title: H3_Sal + Das-treated cells replica 3

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using HiSeq4000 sequencer with single-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCh37 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Gene expression profiles were constructed using the DESeq2 package.
The resulting corrected p-values were calculated based on the Benjamin-Hochberg’s method to adjust multiple testing and control the false discovery rate.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include raw read counts at gene level for each samples.  Excel file includes output from DESeq2.

source_name: MDA-MB-468 cell line

growth_protocol: MDA-MB-468 cells were cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), penicillin (50,000 units/L), and streptomycin (50 mg/mL), and then maintained in 5% of CO2 at 37˚C.

extract_protocol:
The total RNA was extracted and purified using the Rneasy Mini Kit (Qiagen), according to the manufacturer's instructions. The final RNAs were quality controlledusing Agilent 2100 Bioanalyzer and quantified by absorbance using NanoDrop, prior RNA-seq analysis.
Library was constructed on the purified RNAs obtained from the PBS- or drug-treated MDA-MB-468 cells (4 biological replicates per condition), using Illumina TruSeq RNA preparation kit.

treatment_protocol: Cells were seeded on a T25 culture flask (1 million cells per flask) overnight and then treated with PBS (control), the drugs alone (salinomycin or dasatinib), or the drug combination (Sal + Das) for 24 or 72 h.

tag: cell line

value: Triple negative breast tumor

tag: drug incubation time

tag: drug concentration

value: 15.5 microM


title: OTTA2014_0219_Clinical

status: Public on Jul 22 2020

type: RNA

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

description: single-sample normalized data

hyb_protocol: NanoString Gene Expression protocol using 500ng of Total RNA as measured by NanoDrop spectrophotmeter. RNA is combined with capture and reporter codesets, and hybridization buffer. Reaction mixtures are hybridized in a thermal cycler at 65C for either short (16H) or long (20H) hybridization. Samples are then washed and fixed to cartridges using the nCounter Prep Station (high-sensitivity mode) for imaging.

scan_protocol: imaging on nCounter Digital Analyzer at maximum FOV

data_processing: Samples data is processed and normalized following protocols described in Talhouk et al (PMID: 27096160) using PrOTYPE. Briefly: Count data is Log2 transformed, the mean of housekeeping genes (ACTB, RPL19, SDHA, POLR1B, and PGK1) subtracted on a per-sample basis, and then normalized relative to reference samples (denoted as Pool1, Pool2, and Pool3). Code available at https://github.com/AlineTalhouk/PrOType

molecule: total RNA

organism: Homo sapiens

source_name: primary high-grade serous tubo-ovarian carcinoma

label_protocol: NanoString probe-specific unique barcode

extract_protocol: Total RNA extracted with the Qiagen miRNeasy FFPE kit (modified protocol)

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC

tag: site id


title: OSKM Day 4 shRNA-Jmjd3 overexpression rep 1

type: SRA

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

library_source: transcriptomic

data_processing:
rsem v1.2.22/bowtie2 v2.2.5 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 63 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript

organism: Mus musculus

source_name: Mouse MEFs, OSKM day 4

growth_protocol: MEFs were maintained in DMEM/high glucose (Hyclone) containing 10% fetal bovine serum (FBS, PAA), Glutamax (Invitrogen), nonessential amino acids (Invitrogen), and penicillin/streptomycin (Hyclone). Mouse ESCs and iPSCs were cultured on feeder layer (MEF treated with mitomycin-C) in ESC medium containing DMEM/high glucose (Hyclone) supplemented with 15% FBS (GIBCO), Glutamax, nonessential amino acids, sodium pyruvate, penicillin/streptomycin, beta-mercaptoethanol and leukaemia inhibitory factor (LIF). Reprogramming of MEFs was performed either in mES medium or iSF1 medium (DMEM/high glucose supplemented with 10% Knockout Serum Replacement, nonessential amino acids, basic fibroblast growth factor (bFGF) and LIF). Vitamin C was purchased from Sigma and used at concentration of 50 µg/ml. Drosophila S2 cells were obtained from Dr. Jianguo He’s lab and cultured in Schneider’s Drosophila medium (Life technologies, 21720-024) supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from cells using TRIzol following the manufacture’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plat-E cells were transfected with pMXs vectors for OSKM to produce virus. Plat-E cells were maintained in DMEM/high glucose containing 10% FBS.  MEFs within 3 passages were plated at 4000-5000 per square centimetre and infected with retrovirus. We marked the first infection time point as day0, after 2 rounds of 24h infection, the medium was changed to ESC medium, including Vitamin C.

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

value: OSKM lentiviral transfection

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: OTTA2014_0218_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: any

value: all wildtypes

value: hispanic

value: dead

value: adnexal


title: OSKM Day 4 Jmjd3 overexpression rep 2


title: OTTA2014_0217_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: H2_Sal + Das-treated cells replica 2

city: New York

country: USA

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: H1_Sal + Das-treated cells replica 1


title: OSKM Day 4 Jmjd3 overexpression rep 1

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

tag: presumed cell type

tag: strain


title: TRN115

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
nuclear RNA
TPM.TRN.tsv
no processed data

data_processing:
RSEM v1.2.87 was run on raw fastq fileswith default parameters on alignments created by Bowtie on UCSC gene annotation
TPM estimates were tranformed to log space by taking log TPM +1
TopHat2 v2.0.10 was used to map fastq files to mm10 reference
RNASeq-QC was run on the TopHat2 bamfiles to get QC metrics
For TRN and patch-seq samples, cells were removed if they had less than 40% genome mapping rate or or less than 1500 detected genes
Clustering and DE analysis of TRN samples was perfomed with biSNE software (https://github.com/yinqingl/nucseq_analysis), including normalizing the log TPM data to a normalized log TPM
For non-TRN samples, nuclei expressing <1500 genes were removed
Seurat v2.2.0 was used for clustering of the non-TRN samples
Genome_build: mm10
Supplementary_files_format_and_content: Formatted expression matrix (tab deliminated text file) with cells as columns, genes as rows, and TPM values as entries

source_name: TRN

extract_protocol:
Sucrose gradient nuclei isolation followed by FACS sorting for Violet+, Violet+ GFP+ or Violet+ NeuN+ nuclei
Modified SMARTseq2 single nuclei RNA-Seq

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: H_Sal + Das-treated cells

description: H

value: Triple negative breast tumor

value: 15.5 microM


title: OSKM Day 4 FLAG overexpression rep 2

value: FLAG


title: G3_Dasatinib-treated cells replica 3

value: 15 microM


title: TRN113


title: TRN112


title: OTTA2014_0216_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0215_Clinical

description: single-sample normalized data

value: high

tag: overall survival time

tag: progression-free survival time


title: OSKM Day 4 FLAG overexpression rep 1

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

value: OSKM lentiviral transfection

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: G2_Dasatinib-treated cells replica 2

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: TRN111

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0214_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: OSKM Day 4 shRNA-Jmjd3 overexpression rep 2

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

tag: presumed cell type

tag: strain


title: TRN110

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN109

value: No


title: G_Dasatinib-treated cells

description: G

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: OTTA2014_0212_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal


title: TRN108

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN114


title: OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression anti-H3K27me3

library_source: genomic

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.0
Peaks were discovered using Dfilter (H3K27me3)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are peak bed files and bigWig tracks

molecule: genomic DNA

source_name: Mouse MEFs, OSKM day 5

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and then add glycine at 0.125M to quench formaldehyde. Cells were rinsed twice with cold PBS, then lysed in ChIP Lysis Buffer A (50mM HEPES-KOH pH7.3; 140mM NaCl; 1mM EDTA pH8.0; 10% glycerol; 0.5% NP-40; 0.25% Triton-100; protease inhibitor cocktail) for 10 min at 4 ℃. Samples were centrifuged at 1,400g for 5min at 4 ℃, discard the supernatant and re-suspend the samples with ChIP Lysis Buffer B (1% SDS; 50mM Tris-HCl pH8.0; 10mM EDTA; protease inhibitor cocktail) for 10min at 4 ℃. Lysates were sonicated into about 150-300 bp fragments using Bioruptor (Diagenode), and centrifuged at 14,500 g at 4 ℃ for 10 minutes to discard insoluble pellets, and the supernatant was diluted ten times with ChIP IP Buffer (0.01% SDS, 1% Triton-100, 2mM EDTA, 50mM Tris-HCl pH8.0, 150mM NaCl, protease inhibitor cocktail), then incubated with specific antibody overnight at 4 ℃, and add protein A/G Dynabeads (Invitrogen) to capture specific immunoprecipitates. Wash the beads 3 times with low salt buffer (0.1% SDS, 1% Triton-100, 2mM EDTA, 20mM Tris-HCl pH8.0, 150mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton-100, 2mM EDTA, 20mM Tris-HCl pH8.0, 500mM NaCl), once with LiCl buffer 0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.1), and twice with TE buffer (10mM Tris-HCl, 1mM EDTA pH8.0). After washing, add 200ul 10% Chelex-100 and 2ul of Proteinase K (PK,20mg/ml) to incubate in a Mixing Block (BIOER) at 56 ℃ for 30 min, followed by boiling in water for 10 min, then centrifuged at 5,000 rpm for 5 min, and transfer the supernatant to a new tube. Antibodies used were: anti-H3K27me3 (Millipore, 07-449). Drosophila S2 cells were cross-linked in the same way mentioned above, and lysed in ChIP Lysis Buffer A for 10 min, centrifuged, and re-suspended with ChIP Lysis Buffer B, then mixed together with reprogramming mouse cells with the ratio of 1:2. Once Drosophila S2 cells and reprogramming cells were combined, the sample was treated as a single sample throughout the ChIP-seq experiment. After sonication, samples were centrifuged at 13.200 rpm at 4 ℃ for 10 min, the supernatant was diluted twice with ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl, protease inhibitor cocktail) and dialyzed with Slide-A-Lyzer Dialysis cassette (Thermo Scientific, 66380) to reduce the high level of SDS followed with incubation with antibody and Dynabeads. Washed beads were eluted with fresh Elution Buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA, 1.0% SDS) at 56 ℃ for 30 minutes. Centrifuge and incubate the supernatant at 65 4 ℃ for 8-16 h to reverse crosslink the immunoprecipitation DNA. After incubated with RNase A and PK, DNA was purified with phenol:chloroform:isoamyl alcohol (P:C:IA).
Standard Illumina protocols

tag: day

tag: transfection

tag: overexpression

tag: knockout

value: Wildtype

tag: presumed cell type

tag: strain


title: OSKM Day 5 Jmjd3+/+ FLAG overexpression anti-H3K27me3

value: FLAG


title: OSKM Day 5 Jmjd3-/- Jmjd3 overexpression anti-H3K27me3


title: OTTA2014_0211_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: experiment site

value: AOC

tag: site id


title: F3_Salinomycin-treated cells replica 3

tag: cell line

tag: tissue

value: Triple negative breast tumor

tag: drug incubation time

tag: drug concentration

value: 0.5 microM


title: F2_Salinomycin-treated cells replica 2


title: TRN107

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0210_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: high

value: any

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0209_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

value: omentum

tag: experiment site

tag: site id


title: TRN106

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: F1_Salinomycin-treated cells replica 1

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: OSKM Day 10 Jmjd3+/+ Jmjd3 overexpression anti-H3K27me3

source_name: Mouse MEFs, OSKM day 10

tag: day

tag: transfection

value: OSKM lentiviral transfection

tag: overexpression

tag: knockout

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: TRN105


title: OSKM Day 10 Jmjd3+/+ FLAG overexpression anti-H3K27me3


title: F_Salinomycin-treated cells

description: F


title: TRN104


title: G1_Dasatinib-treated cells replica 1

value: 15 microM


title: OTTA2014_0208_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal


title: E3_Control cells replica 3

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: OSKM Day 10 Jmjd3-/- Jmjd3 overexpression anti-H3K27me3

tag: day

tag: transfection

tag: overexpression

tag: knockout

tag: presumed cell type

tag: strain


title: OTTA2014_0213_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

value: alive

tag: experiment site

tag: site id


title: TRN103

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: OTTA2014_0206_Clinical

description: single-sample normalized data

value: HGSOC

value: high

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: AOC


title: TRN102


title: E2_Control cells replica 2

tag: cell line

tag: tissue

value: Triple negative breast tumor

tag: drug incubation time

tag: drug concentration


title: E1_Control cells replica 1


title: OSKM Day 10 Jmjd3-/- FLAG overexpression anti-H3K27me3

tag: day

tag: transfection

tag: overexpression

value: FLAG

tag: knockout

tag: presumed cell type

tag: strain


title: OSKM Day 5 Jmjd3-/- FLAG overexpression anti-H3K27me3


title: TRN101

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: MEF Jmjd3+/+ input

source_name: Mouse MEFs

value: Wildtype

value: mouse embryonic fibroblast


title: OTTA2014_0205_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum

tag: experiment site

tag: site id


title: OTTA2014_0204_Clinical

description: single-sample normalized data

value: any

value: dead

tag: study entry delay

tag: anatomical site

value: adnexal


title: E_Control cells

description: E

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: MEF Jmjd3+/+ anti-H3K27me3

tag: day

tag: transfection

tag: overexpression

tag: knockout

tag: presumed cell type

tag: strain


title: TRN100

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: D3_Sal + Das-treated cells replica 3

value: 15.5 microM


title: OTTA2014_0203_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: experiment site

tag: site id


title: MEF Jmjd3-/- input

tag: day

tag: transfection

tag: overexpression

tag: knockout

tag: presumed cell type

tag: strain


title: MEF Jmjd3-/- anti-H3K27me3


title: TRN99

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: D2_Sal + Das-treated cells replica 2

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration


title: TRN98


title: OTTA2014_0202_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: AOC


title: OTTA2014_0207_Clinical

description: single-sample normalized data

value: pathogenic BRCA2 mutation

tag: experiment site

tag: site id


title: D1_Sal + Das-treated cells replica 1

tag: cell line

tag: tissue

value: Triple negative breast tumor

tag: drug incubation time

tag: drug concentration


title: D_Sal + Das-treated cells

description: D


title: OTTA2014_0201_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: hispanic


title: TRN97

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: TRN96


title: OTTA2014_0200_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_0199_Clinical

description: single-sample normalized data

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: C3_Dasatinib-treated cells replica 3

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration

value: 15 microM


title: C2_Dasatinib-treated cells replica 2


title: TRN95

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0198_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: adnexal


title: TRN94

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H7_S379


title: C1_Dasatinib-treated cells replica 1


title: C_Dasatinib-treated cells

description: C


title: TRN93

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H6_S378


title: TRN92

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H5_S377


title: OTTA2014_0197_Clinical

description: single-sample normalized data

value: all wildtypes

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: B3_Salinomycin-treated cells replica 3

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration

value: 0.5 microM


title: TRN91

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H4_S376

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type


title: B2_Salinomycin-treated cells replica 2


title: TRN90

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H3_S375

value: TRN no Neun selection


title: B1_Salinomycin-treated cells replica 1


title: OTTA2014_0193_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: TRN89

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H2_S374


title: OTTA2014_0192_Clinical

description: single-sample normalized data

value: high

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: DE71_50_rep5

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: X20001_1160_DE71.18.4117_Rep_5_.Rat230_2..CEL

hyb_protocol: Of all, 15 μg of amplified biotin-aRNAs were fragmented and 12.5 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data were obtained using the GeneChip Command Console and Expression Console Software (AGCC; version 3.2 and Expression Console; version 1.2).

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized across all three groups.

label: biotin

organism: Rattus norvegicus

label_protocol: One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3’ IVT Plus kit protocol.

growth_protocol: Timed-mated, female Wistar Han rats (Crl: WI (Han)) were obtained from Charles River Laboratories (Raleigh, North Carolina) at 11 to 12 weeks of age at gestation day 2 (GD 2). Tap water and National Institutes of Health (NIH) 07 diet (Ziegler Brothers, Inc, Gardners, Pennsylvania) were available ad libitum. The care of animals on this study was according to NIH procedures as described in the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals (available online at: https://olaw.nih.gov). The study protocols were approved by the institutional animal care and use committee.

extract_protocol: The liver was weighed and a section of the liver (*500 mg) was taken from the left lobe, placed in a cryotube, flash frozen and stored at -80° C for toxicogenomic analysis. RNA was extracted from frozen liver samples (approximately 3-4 mm cubes) from the PND 4 left lateral hepatic lobe, using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, California) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, California). Samples were aliquoted and stored at -80°C until they were analyzed for gene expression studies.

treatment_protocol: Pentabromodiphenyl ether-mixture (DE-71) dose formulations were prepared at 0 (vehicle control), 0.02, 3, and 10 mg/mL in corn oil to provide oral gavage doses of 0, 0.1, 15, and 50 mg/kg/day when dams were dosed with a dosing volume of 5 mL/kg/day from GD 6 through PND 4, 7 days per week. Controls received corn oil vehicle.

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: treatment

value: 50 mg/kg DE-71

tag: tissue

value: liver


title: TRN88

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H1_S373

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0196_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

value: AOC


title: DE71_0.1_rep5

description: X20003_1160_DE71.20.4134_Rep_5_.Rat230_2..CEL


title: DE71_15_rep5

description: X20000_1160_DE71.17.4024_Rep_5_.Rat230_2..CEL

value: 15 mg/kg DE-71


title: OTTA2014_0191_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: DE71_Veh_rep5

description: X20002_1160_DE71.19.4169_Rep_5_.Rat230_2..CEL

tag: strain

tag: Sex

tag: treatment

value: vehicle control

tag: tissue


title: DE71_15_rep4

description: X19997_1160_DE71.14.3095_Rep_4_.Rat230_2..CEL


title: DE71_15_rep3

description: X19996_1160_DE71.13.3075_Rep_3_.Rat230_2..CEL


title: OTTA2014_0195_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: any

value: presumed adnexal


title: DE71_0.1_rep4

description: X19999_1160_DE71.16.4082_Rep_4_.Rat230_2..CEL


title: DE71_Veh_rep4

description: X19998_1160_DE71.15.4049_Rep_4_.Rat230_2..CEL


title: DE71_0.1_rep3

description: X19995_1160_DE71.12.3044_Rep_3_.Rat230_2..CEL


title: TRN87

description:
nuclear RNA
TPM.TRN.tsv
no processed data

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: OTTA2014_0194_Clinical

description: single-sample normalized data

value: HGSOC

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: peritoneal


title: A2_Control cells replica 2

tag: cell line

tag: tissue

value: Triple negative breast tumor

tag: drug incubation time

tag: drug concentration


title: TRN86

value: TRN no Neun selection


title: OTTA2014_0190_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

value: unknown

value: alive

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: OTTA2014_0189_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: omentum

value: AOC


title: A1_Control cells replica 1


title: TRN85

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_H10_S382

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: B_Salinomycin-treated cells

description: B

tag: cell line

tag: tissue

tag: drug incubation time

tag: drug concentration

value: 0.5 microM


title: DE71_Veh_rep3

description: X19993_1160_DE71.10.3009_Rep_3_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: treatment

value: vehicle control

value: liver


title: OTTA2014_0188_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA1 mutation

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: upper genital track

tag: experiment site


title: A3_Control cells replica 3

tag: cell line

tag: tissue

value: Triple negative breast tumor


title: A_Control cells

description: A

tag: drug incubation time

tag: drug concentration


title: DE71_Veh_rep2

description: X19992_1160_DE71.9.3018_Rep_2_.Rat230_2..CEL

tag: strain

tag: Sex


title: DE71_15_rep2

description: X19991_1160_DE71.8.2132_Rep_2_.Rat230_2..CEL

tag: treatment

value: 15 mg/kg DE-71


title: DE71_0.1_rep2

description: X19994_1160_DE71.11.3035_Rep_2_.Rat230_2..CEL


title: TRN84

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN83


title: OTTA2014_0187_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

value: adnexal

tag: site id


title: S15P4_2

city: Beijing

first: Kai

last: Yu

address: Yiheyuan Rd. 5th

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The first 8bp of read2 were used to split the pooled data into single cells according to the barcode sequences. The following 8bp were unique molecular identifier (UMI). The split reads1 were trimmed off ploy(A) tail sequence and template switch oligo (TSO) sequence. Then we did quality control by removing out reads with adaptor contaminants (length < 37bp) and low-quality bases (N > 10%).
Prepared clean data were aligned to hg38 human reference genome with Hisat2 (version 2.0.5). Uniquely mapped reads on each gene were calculated with htseq-count, and PCR redundant reads were eliminated with UMI sequences in each paired-reads, generated a UMI count matrix of each gene in each cell.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include UMI count values for each Sample.

molecule: polyA RNA

source_name: Brain

extract_protocol:
Briefly, we used a mouth pipette to pick single cells into cell lysis buffer. The cell lysis buffer contained barcode-containing reverse transcriptase primers (5′-TCAGACGTGTGCTCTTCCGATCTXXXXXXXXNNNNNNNNT25-3′; X represents the nucleotides of predesigned cell-specific barcodes and N is the unique molecular identifier (UMI).
Single-cell RNA-seq libraries were constructed following STRT-seq protocol with minor modifications. After reverse transcription and cDNA amplification, the PCR products with different cell-specific barcodes were pooled into one tube. The pooled cDNA was purified and tagged with biotin at the 3′ ends using biotin index primers (5′-/biotin/CAAGCAGAAGACGGCATACGAGAT/index/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3′). After fragmentation, the biotin-tagged 3′ ends were enriched by Dynabeads MyOne streptavidin C1 (Invitrogen, 65002). We used KAPA Hyper Prep Kits (KK8505) to perform library construction. The library amplification primers were an Illumina QP2 primer (5′-CAAGCAGAAGACGGCATACGA-3′) and a short universal primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC-3′).

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: OTTA2014_0186_Clinical

description: single-sample normalized data

value: high

value: all wildtypes

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC


title: TRN82

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G7_S367

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: S15P5_2


title: S15P2_2


title: S15P1_2


title: DE71_Veh_rep1

description: X19989_1160_DE71.6.2052_Rep_1_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: treatment

value: vehicle control

value: liver


title: TRN80

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G5_S365

value: No

value: Violet+


title: OTTA2014_0184_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

value: peritoneal

tag: site id


title: OTTA2014_0185_Clinical

description: single-sample normalized data

value: low

value: unknown

value: hispanic

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site


title: DE71_50_rep4

description: X19988_1160_DE71.5.2032_Rep_4_.Rat230_2..CEL

tag: strain

tag: Sex

tag: treatment

value: 50 mg/kg DE-71

tag: tissue


title: OTTA2014_0183_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

value: any

value: omentum

value: AOC


title: S14P5_2

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: S14P3_2


title: TRN78

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G3_S363

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type

value: TRN no Neun selection


title: OTTA2014_0182_Clinical

description: single-sample normalized data

value: HGSOC

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

tag: site id


title: TRN79

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G4_S364

value: Violet+


title: OTTA2014_0181_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: hispanic


title: DE71_50_rep3

description: X19987_1160_DE71.4.2019_Rep_3_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

tag: treatment

value: 50 mg/kg DE-71

tag: tissue

value: liver


title: S14P1_2

tag: patient id

tag: point

tag: pool

tag: gender


title: DE71_50_rep1

description: X19985_1160_DE71.2.1306_Rep_1_.Rat230_2..CEL


title: TRN77

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G2_S362

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0180_Clinical

description: single-sample normalized data

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: DE71_50_rep2

description: X19986_1160_DE71.3.1336_Rep_2_.Rat230_2..CEL

tag: strain

tag: Sex

tag: treatment

tag: tissue


title: DE71_0.1_rep1

description: X19984_1160_DE71.1.1204_Rep_1_2.Rat230_2..CEL


title: TRN81

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G6_S366

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: PBDE47_50_rep5

description: X20023_1160_BDE47.40.4145_Rep_5_.Rat230_2..CEL

treatment_protocol: Pentabromodiphenyl ether-47 dose formulations were prepared at 0 (vehicle control), 0.02, 3, and 10 mg/mL in corn oil to provide oral gavage doses of 0, 0.1, 15, and 50 mg/kg/day when dams were dosed with a dosing volume of 5 mL/kg/day from GD 6 through PND 4, 7 days per week. Controls received corn oil vehicle.

tag: group

value: 50 mg/kg PBDE-47


title: S13P6_2

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: S13P5_4


title: TRN75

description:
nuclear RNA
TPM.TRN.tsv
no processed data

value: sNuc-seq

value: No


title: TRN76

value: TRN no Neun selection


title: PBDE47_15_rep5

description: X20022_1160_BDE47.39.4139_Rep_5_.Rat230_2..CEL

value: female

value: 15 mg/kg PBDE-47


title: S13P5_3


title: TRN74

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G11_S371


title: OTTA2014_0179_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

value: AOC


title: S13P5_2

tag: tissue

tag: patient id


title: OTTA2014_0177_Clinical

description: single-sample normalized data

value: pathogenic BRCA1 mutation

value: hispanic

tag: anatomical site

tag: experiment site

tag: site id


title: PBDE47_50_rep4

description: X20019_1160_BDE47.36.3145_Rep_4_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

tag: group

tag: treatment

value: liver


title: OTTA2014_0176_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: white

value: alive

value: presumed adnexal


title: TRN73

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_G10_S370

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: S13P4_4

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: PBDE47_0.1_rep5

description: X20020_1160_BDE47.37.4024_Rep_5_.Rat230_2..CEL

tag: strain

tag: Sex

value: female

tag: group

value: 0.1 mg/kg PBDE-47


title: TRN72

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F9_S357

value: TRN no Neun selection


title: OTTA2014_0175_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

value: unknown

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: PBDE47_15_rep4

description: X20018_1160_BDE47.35.3142_Rep_4_.Rat230_2..CEL

value: Wistar Han rats (Crl:WI (Han))

tag: treatment

value: 15 mg/kg PBDE-47

tag: tissue

value: liver


title: S13P4_3

tag: patient id

tag: point

tag: pool

tag: gender


title: TRN71

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F8_S356

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN70

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F7_S355

value: No


title: OTTA2014_0178_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: presumed adnexal


title: OTTA2014_0174_Clinical

description: single-sample normalized data

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: S13P2_2

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: OTTA2014_0173_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: omentum


title: PBDE47_Veh_control_rep5

description: X20021_1160_BDE47.38.4130_Rep_5_.Rat230_2..CEL

tag: strain

tag: Sex

value: female

tag: group

tag: treatment

value: vehicle control


title: TRN69

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F6_S354

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: PBDE47_15_rep3

description: X20016_1160_BDE47.33.3026_Rep_3_.Rat230_2..CEL

value: Wistar Han rats (Crl:WI (Han))

tag: tissue


title: PBDE47_0.1_rep4

description: X20017_1160_BDE47.34.3130_Rep_4_.Rat230_2..CEL

value: 0.1 mg/kg PBDE-47


title: TRN68

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F5_S353


title: PBDE47_Veh_control_rep4

description: X20015_1160_BDE47.32.3018_Rep_4_.Rat230_2..CEL

value: liver


title: S12P5_2

tag: patient id

tag: point


title: OTTA2014_0172_Clinical

description: single-sample normalized data

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0171_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

value: any

value: peritoneal


title: S12P2_3

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: TRN66

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F3_S351

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: TRN67

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F4_S352


title: PBDE47_15_rep2

description: X20012_1160_BDE47.29.2065_Rep_2_.Rat230_2..CEL

tag: strain

tag: Sex

value: female

tag: group

tag: treatment

value: 15 mg/kg PBDE-47


title: S13P4_2


title: S12P2_2


title: TRN65

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F2_S350

value: Violet+

value: TRN no Neun selection


title: OTTA2014_0169_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

tag: site id


title: OTTA2014_0168_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: hispanic

value: omentum


title: S12P1_3

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: TRN64

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F1_S349

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: PBDE47_50_rep2

description: X20013_1160_BDE47.30.2069_Rep_2_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

tag: group

tag: treatment

value: 50 mg/kg PBDE-47

value: liver


title: PBDE47_0.1_rep3

description: X20011_1160_BDE47.28.2061_Rep_3_.Rat230_2..CEL

value: 0.1 mg/kg PBDE-47


title: PBDE47_Veh_control_rep3

description: X20010_1160_BDE47.27.2059_Rep_3_.Rat230_2..CEL

value: vehicle control


title: TRN63

description:
nuclear RNA
TPM.TRN.tsv
no processed data


title: S12P3_2

value: Brain

value: male


title: S11P6_7


title: PBDE47_Veh_control_rep2

description: X20009_1160_BDE47.26.2055_Rep_2_.Rat230_2..CEL


title: S11P6_6


title: OTTA2014_0166_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: TRN62

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F11_S359

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: OTTA2014_0167_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: hispanic

value: alive

value: peritoneal


title: TRN61

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_F10_S358


title: OTTA2014_0170_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: race/ethnicity


title: PBDE47_50_rep1

description: X20008_1160_BDE47.25.1179_Rep_1_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: group

tag: treatment

value: 50 mg/kg PBDE-47

tag: tissue

value: liver


title: TRN60

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_E9_S345

tag: sample type


title: OTTA2014_0165_Clinical

description: single-sample normalized data

value: low

value: unknown

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0163_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: any

value: all wildtypes

value: white

value: dead

value: adnexal


title: S11P6_4

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: TRN59

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: S12P1_2

tag: tissue


title: OTTA2014_0164_Clinical

description: single-sample normalized data

value: HGSOC

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC


title: OTTA2014_0162_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

value: alive

value: omentum

tag: site id


title: PBDE47_0.1_rep1

description: X20005_1160_BDE47.22.1097_Rep_1_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: group

tag: treatment

value: 0.1 mg/kg PBDE-47

tag: tissue

value: liver


title: PBDE47_15_rep1

description: X20007_1160_BDE47.24.1101_Rep_1_.Rat230_2..CEL

value: 15 mg/kg PBDE-47


title: S11P6_3

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: PBDE47_Veh_control_rep1

description: X20004_1160_BDE47.21.1025_Rep_1_.Rat230_2..CEL

value: vehicle control


title: TRN58

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: S11P6_2


title: OTTA2014_0161_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: low

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site


title: S11P5_7

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: OTTA2014_0160_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: Stage

value: high

tag: residual disease status

value: any

value: all wildtypes

value: AOC

tag: site id


title: TRN57

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type

value: TRN no Neun selection


title: S11P6_5


title: TRN56

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_E5_S341


title: Splenic T cells Rapamycin-treated mouse, biological rep3

city: Ulm

first: Jasmin

last: Scheurer

address: Eythstraße 24

country: Germany

institute: Dept of Pediatrics and Adolsecent medicine

description: Gene expression data from splenic T cells isolated 10 days after allogeneic bone marrow transplantation (parent into F1 bone marrow transplantation mouse model)

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

source_name: splenic T cells isolated 10 days post-transplantation

growth_protocol: 10 days after allogeneic bone marrow transplantation splenic single cell suspensions were prepared and stained with anti-CD3 specific antibodies followed by FACS sorting of CD3+ T cells using a FACSAriaTM II flow cytometer

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Zymo Research)

treatment_protocol: Lethally irradiated B6D2F1 recipient mice were reconstituted with T cell depleted bone marrow  from B6 mice  in the presence or absence of B6-derived spleen cells. 1.5 mg/kg rapamycin or PBS i.p. injections were administered every second day until day 10 post-trasplantion.

tag: mouse strain

tag: agent

value: Rapamycin


title: OTTA2014_0159_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site


title: PBDE47_0.1_rep2

description: X20006_1160_BDE47.23.1099_Rep_2_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: group

tag: treatment

value: 0.1 mg/kg PBDE-47

tag: tissue

value: liver


title: S11P5_6

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: Splenic T cells Rapamycin-treated mouse, biological rep2

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

tag: mouse strain

tag: agent


title: TRN55

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_E4_S340

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: S11P5_5


title: OTTA2014_0158_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: site id


title: TRN54

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: TRN no Neun selection


title: TRN53

tag: plate type


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_yfp_rep1

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC_011916.1) using Bowtie 1 and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, the same procedure as above was applied, except that short reads were map to the reference genome of the E. coli MG1655 (NCBI Reference Sequence: NC_000913.3). Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1 (C. crescentus)
Genome_build: NC_000913.3 (E. coli)
Supplementary_files_format_and_content: *_coverage_output.txt: The processed data files for ChIP-seq are tab-delimited files containing three fields: the genome build, the nucleotide position, and the coverage at that position.

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus NA1000

growth_protocol: For E. coli ChIP-seq, cells harboring pUT18C-1xFLAG-ParB were grown in LB (25 mL) at 28oC to mid-exponential phase (OD600 ~0.4) before 1 mM IPTG was added for 1-3 hours. The induction time (either 1, 2 or 3 hours) was chosen so that all ParB variants were produced to a similar protein level as judged by an α-FLAG immunoblot. Subsequently, formaldehyde was added to a final concentration of 1% to fix the cells. For C. crescentus ChIP-seq, MT148 cells harboring van::Pvan-FLAG-ParB (WT)/mutants were grown in PYE (25 mL) + 0.3% glucose + 0.5 mM vanillate to mid-exponential phase (OD600 ~0.4) before formaldehyde was added to a final concentration of 1% to fix the cells.

extract_protocol:
For ChIP-seq, DNA was isolated using Qiagen PCR purification columns.
For ChIP-seq libraries, a standard library construction procedure (using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina sequencing) was employed.

treatment_protocol: FLAG-ParB were produced in medium supplemented with 0.3 % glucose and 0.5 mM vanillate before formaldehyde to 1% (final concentration) was added to fix cells for ChIP-seq.

tag: genotype

tag: developmental stage

value: mixed population, exponential phase

tag: chip-seq antibody

value: FLAG


title: S11P5_4

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_rep2


title: OTTA2014_0155_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

value: adnexal

tag: experiment site

value: AOC


title: S11P5_2

tag: tissue


title: TRN52

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: PBDE47_50_rep3

description: X20014_1160_BDE47.31.2071_Rep_3_.Rat230_2..CEL

tag: strain

value: Wistar Han rats (Crl:WI (Han))

tag: Sex

value: female

tag: group

tag: treatment

value: 50 mg/kg PBDE-47

value: liver


title: Splenic T cells PBS-treated mouse, biological rep3

tag: mouse strain

tag: agent

value: PBS


title: Splenic T cells PBS-treated mouse, biological rep2


title: S11P4_2

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_rep1

tag: genotype

tag: developmental stage

tag: chip-seq antibody


title: TRN50

tag: sample type

value: sNuc-seq

value: No

value: Violet+


title: OTTA2014_0154_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_5K_rep2

tag: genotype

tag: developmental stage

value: mixed population, exponential phase

tag: chip-seq antibody

value: FLAG


title: Splenic T cells PBS-treated mouse, biological rep1

tag: mouse strain

tag: agent


title: S9P3_2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: S11P2_2


title: TRN49

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_E10_S346

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type

value: TRN no Neun selection


title: Splenic T cells Rapamycin-treated mouse, biological rep1

value: Rapamycin


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_5K_rep1


title: OTTA2014_0152_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

value: AOC


title: OTTA2014_0153_Clinical

description: single-sample normalized data

value: all wildtypes

value: hispanic

value: adnexal

tag: experiment site

tag: site id


title: TRN48

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: OTTA2014_0156_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis


title: S11P5_3

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: OTTA2014_0157_Clinical

description: single-sample normalized data

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay


title: OTTA2014_0151_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: dead

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_4K_rep2

tag: genotype

tag: developmental stage

value: mixed population, exponential phase

tag: chip-seq antibody

value: FLAG


title: S9P2_2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: S9P1_3


title: TRN47

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D8_S332

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN51


title: OTTA2014_0150_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

value: AOC


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_3K_rep2

tag: genotype

tag: developmental stage

tag: chip-seq antibody


title: TRN46

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D7_S331

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: OTTA2014_0149_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: hispanic

tag: anatomical site

tag: experiment site

tag: site id


title: S9P1_2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_3K_rep1

tag: genotype


title: S8P4_2


title: OTTA2014_0148_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay


title: TRN44

description:
nuclear RNA
TPM.TRN.tsv
no processed data

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: 800TI_0_G_runTD01376

city: NEW YORK

first: Miriam

last: Merad

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

data_processing:
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

source_name: lung

extract_protocol: 10,000 cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. Libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed using CyberGreen qPCR library quantification assay. Sequencing was performed on Illumina sequencers to a depth of at least 80 million reads per library.

tag: tissue

value: lung

tag: tissue type

value: Tumor

tag: patient id

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: OTTA2014_0147_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: 7002T5_run9

tag: tissue

tag: tissue type

value: male


title: S8P1_2

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender


title: TRN42

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D3_S327

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: OTTA2014_0146_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay


title: 7002T5_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: TRN41

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D2_S326

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: S7P5_2

tag: point

tag: pool

tag: gender


title: OTTA2014_0145_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: anatomical site

value: presumed adnexal

tag: experiment site

tag: site id


title: LeLab_ChIP_seq_MT148_vanA_Pvan_1xFLAG_Caulobacter_crescentus_ParB_4K_rep1

tag: genotype

tag: developmental stage

value: mixed population, exponential phase

tag: chip-seq antibody

value: FLAG


title: OTTA2014_0144_Clinical

description: single-sample normalized data

tag: diagnosis

value: any

value: all wildtypes

tag: progression-free survival time

tag: study entry delay

value: AOC


title: S7P4_3

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: S7P4_2


title: 7002N5_run9

value: lung

tag: tissue type

value: Normal

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: 7002N5_run8

value: male


title: TRN45

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D6_S330

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN40

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D1_S325

value: No


title: 7002v2G-H_run9

data_processing:
Library strategy: CITE-seq
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

extract_protocol: Cell suspensions were split and barcoded using “hashing antibodies” staining beta-2-microglobulin and CD298 and conjugated to “hash-tag” oligonucleotides (HTOs). Hashed samples were pooled and stained with CITEseq antibodies that had been purchased either from the Biolegend TOTALseq catalog or conjugated using the Thunder-Link PLUS Oligo Conjugation kit (Expedeon). Stained cells were then encapsulated for single-cell reverse transcription using the 10X Chromium platform and libraries were prepared as previously described (Stoeckius, Marlon, et al. "Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics." Genome biology 19.1 (2018): 1-12.).

value: Normal, Tumor, PBMC, spiked mouse cells

value: HTO


title: TRN39

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D12_S336

value: Violet+


title: OTTA2014_0143_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: OTTA2014_0142_Clinical

description: single-sample normalized data

value: unknown

value: hispanic

value: dead

tag: progression-free survival time

tag: study entry delay

value: adnexal


title: 7002v2G-H_run8

tag: tissue

value: lung

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S8P1_3

value: Brain

tag: point

tag: pool

tag: gender


title: S7P1_2


title: TRN43

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type

value: TRN no Neun selection


title: TRN38

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D11_S335


title: OTTA2014_0141_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: anatomical site

tag: experiment site

value: AOC

tag: site id


title: TRN37

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_D10_S334

tag: sample type

value: sNuc-seq

tag: used for patch-seq


title: S6P5_4

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: OTTA2014_0140_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: any

value: alive

tag: progression-free survival time

tag: study entry delay


title: 7002v2G-A_run9

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: TRN36

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C9_S321

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: 7002v2G-A_run8

tag: tissue

tag: patient id


title: OTTA2014_0139_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: anatomical site

value: presumed adnexal

tag: experiment site

tag: site id


title: S6P5_3

tag: point

tag: pool

tag: gender


title: TRN35

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C8_S320

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: S6P5_2

tag: tissue

tag: patient id


title: 7002v2G_run9

value: lung

tag: tissue type

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: OTTA2014_0138_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: omentum


title: S5P3_2

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: S7P3_2

value: male


title: OTTA2014_0137_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: any

value: pathogenic BRCA1 mutation

value: alive

tag: experiment site

value: AOC

tag: site id


title: TRN33

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: S5P2_3


title: 7002v2G_run8

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: OTTA2014_0136_Clinical

description: single-sample normalized data

value: HGSOC

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: 7002v2F-H_run9

tag: tissue

tag: patient id

value: HTO


title: S5P2_2

value: Brain

tag: point

tag: pool

tag: gender

value: female


title: OTTA2014_0135_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: low

value: unknown

value: dead

value: presumed adnexal

tag: experiment site

tag: site id


title: TRN31

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: 7002v2F-H_run8

tag: tissue type

tag: libraryname

tag: Sex

value: male

tag: library type

tag: 10x chromium encapsulation kit


title: 7002v2F-A_run9

tag: tissue

tag: patient id

value: ADT


title: 7002v2F-A_run8


title: S2P3_2

tag: point

tag: pool

tag: gender


title: OTTA2014_0134_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal

value: AOC


title: S3P4_2

tag: tissue

tag: patient id

tag: point


title: TRN30

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C3_S315

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: OTTA2014_0133_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: white

tag: experiment site

tag: site id


title: TRN29

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C2_S314


title: S2P2_2

value: Brain

tag: pool

tag: gender


title: TRN34

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C7_S319


title: 7002v2F_run9

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: 7002v2F_run8

tag: tissue

tag: patient id


title: OTTA2014_0132_Clinical

description: single-sample normalized data

value: high

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: peritoneal


title: TRN28

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C1_S313

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: S1P8_2

tag: point

tag: pool

tag: gender

value: female


title: TRN27


title: 7002v2E-H_run9

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

value: male

tag: library type

value: HTO

tag: 10x chromium encapsulation kit


title: S1P7_2


title: OTTA2014_0131_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0130_Clinical

description: single-sample normalized data

value: HGSOC

tag: study entry delay

tag: anatomical site

value: omentum


title: S1P6_2

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender


title: 7002v2E-H_run8

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: TRN32

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C5_S317

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN25

value: sNuc-seq


title: TRN26

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_C11_S323


title: OTTA2014_0129_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: experiment site

tag: site id


title: S1P5_2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: OTTA2014_0128_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: any

value: pathogenic BRCA1 mutation

value: dead

tag: study entry delay

tag: anatomical site


title: TRN24

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B9_S309

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: S1P4_2


title: TRN23

description:
nuclear RNA
TPM.TRN.tsv
no processed data


title: 7002v2E_run9

tag: tissue type

tag: libraryname

tag: Sex

value: male

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: 7002v2E-A_run8

tag: tissue

tag: patient id

value: ADT


title: OTTA2014_0127_Clinical

description: single-sample normalized data

value: HGSOC

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: TRN22

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: S1P3_2

tag: tissue

value: Brain

tag: point

tag: pool

tag: gender


title: TRN21

value: sNuc-seq

value: TRN no Neun selection


title: 7002v2E_run8

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: OTTA2014_0126_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: omentum


title: S1P2_2

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: OTTA2014_0124_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: dead

tag: experiment site

tag: site id


title: OTTA2014_0125_Clinical

description: single-sample normalized data

value: HGSOC

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: S15P5

value: male


title: 7002v2D-H_run9

tag: tissue type

tag: libraryname

tag: Sex

tag: library type

value: HTO

tag: 10x chromium encapsulation kit


title: S1P1_2

tag: tissue

tag: patient id

tag: point

tag: pool


title: TRN20

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B5_S305

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: 7002v2E-A_run9

value: ADT


title: OTTA2014_0122_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: pathogenic BRCA1 mutation

value: hispanic

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC

tag: site id


title: 7002v2D-H_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S15P4

value: Brain

tag: point

tag: pool

tag: gender


title: TRN19

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: 7002v2D-A_run9

value: lung

value: Normal, Tumor, PBMC, spiked mouse cells


title: 7002v2D-A_run8


title: S15P3


title: TRN18

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B3_S303


title: OTTA2014_0121_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal


title: 7002v2D_run9

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

value: male

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: S15P2

tag: point

tag: pool

tag: gender


title: TRN17

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B2_S302

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: S15P1


title: TRN16


title: 7002v2D_run8


title: S14P5

value: female


title: 7002v2C-H_run9

value: HTO


title: OTTA2014_0119_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum

tag: experiment site

tag: site id


title: 7002v2C-H_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S14P4

value: Brain

tag: point

tag: pool

tag: gender


title: OTTA2014_0117_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: study entry delay

tag: anatomical site

value: AOC


title: OTTA2014_0116_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: experiment site

tag: site id


title: TRN13

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B10_S310

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: S14P3

tag: tissue

tag: patient id

tag: point

tag: pool

tag: gender


title: S14P2


title: 7002v2C_run9

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: libraryname

tag: Sex

value: male

tag: library type

tag: 10x chromium encapsulation kit


title: 7002v2C-A_run9

value: ADT


title: OTTA2014_0115_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA2 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: adnexal


title: TRN12

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A9_S297

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN9


title: OTTA2014_0114_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: high

tag: experiment site

tag: site id


title: 7002v2C-A_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S13P6

value: Brain

tag: point

tag: pool

tag: gender


title: TRN10

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A7_S295

tag: sample type

tag: used for patch-seq


title: OTTA2014_0120_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0118_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: experiment site

value: AOC

tag: site id


title: 7002v2C_run8

tag: tissue

tag: tissue type

tag: patient id

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: S13P5

tag: point

tag: pool

tag: gender


title: S13P4


title: OTTA2014_0123_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: presumed adnexal


title: 7002v2B-H_run8

tag: tissue

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

value: HTO


title: TRN15

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN14

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_B11_S311


title: OTTA2014_0111_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: unknown

value: dead

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: TRN7

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A4_S292


title: OTTA2014_0110_Clinical

description: single-sample normalized data

tag: Stage

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: S14P1

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: female


title: 7002v2B-A_run9

value: lung

tag: tissue type

tag: libraryname

tag: Sex

value: male

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: OTTA2014_0113_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: white

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: 7002v2B-H_run9

tag: tissue

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

value: HTO


title: TRN6

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A3_S291

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN8


title: 7002v2B-A_run8

tag: tissue type

tag: libraryname

tag: Sex

tag: library type

tag: 10x chromium encapsulation kit


title: S13P2

tag: point

tag: pool

tag: gender


title: S13P1


title: OTTA2014_0109_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0112_Clinical

description: single-sample normalized data

value: unknown

value: pathogenic BRCA1 mutation

value: alive

value: omentum

tag: experiment site

tag: site id


title: S12P4

tag: tissue

value: Brain

tag: patient id

tag: point

tag: pool

tag: gender

value: male


title: S12P5


title: TRN5

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A2_S290

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: 7002v2B_run9

value: lung

tag: tissue type

tag: libraryname

tag: Sex

tag: library type

value: GEX

tag: 10x chromium encapsulation kit


title: TRN3


title: S12P3


title: OTTA2014_0108_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

value: AOC


title: OTTA2014_0107_Clinical

description: single-sample normalized data

value: all wildtypes

value: hispanic

value: adnexal

tag: experiment site

tag: site id


title: 7002v2A-H_run8

tag: tissue

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

tag: Sex

tag: library type

value: HTO

tag: 10x chromium encapsulation kit


title: 7002v2A-H_run9


title: S12P2

tag: point

tag: pool

tag: gender


title: TRN2

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: OTTA2014_0106_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: low

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0105_Clinical

description: single-sample normalized data

value: high

value: any

value: dead

value: omentum

tag: experiment site

tag: site id


title: TRN1

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A10_S298

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0104_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA2 mutation

value: white

value: AOC


title: 7002v2A-A_run9

tag: tissue

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

tag: Sex

value: male

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: S12P1

value: Brain

tag: point

tag: pool

tag: gender


title: 7002v2A-A_run8


title: LATS1/2 KO Intestinal stromal cell-5

city: Daejeon

first: Hyunsoo

last: Cho

address: Yuseonggu

country: South Korea

institute: IBS/KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: PDGFRb+ intestinal stromal cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: strain

tag: developmental stage

value: Adult

tag: genotype

tag: cell type

value: PDGFRb+ intestinal stromal cells

tag: sorting method

value: FACS sorted


title: TRN4

description:
nuclear RNA
TPM.TRN.tsv
X012116_1TRNp2_A1_S289

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection