10


title: CD8-Adverse CD8_P1


title: CD8-Ctrl CD8_C9


title: CD8-Ctrl CD8_C7


title: CD8-Ctrl CD8_C8


title: CD8-Ctrl CD8_C10


title: LPC-Adverse CD38_P5

source_name: LPC-Adverse


title: CD8-Ctrl CD8_C11


title: CD8-Ctrl CD8_C4


title: LPC-Intermediate CD38_P4

source_name: LPC-Intermediate


title: LPC-Adverse CD38_P6


title: LPC-Intermediate CD38_P7


title: LPC-Adverse CD38_P9


title: LPC-Intermediate CD38_P33


title: LPC-Favorable CD38_P32

source_name: LPC-Favorable


title: LPC-Adverse CD38_P8


title: CD8-Ctrl CD8_C6


title: LPC-Favorable CD38_P31


title: LPC-Adverse CD38_P3


title: LPC-Intermediate CD38_P24


title: LPC-Adverse CD38_P30


title: LPC-Intermediate CD38_P29


title: LPC-Intermediate CD38_P28


title: LPC-Intermediate CD38_P20


title: LPC-Intermediate CD38_P21


title: LPC-Adverse CD38_P2


title: LPC-Favorable CD38_P14


title: LPC-Adverse CD38_P19


title: LPC-Intermediate CD38_P22


title: LPC-Favorable CD38_P17


title: LPC-Intermediate CD38_P18


title: LPC-Favorable CD38_P12


title: LPC-Favorable CD38_P13


title: LPC-Intermediate CD38_P23


title: LPC-Favorable CD38_P16


title: LPC-Favorable CD38_P15


title: LPC-Favorable CD38_P11


title: HPC-Ctrl CD38_C9

source_name: HPC-Ctrl


title: HPC-Ctrl CD38_C8


title: LPC-Adverse CD38_P10


title: LPC-Adverse CD38_P1


title: HPC-Ctrl CD38_C6


title: HPC-Ctrl CD38_C7


title: LSC-Adverse CD34_P9

source_name: LSC-Adverse


title: HPC-Ctrl CD38_C10


title: HPC-Ctrl CD38_C4


title: HPC-Ctrl CD38_C11


title: LSC-Favorable CD34_P32

source_name: LSC-Favorable


title: LSC-Adverse CD34_P8


title: LSC-Intermediate CD34_P7

source_name: LSC-Intermediate


title: LSC-Adverse CD34_P5


title: LSC-Adverse CD34_P6


title: LSC-Intermediate CD34_P33


title: LSC-Intermediate CD34_P4


title: LSC-Favorable CD34_P31


title: LSC-Adverse CD34_P30


title: LSC-Adverse CD34_P3


title: LSC-Intermediate CD34_P28


title: LSC-Intermediate CD34_P24