title: OTTA2014_0355_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time


title: TRN247

status: Public on Jul 22 2020

type: SRA

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

country: USA

institute: Broad Institute

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E4_S244

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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 adjacent


title: TRN249

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


title: TRN251

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E8_S248


title: OTTA2014_0351_Clinical

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

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

value: all wildtypes

tag: race/ethnicity

value: hispanic

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0358_Clinical

description: single-sample normalized data

value: high

value: any

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum


title: OTTA2014_0360_Clinical

description: single-sample normalized data

value: white


title: TRN246

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0353_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis


title: TRN254


title: OTTA2014_0352_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: adnexal


title: set4∆ Hypoxia rep 3

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Tophat2 v 2.1.0 was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60,  and strandedness set to "fr-firststrand".
HTSeq Count v. 0.6.1  was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
EdgeR v. 3.12.1 (using Bioconductor v 3.2) were used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes (false discovery raye of 1%)
Genome_build: Saccharomyces_cerevisiae.R64-1-1
Supplementary_files_format_and_content: BriggsGeneCounts_set4WT_forGEO.txt - raw abundance measurements
briggs_set1set4_rnaseq_CPM_WTset4_GEO.txt - CPM normalized abundance estimates

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: S. cerevisiae (BY4741 WT, BY4741 set4∆ strains) Strains were grown to saturation overnight in SC media at 30 degrees C. Cells were back diluted to an OD600: 0.1 and grown to log phase at 30 degrees C in SC media for 8 hours under hypoxic conditions or 5.5 hours under aerobic conditions.

extract_protocol:
Cells were harvested following 8 hours of growth under hypoxia or 5.5 hours of growth under aerobic conditions. At the indicated time points cells were pelleted and frozen using liquid nitrogen. Total RNA was isolated using phenol extraction protocol and treated with DNAse (Ambion).
An Illumina TruSeq Stranded kit was used to construct a cDNA library
RNA sequencing by Illumina HiSeq2500 next generation sequencer

treatment_protocol: Both BY4741 WT and BY4741 set4∆ strains were grown for 8 hours under hypoxia or 5.5 hours under aerobic conditions

tag: genotype

tag: stress

value: Hypoxia


title: OTTA2014_0354_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: set4∆ Hypoxia rep 2


title: TRN244

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E1_S241

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0347_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA1 mutation

tag: overall survival time

tag: progression-free survival time


title: WT Hypoxia rep 3

tag: genotype

value: WT

tag: stress


title: set4∆ Hypoxia rep 1


title: TRN243

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E12_S252

value: No

value: Violet+

value: TRN adjacent


title: OTTA2014_0349_Clinical

description: single-sample normalized data

value: HGSOC

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: alive


title: OTTA2014_0346_Clinical

description: single-sample normalized data

value: unknown

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC

tag: site id


title: TRN242

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: WT Hypoxia rep 2


title: OTTA2014_0356_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

value: all wildtypes

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_0350_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white

value: omentum


title: TRN241

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E10_S250


title: WT Hypoxia rep 1

tag: genotype

tag: stress

value: Hypoxia


title: TRN245

value: sNuc-seq


title: OTTA2014_0348_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0344_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: hispanic

value: adnexal


title: WT Aerobic rep 3

value: WT

value: Aerobic


title: TRN240

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D9_S237

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN adjacent


title: OTTA2014_0345_Clinical

description: single-sample normalized data

value: HGSOC

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: unknown

tag: overall survival time

tag: progression-free survival time


title: TRN239


title: OTTA2014_0343_Clinical

description: single-sample normalized data

value: high

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: AOC


title: OTTA2014_0342_Clinical

description: single-sample normalized data

tag: study entry delay

tag: anatomical site

value: peritoneal

tag: experiment site

tag: site id


title: WT Aerobic rep 2

tag: genotype

tag: stress


title: TRN238

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D7_S235

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: WT Aerobic rep 1


title: TRN235


title: OTTA2014_0339_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


title: OTTA2014_0341_Clinical

description: single-sample normalized data

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


title: OTTA2014_0340_Clinical

description: single-sample normalized data

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: TRN236

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN234


title: TRN233

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D2_S230


title: OTTA2014_0337_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: low

value: alive


title: OTTA2014_0338_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: hispanic

value: dead


title: TRN232

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D1_S229


title: OTTA2014_0335_Clinical

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: presumed adnexal


title: TRN230

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D11_S239

value: No


title: OTTA2014_0336_Clinical

description: single-sample normalized data

value: pathogenic BRCA1 mutation

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0334_Clinical

description: single-sample normalized data


title: TRN231

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_D12_S240

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN adjacent


title: TRN237


title: OTTA2014_0332_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: white


title: TRN228

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C9_S225


title: OTTA2014_0333_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: adnexal

value: AOC


title: OTTA2014_0331_Clinical

description: single-sample normalized data

value: any

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_0330_Clinical

description: single-sample normalized data

value: all wildtypes

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: TRN225

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN227


title: TRN226

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C7_S223


title: TRN229


title: OTTA2014_0328_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: peritoneal


title: OTTA2014_0329_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: dead


title: TRN224


title: OTTA2014_0326_Clinical

description: single-sample normalized data

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: TRN222

value: No


title: OTTA2014_0327_Clinical

description: single-sample normalized data

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0324_Clinical

description: single-sample normalized data

value: presumed adnexal


title: Control 32

city: Edirne

first: Mehmet

middle: Ali

last: Balci

address: Balkan campus

department: Rheumatology

country: Turkey

institute: Trakya University

description: Gene expression after extracting total RNA from peripheral blood

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by  Absolutely RNA Nanoprep Kit Agilent).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. 1.5 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent One-Color Microarray-Based Gene Expression Kit (Low Input Quick Amp Labeling)   Microarrays (G4851B) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

extract_protocol: Peripheral blood from patient and healthy volunteers was obtained, then RNA was prepared using the InnuPrep RNA miniprep kit (Analytik Jena GMBH, Germany) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: whole blood

tag: gender

value: female

tag: age


title: Control 31


title: TRN221

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C2_S218

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN adjacent


title: Control 27


title: Control 29


title: Control 23


title: Control 30


title: Control 25


title: Control 21


title: Control 22


title: TRN220

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C1_S217


title: TRN223

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C4_S220


title: Control 18


title: Control 17


title: Control 19


title: TRN219

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


title: Control 20


title: OTTA2014_0323_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: unknown

tag: brca1 and brca2 germline mutation status


title: OTTA2014_0325_Clinical

description: single-sample normalized data

value: high

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: adnexal


title: OTTA2014_0322_Clinical

description: single-sample normalized data

tag: experiment site

value: AOC

tag: site id


title: Control 16

tag: tissue

tag: gender

tag: age


title: OTTA2014_0321_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis


title: OTTA2014_0320_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: alive


title: TRN216

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0319_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

tag: study entry delay

value: omentum


title: OTTA2014_0318_Clinical

description: single-sample normalized data

tag: diagnosis

value: dead

tag: anatomical site

tag: experiment site

tag: site id


title: Control 28

tag: tissue

tag: gender

tag: age


title: TRN215

tag: sample type

tag: used for patch-seq


title: TRN214

tag: facs sorting signal

tag: plate type


title: Control 15


title: Control 26


title: OTTA2014_0317_Clinical

description: single-sample normalized data

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: TRN218


title: OTTA2014_0316_Clinical

description: single-sample normalized data

tag: diagnosis

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: lower genital track


title: OTTA2014_0315_Clinical

description: single-sample normalized data

value: any

value: hispanic

tag: experiment site

tag: site id


title: TRN212

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: TRN217

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_C10_S226


title: Control 14

tag: tissue

value: whole blood

tag: gender

value: female

tag: age


title: TRN211

value: Violet+

value: TRN adjacent


title: Control 12


title: OTTA2014_0314_Clinical

description: single-sample normalized data

value: HGSOC

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


title: TRN210


title: Control 11


title: Control 13


title: Control 24


title: OTTA2014_0313_Clinical

description: single-sample normalized data

tag: diagnosis

value: low

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


title: Control 9

tag: tissue


title: OTTA2014_0312_Clinical

description: single-sample normalized data

value: high

value: white

tag: experiment site

value: AOC

tag: site id


title: TRN209

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_B2_S206

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: Control 8

tag: gender

tag: age


title: TRN207


title: TRN206


title: OTTA2014_0311_Clinical

description: single-sample normalized data

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: dead

value: omentum


title: TRN208

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_B1_S205


title: OTTA2014_0310_Clinical

description: single-sample normalized data

tag: diagnosis

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site


title: TRN205

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_B10_S214

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0309_Clinical

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

value: any

tag: experiment site

tag: site id


title: OTTA2014_0308_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: hispanic


title: Control 6

tag: tissue

tag: gender

tag: age


title: Control 5


title: Control 7


title: Control 2


title: Control 3


title: MB-231-maspin #3

city: Yonago

first: Tomohiko

last: Sakabe

state: Tottori

address: Nishi-cho 86

country: Japan

institute: Tottori University

hyb_protocol: Fragmented RNA was hybridized onto the 3D-Gene human mRNA oligo chip 25k Ver 2.1 for 16 hour at 37˚C.

scan_protocol: Oligo chip was scanned by a 3D-Gene Scanner 3000.

data_processing: To generate the global normalization data, the raw signal intensity were subtracted with the background mean and normalized to the value in which the median intensity was 25.

source_name: MDA-MB-231_stably expressing maspin and ZsGreen (Maspin-P2A-ZsGreen)

label_protocol: Amino Allyl aRNA was synthesis using Ambion Amino Allyl MessageAmp II aRNA Amplification Kit. CyDye labeling was performed using Amersham Cy5 Mono-Reactive Dye.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit.

tag: cell line

tag: cell type

value: breast cancer cells

tag: genotype/variation


title: Control 4

value: whole blood


title: MB-231-maspin #2

value: stably expressing maspin and ZsGreen (Maspin-P2A-ZsGreen)


title: TRN204

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_A9_S201

tag: sample type

tag: used for patch-seq

value: No

value: Violet+


title: OTTA2014_0307_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

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


title: Patient 38

value: female


title: Control 1


title: TRN203

tag: facs sorting signal

tag: plate type

value: TRN adjacent


title: OTTA2014_0306_Clinical

description: single-sample normalized data

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

value: alive

tag: experiment site

tag: site id


title: MB-231-control #3

source_name: MDA-MB-231_stably expressing ZsGreen

tag: cell line

tag: cell type

tag: genotype/variation

value: stably expressing ZsGreen


title: Patient 37

tag: tissue

tag: gender

tag: age


title: TRN202

tag: sample type

value: sNuc-seq

tag: used for patch-seq


title: TRN201

tag: facs sorting signal

tag: plate type


title: Total CD45+ Leukocytes from Ldlr-/- Aorta

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.2)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.2)
alignment, Cell Ranger Single Cell Software Suite (v2.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

extract_protocol:
The thoracic aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live CD45+ cells were sorted out using BD FACSAriaIII.
The cells are resuspended in final concentration of 1000cells/µL in 1X PBS containing 0.04% BSA to minimize cell loss and aggregation. ~17,400 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3’ Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

treatment_protocol: Sample 1: no treatment. Sample 2: at 8 weeks of age mice were treated by tamoxifen gavage (200 uL, 20 mg/mL) to turn on fluorescent tomato-reporter allele. Mice were then started on high fat diet (HFD) at 11 weeks of age for 21 days prior to sacrifice.

tag: strain

tag: genotype

value: CX3CR1creER/+ Rosa26-lsl-Tomato Ldlr KO

value: Aorta

value: Total CD45+ Leukocytes


title: TRN198


title: OTTA2014_0305_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: 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: AOC


title: OTTA2014_0303_Clinical

description: single-sample normalized data

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: white

value: presumed adnexal

tag: experiment site

tag: site id


title: OTTA2014_0304_Clinical

description: single-sample normalized data

value: HGSOC


title: OTTA2014_0301_Clinical

description: single-sample normalized data

value: adnexal


title: C_4685_S30

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

address: 320 West 15th Street

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

data_processing:
FastQC 0.11.5 quality control
STAR 2.5 "--outSAMmapqUnique 60"
NGSUtils/bamutils 0.5.9
subread/featureCounts 1.5.1 "-s 2 -p –Q 10"
MultiQC. Genes with read count per million (CPM) > 0.5 in more than 3 of the samples were kept.
edgeR 3.12.1 differential expression
Genome_build: mm10

source_name: WT cerebellum

growth_protocol: Tg-FDD and wild type C57/BL6J (WT) (JAX stock #000664) male and female mice were used for our experiments, including cellular, biochemical and immunohistochemistry (IHC) analyses. The Tg-FDD mouse model expresses a FDD-associated human mutant BRI2 transgene that leads to the vascular accumulation of ADan amyloid [37]. Mice were housed at the Indiana University School of Medicine (IUSM) animal care facility and were maintained according to USDA standards (12-hr. light/dark cycle, food and water ad libitum), in accordance with the Guide for the Care and Use of Laboratory Animals (National Institutes of Health, Bethesda, MD).

extract_protocol:
Brain tissue was homogenized in Trizol, and total RNA was isolated by chloroform extraction (Toni, L.S., et al., Optimization of phenol-chloroform RNA extraction. MethodsX, 2018. 5: p. 599-608.)
The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. Then five hundred nanogram of RNA per sample were used prepare dual-indexed strand-specific cDNA library using TruSeq Stranded mRNA Library Prep Kit (Illumina). The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Two hundred pico molar pooled libraries were utilized per flowcell for clustering amplification on cBot using HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 97% of the sequencing reads reached Q30 (99.9% base call accuracy).

tag: tissue

value: brain

tag: genotype

value: WT

tag: age

value: 9 months


title: OTTA2014_0300_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: any


title: Total CD45+ Leukocytes from C57BL/6 Aorta

tag: strain

value: Wild type


title: MB-231-maspin #1

tag: cell line

tag: cell type

value: breast cancer cells

tag: genotype/variation

value: stably expressing maspin and ZsGreen (Maspin-P2A-ZsGreen)


title: MB-231-control #2

value: stably expressing ZsGreen


title: OTTA2014_0299_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: pathogenic BRCA1 mutation

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time


title: C_4684_S29

tag: tissue


title: Patient 35

value: whole blood

tag: gender

value: female


title: Patient 30

tag: age


title: Patient 34


title: TRN199

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_A4_S196

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN adjacent


title: TRN197


title: TRN196

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_A1_S193


title: Patient 33


title: TRN213


title: TRN195


title: C_1673_S28

source_name: Tg-FDD cerebellum

tag: genotype

value: Tg-Familial Danish Dementia (FDD)


title: C_1672_S27

value: brain


title: OTTA2014_0298_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: hispanic

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0297_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: unknown

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

value: adnexal


title: TRN194

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_A11_S203

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN200

description:
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_A5_S197


title: OTTA2014_0296_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: any

value: presumed adnexal


title: TRN193


title: OTTA2014_0295_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

tag: study entry delay

tag: anatomical site

tag: experiment site


title: TRN192

value: TRN no Neun selection


title: OTTA2014_0294_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: race/ethnicity

tag: site id


title: WT CD8+ T cell1 spleen

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: 2506 Speedway A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
Isolated splenocytes from mechanically dissocaited spleen and enriched CD8 T cells with isolation kit
WT_spl_1

data_processing:
FastQ files were assessed for quality issues using fastQC.
Reads were pseudoaligned to the mouse transcriptome (GRCm38) and transcript abundances were estimated using Kallisto (version 0.46.1).
The transcript-level counts were aggregated to gene-level counts using tximport in R, normalized using DESeq2 size factors and transformed with variance stabilizing transformation.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files including raw counts for each gene or variance-stabilized counts for each gene.

source_name: spleen

extract_protocol:
The thymuses and spleens were removed from overtly sick LN3 mice or tumor-free wild-type mice. Thymic and splenic T-ALL cells, and wild-type thymocytes were isolated by mechanically dissociating organs on ice. CD8+ T cells from the spleens of tumor-free mice were enriched using the MojoSort™ Mouse CD8 T Cell Isolation Kit (BioLegend), according to manufacturer’s instructions. Total RNA was purified using an RNeasy Mini Kit (Qiagen).
Poly(A) RNA was enriched from total RNA using the Poly(A)Purist Mag kit (Life Technologies). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (NEB) for Illumina.

tag: strain

tag: genotype

value: wildtype

tag: tissue

value: spleen


title: WT CD8+ T cell2 spleen

description:
Isolated splenocytes from mechanically dissocaited spleen and enriched CD8 T cells with isolation kit
WT_spl_2


title: WT CD8+ T cell3 spleen

description:
Isolated splenocytes from mechanically dissocaited spleen and enriched CD8 T cells with isolation kit
WT_spl_3


title: TRN189

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H6_S282

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+


title: Patient 26

description: Gene expression after extracting total RNA from peripheral blood

value: whole blood

tag: gender

value: female

tag: age


title: TRN190

tag: plate type


title: OTTA2014_0293_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

value: high

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: white

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

value: peritoneal


title: Patient 31


title: Patient 29


title: Patient 25


title: C_1671_S26

value: brain

tag: genotype

value: Tg-Familial Danish Dementia (FDD)

value: 9 months


title: Patient 28

tag: tissue


title: Control 10


title: Patient 24


title: Patient 27


title: Patient 23


title: TRN191

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H8_S284

tag: sample type


title: MB-231-control #1

tag: cell line

tag: cell type

value: breast cancer cells

tag: genotype/variation

value: stably expressing ZsGreen


title: OTTA2014_0302_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

value: any

tag: race/ethnicity

value: hispanic

value: dead

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

value: AOC

tag: site id


title: Patient 32

value: whole blood

tag: gender

tag: age


title: C_4686_S31

value: WT


title: WT thymocyte2 thymus

description:
Isolated thymocytes from mechanically dissociated tumor-free thymus
WT_thy_2

source_name: thymus

tag: strain

value: wildtype

value: thymus


title: WT thymocyte3 thymus

description:
Isolated thymocytes from mechanically dissociated tumor-free thymus
WT_thy_3


title: WT thymocyte1 thymus

description:
Isolated thymocytes from mechanically dissociated tumor-free thymus
WT_thy_1


title: OTTA2014_0292_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

value: high

tag: residual disease status

value: unknown

tag: brca1 and brca2 germline mutation status

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: TRN188

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H5_S281

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_0290_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: race/ethnicity

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: OTTA2014_0289_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: hispanic


title: LN3 T-ALL2 spleen

description:
Isolated LN3 T-ALL from mechanically dissociated spleen of tumor-bearing mice
LN3_spl_2

tag: strain

tag: genotype

value: LN3 tg

tag: tissue

value: spleen


title: LN3 T-ALL3 spleen

description:
Isolated LN3 T-ALL from mechanically dissociated spleen of tumor-bearing mice
LN3_spl_3


title: OTTA2014_0288_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

value: adnexal

value: AOC


title: TRN185

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H2_S278

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: TRN187

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


title: TRN186

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H3_S279


title: OTTA2014_0291_Clinical

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: race/ethnicity

value: alive

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: LN3 T-ALL1 spleen

description:
Isolated LN3 T-ALL from mechanically dissociated spleen of tumor-bearing mice
LN3_spl_1

tag: strain

tag: genotype

tag: tissue


title: TRN183


title: LN3 T-ALL3 thymus

description:
Isolated LN3 T-ALL from mechanically dissociated thymus of tumor-bearing mice
LN3_thy_3

value: thymus


title: TRN184

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_H1_S277


title: OTTA2014_0287_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: year of diagnosis

tag: vital status

value: presumed adnexal


title: OTTA2014_0286_Clinical

description: single-sample normalized data

tag: age at diagnosis

value: low

value: white

tag: overall survival time

tag: progression-free survival time


title: LN3 T-ALL2 thymus

description:
Isolated LN3 T-ALL from mechanically dissociated thymus of tumor-bearing mice
LN3_thy_2


title: TRN182

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: Patient 22

value: whole blood

tag: gender

value: female

tag: age


title: TRN181

value: TRN no Neun selection


title: OTTA2014_0285_Clinical

description: single-sample normalized data

tag: Stage

value: high

value: unknown

tag: race/ethnicity

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: Total CD45+ cells from regression group treated with isotype IgG control antibody

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

description: Control

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
single cell 3' gene counting, Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene expression by cell, file with barcodes and file with expressed genes.  Files are ready to be import into Seurat package or similar.

source_name: aorta

extract_protocol: The whole aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into as small pieces as possible and incubated at 37°C for 15 minutes with enzyme mixture containing DNase I (40 U/ml), liberase (4 U/ml), hyaluronidase (60 U/ml). Live CD45+ cells were sorted out using BD FACSAriaIII. The cells are resuspended in final concentration of ~500 cells/µL in 1X HBSS containing 0.04% BSA to minimize cell loss and aggregation. ~12,000 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3' Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

tag: tissue

value: aorta

tag: cell type

value: CD45+ cells

tag: treatment

value: isotype IgG control antibody

tag: strain

tag: genotype

value: injected with PCSK9 AAV

value: 28 weeks

tag: phenotype

value: amelioration of atherosclerosis


title: OTTA2014_0284_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

value: AOC


title: TRN180

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: OTTA2014_0283_Clinical

description: single-sample normalized data

tag: Stage

value: low

tag: race/ethnicity

value: hispanic

value: alive

tag: study entry delay

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: TRN179

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G8_S272

value: Violet+

value: TRN no Neun selection


title: Total CD45+ cells from regression group treated with anti-CD25 antibody

description: Treated

tag: tissue

value: aorta

tag: cell type

tag: treatment

value: anti-CD25 antibody

tag: strain

tag: genotype

tag: age

tag: phenotype

value: unchanged atherosclerosis


title: Patient 18

value: whole blood

tag: gender

value: female


title: Patient 20


title: Patient 19


title: Patient 21


title: OTTA2014_0282_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

tag: residual disease status

value: any

tag: brca1 and brca2 germline mutation status

value: pathogenic BRCA1 mutation

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: omentum


title: Patient 16

tag: tissue


title: Patient 15


title: Patient 17


title: Patient 14


title: Total CD45+ cells from progression group.

description: Baseline

tag: cell type

value: CD45+ cells

tag: treatment

value: progression group

value: injected with PCSK9 AAV

value: 28 weeks

value: severe atherosclerosis


title: TRN178

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G7_S271

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: LN3 T-ALL1 thymus

description:
Isolated LN3 T-ALL from mechanically dissociated thymus of tumor-bearing mice
LN3_thy_1

tag: strain

tag: genotype

value: LN3 tg

value: thymus


title: Patient 13

description: Gene expression after extracting total RNA from peripheral blood

tag: gender

tag: age


title: TRN177

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G6_S270

value: Violet+

value: TRN no Neun selection


title: OTTA2014_0280_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: race/ethnicity

value: hispanic

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

value: AOC

tag: site id


title: TRN176

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: OTTA2014_0281_Clinical

description: single-sample normalized data

value: unknown

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

value: adnexal


title: Patient 36

tag: tissue

value: whole blood

tag: gender

value: male

tag: age


title: TRN174

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G3_S267

tag: plate type


title: OTTA2014_0279_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: race/ethnicity


title: OTTA2014_0277_Clinical

description: single-sample normalized data

value: high

value: white

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: Patient 12

value: female


title: Patient 11


title: Patient 10


title: TRN172

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G1_S265

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal


title: OTTA2014_0276_Clinical

description: single-sample normalized data

value: low

tag: brca1 and brca2 germline mutation status

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: presumed adnexal


title: TRN171

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN173

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G2_S266


title: OTTA2014_0273_Clinical

description: single-sample normalized data

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: any

value: hispanic

value: omentum


title: OTTA2014_0274_Clinical

description: single-sample normalized data

tag: Stage

tag: residual disease status

value: unknown

tag: race/ethnicity

value: dead

tag: study entry delay

value: AOC


title: TRN170

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G11_S275

tag: sample type


title: Patient 8

tag: tissue

value: whole blood

tag: gender

value: male

tag: age


title: Patient 7


title: Patient 5


title: TRN168

tag: used for patch-seq

tag: facs sorting signal


title: OTTA2014_0271_Clinical

description: single-sample normalized data

value: high

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: FM rep2 (FH rep2)

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: Drosophila dmel6
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

organism: Drosophila melanogaster

source_name: intestinal stem cells

extract_protocol:
Samples were fixed in 1 ml of PBS containing 1% formaldehyde (Sigma-Aldrich) and 0.5% Igepal CA-630 (Sigma-Aldrich) for 1 h on ice, then, incubated for 5 min after addition of 140 μl of 2 M glycine. Samples were then rinsed three times with ice cold PBS and homogenized by sonication in 2 ml of homogenization buffer (150 mM NaCl, 50 mM HEPES buffer at pH 7.6, 1 mM EGTA, 15 mM EDTA and 10% glycerol) supplied with 8 mM vanadyl ribonucleoside complex (Sigma-Aldrich), 50 U/ml SUPERase-In (Thermo Fisher Scientific), and 1 tablet/50 ml protease inhibitor cocktail tablet (Roche). After centrifugation at 13,000 g for 30 min, the supernantant was incubated with anti-FLAG-M2 affinity agarose beads (Thermo Fisher Scientific) at 4°C O/N. The beads were then washed four times with homogenization buffer. And the RNAs bound to the pAbp were recovered in 100 ml of elution buffer (50 mM Tris–HCl, pH 7.0, 10 mM EDTA, 1.3% SDS and 50 U/ml SUPERase-In) by proteinase K (40 μg/mL) treatment 2h at 60°C and O/N at 65°C after addition of NaCl (200mM). Eluant was then mixed with 4V of Trizol (Thermo Fisher Scientific) and 1V of chloroform (Sigma-Aldrich) with vigorously shaking, incubated at room temperature for 10 min, and then centrifuged at 12,000 g for 15 min at 4°C. The supernatant was transferred and mix with 2.5V of isopropanol, chilled at -80°C O/N, and centrifuged at 12,000 g for 30 min at 4°C. The RNA pellet was rinsed twice with 70% ethanol and then dissolved in RNase free water.
RNA libraries were generated with standard Illumina protocols

tag: cell type

value: intestinal stem cells

tag: genotype/variation

value: Mutant mtDNAs, FOXO knockdown


title: OTTA2014_0278_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: race/ethnicity

value: white

tag: progression-free survival time


title: TRN167

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type


title: TRN169

value: TRN no Neun selection


title: OTTA2014_0272_Clinical

description: single-sample normalized data

value: HGSOC

value: low

tag: brca1 and brca2 germline mutation status

value: hispanic

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: study entry delay

tag: anatomical site


title: OTTA2014_0270_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

value: any

value: pathogenic BRCA1 mutation

value: dead

value: omentum

tag: experiment site

value: AOC

tag: site id


title: TRN166


title: FM rep1 (FH rep1)

tag: cell type

tag: genotype/variation


title: TRN175

description:
nuclear RNA
TPM.TRN.tsv
X012116_TRNtest_G4_S268


title: FC rep2

value: Control mtDNAs, FOXO knockdown


title: OTTA2014_0275_Clinical

description: single-sample normalized data

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: high

tag: residual disease status

tag: race/ethnicity

tag: progression-free survival time


title: Patient 6

tag: tissue

value: whole blood

tag: gender

value: female

tag: age


title: OTTA2014_0268_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: study entry delay


title: OTTA2014_0269_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: anatomical site

value: adnexal

tag: experiment site

tag: site id


title: CD150NEG_D2_Mysm1-WT_Puma-WT

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

description: rRNA-depleted stranded RNA. Both males and females were used, and sex-matched between experimental groups.

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
Low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.4.2).
Pairwise comparisons were performed between samples across different mouse genotypes and genes with changes in expression ≥ |1.5| folds and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

source_name: Lin-cKit+Sca1+CD150- bone marrow cells

extract_protocol:
Mouse bone marrow was flushed from femurs, tibiae, humeri, and ilia of mice with a 26-G needle in PBS supplemented with 0.1% BSA and 2 mM EDTA, filtered through 40-μm cell strainers, and subjected to red blood cell lysis in ACK buffer (0.15 M NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA). The cells were stained with Biotin anti-mouse Lineage Panel (BioLegend) and lineage-positive cells depleted using biotin-binding Dynabeads (Life Technologies). The lineage-negative fraction was stained with PeCy7-cKit/CD117 (clone 2B8, BD Biosciences), APC-Sca1 (E13–161.7, BioLegend), FITC-CD48 (HM48-1, eBioscience), PE-CD150 (mShad150, eBioscience), and streptavidin-PECy5 (BioLegend). Propidium iodide or DAPI was added immediately before sorting for dead cell exclusion. Cell sorting was performed on the FACSAria instrument and was analyzed with FACS Diva software (BD Biosciences). The extracted BM cells were sorted into Lin-cKit+Sca1+ CD150+ and CD150- populations.
RNA was isolated from FACS-sorted HSPCs using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech).The libraries were sequenced on an Illumina HiSeq 2000 sequencer in paired-end 50bp configuration.

tag: strain

value: Mice were 8-12 weeks of age.

value: pooled male and female

tag: genotype

value: Mysm1+/+ Puma+/+


title: Patient 9


title: CD150NEG_D3_Mysm1-WT_Puma-WT


title: Patient 3


title: FC rep1

tag: cell type

value: intestinal stem cells

tag: genotype/variation


title: Patient 2

tag: tissue


title: TRN165

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

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: Patient 4

tag: gender

tag: age


title: TRN164


title: OTTA2014_0267_Clinical

description: single-sample normalized data

value: HGSOC

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

value: hispanic

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay


title: CD150NEG_C5_Mysm1-WT_Puma-KO

tag: strain

tag: genotype

value: Mysm1+/+ Puma-/-


title: CD150NEG_D4_Mysm1-WT_Puma-WT


title: TRN163

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: CD150NEG_C3_Mysm1-WT_Puma-KO

tag: age

tag: gender


title: M rep1 (H rep1)

tag: cell type

tag: genotype/variation

value: Mutant mtDNAs


title: Patient 1

tag: tissue

value: whole blood

value: female


title: OTTA2014_0266_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

value: alive

tag: anatomical site

value: omentum

tag: experiment site

value: AOC

tag: site id


title: OTTA2014_0265_Clinical

description: single-sample normalized data

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

value: adnexal


title: TRN161

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: CD150NEG_C2_Mysm1-WT_Puma-KO

tag: strain

tag: age

value: Mice were 8-12 weeks of age.

tag: gender

value: pooled male and female

tag: genotype


title: C rep1

tag: cell type

value: intestinal stem cells

tag: genotype/variation

value: Control mtDNAs


title: CD150NEG_B3_Mysm1-KO_Puma-KO

value: Mysm1-/- Puma-/-


title: CD150NEG_B5_Mysm1-KO_Puma-KO


title: OTTA2014_0263_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: all wildtypes

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0264_Clinical

description: single-sample normalized data

value: any

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


title: BC51_ile10_WT_RNA

first: Darren

middle: John

last: Parker

address: 31 Ames Street

department: Biology

institute: MIT

description: Total RNA

data_processing:
Bam files were converted to fastq files using bedtools command bamtofastq.
Fastq files were stripped of polyA tail by finding and keeping sequence before first instance of 10 sequential A nt.
Stripped fastq files were aligned to B. subtilis 168 chromosome NC_000964.3 using bowtie with options -v 2 -k 1 --best.
2 wig files per sample: 5' of reads counted singly for both strands.
Genome_build: NC_000964.3
Supplementary_files_format_and_content: 2 wig files per sample.

organism: Bacillus subtilis

source_name: Inducible ileS with 10 μM IPTG

growth_protocol: Overnight cultures in MCCG media (see Methods in publication for details) were backdiluted 1:1000 into fresh media and grown to OD600 0.3 in shaking flasks at 37°C with the listed [IPTG].

extract_protocol:
Cells were mixed 1:1 with 50% Methanol and incubated on ice for 5 minutes before spin down for 10 minutes at 4°C. Methanol was removed, cells were lysed with lysozyme and RNA was purified using RNeasy kit as per manufacturer's instruction (Qiagen).
RNA was fragmented (ThermoFischer #AM8740), dephosphorylated, polyadenylated, and reverse transcribed using Superscript III and custom oligo-dT reverse transcription primers. Resulting cDNA was ligated with Illumina sequencing adapters and PCR amplified. Single end (50 bp) sequencing was performed on an Illumina HiSeq 2000.

tag: strain


title: M rep2 (H rep2)

tag: cell type

tag: genotype/variation

value: Mutant mtDNAs


title: BC49_ile20_WT_RNA

description: Total RNA

source_name: Inducible ileS with 20 μM IPTG


title: BC50_ile15_WT_RNA

description: Total RNA

source_name: Inducible ileS with 15 μM IPTG


title: CD150NEG_B1_Mysm1-KO_Puma-KO

tag: age

tag: gender

tag: genotype


title: OTTA2014_0261_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: alive

value: peritoneal


title: TRN159

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: CD150NEG_A3_Mysm1-KO_Puma-HET

value: Mice were 8-12 weeks of age.

value: pooled male and female

value: Mysm1-/- Puma+/-


title: TRN158

value: sNuc-seq


title: OTTA2014_0262_Clinical

description: single-sample normalized data

value: HGSOC

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

value: AOC

tag: site id


title: TRN157


title: BC48_ile25_WT_RNA

description: Total RNA

source_name: Inducible ileS with 25 μM IPTG

tag: strain


title: CD150NEG_A2_Mysm1-KO_Puma-HET

tag: age

tag: gender

tag: genotype


title: TRN162

source_name: TRN

tag: sample type

tag: used for patch-seq


title: OTTA2014_0260_Clinical

description: single-sample normalized data

source_name: primary high-grade serous tubo-ovarian carcinoma

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

value: any


title: BC47_ile30_WT_RNA

description: Total RNA

source_name: Inducible ileS with 30 μM IPTG


title: CD150NEG_A1_Mysm1-KO_Puma-HET


title: OTTA2014_0259_Clinical

description: single-sample normalized data

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: omentum


title: TRN156

tag: facs sorting signal

tag: plate type


title: TRN160


title: C rep2

tag: cell type

value: intestinal stem cells

tag: genotype/variation

value: Control mtDNAs


title: TRN155

tag: sample type

tag: used for patch-seq


title: BC46_ile40_WT_RNA

description: Total RNA

source_name: Inducible ileS with 40 μM IPTG

tag: strain


title: CD150POS_W1_Mysm1-WT_Puma-WT

source_name: Lin-cKit+Sca1+CD150+ bone marrow cells

tag: age

tag: gender

tag: genotype

value: Mysm1+/+ Puma+/+


title: OTTA2014_0257_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: unknown

value: hispanic

value: dead

tag: study entry delay

tag: anatomical site

tag: experiment site

tag: site id


title: TRN154

value: No

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: BC45_ile70_WT_RNA

description: Total RNA

source_name: Inducible ileS with 70 μM IPTG


title: TRN153

tag: sample type

value: sNuc-seq

tag: used for patch-seq


title: CD150POS_D3-4_Mysm1-WT_Puma-WT

tag: strain

tag: age

value: Mice were 8-12 weeks of age.

value: pooled male and female


title: OTTA2014_0256_Clinical

description: single-sample normalized data

value: HGSOC

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

value: adnexal

value: AOC


title: BC44_ile500_WT_RNA

description: Total RNA

source_name: Inducible ileS with 500 μM IPTG


title: CD150POS_D2_Mysm1-WT_Puma-WT

tag: gender

tag: genotype


title: TRN152


title: TRN151


title: BC41_arg10_WT_RNA

description: Total RNA

source_name: Inducible argS with 10 μM IPTG


title: CD150POS_D1_Mysm1-WT_Puma-WT


title: BC40_arg15_WT_RNA

description: Total RNA

source_name: Inducible argS with 15 μM IPTG


title: CD150POS_C2-5_Mysm1-WT_Puma-KO

value: Mysm1+/+ Puma-/-


title: OTTA2014_0255_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: all wildtypes

tag: study entry delay

tag: anatomical site

value: presumed adnexal


title: BC38_arg25_WT_RNA

description: Total RNA

source_name: Inducible argS with 25 μM IPTG

tag: strain


title: CD150POS_C1-4_Mysm1-WT_Puma-KO

tag: age


title: TRN149

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0253_Clinical

description: single-sample normalized data

value: high

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: experiment site

tag: site id


title: OTTA2014_0254_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: omentum


title: CD150POS_P3_Mysm1-KO_Puma-KO

tag: strain

tag: age

tag: gender

tag: genotype

value: Mysm1-/- Puma-/-


title: TRN148

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: BC36_arg40_WT_RNA

description: Total RNA

source_name: Inducible argS with 40 μM IPTG


title: BC37_arg30_WT_RNA

description: Total RNA

source_name: Inducible argS with 30 μM IPTG


title: CD150POS_P2_Mysm1-KO_Puma-KO


title: OTTA2014_0258_Clinical

description: single-sample normalized data

tag: brca1 and brca2 germline mutation status

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


title: OTTA2014_0251_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: white

tag: experiment site

tag: site id


title: OTTA2014_0252_Clinical

description: single-sample normalized data

value: alive


title: CD150POS_P1_Mysm1-KO_Puma-KO

tag: strain

tag: age

value: Mice were 8-12 weeks of age.

tag: gender

tag: genotype


title: BC35_arg70_WT_RNA

description: Total RNA

source_name: Inducible argS with 70 μM IPTG


title: TRN146

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: CD150POS_B6_Mysm1-KO_Puma-KO

value: pooled male and female


title: BC34_arg500_WT_RNA

description: Total RNA

source_name: Inducible argS with 500 μM IPTG


title: TRN145


title: TRN150


title: OTTA2014_0250_Clinical

description: single-sample normalized data

value: HGSOC

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: AOC


title: 168_WT_RNA

description: Total RNA


title: CD150POS_B5_Mysm1-KO_Puma-KO


title: CD150POS_B1_Mysm1-KO_Puma-KO


title: TRN143


title: S. cerevisiae Aligned to C. albicans Genome

city: Chicago

first: Ryan

middle: Patrick

last: Dohn

state: IL

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

description:
Sample 12
Processed file required for samples 10 and 11 analysis. Contains genes misaligned to the wrong genome for use in species mixing.

data_processing:
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.
Supplementary_files_format_and_content: Tab delimited raw count table with gene and barcode ids (Samples 3 and 4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Samples 14 and 15)

source_name: S. cerevisiae cells

growth_protocol: Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.

extract_protocol:
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.

treatment_protocol: Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.

tag: treatment

value: 42°C Heat Shock


title: OTTA2014_0248_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: omentum

tag: experiment site

tag: site id


title: CD150POS_B3_Mysm1-KO_Puma-KO

tag: strain

tag: age

tag: gender

tag: genotype

value: Mysm1-/- Puma-/-


title: TRN144

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0246_Clinical

description: single-sample normalized data

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

value: adnexal


title: OTTA2014_0249_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: alive

tag: experiment site

tag: site id


title: OTTA2014_0245_Clinical

description: single-sample normalized data

value: pathogenic BRCA1 mutation


title: CD150POS_A4_Mysm1-KO_Puma-HET

tag: strain

tag: age

value: Mice were 8-12 weeks of age.

tag: gender

tag: genotype

value: Mysm1-/- Puma+/-


title: CD150POS_A3_Mysm1-KO_Puma-HET


title: TRN147

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: TRN140


title: OTTA2014_0244_Clinical

description: single-sample normalized data

value: HGSOC

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: AOC


title: S. cerevisiae cells - Heat Shock - rep 2

description: Sample 6

tag: treatment

value: 42°C Heat Shock


title: TRN141


title: OTTA2014_0242_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: presumed adnexal

tag: experiment site

tag: site id


title: CD150POS_A2_Mysm1-KO_Puma-HET

tag: strain

tag: age

tag: gender

value: pooled male and female

tag: genotype


title: TRN139

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: CD150POS_A1_Mysm1-KO_Puma-HET


title: OTTA2014_0243_Clinical

description: single-sample normalized data

value: low

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


title: S. cerevisiae Bulk RNA

description: Sample 14

tag: treatment

value: untreated


title: TRN138


title: S. cerevisiae cells - 20 minute Lysis - rep 1

description: Sample 2

tag: strain


title: OSlowKM Day 5 FLAG-JMJD3 overexpression input

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: genomic

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.0
Peaks were discovered using MACS2 (Klf4)
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

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:
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

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: transfection

value: OSlowKM lentiviral transfection

tag: overexpression

tag: knockout

value: Wildtype

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells


title: OTTA2014_0241_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: pathogenic BRCA2 mutation

value: white

value: alive

value: peritoneal

tag: experiment site

tag: site id


title: OTTA2014_0247_Clinical

description: single-sample normalized data

value: HGSOC

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: TRN142

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_0240_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

value: high

value: unknown

value: hispanic

tag: anatomical site

value: adnexal


title: S. cerevisiae cells - 15 minute Lysis - rep 1

description: Sample 1

tag: strain

tag: treatment

value: untreated


title: TRN136


title: KLF3i_CBP_CHIP_rep_2

city: La Jolla

first: George

last: Sen

state: California

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

description:
ChIP-seq protocol
KLF3i_CBP_CHIP_Diffreps

data_processing:
Raw ChIP-seq reads were aligned using Bowtie2 and low quality reads and duplicates were filtered out of the data.
HOMER's findPeaks was used for call peaks in individual replicates using Input ChIP-seq as the control sample. Common peaks among replicates were identified using HOMER's mergePeaks function.
Differential peaks between CBP and KLF3i_CBP CHIP samples were obtained by DiffReps 1.55.4 (4) using negative binomial test with a scanning window size of 1000 bp, step size of 100 bp, and a cutoff p-value of 0.0001.
Genome_build: hg19
Supplementary_files_format_and_content: called peaks

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes and maintained in keratinocyte EpiLife medium plus HKGS (Thermo Scientific).

extract_protocol:
DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: 20 million cells were crosslinked with 2mM DSG and 1% formaldehyde and used to pulldown KLF3 or CBP.

tag: tissue

value: Neonatal foreskin

tag: cell type

value: primary keratinocytes

tag: antibody

value: CBP (Cell Signaling D6C5 #7389)


title: OSKM Day 5 FLAG-JMJD3 overexpression input

tag: day

tag: transfection

value: OSKM lentiviral transfection

tag: overexpression

tag: knockout

value: Wildtype

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells


title: TRN135

source_name: TRN

tag: sample type

tag: used for patch-seq


title: KLF3i_CBP_CHIP_rep_1


title: OTTA2014_0239_Clinical

description: single-sample normalized data

source_name: primary high-grade serous tubo-ovarian carcinoma

value: HGSOC

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

value: omentum

tag: experiment site

tag: site id


title: OSKM Day 5 FLAG-JMJD3 overexpression anti-FLAG

tag: day

tag: transfection

tag: overexpression

tag: strain


title: CBP_CHIP_rep_2

description:
ChIP-seq protocol
CBP_peaks

tag: tissue

tag: cell type

tag: antibody


title: TRN134

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: OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression anti-H3K27ac

tag: knockout

tag: presumed cell type


title: TRN133


title: OSKM Day 5 Jmjd3+/+ FLAG overexpression anti-H3K27ac

value: FLAG


title: OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression Klf4


title: Input_CBP_CHIP

description: ChIP-seq protocol

value: none (input)


title: TRN132


title: TRN131


title: KLF3_CHIP_rep_2

description:
ChIP-seq protocol
KLF3_peaks

value: Neonatal foreskin

value: KLF3 (Sigma HPA049512)


title: TRN137


title: OSKM Day 5 Jmjd3+/+ FLAG overexpression Klf4


title: TRN130


title: OSKM Day 8 shRNA-Utx overexpression rep 2

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

source_name: Mouse MEFs, OSKM day 8

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

tag: overexpression transfection

tag: shRNA transfection

value: shRNA-Utx


title: OTTA2014_0237_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: unknown

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

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: AOC


title: OTTA2014_0234_Clinical

description: single-sample normalized data

value: HGSOC

value: any

value: dead

value: adnexal

tag: site id


title: OTTA2014_0233_Clinical

description: single-sample normalized data

value: all wildtypes

value: omentum


title: OTTA2014_0236_Clinical

description: single-sample normalized data


title: CBP_CHIP_rep_1

description:
ChIP-seq protocol
CBP_peaks

tag: tissue

tag: cell type

value: primary keratinocytes

tag: antibody

value: CBP (Cell Signaling D6C5 #7389)


title: OTTA2014_0238_Clinical

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis


title: OSlowKM Day 5 FLAG-JMJD3 overexpression anti-FLAG

tag: day

tag: transfection

value: OSlowKM lentiviral transfection

tag: overexpression

tag: knockout

value: Wildtype

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: Input_KLF3_CHIP

description: ChIP-seq protocol

value: Neonatal foreskin

value: none (input)


title: TRN129

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: OSKM Day 8 shRNA-Utx overexpression rep 1

tag: overexpression transfection

tag: shRNA transfection

value: shRNA-Utx

value: OSKM lentiviral transfection


title: OTTA2014_0232_Clinical

description: single-sample normalized data

value: HGSOC

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: 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: TRN128

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: KLF3_CHIP_rep_1

description:
ChIP-seq protocol
KLF3_peaks

tag: tissue

tag: cell type

value: primary keratinocytes

tag: antibody

value: KLF3 (Sigma HPA049512)


title: OSKM Day 8 shRNA-Luc overexpression rep 2

tag: day

tag: overexpression transfection

tag: shRNA transfection

value: shRNA-Luciferase

tag: transfection

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: OTTA2014_0231_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

value: all wildtypes

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: alive

tag: overall survival time

tag: progression-free survival time

value: adnexal


title: OTTA2014_0230_Clinical

description: single-sample normalized data

tag: study entry delay

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: OTTA2014_0235_Clinical

description: single-sample normalized data


title: P300i_RNAseq_rep_1

description:
RNA-seq protocol
P300i_RNAseq

data_processing:
Illumina Hiseq 4000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using STAR.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts).  Genes with less than 10 reads in every sample were excluded.
Statistics were calculated by ANOVA and differential genes with significant p-values and FDR(<0.05) with a >2 fold change (+/-) were selected as differentially expressed.
Genome_build: hg19

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: KLF3, KLF4, KLF3/KLF4 double knockdown (DKD), CBP, and P300 siRNA knockdown

tag: tissue

value: Neonatal foreskin

tag: cell type

tag: knockdown


title: TRN126

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

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: CBPi_RNAseq_rep_2

description:
RNA-seq protocol
CBPi_RNAseq

value: CBPi


title: OSKM Day 8 shRNA-Jmjd3 overexpression rep 1

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

value: OSKM lentiviral transfection

tag: presumed cell type

tag: strain


title: CBPi_RNAseq_rep_1

description:
RNA-seq protocol
CBPi_RNAseq


title: TRN125


title: OSKM Day 8 Jmjd3 overexpression rep 2


title: TRN124


title: OSKM Day 8 Jmjd3 overexpression rep 1


title: TRN123


title: OTTA2014_0229_Clinical

description: single-sample normalized data

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

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: 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: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

value: peritoneal

value: AOC


title: KLF3i_KLF4i_DKD_RNAseq_rep_1

description:
RNA-seq protocol
KLF3i_KLF4i_DKD_RNAseq

tag: tissue

tag: cell type

value: primary keratinocytes

tag: knockdown

value: KLF3i_KLF4i_double knockdown


title: KLF3i_KLF4i_DKD_RNAseq_rep_2

description:
RNA-seq protocol
KLF3i_KLF4i_DKD_RNAseq


title: P300i_RNAseq_rep_2

description:
RNA-seq protocol
P300i_RNAseq


title: OSKM Day 8 FLAG overexpression rep 2

tag: day

tag: overexpression transfection

value: FLAG

tag: shRNA transfection

tag: transfection

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: KLF4i_RNAseq_rep_2

description:
RNA-seq protocol
KLF4i_RNAseq

value: Neonatal foreskin


title: TRN122

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: OTTA2014_0227_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

value: alive

tag: anatomical site

value: omentum

tag: experiment site

tag: site id


title: OTTA2014_0228_Clinical

description: single-sample normalized data

value: HGSOC

value: high

value: all wildtypes

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

value: adnexal


title: TRN121

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN127


title: KLF4i_RNAseq_rep_1

description:
RNA-seq protocol
KLF4i_RNAseq

tag: tissue

tag: cell type

value: primary keratinocytes

tag: knockdown


title: OTTA2014_0226_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: dead

value: AOC


title: OTTA2014_0225_Clinical

description: single-sample normalized data

tag: race/ethnicity

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: anatomical site

tag: experiment site

tag: site id


title: OTTA2014_0224_Clinical

description: single-sample normalized data

tag: progression-free survival time

tag: study entry delay


title: OSKM Day 8 FLAG overexpression rep 1

tag: day

tag: overexpression transfection

value: FLAG

tag: shRNA transfection

tag: transfection

value: OSKM lentiviral transfection

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells

tag: strain


title: OSKM Day 8 shRNA-Luc overexpression rep 1

value: shRNA-Luciferase


title: OSKM Day 8 shRNA-Jmjd3 overexpression rep 2


title: TRN120

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: No

tag: facs sorting signal

tag: plate type


title: OTTA2014_0223_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

value: hispanic

tag: year of diagnosis

tag: vital status


title: OSKM Day 4 shRNA-Utx overexpression rep 2

source_name: Mouse MEFs, OSKM day 4

tag: day

tag: overexpression transfection

tag: shRNA transfection

value: shRNA-Utx

tag: transfection


title: KLF3i_RNAseq_rep_2

description:
RNA-seq protocol
KLF3i_RNAseq

tag: tissue

value: Neonatal foreskin

tag: cell type

tag: knockdown


title: OSKM Day 4 shRNA-Utx overexpression rep 1

tag: presumed cell type

tag: strain


title: KLF3i_RNAseq_rep_1

description:
RNA-seq protocol
KLF3i_RNAseq


title: TRN119

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

value: Violet+

tag: plate type

value: TRN no Neun selection


title: TRN118


title: OTTA2014_0222_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

value: all wildtypes

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: OSKM Day 4 shRNA-Luc overexpression rep 2

tag: day

tag: overexpression transfection

tag: shRNA transfection

tag: transfection

tag: presumed cell type

tag: strain


title: CTLi_RNAseq_rep_2

description: RNA-seq protocol

treatment_protocol: KLF3, KLF4, KLF3/KLF4 double knockdown (DKD), CBP, and P300 siRNA knockdown. Non-targeting siRNA: Ambion Silencer Select negative control 4390844.

tag: tissue

tag: cell type

value: primary keratinocytes

tag: knockdown

value: control non-targeting RNAi


title: OSKM Day 4 shRNA-Luc overexpression rep 1

value: OSKM lentiviral transfection

value: Intermediate pluripotent reprogrammed cells


title: TRN117

tag: sample type

value: sNuc-seq

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_0221_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: progression-free survival time

tag: study entry delay

value: omentum

value: AOC


title: CTLi_RNAseq_rep_1

description: RNA-seq protocol

tag: tissue

tag: cell type

tag: knockdown


title: OTTA2014_0220_Clinical

description: single-sample normalized data

value: HGSOC

value: hispanic

value: alive

tag: anatomical site

tag: experiment site

tag: site id


title: TRN116

tag: sample type

tag: used for patch-seq

value: No

tag: facs sorting signal

value: Violet+

tag: plate type