title: YAP_KO_Starvation_Rep1

value: Starvation


title: YAP_KO_LPA_Rep2

status: Public on May 25 2018

type: SRA

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

country: USA

institute: University of California, San Diego School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

molecule: total RNA

organism: Homo sapiens

source_name: HEK293A cells

growth_protocol: HEK293A cells were plated at 1.5x10^5 cells/well in a 6-well plate under normal growth conditions (DMEM with 10% FBS, 1% P/S). Once cells adhered to the plate, cells were starved with serum-free culture media (DMEM with 1% P/S) for 16 hours before harvesting (for starvation conditions) or stimulation.

extract_protocol:
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from HEK293A cells from different conditions.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).

treatment_protocol: Following 16 hours of serum starvation, cells were stimulated with LPA (100 nM) for 90 minutes before harvesting.

tag: genotype

value: YAP-KO

tag: condition

value: LPA


title: WT_Starvation_Rep2

value: WT


title: YAP_KO_Starvation_Rep3


title: E09990_T_Xba

type: genomic

city: Washington

first: Krithika

last: Bhuvaneshwar

state: DC

address: 2115 Wisconsin Ave NW

institute: Georgetown University

description: Xba

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
The CHP file contains genotype calls and CBCHP files contain copy number data.  Calls were determined by the GTYPE software version 3.0 with 25% level of confidence.
CINDEX output is available on the series record in REMBRANDT_CIN*txt files. Column 1 of the REMBRANDT_CIN_CHROMOSOMES files refers to chromosome number.

label: biotin

molecule: genomic DNA

source_name: Brain

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tissue (Approximately 10 μg from each tumor) was used to extract high molecular weight, genomic DNA using QIAamp DNA Micro DNA extraction kit (Qiagen) following the manufacturer's instructions. The quality of DNA was checked by electrophoresis run in a 2% agarose gel.

tag: patient id

tag: analyzed with cindex?

value: yes

tag: disease state

value: UNKNOWN

tag: provider

value: H. LEE MOFFITT CANCER CENTER


title: E10010_B_Xba

description:
Duplicate
Xba

value: GBM

value: DANA-FARBER CANCER INSTITUTE


title: YAP_KO_LPA_Rep3


title: YAP_KO_Starvation_Rep2


title: E10002_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE

tag: tumorgrade

value: IV


title: E09990_B_Xba

description:
Duplicate
Xba


title: E10002_B_Xba

description:
Duplicate
Xba


title: E09989_B_Xba

description:
Duplicate
Xba

value: HENRY FORD HOSPITAL


title: WT_LPA_Rep2


title: WT_LPA_Rep1


title: E09989_T_Xba

description: Xba


title: WT_Starvation_Rep1


title: TAZ_YAP_KO_Starvation_Rep3

value: TAZ/YAP-dKO


title: E09987_B_Xba

description:
Duplicate
Xba


title: E09987_T_Xba

description: Xba


title: E09985_B_Xba

description:
Duplicate
Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: TAZ_YAP_KO_Starvation_Rep2


title: TAZ_YAP_KO_Starvation_Rep1


title: WT_Starvation_Rep3


title: TAZ_YAP_KO_LPA_Rep3


title: E09982_T_Xba

description: Xba


title: TAZ_YAP_KO_LPA_Rep2


title: E09982_B_Xba

description:
Duplicate
Xba


title: E09975_T_Xba

description: Xba


title: TAZ_KO_Starvation_Rep2

value: TAZ-KO


title: TAZ_KO_Starvation_Rep1


title: TAZ_KO_LPA_Rep3


title: TAZ_KO_LPA_Rep1


title: E09975_B_Xba

description:
Duplicate
Xba


title: TAZ_KO_Starvation_Rep3


title: E09971_B_Xba

description:
Duplicate
Xba


title: E09978_B_Xba

description:
Duplicate
Xba


title: E09976_T_Xba

description: Xba


title: TAZ_KO_LPA_Rep2


title: Transformed HMECs rep3

city: Durham

first: Matthew

middle: Burk

last: Friedersdorf

state: NC

address: 207 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

description:
HMEC_RNAseq.DiffGeneExp.tdt
tfo3

data_processing:
Sequenced reads were mapped to the hg19 genome using Tophat2 with parameters -N 2 --read-edit-dist 3 -r 50 --mate-std-dev 325 -G hg19_refFlat.gtf --no-coverage-search
Transcript abundance and differential expression were estimated using Cufflinks with parameters -M ncRNAs.gtf, gtf file includes rRNA, tRNA, snoRNA, miRNA, srpRNA, snRNA, 7SK and chrM genes from UCSC Table browser, hg19 build 37.2
cuffmerge run with parameters -g hg19_refFlat.gtf -s
cuffdiff run with parameters -F 0.04 -M ncRNAs.gtf -b hg19.fa
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files, cuffdiff output, value1 & value2 in table are FPKM normalized counts

source_name: mammary epithelial cells (HMECs)

growth_protocol: HMECs were maintained in Mammary Epithelial Growth Medium (MEGM; Lonza, Walkersville, MD, USA). IMO and TFO HMECs were maintained in MEGM+10% fetal bovine serum. Cells were passaged at 50-70% confluency using a Reagent Pack (Lonza) according to the manufacturer’s subculturing protocol.

extract_protocol:
Total RNA was obtained from cells using the TRIsure reagent (Bioline, Luckenwalde Germany) according to the manufacturer’s protocol. RNA quantity was analyzed using a NanoDrop spectrophotometer, and ribosomal RNA was depleted using the Ribozero Gold kit (Epicentre, Madison, WI, USA).
50ng of rRNA depleted RNA was used as input for sequencing libraries, which were made using the ScriptSeq v2 RNA-seq library preparation kit (Epicentre) according to the manufacturer’s instructions. 16 amplification cycles were used in the final PCR amplification step.  Barcodes: Prim rep 1: GATCAG; Prim rep 2: CAGATC; Prim rep 3: ACTTGA; Imo rep 1: TAGCTT; Imo rep 2: ATCACG; Imo rep 3: CGATGT; Tfo rep 1: GGCTAC; Tfo rep 2:  TTAGGC; Tfo rep 3: TGACCA

tag: cell type

value: Transformed HMECs

tag: transgenes

value: Immortalized HMECs+ HRASG12V

tag: passages


title: E09971_T_Xba

description: Xba


title: E09967_T_Xba

description: Xba


title: TAZ_YAP_KO_LPA_Rep1


title: E09967_B_Xba

description:
Duplicate
Xba


title: Immortalized HMECs rep3

description:
HMEC_RNAseq.DiffGeneExp.tdt
imo3

value: Immortalized HMECs

value: HMECs+ hTERT, p53DD, cyclin D1, CDK4R24C and c-MYCT58A


title: E09983_B_Xba

description:
Duplicate
Xba


title: WT_LPA_Rep3

value: LPA


title: Immortalized HMECs rep2

description:
HMEC_RNAseq.DiffGeneExp.tdt
imo2


title: Primary HMECs rep3

description:
Obtained from Lonza at p9; 50Y female healthy donor
HMEC_RNAseq.DiffGeneExp.tdt
prim3

value: Primary HMECs

value: normal HMECs


title: E09966_T_Xba

description: Xba

value: yes

value: ASTROCYTOMA

value: III


title: E09966_B_Xba

description:
Duplicate
Xba

value: H. LEE MOFFITT CANCER CENTER


title: E09965_T_Xba

description: Xba

value: UNKNOWN


title: E09965_B_Xba

description:
Duplicate
Xba


title: E09976_B_Xba

description:
Duplicate
Xba

value: GBM


title: Primary HMECs rep2

description:
Obtained from Lonza at p9; 50Y female healthy donor
HMEC_RNAseq.DiffGeneExp.tdt
prim2


title: E09978_T_Xba

description: Xba


title: E09263_duplicate

type: RNA

description: duplicate specimen: no data in matrix.

hyb_protocol: Per manufacturer (Affymetrix)

scan_protocol: Per manufacturer (Affymetrix)

data_processing: The .cel and .txt files of all the arrays that passed the minimal quality-control were input into dChip for normalization. The model-based expression index algorithm implemented in dChip selects an invariant set with a small within-subset rank difference to serve as basis for adjusting the brightness of the arrays to a comparable level. The normalization was done at the PM and MM probe levels, and model-based expression levels were calculated using normalized probe level data. We choose the average difference model (PM > MM) to compute expression values; negative average differences were truncated to 1 or log-transformed values of zeros to flag negative signal intensities with no biological meaning.  For data preprocessing, probe-level data were consolidated into probe-set data using the Affymetrix MAS5 algorithm, with the target scaling value at 500. Probe-level data were also processed with custom Chip Definition Files that rearranged Affymetrix probes into gene-based probe sets. Probes mapped to alternatively spliced exons were grouped into distinct probe sets. Most 3′ probes were selected for processing. Nonspecific probes were masked before processing.  The data matrix was constructed such that every sample has only one matching gene expression biospecimen.  Duplicate  specimens were excluded. The duplicate samples are inidicated in the titles and  'description' field.

source_name: brain

label_protocol: Per manufacturer (Affymetrix)

extract_protocol: Total RNA was extracted from the tumor tissue (50-80 mg) using the Trizol reagent (Invitrogen) and following the manufacturer's instructions. The quality of RNA extracted was verified using Agilent’s Bioanalyzer System with the help of RNA Pico Chips. 5 μg RNA extracted from each sample was processed using the Affymetrix U1332 Plus gene expression microarray chips 2.

tag: disease

value: unknown

tag: tissue

value: brain

tag: extract name

tag: assay name


title: E10252_duplicate C_T

description: duplicate specimen: no data in matrix.

value: NIH NEURO-ONCOLOGY BRANCH

value: glioblastoma multiforme


title: E09964_T_Xba

description: Xba


title: Transformed HMECs rep2

description:
HMEC_RNAseq.DiffGeneExp.tdt
tfo2

value: Transformed HMECs


title: E09907_duplicate

description: duplicate specimen: no data in matrix.

value: NABTT/H. LEE MOFFITT CANCER CENTER

tag: tumor grade

value: grade 4


title: E09964_B_Xba

description:
Duplicate
Xba


title: E10252_duplicate C_NT

description: duplicate specimen: no data in matrix.


title: E10252_duplicate B

description: duplicate specimen: no data in matrix.


title: E09963_T_Xba

description: Xba


title: E09963_B_Xba

description:
Duplicate
Xba


title: E09960_T_Xba

description: Xba

value: UNIV OF PITTSBURGH


title: E09833_duplicate

description: duplicate specimen: no data in matrix.


title: E09958_T_Xba

description: Xba

value: HENRY FORD HOSPITAL


title: E09960_B_Xba

description:
Duplicate
Xba


title: E09137_duplicate

description: duplicate specimen: no data in matrix.


title: E09958_B_Xba

description:
Duplicate
Xba


title: E09278_duplicate

description: duplicate specimen: no data in matrix.


title: E09957_T_Xba

description: Xba

value: Unknown


title: E09956_T_Xba

description: Xba


title: E09957_B_Xba

description:
Duplicate
Xba


title: E09951_T_Xba

description: Xba


title: E09956_B_Xba

description:
Duplicate
Xba


title: E09951_B_Xba

description:
Duplicate
Xba


title: E09948_T_Xba

description: Xba


title: E09948_B_Xba

description:
Duplicate
Xba


title: E09945_B_Xba

description:
Duplicate
Xba

value: UNIVERSITY OF WISCONSIN


title: E09941_B_Xba

description:
Duplicate
Xba

value: OLIGODENDROGLIOMA


title: E09941_T_Xba

description: Xba

value: yes


title: MD552910

value: M. D. ANDERSON CANCER CENTER

value: grade 3


title: E09938_T_Xba

description: Xba

value: H. LEE MOFFITT CANCER CENTER

value: IV


title: E09937_T_Xba

description: Xba

value: II


title: E09945_T_Xba

description: Xba

value: UNKNOWN


title: E10059

value: NABTT/MASSACHUSETTS GENERAL HOSPITAL

value: unknown

value: brain


title: E10067


title: E10058


title: E09936_T_Xba

description: Xba

value: GBM


title: E10037


title: E09936_B_Xba

description:
Duplicate
Xba


title: E10044


title: E10030

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: E10036


title: E10038


title: E10023


title: E09935_T_Xba

description: Xba


title: E10022


title: E09932_B_Xba

description:
Duplicate
Xba

value: MIXED

value: NIH NEURO-ONCOLOGY BRANCH


title: E10027

value: HENRY FORD HOSPITAL


title: E10003


title: E09998

value: UNIVERSITY OF SAN FRANCISCO


title: E10024


title: E10008


title: E09930_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E09993


title: E09924_B_Xba

description:
Duplicate
Xba


title: E09924_T_Xba

description: Xba

value: yes


title: E09930_B_Xba

description:
Duplicate
Xba


title: E09923_T_Xba

description: Xba

value: UNIVERSITY OF WISCONSIN


title: E09923_B_Xba

description:
Duplicate
Xba


title: E09990


title: E09996


title: E09922_T_Xba

description: Xba


title: E09922_B_Xba

description:
Duplicate
Xba


title: E09921_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA


title: E09989


title: E10019

value: H. LEE MOFFITT CANCER CENTER


title: E09920_B_Xba

description:
Duplicate
Xba

value: III


title: E09917_T_Xba

description: Xba


title: E09917_B_Xba

description:
Duplicate
Xba


title: E09916_T_Xba

description: Xba


title: E09985


title: E09916_B_Xba

description:
Duplicate
Xba


title: E09971


title: E09965


title: E09975


title: E09978


title: E09914_T_Xba

description: Xba


title: E09982


title: E09963


title: E09964


title: E09914_B_Xba

description:
Duplicate
Xba


title: E09955


title: E09921_T_Xba

description: Xba


title: E09910_T_Xba

description: Xba


title: E09907B_T_Xba

description: Xba

value: IV


title: E09907_T_Xba

description: Xba


title: E09928


title: E09907_B_Xba

description:
Duplicate
Xba


title: E09906_T_Xba

description: Xba


title: E09910_B_Xba

description:
Duplicate
Xba

value: UNKNOWN


title: E09902_T_Xba

description: Xba


title: E09900_T_Xba

description: Xba


title: E09900_B_Xba

description:
Duplicate
Xba


title: E09916


title: E09945


title: E09935


title: E09899_T_Xba

description: Xba

value: UNIV OF PITTSBURGH


title: E09899

value: unknown


title: E09893_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: E09958

value: brain


title: E09910


title: E09924


title: E09893_B_Xba

description:
Duplicate
Xba


title: E09906_B_Xba

description:
Duplicate
Xba

value: GBM


title: E09894


title: E09923


title: E09885


title: E09902_B_Xba

description:
Duplicate
Xba


title: E09892_B_Xba

description:
Duplicate
Xba


title: E09774

value: NABTT/JOHNS HOPKINS


title: E09922


title: E09708


title: E09770


title: E09888


title: E09868


title: E09899_B_Xba

description:
Duplicate
Xba


title: E09657

value: NIH NEURO-ONCOLOGY BRANCH


title: E09704

value: DANA-FARBER CANCER INSTITUTE


title: E09890_B_Xba

description:
Duplicate
Xba

value: II


title: E09900


title: E09871_T_Xba

description: Xba


title: E09868_B_Xba

description:
Duplicate
Xba


title: E09868_T_Xba

description: Xba


title: E09871_B_Xba

description:
Duplicate
Xba


title: E09860_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E09644


title: E09641

value: UNIVERSITY OF SAN FRANCISCO


title: E09629


title: E09860_B_Xba

description:
Duplicate
Xba


title: E09595


title: E09857_B_Xba

description:
Duplicate
Xba


title: E09857_T_Xba

description: Xba

value: yes


title: E09858_B_Xba

description:
Duplicate
Xba


title: E09852_T_Xba

description: Xba


title: E09587


title: E09546


title: E09495


title: E09852_B_Xba

description:
Duplicate
Xba


title: E09862_T_Xba

description: Xba


title: E09848_T_Xba

description: Xba

value: MIXED


title: E09862_B_Xba

description:
Duplicate
Xba

value: H. LEE MOFFITT CANCER CENTER


title: E09891_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA


title: E09846_T_Xba

description: Xba


title: E09848_B_Xba

description:
Duplicate
Xba


title: E09494


title: E09846_B_Xba

description:
Duplicate
Xba


title: E09611


title: E09264


title: E09842_B_Xba

description:
Duplicate
Xba

value: IV


title: E09842_T_Xba

description: Xba


title: E09834_B_Xba

description:
Duplicate
Xba


title: E09833B_T_Xba

description: Xba


title: E09833_T_Xba

description: Xba


title: E09167


title: 900_00_5315

value: THOMAS JEFFERSON UNIVERSITY

value: unclassified


title: E09378

value: unknown


title: E09833_B_Xba

description:
Duplicate
Xba


title: HF1502

value: HENRY FORD HOSPITAL (RETRO)

value: oligodendroglioma

value: grade 3


title: MD549279

value: M. D. ANDERSON CANCER CENTER

value: brain


title: E09151

value: NIH NEURO-ONCOLOGY BRANCH


title: E09832_T_Xba

description: Xba

value: GBM


title: E09238


title: MD508984


title: HF1702


title: HF1493


title: E09829B_T_Xba

description: Xba


title: HF1357


title: HF1458


title: HF1227

value: grade 2


title: HF1487


title: E09835_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E09263


title: E09829_T_Xba

description: Xba

value: yes


title: HF1167


title: E09829_B_Xba

description:
Duplicate
Xba


title: E09825_T_Xba

description: Xba


title: HF1090


title: E09825_B_Xba

description:
Duplicate
Xba


title: HF0962


title: E09819_T_Xba

description: Xba


title: HF1057


title: E07733

value: DANA-FARBER CANCER INSTITUTE


title: E09819_B_Xba

description:
Duplicate
Xba


title: E09811_T_Xba

description: Xba

value: H. LEE MOFFITT CANCER CENTER

value: II


title: E09810_T_Xba

description: Xba

value: IV


title: E09803_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

value: NIH

value: III


title: HF0960

value: HENRY FORD HOSPITAL (RETRO)


title: E09802_T_Xba

description: Xba


title: E09801_T_Xba

description: Xba


title: E09801_B_Xba

description:
Duplicate
Xba


title: E09800_B_Xba

description:
Duplicate
Xba


title: HF0920

value: oligodendroglioma


title: E09785_B_Xba

description:
Duplicate
Xba


title: HF0897


title: HF0816

value: grade 3


title: E09786_T_Xba

description: Xba


title: HF0828


title: E09782_T_Xba

description: Xba

value: NABTT/JOHNS HOPKINS


title: HF0599

value: brain


title: HF0510


title: E09786_B_Xba

description:
Duplicate
Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: HF0835


title: HF0327


title: HF0285


title: E09800_T_Xba

description: Xba

value: GBM


title: HF0460


title: HF0251


title: E09785_T_Xba

description: Xba


title: HF0291

value: grade 2


title: E09759_T_Xba

description: Xba

value: UWI


title: E10470


title: HF0218


title: E10278

value: NABTT/HENRY FORD HOSPITAL


title: E10691


title: E10097

value: HENRY FORD HOSPITAL


title: E09755_T_Xba

description: Xba

value: yes

value: OLIGODENDROGLIOMA

value: H. LEE MOFFITT CANCER CENTER


title: E09752_B_Xba

description:
Duplicate
Xba

value: IV


title: E09755_B_Xba

description:
Duplicate
Xba

value: II


title: E09774_B_Xba

description:
Duplicate
Xba

value: UNKNOWN


title: E10054


title: HF0184

value: HENRY FORD HOSPITAL (RETRO)


title: E10163

value: UNIVERSITY OF SAN FRANCISCO

value: oligodendroglioma


title: E10072


title: E09752_T_Xba

description: Xba


title: E09744_B_Xba

description:
Duplicate
Xba

value: NABTT/JOHNS HOPKINS


title: E09756_B_Xba

description:
Duplicate
Xba


title: E09743_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

value: III


title: E09743_T_Xba

description: Xba


title: E09742_T_Xba

description: Xba

value: GBM


title: E10001

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE

value: brain

value: grade 3


title: E10011

value: grade 2


title: E09988


title: E09949


title: E09937


title: E10021


title: E09730_B_Xba

description:
Duplicate
Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: E09730_T_Xba

description: Xba

value: yes


title: E09759_B_Xba

description:
Duplicate
Xba

value: UWI


title: E09722_T_Xba

description: Xba

value: IV


title: E09744_T_Xba

description: Xba


title: E09893

value: H. LEE MOFFITT CANCER CENTER


title: E09742_B_Xba

description:
Duplicate
Xba


title: E09740_T_Xba

description: Xba


title: E09804


title: E09681


title: E09860


title: E09890


title: E09699_B_Xba

description:
Duplicate
Xba

value: OLIGODENDROGLIOMA

value: II


title: E09699


title: E09867

value: UNIVERSITY OF SAN FRANCISCO


title: E09740_B_Xba

description:
Duplicate
Xba


title: E09722_B_Xba

description:
Duplicate
Xba


title: E09681_T_Xba

description: Xba


title: E09708_T_Xba

description: Xba

value: UNKNOWN


title: E09755

value: oligodendroglioma


title: E09708_B_Xba

description:
Duplicate
Xba


title: E09699_T_Xba

description: Xba


title: E09664


title: E09698_T_Xba

description: Xba


title: E09680_B_Xba

description:
Duplicate
Xba


title: E09679_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E09661


title: E09656


title: E08021


title: E09681_B_Xba

description:
Duplicate
Xba

value: III


title: E09858


title: E09680_T_Xba

description: Xba

value: GBM


title: 900_00_5550

value: THOMAS JEFFERSON UNIVERSITY


title: 900_00_5552

value: brain


title: E09503


title: E09645


title: E09419

value: grade 3


title: E09448


title: E09670_T_Xba

description: Xba


title: E09679_B_Xba

description:
Duplicate
Xba


title: 900_00_5412


title: E09670_B_Xba

description:
Duplicate
Xba


title: E09657_T_Xba

description: Xba


title: E09657_B_Xba

description:
Duplicate
Xba


title: E09655_B_Xba

description:
Duplicate
Xba


title: E09649_T_Xba

description: Xba

value: UCSF


title: 900_00_5476

value: grade 2


title: Organoid on day 5

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Mus musculus

source_name: Organoid on day 5

label_protocol: Extracted total RNA was labeled with Cy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: Organoid on day 5


title: Organoid on day 1

source_name: Organoid on day 1

value: Organoid on day 1


title: 900_00_5345


title: Villus

source_name: Villus

value: Villus


title: 900_00_5547


title: 900_00_5380


title: 900_00_5341


title: Crypt

source_name: Crypt

value: Crypt


title: E09649_B_Xba

description:
Duplicate
Xba

value: IV


title: E09513


title: NT6

value: NIH NEURO-ONCOLOGY BRANCH

value: normal


title: NT4


title: NT3


title: E09756_T_Xba

description: Xba

value: yes

value: H. LEE MOFFITT CANCER CENTER


title: HF0533

value: HENRY FORD HOSPITAL (RETRO)


title: HF0523


title: E09645_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: HF0593


title: NT1


title: NT2


title: HF0512


title: HF0526


title: NT5


title: E09644_T_Xba

description: Xba

value: UNKNOWN


title: E09644_B_Xba

description:
Duplicate
Xba


title: E09641_B_Xba

description:
Duplicate
Xba

value: Unknown


title: E09624_T_Xba

description: Xba

value: GBM


title: HF0467

value: brain


title: E09624_B_Xba

description:
Duplicate
Xba


title: HF0616


title: E09622_T_Xba

description: Xba


title: HF0383


title: E09622_B_Xba

description:
Duplicate
Xba


title: HF0295


title: HF0377


title: HF0232


title: HF0211


title: HF0178


title: HF0171


title: HF0303


title: E09611_T_Xba

description: Xba


title: E09611_B_Xba

description:
Duplicate
Xba


title: HF0131


title: NT7


title: HF0137


title: HF0120


title: E10690

value: mixed


title: HF0088


title: HF0183

value: grade 2


title: HF0151


title: E09848


title: E09511

value: UNIVERSITY OF SAN FRANCISCO

value: grade 3


title: E09688


title: E09615_T_Xba

description: Xba


title: HF0163


title: E09606_B_Xba

description:
Duplicate
Xba

value: UCSF


title: E09610_T_Xba

description: Xba


title: E09606_T_Xba

description: Xba


title: E09688_B_Xba

description:
Duplicate
Xba

value: MIXED

value: II


title: E09605_B_Xba

description:
Duplicate
Xba

value: IV


title: E09605_T_Xba

description: Xba


title: E09358


title: E09334


title: MD621233

value: M. D. ANDERSON CANCER CENTER

value: glioblastoma multiforme


title: E09289

value: NIH NEURO-ONCOLOGY BRANCH


title: E09440


title: E09394

value: UNIVERSITY OF WISCONSIN


title: E09602_T_Xba

description: Xba

value: yes


title: MD545226

value: grade 4


title: MD602958


title: MD607216


title: HF1671

value: HENRY FORD HOSPITAL (RETRO)


title: E09262


title: MD607103


title: MD608660


title: E09601_T_Xba

description: Xba

value: GBM


title: E09602_B_Xba

description:
Duplicate
Xba


title: HF1640

value: brain


title: E09601_B_Xba

description:
Duplicate
Xba


title: E09587_T_Xba

description: Xba

value: UNKNOWN


title: HF1628


title: HF1608


title: E09610_B_Xba

description:
Duplicate
Xba


title: E09595_T_Xba

description: Xba


title: HF1540


title: HF1589


title: HF1667


title: HF1534


title: HF1492


title: HF1618


title: HF1585


title: ASD patient [SNP234 OP]

city: Olomouc

first: Josef

last: Srovnal

address: Hnevotinska 5

department: IMTM

country: Czech Republic

institute: Palacky University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (version 4.0.0.1567G). Copy number values were extracted and converted from CEL files into CYCHP files using Chromosome Analysis Suite software (v.3.3.0.139) in default manner using CYTO2 algorythm v.s. 2.2.0. Reference file was CytoScan HD Array.na33.r2, ChAS Browser was NefAffx Build hg19 (20170803).

label: Biotin

source_name: ASD patient

extract_protocol: Genomic DNA was extracted from mononuclear cell  of peripheral blood using saline method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: Peripheral blood

tag: gender

value: F

tag: adhd

value: no


title: E09569_T_Xba

description: Xba


title: HF1397


title: E09587_B_Xba

description:
Duplicate
Xba


title: Mother of SNP136 [SNP218]

source_name: Mother of SNP136


title: HF1509


title: E09569_B_Xba

description:
Duplicate
Xba


title: HF1469


title: Father of SNP136 [SNP219]

source_name: Father of SNP136

value: M


title: HF1382


title: ASD patient [SNP223]


title: E09546_T_Xba

description: Xba

value: Unknown

value: UCSF


title: HF1356


title: HF1517


title: HF1338


title: ASD patient [SNP217]


title: HF1292


title: HF1297


title: E09531_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

value: UNIV OF PITTSBURGH


title: HF1269

value: glioblastoma multiforme


title: E09531_T_Xba

description: Xba


title: HF1191


title: HF1318


title: HF1262


title: E09535_T_Xba

description: Xba

value: NIH NEURO-ONCOLOGY BRANCH

value: IV


title: E09515_T_Xba

description: Xba

value: yes


title: HF1220

value: grade 4


title: HF1178

value: HENRY FORD HOSPITAL (RETRO)


title: HF1538


title: E09515_B_Xba

description:
Duplicate
Xba


title: HF1139


title: ASD patient [SNP213]


title: ASD patient [SNP205]


title: E09511_T_Xba

description: Xba

value: mixed

value: III


title: ASD patient [SNP216]


title: ASD patient [SNP206]


title: E09511_B_Xba

description:
Duplicate
Xba


title: HF1097

value: brain


title: HF1078


title: HF1077


title: HF1122


title: E09503_T_Xba

description: Xba

value: OLIGODENDROGLIOMA

value: II


title: HF0992


title: HF1058


title: E09503_B_Xba

description:
Duplicate
Xba


title: HF1137


title: HF0990


title: Mother of SNP201 [SNP202]

source_name: Mother of SNP201

value: Peripheral blood

value: F

value: no


title: HF0996


title: HF0986


title: E09495_T_Xba

description: Xba

value: UNKNOWN


title: HF0963


title: ASD patient [SNP201]

value: M


title: ASD patient [SNP207]


title: ASD patient [SNP198]


title: HF0894


title: ASD patient [SNP204]


title: ASD patient [SNP199]


title: HF0891


title: HF0654


title: ASD patient [SNP200]


title: ASD patient [SNP197]


title: HF0627


title: E09494_T_Xba

description: Xba


title: HF0543


title: HF0520


title: E09489_T_Xba

description: Xba

value: GBM


title: HF0505

value: glioblastoma multiforme


title: HF0583


title: HF0445


title: E09483_T_Xba

description: Xba

value: UCSF


title: HF0442.5


title: ASD patient [SNP194]


title: ASD patient [SNP203]


title: ASD patient [SNP195]


title: ASD patient [SNP193]


title: E09495_B_Xba

description:
Duplicate
Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: HF0300.3


title: E09483_B_Xba

description:
Duplicate
Xba

value: IV


title: HF0268

value: grade 1


title: HF0408

value: HENRY FORD HOSPITAL (RETRO)

value: grade 4


title: E09471_T_Xba

description: Xba

value: yes

value: Astrocytoma


title: ASD patient [SNP192]


title: E09494_B_Xba

description:
Duplicate
Xba


title: E09454_T_Xba

description: Xba


title: HF0180

value: brain


title: HF0212


title: Father of SNP104 [SNP190]

source_name: Father of SNP104


title: HF0138


title: E09489_B_Xba

description:
Duplicate
Xba


title: E09454_B_Xba

description:
Duplicate
Xba


title: HF0066


title: ASD patient [SNP196]


title: Mother of SNP104 [SNP189]

source_name: Mother of SNP104


title: E09451_T_Xba

description: Xba

value: UNIVERSITY OF WISCONSIN


title: ASD patient [SNP191]

value: Peripheral blood


title: Father of SNP181 [SNP186]

source_name: Father of SNP181


title: E09451_B_Xba

description:
Duplicate
Xba


title: E50123


title: HF0050


title: ASD patient [SNP188]


title: HF0024


title: E50057

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: E09449_B_Xba

description:
Duplicate
Xba


title: HF0031


title: E50091

value: MEMORIAL SLOAN KETTERING CANCER CENTER


title: E50074

value: DANA-FARBER CANCER INSTITUTE


title: E10662_duplicate


title: E10596


title: ASD patient [SNP184]

value: M


title: E09448_T_Xba

description: Xba

value: OLIGODENDROGLIOMA

value: III


title: ASD patient [SNP187]


title: E09448_B_Xba

description:
Duplicate
Xba

value: UCSF


title: HF0048

value: glioblastoma multiforme


title: Mother of SNP24 [SNP182]

source_name: Mother of SNP24

value: F

value: no


title: E09440_T_Xba

description: Xba

value: mixed

value: II


title: E10514

value: NIH NEURO-ONCOLOGY BRANCH


title: Father of SNP24 [SNP183]

source_name: Father of SNP24


title: E10512


title: E10662


title: E09440_B_Xba

description:
Duplicate
Xba


title: ASD patient [SNP181]


title: E10488

value: grade 4


title: E10444

value: brain


title: HF0790

value: HENRY FORD HOSPITAL (RETRO)


title: HF0142


title: E09419_T_Xba

description: Xba

value: yes


title: Mother of SNP181 [SNP185]

source_name: Mother of SNP181

value: Peripheral blood


title: ASD patient [SNP178]


title: E10462


title: E10312


title: E09405_T_Xba

description: Xba

source_name: Brain

value: GBM

value: IV


title: E10313

value: UNIV OF PITTSBURGH


title: E10306


title: E10318


title: E10305


title: E10300


title: E10551


title: E09405_B_Xba

description:
Duplicate
Xba


title: E10292


title: E10271

value: DANA-FARBER CANCER INSTITUTE


title: E10433


title: E10264

value: NABTT/HENRY FORD HOSPITAL


title: E09398_B_Xba

description:
Duplicate
Xba

value: Astrocytoma

value: UCSF


title: E10284

value: glioblastoma multiforme


title: E09449_T_Xba

description: Xba


title: E10290


title: Mother of SNP169 [SNP170]

source_name: Mother of SNP169

value: F

value: no


title: ASD patient [SNP174]

value: M


title: ASD patient [SNP173]


title: E10262

source_name: brain


title: E10267


title: E09378_T_Xba

description: Xba

value: UNKNOWN

value: NIH NEURO-ONCOLOGY BRANCH


title: E09378_B_Xba

description:
Duplicate
Xba


title: ASD patient [SNP175]


title: E09398_T_Xba

description: Xba

value: II


title: E10252

value: brain


title: E10258

value: UNIVERSITY OF SAN FRANCISCO


title: E09369_T_Xba

description: Xba

value: yes


title: ASD patient [SNP180]

value: Peripheral blood


title: Father of SNP169 [SNP171]

source_name: Father of SNP169


title: ASD patient [SNP167]


title: E09369_B_Xba

description:
Duplicate
Xba

value: GBM

value: IV


title: ASD patient [SNP166]


title: E09362_T_Xba

description: Xba

value: ASTROCYTOMA


title: E10203


title: E10193

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: E10211


title: E09419_B_Xba

description:
Duplicate
Xba

value: OLIGODENDROGLIOMA

value: III


title: E10226

value: NABTT/HENRY FORD HOSPITAL

value: glioblastoma multiforme


title: E10227


title: E09362_B_Xba

description:
Duplicate
Xba


title: E10249


title: ASD patient [SNP172]

value: no


title: E10191


title: E10184


title: E10172


title: E09358_T_Xba

description: Xba

value: mixed

value: UCSF


title: ASD patient [SNP164]

value: F


title: ASD patient [SNP165]


title: E09358_B_Xba

description:
Duplicate
Xba

value: II


title: E10144

value: NIH NEURO-ONCOLOGY BRANCH

value: brain

value: grade 4


title: E10140

value: MEMORIAL SLOAN KETTERING CANCER CENTER


title: ASD patient [SNP163]

value: Peripheral blood

value: M

value: yes


title: E10158


title: E09355_T_Xba

description: Xba

value: GBM

value: DANA-FARBER CANCER INSTITUTE


title: E09355_B_Xba

description:
Duplicate
Xba


title: E09348_T_Xba

description: Xba


title: E10041


title: E10077

value: UNIVERSITY OF SAN FRANCISCO


title: E10031

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: E09348_B_Xba

description:
Duplicate
Xba


title: ASD patient [SNP154]


title: E10102

value: glioblastoma multiforme


title: E10029

value: H. LEE MOFFITT CANCER CENTER


title: E10110


title: E10016


title: E10250

value: NABTT/HENRY FORD HOSPITAL


title: E10026


title: E09331_T_Xba

description: Xba

value: IV


title: E10012


title: E10013


title: Father of SNP152 [SNP153]

source_name: Father of SNP152

value: no


title: E09296_T_Xba

description: Xba

value: ASTROCYTOMA

value: II


title: E09331_B_Xba

description:
Duplicate
Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: E09967

value: brain

value: grade 4


title: E09951

value: UNIV OF PITTSBURGH


title: ASD patient [SNP152]

value: Peripheral blood

value: M


title: E09278B_T_Xba

description: Xba

value: GBM


title: E09956


title: E09278_T_Xba

description: Xba

value: yes


title: E09930


title: E10002


title: E09907

value: NABTT/H. LEE MOFFITT CANCER CENTER


title: E09917

value: UNIVERSITY OF WISCONSIN


title: E09278_B_Xba

description:
Duplicate
Xba


title: Mother of SNP152 [SNP151]

source_name: Mother of SNP152

value: F


title: E09938

value: H. LEE MOFFITT CANCER CENTER

value: glioblastoma multiforme


title: E09906


title: E09264_T_Xba

description: Xba

value: UNKNOWN


title: ASD patient [SNP168]

value: no


title: ASD patient [SNP155]


title: ASD patient [SNP169]


title: E09264_B_Xba

description:
Duplicate
Xba


title: ASD patient [SNP149]


title: ASD patient [SNP150]


title: ASD patient [SNP145]


title: E09847

value: UNIVERSITY OF SAN FRANCISCO


title: ASD patient [SNP148]


title: ASD patient [SNP141]


title: E09846


title: E09833


title: E09852

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: E09842


title: E09857


title: E09832


title: E09263_T_Xba

description: Xba

value: Unknown

value: NIH NEURO-ONCOLOGY BRANCH


title: E09862

value: brain

value: grade 4


title: E09829


title: Mother of SNP65 [SNP134]

source_name: Mother of SNP65

value: Peripheral blood


title: E09263_B_Xba

description:
Duplicate
Xba


title: E09263B_NT_Xba

description:
second resection/operation - nontumor
Xba


title: E09810


title: E09825


title: E09802


title: E09262_T_Xba

description: Xba

value: MIXED


title: Father of SNP65 [SNP137]

source_name: Father of SNP65

value: M


title: ASD patient [SNP133]

source_name: ASD patient


title: E09791


title: E09787


title: E09800


title: E09262_B_Xba

description:
Duplicate
Xba


title: ASD patient [SNP115]


title: E09239_T_Xba

description: Xba

value: yes

value: ASTROCYTOMA

value: III


title: E09239_B_Xba

description:
Duplicate
Xba


title: E09782

value: NABTT/JOHNS HOPKINS


title: ASD patient [SNP125]

value: F


title: E09752

value: H. LEE MOFFITT CANCER CENTER

value: glioblastoma multiforme


title: E09759

value: UNIVERSITY OF WISCONSIN


title: ASD patient [SNP131]


title: ASD patient [SNP146]


title: E09742


title: E09238_T_Xba

description: Xba

value: UNKNOWN


title: ASD patient [SNP124]

value: no


title: E09744


title: E09730


title: E09233_B_Xba

description:
Duplicate
Xba

value: GBM

value: IV


title: E09263B_T_Xba

description:
second resection/operation-tumor
Xba

value: Unknown

value: NIH NEURO-ONCOLOGY BRANCH


title: E09722

value: brain

value: grade 4


title: E09740


title: E09786


title: ASD patient [SNP111]

value: Peripheral blood

value: M


title: ASD patient [SNP144]


title: E09698


title: ASD patient [SNP147]


title: E09232_T_Xba

description: Xba

value: yes


title: E09680


title: ASD patient [SNP110]


title: E09232_B_Xba

description:
Duplicate
Xba


title: E09670


title: E09231_T_Xba

description: Xba

value: ASTROCYTOMA


title: E09655


title: Control

city: Yangzhou

first: Shaohua

last: Shi

state: Jiangsu

address: 48 East Wenhui Road

department: College of Veterinary Medicine

country: China

institute: Yangzhou University

description:
15 days
control

data_processing:
Illumina Casava1.7 software used for basecalling.
Get Raw sequencing Reads may contain low overall quality, contain sequencing primers, low end quality unqualified Reads, the unqualified Reads is likely a certain effects on the quality analysis, so it must be filtered, the analysis of the data obtained can be used to clean Reads, application Seqtk [1]
Application Hisat2 (version: 2.0.4) spliced mapping algorithm reads after pretreatment for Genome mapping, this algorithm allows the length will not be able to match the mapping reads segmentation, more suitable for eukaryotic (area) between have introns transcriptome sequencing data; The default parameters
Reads into FPKM (Fragments could Per Kilobase of exon model Per m letters mapped reads) for the standardization of amount of gene expression. Application Stringtie (version: 1.3.0) in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) [6] normalization method, finally calculated using perl script FPKM value of each gene.
Genome_build: galgal4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts

organism: Gallus gallus

source_name: Lung

extract_protocol:
Lungs were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: White Leghorn

value: lung

tag: infection

value: Control


title: E09756

value: H. LEE MOFFITT CANCER CENTER

value: glioblastoma multiforme


title: E09654


title: E09231_B_Xba

description:
Duplicate
Xba

tag: patient id


title: ASD patient [SNP104]


title: E09649

value: UNIVERSITY OF SAN FRANCISCO


title: E09233_T_Xba

description: Xba

tag: analyzed with cindex?


title: E09624


title: Lung of SPF chicken infected with H5N1 NS1-truncated S strain

description:
15 days
SY


title: E09214_B_Xba

description:
Duplicate
Xba

tag: disease state


title: E09214_T_Xba

description: Xba

tag: provider


title: E09623

value: UNIV OF PITTSBURGH


title: E09615


title: E09622


title: Mother of SNP54 [SNP102]

source_name: Mother of SNP54

value: F

value: no


title: E09606


title: E09192_T_Xba

description: Xba

value: GBM

tag: tumorgrade

value: IV


title: E09605

value: brain


title: E09602

value: UNIVERSITY OF WISCONSIN

value: grade 4


title: E09610

value: NIH NEURO-ONCOLOGY BRANCH


title: E09192_B_Xba

description:
Duplicate
Xba


title: E09690


title: E09176_B_Xba

description:
Duplicate
Xba


title: E09601


title: E09167_T_Xba

description: Xba

value: UNKNOWN

value: DANA-FARBER CANCER INSTITUTE


title: E09176_T_Xba

description: Xba

value: yes

value: ASTROCYTOMA


title: Father of SNP46 [SNP76]

source_name: Father of SNP46

value: Peripheral blood

value: M


title: E09535

value: glioblastoma multiforme


title: E09489


title: E09483

value: UNIVERSITY OF SAN FRANCISCO


title: ASD patient [SNP59]


title: Lung of SPF chicken infected with H5N1 S strain

description:
15 days
99V

value: White Leghorn

value: lung

value: infected with H5N1 S strain


title: E09151_T_Xba

description: Xba


title: E09451


title: E09449


title: E09454


title: E09151_B_Xba

description:
Duplicate
Xba


title: E08021_T_Xba

description: Xba

value: OLIGODENDROGLIOMA

value: UCSF

value: III


title: Mother of SNP46 [SNP75]

source_name: Mother of SNP46

value: F

value: no


title: E09405

value: brain

value: grade 4


title: E09430

value: NIH NEURO-ONCOLOGY BRANCH


title: E09647


title: Mother of SNP59 [SNP108]

source_name: Mother of SNP59


title: E09348


title: Father of SNP54 [SNP103]

source_name: Father of SNP54


title: ASD patient [SNP136]


title: E08021_B_Xba

description:
Duplicate
Xba


title: E09278


title: ASD patient [SNP65]


title: E09331


title: E07733_T_Xba

description: Xba

value: yes

value: UNKNOWN

value: DANA-FARBER CANCER INSTITUTE


title: ASD patient [SNP24]

value: Peripheral blood

value: M


title: ASD patient [SNP54]


title: ASD patient [SNP46]


title: 88375506_T_Xba

description: Xba

value: GBM

value: TJU


title: E07733_B_Xba

description:
Duplicate
Xba


title: Sample147: Umbilical cord blood - Control

city: New York

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All statistical analyses were conducted in the statistical package R. All gene expression data were  processed,  normalized  and  quality  treated. Raw  data  were  background corrected,  quantile  normalized  and  log2 ransformed  using  the neqc function  of  limma,  a  robust  method  for  Illumina BeadChips. Non-specific  filtering retained  probes  expressed  in  at  least  50  arrays  with  a  detection P-value  <0.05. When multiple  microarray  probes  mapped  to  the  same  HGNC  symbol, we  used  a  median reduction technique and used the resulting collapsed expression profile for each gene for further  analysis. Resulting  normalized  data  were  inspected  for  outlying  samples  using unsupervised  hierarchical  clustering  of  samples  and  principal  component  analysis  to identify  potential  outliers  outside  two  standard  deviations  from  these  grand  averages. Based  on  these  metrics, 19 samples  were  labeled  as  outliers and 149 samples  passed into  the subsequent analyses.

source_name: Umbilical cord blood

label_protocol: Complementary DNA was derived from RNA and then hybridized, and raw probe intensities were generated on Illumina HumanHT-12 v4 BeadChip arrays.

extract_protocol: RNA was extracted from PAXgene RNA tubes as per the manufacturer's instructions. All samples had a Bioanalyzer RNA Integrity Number (RIN) >7.

treatment_protocol: Umbilical cord blood was collected by trained staff after offspring delivery but before delivery of the placenta. The cord was clamped and cut, after which the clamp was released and cord blood drained by gravity into a kidney collection dish. Cord blood was collected using a syringe for processing and storage at -80C in PAXgene RNA tubes.

value: Umbilical cord blood

tag: maternal diagnosis

value: Control

tag: neonate gender

value: Female

tag: rin

tag: microarray batch

value: Two


title: Sample148: Umbilical cord blood - Control

tag: tissue

value: One


title: Father of SNP59 [SNP107]

source_name: Father of SNP59


title: Sample145: Umbilical cord blood - Control


title: E09139

tag: disease

value: glioblastoma multiforme

tag: extract name


title: E09214

tag: tumor grade

tag: assay name


title: Sample146: Umbilical cord blood - Control

value: Male


title: E09192

value: brain


title: E09569

value: grade 4


title: 88295267_T_Xba

description: Xba

source_name: Brain


title: 900_0053_03

value: THOMAS JEFFERSON UNIVERSITY


title: E09137

value: NIH NEURO-ONCOLOGY BRANCH


title: E09233


title: 900_00_5554


title: E09478

value: UNIVERSITY OF WISCONSIN


title: 88375506_B_Xba

description:
Duplicate
Xba


title: 860772_T_Xba

description: Xba

value: yes

value: TBD


title: 860772_B_Xba

description:
Duplicate
Xba


title: 900_00_5551


title: ASD patient [SNP83]

value: Peripheral blood

tag: gender

value: M

tag: adhd

value: no


title: 900_0052_99


title: Sample149: Umbilical cord blood - Control

value: Umbilical cord blood


title: Sample142: Umbilical cord blood - Control

value: Control


title: Sample143: Umbilical cord blood - Control

value: Female


title: 81668782_B_Xba

description:
Duplicate
Xba

value: TJU


title: 900_00_5546


title: 900_00_5544


title: 81668782_T_Xba

description: Xba


title: 900_00_5548


title: Sample140: Umbilical cord blood - Control

value: Two


title: 900_00_5541

value: glioblastoma multiforme


title: 3525342_B_Xba

description:
Duplicate
Xba


title: 900_00_5543


title: E09369


title: Sample141: Umbilical cord blood - Control

value: Male

value: One


title: 900_00_5540

value: brain


title: 900_00_5542

value: THOMAS JEFFERSON UNIVERSITY


title: Sample139: Umbilical cord blood - Control


title: 900_00_5489


title: 3525342_T_Xba

description: Xba


title: 3523498_T_Xba

description: Xba


title: Sample138: Umbilical cord blood - Control


title: 3523498_B_Xba

description:
Duplicate
Xba


title: 900_00_5488


title: 3522254_T_Xba

description: Xba


title: 900_00_5462


title: Sample137: Umbilical cord blood - Control


title: Sample136: Umbilical cord blood - Control


title: 900_00_5458


title: 900_00_5445


title: 900_00_5414


title: Sample135: Umbilical cord blood - Control


title: 900_00_5404_B


title: 900_00_5413


title: 3514945_B_Xba

description:
Duplicate
Xba


title: 900_00_5384


title: 3513467_T_Xba

description: Xba


title: Sample134: Umbilical cord blood - Control


title: Sample133: Umbilical cord blood - Control


title: 900_00_5404


title: 3522254_B_Xba

description:
Duplicate
Xba


title: 900_00_5396


title: ASD patient [SNP32]

value: F


title: 3514945_T_Xba

description: Xba


title: Sample132: Umbilical cord blood - Control


title: Sample131: Umbilical cord blood - Control


title: 900_00_5381


title: 900_00_5338


title: 3513467_B_Xba

description:
Duplicate
Xba


title: 900_00_5342


title: 900_00_5317


title: ASD patient [SNP16]


title: 900_00_5346


title: 900_00_53_32


title: 3512529_T_Xba

description: Xba


title: Sample130: Umbilical cord blood - Control


title: 900_00_5316


title: Sample129: Umbilical cord blood - Control


title: 900_00_5379


title: 3512529_B_Xba

description:
Duplicate
Xba


title: MD570013

value: M. D. ANDERSON CANCER CENTER

value: astrocytoma

value: grade 3


title: 3506280_T_Xba

description: Xba

value: yes

value: TBD


title: E09138

value: NIH NEURO-ONCOLOGY BRANCH

value: grade 4


title: 3506280_B_Xba

description:
Duplicate
Xba


title: MD550715


title: 3504050_T_Xba

description: Xba


title: MD554082


title: 3504050_B_Xba

description:
Duplicate
Xba


title: Sample128: Umbilical cord blood - Control

value: Umbilical cord blood

value: Control


title: 3497265_T_Xba

description: Xba

value: TJU


title: Sample126: Umbilical cord blood - Control

value: Female


title: MD550239


title: MD548457


title: HF1677

value: HENRY FORD HOSPITAL (RETRO)

value: grade 2


title: MD547038


title: HF1708


title: Sample127: Umbilical cord blood - Control

value: One


title: HF1581

value: brain


title: HF1587


title: HF1606


title: 3497265_B_Xba

description:
Duplicate
Xba


title: 3495697_T_Xba

description: Xba


title: Sample123: Umbilical cord blood - Control

value: Male

value: Two


title: Sample122: Umbilical cord blood - Control


title: Sample144: Umbilical cord blood - Control


title: HF1568


title: HF1588


title: MD548092

value: M. D. ANDERSON CANCER CENTER


title: HF1551

value: astrocytoma


title: HF1613

value: grade 3


title: 3495697_B_Xba

description:
Duplicate
Xba


title: Sample120: Umbilical cord blood - Control


title: Sample124: Umbilical cord blood - Control


title: 3089254_T_Xba

description: Xba

value: yes


title: HF1511


title: 3089254_B_Xba

description:
Duplicate
Xba

value: TBD


title: Sample121: Umbilical cord blood - Control


title: HF1490


title: HF1489


title: Sample117: Umbilical cord blood - Control


title: Sample119: Umbilical cord blood - Control


title: HF1494


title: 03486876_T_Xba

description: Xba

value: GBM


title: HF1442


title: HF1409


title: HF1381


title: HF1407


title: 03484586_T_Xba

description: Xba


title: HF1475


title: 03484586_B_Xba

description:
Duplicate
Xba


title: Sample118: Umbilical cord blood - Control


title: Sample114: Umbilical cord blood - Control


title: Sample116: Umbilical cord blood - Control


title: Sample115: Umbilical cord blood - Control


title: Sample113: Umbilical cord blood - Control


title: 03484270_T_Xba

description: Xba

value: Astrocytoma

value: III


title: HF1366


title: HF1344


title: 03484270_B_Xba

description:
Duplicate
Xba


title: HF1380


title: 03480779_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: HF1325


title: HF1334


title: HF1319


title: HF1316


title: Sample112: Umbilical cord blood - Control

value: Umbilical cord blood

value: Control


title: HF1345

value: HENRY FORD HOSPITAL (RETRO)


title: 03480779_B_Xba

description:
Duplicate
Xba

value: TJU


title: 03479212_T_Xba

description: Xba


title: Sample110: Umbilical cord blood - Control

value: One


title: HF1255

value: brain


title: Sample111: Umbilical cord blood - Control

value: Male


title: HF1295


title: HF1286


title: HF1246

value: grade 2


title: HF1242


title: 03477889_T_Xba

description: Xba


title: Sample125: Umbilical cord blood - Control

value: Female


title: HF1280

value: astrocytoma


title: Sample109: Umbilical cord blood - Control


title: HF1235


title: Sample108: Umbilical cord blood - Control


title: 03486876_B_Xba

description:
Duplicate
Xba


title: 03476542_T_Xba

description: Xba


title: 03479212_B_Xba

description:
Duplicate
Xba


title: HF1136

value: grade 3


title: HF1232


title: HF1156


title: 03476542_B_Xba

description:
Duplicate
Xba


title: HF1185


title: HF1150


title: HF1032


title: HF1186


title: Sample106: Umbilical cord blood - Control


title: 03473405_T_Xba

description: Xba

value: yes


title: Sample107: Umbilical cord blood - Control


title: HF1000


title: Sample105: Umbilical cord blood - Control


title: 03473405_B_Xba

description:
Duplicate
Xba


title: HF0982


title: HF0975


title: 03473067_T_Xba

description: Xba


title: 03474525_T_Xba

description: Xba


title: 03473067_B_Xba

description:
Duplicate
Xba


title: HF0954.2


title: HF0953


title: HF0966


title: HF0899


title: Sample102: Umbilical cord blood - Control

value: Two


title: Sample100: Umbilical cord blood - Control


title: Sample103: Umbilical cord blood - Control


title: HF0931


title: HF0855


title: 03471616_T_Xba

description: Xba

value: II


title: HF0822


title: HF0936


title: HF0914


title: Sample104: Umbilical cord blood - Control


title: 03471616_B_Xba

description:
Duplicate
Xba


title: HF0850


title: HF0844


title: Sample99: Umbilical cord blood - Control


title: HF0802


title: HF0757


title: Sample101: Umbilical cord blood - Control


title: Sample98: Umbilical cord blood - Control


title: HF0778


title: 03468400_B_Xba

description:
Duplicate
Xba

value: GBM


title: 03468400_T_Xba

description: Xba


title: 03466950_T_Xba

description: Xba


title: 03466950_B_Xba

description:
Duplicate
Xba


title: 03465304_T_Xba

description: Xba


title: Sample97: Umbilical cord blood - Control


title: Sample96: Umbilical cord blood - Control


title: HF0702


title: Sample93: Umbilical cord blood - Control


title: Sample95: Umbilical cord blood - Control


title: 03465304_B_Xba

description:
Duplicate
Xba


title: HF0670


title: Astro-D2KO mouse with SE induced by Lithium-pilocarpine 4

city: Chicago

first: Gustavo

middle: Werpel

last: Fernandes

state: IL

address: 5841 South Maryland Av.

department: Endocrinology

institute: University of Chicago

description: Gene expression data from the brain of Astro-D2KO mouse with SE induced by Lithium-pilocarpine

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized on GeneChip Affymetrix MoGene 2.0 st Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips underwent a process of scanning, visualization of arrays and quality control analysis.

data_processing: The data were analyzed using Affymetrix default analysis settings and RMA as normalization method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10uL with concentration at least 250ng/3uL (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Lithium-pilocarpine-induced SE protocol: Mice were given lithium chloride (LiCl; Sigma; 10 mEq/Kg, i.p.;) 18 h before administration of pilocarpine or saline.This lowers the animal’s threshold for seizure and a much lower dose of pilocarpine (65 mg/kg, i.p.) was used.

value: Brain

tag: brain region

value: hippocampus

tag: genotype

value: + Flox D2/ + cre Glia

tag: age

value: 8-10 weeks-old

tag: strain


title: Astro-D2KO mouse with SE induced by Lithium-pilocarpine 3


title: HF0726

tag: provider

value: HENRY FORD HOSPITAL (RETRO)


title: Astro-D2KO mouse with SE induced by Lithium-pilocarpine 1


title: Sample94: Umbilical cord blood - Control

value: Umbilical cord blood

value: Control


title: Astro-D2KO mouse treated with saline solution 3

description: Gene expression data from the brain of Astro-D2KO mouse treated with saline solution


title: HF0639

value: brain


title: Astro-D2KO mouse treated with saline solution 4


title: 03463812_B_Xba

description:
Duplicate
Xba

tag: patient id

tag: disease state

value: TJU


title: Sample92: Umbilical cord blood - Control

tag: maternal diagnosis

tag: neonate gender

value: One


title: Astro-D2KO mouse with SE induced by Lithium-pilocarpine 2


title: Sample91: Umbilical cord blood - Control

value: Male

tag: rin

tag: microarray batch


title: Astro-D2KO mouse treated with saline solution 2

tag: tissue


title: HF0488

tag: disease

value: astrocytoma

value: grade 2

tag: extract name


title: Sample90: Umbilical cord blood - Control


title: 03463522_T_Xba

description: Xba

value: Astrocytoma

tag: tumorgrade


title: HF0608

tag: tumor grade

tag: assay name


title: HF0491


title: HF0606


title: HF0450


title: Sample89: Umbilical cord blood - Control

value: Female


title: Astro-D2KO mouse treated with saline solution 1

tag: brain region


title: 03461404_B_Xba

description:
Duplicate
Xba


title: 03461404_T_Xba

description: Xba

tag: analyzed with cindex?

value: yes


title: Control mouse with SE induced by Lithium-pilocarpine 4

description: Gene expression data from the brain of Control mouse with SE induced by Lithium-pilocarpine

tag: genotype

value: wild type/ + cre Glia

tag: age


title: 03461078_T_Xba

description: Xba

value: ASTROCYTOMA

tag: provider

value: III


title: Sample88: Umbilical cord blood - Control


title: Sample87: Umbilical cord blood - ControlTE

value: ControlTE


title: 03460111_B_Xba

description:
Duplicate
Xba

tag: patient id

value: II


title: HF0435

value: HENRY FORD HOSPITAL (RETRO)

value: grade 3


title: HF0434


title: HF0332


title: Control mouse with SE induced by Lithium-pilocarpine 2

value: Brain

value: hippocampus

value: 8-10 weeks-old

tag: strain


title: 03451592_T_Xba

description: Xba

tag: disease state

value: GBM

value: TJU


title: Sample86: Umbilical cord blood - ControlTE

value: Umbilical cord blood

tag: maternal diagnosis

tag: neonate gender

value: One


title: HF0329

value: astrocytoma

value: brain

value: grade 2


title: Control mouse with SE induced by Lithium-pilocarpine 3

value: wild type/ + cre Glia


title: HF0316


title: Control mouse treated with saline solution 4

description: Gene expression data from the brain of Control mouse treated with saline solution


title: Sample84: Umbilical cord blood - ControlTE

value: Female

tag: rin

tag: microarray batch


title: Control mouse with SE induced by Lithium-pilocarpine 1

tag: tissue


title: 03451592_B_Xba

description:
Duplicate
Xba


title: 03460111_T_Xba

description: Xba

value: yes

value: ASTROCYTOMA


title: Sample83: Umbilical cord blood - ControlTE

value: ControlTE

value: Male

value: Two


title: Control mouse treated with saline solution 3

value: Brain


title: Control mouse treated with saline solution 1

value: hippocampus


title: Sample85: Umbilical cord blood - ControlTE


title: Control mouse treated with saline solution 2

value: 8-10 weeks-old


title: HF0305

value: HENRY FORD HOSPITAL (RETRO)

tag: disease

tag: extract name


title: 03450728_T_Xba

description: Xba

value: OLIGODENDROGLIOMA

value: TJU


title: HF0252

tag: tumor grade


title: Sample81: Umbilical cord blood - ControlTE

value: Umbilical cord blood

value: One


title: 03450728_B_Xba

description:
Duplicate
Xba


title: 03448110B_T_Xba

description:
second resection/operation
Xba

value: GBM


title: Sample82: Umbilical cord blood - ControlTE


title: 03444255_T_Xba

description: Xba


title: bovine pituitary_ISe_biological rep6

city: Lexington

first: James

last: Matthews

state: KY

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

institute: University of Kentucky

description: supplemented with sodium selenite

hyb_protocol: The biotinylated cRNAs were further fragmented and used as probes to hybridize the gene chips in the GeneChip Hybridization Oven 640 (Affymetrix).After hybridization, the chips were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G; Affymetrix)

data_processing:
Data were collected using the GeneChip Operating Software (GCOS, version 1.2; Affymetrix). The raw expression intensity values from the GCOS were imported into Partek Genomics Suite software (PGS 7.17.0918; Partek Inc.). For GeneChip background correction, the algorithm of Robust Multichip Averaging adjusted with probe length and GC oligo contents was implemented. The background-corrected data were further converted into expression values using quantile normalization across all the chips and median polish summarization of multiple probes for each probe set.
probe group file: BovGene-1_0-st.pgf
meta-probeset file: BovGene-1_0-st.mps

organism: Bos taurus

source_name: bovine pituitary, ISe

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Pituitary collected right after death of each animal

extract_protocol: Pituirary was placed in a foil pack, flash-frozen in liquid nitrogen, and stored at -80°C. Total RNA was extracted from the whole frozen pituitary tissue using TRIzol Reagent following the manufacturer’s instructions.

treatment_protocol: Not applicable

value: pituitary

tag: supplement

value: sodium selenite (ISe)


title: Sample78: Umbilical cord blood - ControlTE


title: HF0152

source_name: brain

value: astrocytoma

value: brain

value: grade 3

tag: assay name


title: Sample79: Umbilical cord blood - ControlTE

value: ControlTE


title: HF0089


title: bovine pituitary_ISe_biological rep5

description: supplemented with sodium selenite


title: HF0244


title: 03448110_B_Xba

description:
Duplicate
Xba


title: Sample80: Umbilical cord blood - ControlTE

value: Female


title: bovine pituitary_ISe_biological rep1

description: supplemented with sodium selenite


title: 03444255_B_Xba

description:
Duplicate
Xba


title: bovine pituitary_ISe_biological rep2

description: supplemented with sodium selenite


title: HF0223

value: grade 2


title: HF0108


title: HF0026


title: bovine pituitary_OSe_biological rep7

description: supplemented with  SEL-PLEX

source_name: bovine pituitary, OSe

value: SEL-PLEX (OSe)


title: HF0087


title: bovine pituitary_ISe_biological rep3

description: supplemented with sodium selenite


title: 03448110_T_Xba

description: Xba

tag: analyzed with cindex?

value: yes


title: Sample75: Umbilical cord blood - ControlTE

value: Male

value: Two


title: Sample76: Umbilical cord blood - ControlTE


title: Sample77: Umbilical cord blood - ControlTE


title: 03442083_T_Xba

description: Xba


title: Sample74: Umbilical cord blood - ControlTE


title: 03442083_B_Xba

description:
Duplicate
Xba


title: 03441740_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

tag: tumorgrade

value: III


title: 03441740_T_Xba

description: Xba

value: TJU


title: HF0017

value: HENRY FORD HOSPITAL (RETRO)


title: bovine pituitary_OSe_biological rep6

description: supplemented with  SEL-PLEX


title: 03441358_T_Xba

description: Xba

value: GBM


title: bovine pituitary_OSe_biological rep5

description: supplemented with  SEL-PLEX

value: pituitary


title: Sample73: Umbilical cord blood - ControlTE

value: Umbilical cord blood


title: HF0022

value: astrocytoma


title: Sample72: Umbilical cord blood - ControlTE

value: One


title: bovine pituitary_OSe_biological rep4

description: supplemented with  SEL-PLEX


title: Sample70: Umbilical cord blood - ControlTE


title: E10710

value: NIH NEURO-ONCOLOGY BRANCH

value: brain


title: 03439543_T_Xba

description: Xba


title: E10540


title: 03437691_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: bovine pituitary_MIX_biological rep7

description: supplemented with 1: 1 blend of sodium selenite and SEL-PLEX

source_name: bovine pituitary, MIX

value: 1:1 blend (MIX) of ISe and OSe


title: Sample68: Umbilical cord blood - ControlTE

value: ControlTE

value: Female


title: E10645

value: grade 3


title: E10556


title: Sample69: Umbilical cord blood - ControlTE

value: Male

value: Two


title: bovine pituitary_OSe_biological rep1

description: supplemented with  SEL-PLEX

value: SEL-PLEX (OSe)


title: Sample71: Umbilical cord blood - ControlTE


title: 03437691_B_Xba

description:
Duplicate
Xba

value: TJU


title: 03441358_B_Xba

description:
Duplicate
Xba


title: bovine pituitary_OSe_biological rep3

description: supplemented with  SEL-PLEX


title: bovine pituitary_MIX_biological rep6


title: Sample67: Umbilical cord blood - ControlTE


title: E10615


title: bovine pituitary_OSe_biological rep2

description: supplemented with  SEL-PLEX


title: 03463812_T_Xba

description: Xba

value: yes


title: 03437595_T_Xba

description: Xba

value: ASTROCYTOMA

value: II


title: 03437595_B_Xba

description:
Duplicate
Xba


title: 03436958_T_Xba

description: Xba


title: Transformed HMECs rep1

description:
HMEC_RNAseq.DiffGeneExp.tdt
tfo1

source_name: mammary epithelial cells (HMECs)

tag: cell type

value: Transformed HMECs

tag: transgenes

value: Immortalized HMECs+ HRASG12V

tag: passages


title: bovine pituitary_MIX_biological rep5

value: pituitary


title: E10483

tag: provider

value: NIH NEURO-ONCOLOGY BRANCH

value: astrocytoma

value: grade 2


title: Sample66: Umbilical cord blood - ControlTE

value: Umbilical cord blood


title: E10482

value: brain


title: 03436958_B_Xba

description:
Duplicate
Xba

tag: patient id

tag: disease state

value: OLIGODENDROGLIOMA


title: Sample65: Umbilical cord blood - ControlTE

tag: maternal diagnosis

value: ControlTE

tag: neonate gender

value: Female


title: bovine pituitary_ISe_biological rep4

description: supplemented with sodium selenite

value: sodium selenite (ISe)


title: Immortalized HMECs rep1

description:
HMEC_RNAseq.DiffGeneExp.tdt
imo1

value: Immortalized HMECs

value: HMECs+ hTERT, p53DD, cyclin D1, CDK4R24C and c-MYCT58A


title: 03434766_T_Xba

description: Xba

value: yes

value: GBM

value: TJU


title: Primary HMECs rep1

description:
Obtained from Lonza at p9; 50Y female healthy donor
HMEC_RNAseq.DiffGeneExp.tdt
prim1

value: Primary HMECs

value: normal HMECs


title: Sample64: Umbilical cord blood - PTSD

value: PTSD

value: Male

tag: rin

tag: microarray batch

value: Two


title: Sample62: Umbilical cord blood - PTSD

tag: tissue

value: One


title: Sample63: Umbilical cord blood - PTSD

value: Umbilical cord blood


title: 03434174_B_Xba

description:
Duplicate
Xba


title: 03434174_T_Xba

description: Xba


title: bovine pituitary_MIX_biological rep2

value: pituitary

value: 1:1 blend (MIX) of ISe and OSe


title: bovine pituitary_MIX_biological rep1


title: E10285

value: UNIVERSITY OF SAN FRANCISCO

tag: disease

value: astrocytoma

value: brain

tag: extract name


title: E10286

value: UNIV OF PITTSBURGH


title: 03433293_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: Sample61: Umbilical cord blood - PTSD

value: Female


title: E10216

value: NIH NEURO-ONCOLOGY BRANCH


title: Sample59: Umbilical cord blood - PTSD


title: Sample58: Umbilical cord blood - PTSD


title: bovine pituitary_MIX_biological rep3

tag: supplement


title: bovine pituitary_MIX_biological rep4


title: 03434766_B_Xba

description:
Duplicate
Xba

value: GBM

value: TJU


title: E10248

value: NABTT/HENRY FORD HOSPITAL

tag: assay name


title: Sample60: Umbilical cord blood - PTSD

value: PTSD


title: 03433293_B_Xba

description:
Duplicate
Xba


title: Sample57: Umbilical cord blood - PTSD


title: E10192

value: UNIVERSITY OF CALIFORNIA SCHOOL OF MEDICINE


title: 03431774_T_Xba

description: Xba

tag: analyzed with cindex?

value: yes


title: E10196


title: E10182


title: 03431774_B_Xba

description:
Duplicate
Xba


title: 03431712_B_Xba

description:
Duplicate
Xba


title: 03431712_T_Xba

description: Xba


title: 03425149_T_Xba

description: Xba


title: Sample55: Umbilical cord blood - PTSD

value: Two


title: 03425149_B_Xba

description:
Duplicate
Xba


title: Sample56: Umbilical cord blood - PTSD

value: Umbilical cord blood

value: One


title: Sample53: Umbilical cord blood - PTSD

value: Male


title: SER5_CTRL

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: RNAPII SER5P was profiled in RMG-1 clone in ARID1A-WT condition

library_source: genomic

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq): BWA
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: RMG-1 cells were maintained in DMEM/F12 50/50 medium (Corning) supplemented with 10% (v/v) of TET-free fetal bovine serum (Clontech) or super calf serum (GEMcell) and 2 mM of L-glutamine (Corning).

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: Doxycicline (2ug/ml, 72 hours) was used to induced the knock-down of ARID1A with a TET-inducible shRNA.

tag: experiment

value: CHIP-seq

tag: chip antibody

value: ACTIVE MOTIF MOUSE MONOCLONAL (61086)


title: Sample51: Umbilical cord blood - PTSD


title: Sample54: Umbilical cord blood - PTSD


title: SER5_DOX

description: RNAPII SER5P was profiled in RMG-1 clone in ARID1A-KD condition


title: 03421899_T_Xba

description: Xba

value: ASTROCYTOMA

tag: tumorgrade

value: III


title: Sample52: Umbilical cord blood - PTSD


title: SER2_DOX

description: RNAPII SER2P was profiled in RMG-1 clone in ARID1A-KD condition

value: ACTIVE MOTIF MOUSE MONOCLONAL (610864


title: E10162

value: astrocytoma

value: brain

tag: tumor grade

value: grade 3


title: Sample50: Umbilical cord blood - PTSD

value: Female


title: E10138

tag: provider

value: UNIVERSITY OF SAN FRANCISCO


title: E10025

value: H. LEE MOFFITT CANCER CENTER

value: grade 2


title: E10105

value: NIH NEURO-ONCOLOGY BRANCH


title: E10062


title: E10103

value: HENRY FORD HOSPITAL


title: E09997


title: SER2_CTRL

description: RNAPII SER2P was profiled in RMG-1 clone in ARID1A-WT condition


title: E09959


title: Sample49: Umbilical cord blood - PTSD

value: Umbilical cord blood

value: PTSD


title: 03421536_T_Xba

description: Xba

tag: patient id

value: yes

value: UNCLASSIFIED

value: TJU


title: 03421536_B_Xba

description:
Duplicate
Xba

tag: disease state


title: 03418160_T_Xba

description: Xba

value: GBM


title: 03421899_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

value: III


title: E09966

value: astrocytoma


title: Sample48: Umbilical cord blood - PTSD

tag: maternal diagnosis

value: Male

value: Two


city: Jerusalem

first: Ofer

last: Mandelbaum

state: Select a State or Province

address: Hebrew University Medical School

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University Faculty of Medicine, Jerusalem, Israel

description:
annotated peak file: GSE100636_annotated_peaks_ATAC__data.xlsx
sample name in annotated peak file: non_first_P_b_S10_L001_R1_001
Tissue from sample GSM3030146 (positive_primigravidae_dNK) is from a different individual than sample GSM3030147 (positive_multigravidae_subsequent_pregnancy_dNK)

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using Bowtie2 aligner version 2.2.9 (Langmead et al., 2009) with default parameters. The Picard tool MarkDuplicates from the Broad Institute (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates. To identify regions of enrichment (peaks) we used the HOMER package makeTagDirectory followed by findPeaks command “-style factor -size 300 (Heinz et al., 2010). Union peaks file was generated by combining and merging overlapping peaks in all samples. Reads in the union peak file were counted using HOMER annotatePeaks (-raw). Normalization was done using the DESeq2 R-package.
The Picard tool MarkDuplicates from the Broad Institute (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates.
To identify regions of enrichment (peaks) we used the HOMER package makeTagDirectory followed by findPeaks command “-style factor -size 300 (Heinz et al., 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Union peaks file was generated by combining and merging overlapping peaks in all samples. Reads in the union peak file were counted using HOMER annotatePeaks (-raw). Normalization was done using the DESeq2 R-package.

source_name: decidual Natural killer cells

extract_protocol:
NKG2Chigh dNK cells purified from pooled decidua samples (4 for primigravid and 7 for multigravid) were sorted (confirmed by staining with anti CD56 and anti NKG2C antibodies). The same was done with pooled nulligravid and multigravid endometrial NKG2Chigh cells. In multigravid dNK cells also NKG2Cneg cells were sorted. All epidemiological details of these samples are mentioned in tables 8, 14 and 15. 5*105cells from each population were used for the ATACseq assay. The cells were centrifuged at 500g for 3 min, followed by a washing step. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min at 4°C. Next, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C. The samples were purified using a Qiagen MinElute Kit.
Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification, the libraries were purified using a Qiagen MinElute Kit and sequenced.

tag: cell type

value: dNK cells positive for NKG2C

tag: pregnancy status

value: subsequent pregnancy multigravidae


title: positive_multigravidae_eNK

description:
annotated peak file: GSE100636_annotated_peaks_ATAC__data.xlsx
sample name in annotated peak file: enk_were_P_a_S1_L001_R1_001

source_name: endometrial Natural killer cells

value: eNK cells positive for NKG2C

value: were pregnant multigravidae


title: 03418160_B_Xba

description:
Duplicate
Xba


title: positive_nulligravidae_eNK

description:
annotated peak file: GSE100636_annotated_peaks_ATAC__data.xlsx
sample name in annotated peak file: enk_never_P__S5_L001_R1_001

value: were never pregnant nulligravidae


title: E10362

value: NABTT/HENRY FORD HOSPITAL

value: brain


title: 03352571_T_Xba

description: Xba


title: Sample47: Umbilical cord blood - PTSD

value: Umbilical cord blood

value: PTSD

tag: neonate gender

tag: rin

tag: microarray batch

value: One


title: Sample44: Umbilical cord blood - PTSDDep

tag: tissue

value: PTSDDep

value: Female


title: positive_primigravidae_dNK

description:
annotated peak file: GSE100636_annotated_peaks_ATAC__data.xlsx
sample name in annotated peak file: first_P_S7_L001_R1_001
Tissue from sample GSM3030146 (positive_primigravidae_dNK) is from a different individual than sample GSM3030147 (positive_multigravidae_subsequent_pregnancy_dNK)

value: first pregnancy primigravidae


title: Sample45: Umbilical cord blood - PTSD


title: 03352571_B_Xba

description:
Duplicate
Xba

value: GBM

value: TJU


title: 03272709_T_Xba

description: Xba

value: yes


title: Sample42: Umbilical cord blood - PTSDDep

value: Male

value: Two


title: Sample46: Umbilical cord blood - PTSD


title: 03272709_B_Xba

description:
Duplicate
Xba


title: E09921

value: HENRY FORD HOSPITAL

tag: disease

value: astrocytoma

tag: extract name


title: E09892

value: NIH NEURO-ONCOLOGY BRANCH

tag: assay name


title: E09914

value: H. LEE MOFFITT CANCER CENTER

value: grade 3


title: E09948

value: brain


title: 03184579_T_Xba

description: Xba

tag: analyzed with cindex?


title: Sample43: Umbilical cord blood - PTSDDep

value: Umbilical cord blood


title: E09855

value: UNIVERSITY OF SAN FRANCISCO


title: Sample41: Umbilical cord blood - PTSDDep


title: Sample39: Umbilical cord blood - PTSDDep

value: One


title: E09920

value: UNIVERSITY OF WISCONSIN


title: E09826


title: E09819


title: E09818


title: Sample40: Umbilical cord blood - PTSDDep

value: PTSDDep


title: Sample37: Umbilical cord blood - PTSDDep

value: Female


title: Sample38: Umbilical cord blood - PTSDDep


title: E09811

value: grade 2


title: 03184579_B_Xba

description:
Duplicate
Xba

value: GBM

value: TJU


title: 00715851_B_Xba

description:
Duplicate
Xba

value: ASTROCYTOMA

value: II


title: 01113810_B_Xba

description:
Duplicate
Xba


title: Sample36: Umbilical cord blood - PTSDDep


title: Sample33: Umbilical cord blood - PTSDDep

value: Male

value: Two


title: E09471

value: astrocytoma


title: Sample30: Umbilical cord blood - Depression

value: Depression


title: E09797

value: H. LEE MOFFITT CANCER CENTER


title: E09408

value: brain

value: grade 3


title: E09743


title: 00641238_T_Xba

description: Xba

value: yes


title: 00518392_T_Xba

description: Xba


title: 01074569_B_Xba

description:
Duplicate
Xba


title: 00715851_T_Xba

description: Xba


title: 00641238_B_Xba

description:
Duplicate
Xba


title: 13432X6_3-Low

city: Salt Lake City

last: Williams

state: UT

address: 15 N. Medical Dr. E.

department: Pathology

institute: University of Utah

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument, a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents.
Real Time Analysis Software (RTA v1.18.61) performed base calling and assigned a quality score to each base for each cycle.
Reads were aligned to hg19 + splice junctions using novoalign. Spliced alignments were converted back to genomic space, sorted and indexed using Useq 8.8.9 SamTranscriptomeParser.
Normalized coverage tracks (depth per million mapped reads) were generated using USeqSam2USeq and USeq2UCSCExe
Differentially expressed genes were determined using DefinedRegionDifferentialSeq (DRDS). DRDS counts the number of reads aligning to each gene and then calls DESeq2, which normalizes the counts and identifies differently expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts from DRDS in a single tab-delimited file

source_name: CD4+ T cells 5 days post LCMV infection

extract_protocol:
Splenocytes were stained with CD4, Thy1.1, and CD25 and sorted via flow cytometry. Transgenic CD4+ T cells were lysed using QIAzol and total RNA was extracted using QIAGEN miRNeasy Kit.
RNA libraries were prepared for sequencing using NuGEN Ovation RNA-Seq System v2 kit and protocol.

tag: strain

value: Spleen

value: CD4+ T cells

tag: cd25 signature

value: Low


title: 13432X5_2-Low


title: Sample29: Umbilical cord blood - Depression

value: Umbilical cord blood

value: One


title: 01074569_T_Xba

description: Xba

value: GBM


title: Sample28: Umbilical cord blood - Depression


title: NOB1228_NBE_p3Side_Xba

description: Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: 13432X4_1-Low


title: E09531

value: UNIV OF PITTSBURGH


title: E09393

value: UNIVERSITY OF SAN FRANCISCO

tag: tumor grade


title: Sample26: Umbilical cord blood - Depression

value: Male


title: Sample32: Umbilical cord blood - PTSDDep

value: PTSDDep

value: Female


title: Sample31: Umbilical cord blood - Depression

value: Depression


title: E10299

tag: provider

value: astrocytoma


title: 00518392_B_Xba

description:
Duplicate
Xba

tag: patient id

value: TJU


title: E09673

value: brain

value: grade 2


title: E09239

value: grade 3


title: Sample27: Umbilical cord blood - Depression


title: 13432X3_3-High

value: Spleen

value: CD4+ T cells

value: High


title: E09296

value: DANA-FARBER CANCER INSTITUTE


title: E09398


title: E09542


title: NOB0822_NBE_p10_Xba

description: Xba

tag: disease state

value: GBM


title: Sample24: Umbilical cord blood - Depression

value: Umbilical cord blood

tag: maternal diagnosis

value: Two


title: E09515

value: NIH NEURO-ONCOLOGY BRANCH


title: 13432X2_2-High

tag: cell type


title: Sample25: Umbilical cord blood - Depression

value: Male


title: NOB0320_NBE_p2_Xba

description: Xba


title: NOB0822_NBE_p3_Xba

description: Xba


title: 13432X1_1-High


title: E09231


title: E09212


title: E09801

value: H. LEE MOFFITT CANCER CENTER


title: NOB0308_NBE_R1b_Xba

description: Xba

tag: tumorgrade

value: IV


title: NOB0308_NBE_p30_IC2_Xba

description: Xba


title: Sample23: Umbilical cord blood - Depression

value: Depression

tag: neonate gender

value: One


title: 01113810_T_Xba

description: Xba

value: yes

value: TJU


title: NOB0211_NBE_NBE_p3_Xba

description: Xba

value: Unknown


title: NOB0308_NBE_p30_IC1_Xba

description: Xba


title: Sample22: Umbilical cord blood - Depression

tag: rin


title: MD570013_T_Xba

description: Xba

value: Astrocytoma

value: M. D. ANDERSON CANCER CENTER

value: III


title: KR+BAP1 rep1

city: Tokyo

first: Shuhei

last: Asada

address: 4-6-1 Shirokanedai, Minato-ku

department: Cellular Therapy

institute: Institute of Medical Science, The University of Tokyo

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse genome (mm10) using TopHat v2.0.9, with default parameters.
Normalized read counts were calculated using HTSeq 0.6.1p1 (-s reverse -m intersection-strict) and DESeq22 1.6.3 with VST normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: Bone marrow progenitor cells

growth_protocol: Cells were cultured in M3234 methylcellulose containing 20 ng/ml SCF, 10 ng/ml IL-3 and 10 ng/ml IL-6  according to manufacturer’s instructions.

extract_protocol:
Total RNA was prepared using RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol.

value: Bone marrow progenitor cells

tag: age

value: 8- to 12-week-old

tag: transduced genes

value: ASXL1-MT K351R and BAP1


title: MT+BAP1 rep3

tag: tissue

value: ASXL1-MT and BAP1


title: KR+BAP1 rep3


title: KR+BAP1 rep2


title: MT+BAP1 rep2


title: Sample21: Umbilical cord blood - Depression

value: Umbilical cord blood

value: Female

tag: microarray batch

value: Two


title: Sample20: Umbilical cord blood - Depression

value: Male


title: Sample19: Umbilical cord blood - Depression


title: Sample35: Umbilical cord blood - PTSDDep

value: PTSDDep


title: Sample18: Umbilical cord blood - Depression

value: Depression


title: MD550715_T_Xba

description: Xba


title: 900_00_5549

value: THOMAS JEFFERSON UNIVERSITY

tag: disease

value: astrocytoma

value: brain

value: grade 3

tag: extract name

tag: assay name


title: 900_00_5468

value: grade 2


title: 900_00_5545


title: MT+BAP1 rep1

tag: strain


title: 900_00_5459

tag: tumor grade


title: 900_00_5477

tag: provider


title: MD550715_B_Xba

description:
Duplicate
Xba

tag: patient id

value: Astrocytoma

value: M. D. ANDERSON CANCER CENTER


title: Sample17: Umbilical cord blood - Depression


title: ASXL1-MT rep3

value: Bone marrow progenitor cells


title: MD548457_T_Xba

description: Xba

tag: analyzed with cindex?

value: yes

tag: disease state

value: III


title: ASXL1-MT rep2

value: 8- to 12-week-old


title: MD508984_T_Xba

description: Xba

value: OLIGODENDROGLIOMA


title: 900_00_5385


title: BAP1 rep3


title: 900_00_5308


title: MD508984_B_Xba

description:
Duplicate
Xba


title: 900_00_5382


title: ASXL1-MT rep1


title: Sample15: Umbilical cord blood - Depression

value: Umbilical cord blood

tag: maternal diagnosis


title: 900_00_1961


title: Sample12: Umbilical cord blood - Depression

value: Two


title: Sample11: Umbilical cord blood - Depression

value: Female

value: One


title: HF1677_T_Xba

description: Xba

value: HENRY FORD HOSPITAL (RETRO)

tag: tumorgrade

value: II


title: Sample9: Umbilical cord blood - Depression

value: Depression

tag: neonate gender

value: Male


title: Sample13: Umbilical cord blood - Depression

tag: rin


title: Sample14: Umbilical cord blood - Depression


title: BAP1 rep2

tag: age


title: HF1671_T_Xba

description: Xba

value: GBM

value: IV


title: HF1702_T_Xba

description: Xba


title: Sample16: Umbilical cord blood - Depression


title: Sample10: Umbilical cord blood - Depression


title: BAP1 rep1

tag: transduced genes


title: MD548457_B_Xba

description:
Duplicate
Xba

value: Astrocytoma


title: HF1667_T_Xba

description: Xba


title: Sample34: Umbilical cord blood - PTSDDep

tag: tissue

value: PTSDDep


title: Col1 RNA-seq

city: Lyon

first: Antoine

last: Larrieu

address: 46 allée d'Italie

country: France

institute: ENS Lyon

data_processing:
Reads were cleaned (quality threshold: 20, adaptors removed, and reads mapping to rRNA removed) @ the sequencing facility
We first assessed the quality of the reads using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc,  (version 0.11.3)).
Preprocessed reads were then mapped to the Col-0 reference genome using Bowtie 2 (Version 2.2.5) and TopHat (version 2.1.0) and counted using HTSeq (Version 0.6.1)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene

organism: Arabidopsis thaliana

source_name: Inflorescence meristem

growth_protocol: Plants were germinated in short days (8 hours daylight) for 4 weeks and transfered to long days (16 hours daylight) for 2 weeks. Inflorescences were dissected and tissue frozen in liquid N2 within 3 minutes. 10 inflorescences were pooled per replicate

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA extraction kit (ThermoFisher) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Strand specific protocol following manufacturer’s instructions. The three RNA-seq libraries were sequenced using a HiSeq2000 Pair End 2x100bp at the Unité de Recherche en Génomique Végétale (Institute of Plant Sciences Paris-Saclay).

treatment_protocol: Samples were not treated

tag: ecotype

value: 10 Dissected inflorescence meristems were pooled per sample

tag: developmental stage

value: Flowers buds were removed until stage P5


title: HF1640_T_Xba

description: Xba


title: HF1628_T_Xba

description: Xba


title: Col3 RNA-seq


title: Sample8: Umbilical cord blood - Depression

tag: microarray batch


title: Sample3: Umbilical cord blood - Depression


title: Sample4: Umbilical cord blood - Depression


title: 10962X22

status: Public on May 24 2018

first: Alana

last: Welm

state: utah

address: 2000 Cir of Hope Dr

institute: Huntsman cancer institute

data_processing:
fastq files to the human genome reference (hg19) using TopHat ver. 2.0.10
count reads for each gene using HTSeq ver. 0.5.3p9
The gene annotation is taken from Ensembl Homo Sapiens GRCh37.68
Normalized counts calculated using DESeq ver. 1.16
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes FPKM values for each Sample.

source_name: PDX- Breast

growth_protocol: Tumor fragments (solid tumors) or cell suspensions (PE or ascites, with matrigel) implanted into cleared mammary fat pads of NOD/SCID or NSG mice. Estrogen was supplemented in ER+ cases. See DeRose and Gligorich et al 2013 for detailed methods

extract_protocol:
PDX tumor was removed, flash frozen on dry ice, and RNA was harvested using Qiagen kit . 1 ug of total RNA for the construction of sequencing libraries.
Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 125 Cycle Paired-End Sequencing v4

value: breast cancer

tag: library code

value: Index 3 TTAGGC

tag: type

value: TNBC

tag: hci samplename

value: HCI019 P2


title: 10962X19

value: Index 2 CGATGT

value: HCI016 P2


title: Sample6: Umbilical cord blood - Depression

value: Umbilical cord blood

value: Two


title: 10962X17

value: Index 6 GCCAAT

value: ER+

value: luminal B

value: HCI013 P3


title: 10962X20

value: Index 10 TAGCTT

value: HCI017 P2


title: HF1618_T_Xba

description: Xba

value: GBM

tag: provider

value: HENRY FORD HOSPITAL (RETRO)

value: IV


title: 10962X18

value: breast cancer

value: Index 1 ATCACG

value: HCI015 P3


title: HF1708_T_Xba

description: Xba

tag: patient id

value: Astrocytoma

value: II


title: 10962X21

value: Index 20 GTGGCC

value: ER+PR-

value: HCI018 P2


title: 10962X15

value: Index 13 AGTCAA

value: HCI011 P3


title: 10962X14

value: Index 7 CAGATC

value: TNBC

value: basal-like

value: HCI010 P3


title: VCC-treated monolayer

city: Umeå

first: Aziz

last: Bitar

address: Umeå University

country: Sweden

institute: Umeå University

data_processing: Background was first subtracted from the data and then normalized using Beadstudios cubic spline algorithm.

source_name: T84 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from T84 polarized tight monolayers by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

tag: condition

value: 160 ng/ml (VCC)

value: colon carcinoma cell line T84


title: 10962X10

value: Index 12 CTTGTA

value: ER+

value: luminal B

value: HCI007 P3


title: 10962X8

value: breast cancer

value: Index 25 ACTGAT

value: HCI005 P3


title: 10962X9

value: Index 6 GCCAAT

value: HCI006 P3


title: T84 Ctrl

value: LB


title: 10962X16

value: Index 21 GTTTCG

value: HCI012 P4


title: 10962X13

value: Index 3 TTAGGC

value: TNBC

value: HCI009 P6


title: Sample1: Umbilical cord blood - Depression

value: Umbilical cord blood

value: Depression

value: Male

value: Two


title: Sample7: Umbilical cord blood - Depression

value: Female

value: One


title: 10962X12

value: breast cancer

value: Index 14 AGTTCC

value: HCI009 P3


title: 10962X11

value: Index 10 TAGCTT

value: basal-like

value: HCI008 P4


title: 10962X7

value: Index 18 GTCCGC

value: HCI004 P3


title: 10962X6

value: Index 7 CAGATC

value: ER+

value: luminal B

value: HCI003 P6


title: Sample5: Umbilical cord blood - Depression

value: Umbilical cord blood

value: Depression


title: 10962X5

value: Index 4 TGACCA

value: HCI003 P3


title: 10962X3

value: TNBC

value: HCI002 P3


title: Sample2: Umbilical cord blood - Depression

value: Male

value: One


title: MM135

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

description: GEO_processed_MM_10X_raw_UMI_COUNT_matrix.txt

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher) and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
hg19
In 10X genomics data, Cellranger-2.1 was generated UMI count and modified matrix by Seurat.
Genome_build: hg19/GRCh38(10X)
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 173 single cells and the UMI count for 1,339 single cells (from 10X).

extract_protocol:
Plasma cells were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).
In CD138-negative samples, starting with 100-500ng of input RNA, sequencing libraries were constructed with the Truseq RNA Sample Prep Kit v2-setA,B (Illumina). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies) then pooled without index overlapping. Finally pooled libraries were sequenced using the HiSeq2500 (Illumina) as 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit.

tag: cell type

value: Multiple myeloma

tag: prep-site

value: Bone marrow

tag: facs sorting

tag: heavy chain

value: IgG

tag: light chain

value: Lambda

tag: iss

value: I


title: MM34EM_94

value: Ascites

value: CD138 positive

value: kappa

value: III


title: 10962X4

value: breast cancer

value: Index 22 CGTACG

value: basal-like

value: HCI002 P7


title: MM34EM_88


title: MM34EM_91


title: MM34EM_93


title: 10962X1

value: Index 5 ACAGTG

value: TNBC

value: HCI001 P3


title: MM34EM_87


title: MM34EM_85


title: MM34EM_86


title: MM34EM_82


title: MM34EM_81


title: MM34EM_80


title: MM34EM_74


title: MM34EM_73


title: MM34EM_75


title: MM34EM_69


title: MM34EM_66


title: MM34EM_59


title: MM34EM_67


title: MM34EM_58


title: MM34EM_63


title: MM34EM_64


title: MM34EM_72


title: MM34EM_54


title: MM34EM_57


title: MM34EM_51


title: MM34EM_49


title: MM34EM_56


title: MM34EM_48


title: MM34EM_53


title: MM34EM_50


title: MM34EM_78


title: MM34EM_44


title: MM34EM_43


title: MM34EM_37


title: MM34EM_41


title: MM34EM_39


title: Col2 RNA-seq

value: 10 Dissected inflorescence meristems were pooled per sample

value: Flowers buds were removed until stage P5


title: MM34EM_33

value: Multiple myeloma


title: MM34EM_34

value: IgG


title: MM34EM_35


title: MM34EM_30


title: MM34EM_22


title: MM34EM_21


title: MM34EM_46


title: MM34EM_24


title: MM34EM_25


title: MM34EM_18


title: MM34EM_15


title: MM34EM_17


title: MM34EM_13


title: MM34EM_11


title: MM34EM_16


title: MM34EM_7


title: MM34EM_38


title: MM34EM_6


title: MM34EM_3


title: MM34EM_5


title: MM34_96

value: Bone marrow


title: MM34_95


title: MM34EM_1


title: MM34EM_2


title: MM34EM_36


title: MM34EM_20


title: MM34EM_19


title: MM34_94


title: MM34_92


title: MM34EM_23


title: MM34EM_14


title: MM34_88


title: MM34_89


title: MM34_87


title: MM34_86


title: MM34_91


title: MM34_83


title: MM34_85


title: MM34_82


title: MM34_80


title: MM34_8


title: MM34_79


title: MM34_73


title: MM34_78


title: MM34_7


title: MM34_74


title: MM34_71


title: MM34_63


title: MM34_66


title: MM34_70


title: MM34_65


title: MM34_52


title: MM34_51


title: MM34_6


title: MM34_53


title: MM34_61


title: MM34_59


title: MM34_56


title: MM34_47


title: MM34_50


title: MM34_57


title: MM34_49


title: MM34_55


title: MM34_46


title: MM34_58


title: MM34_4


title: MM34_37


title: MM34_35


title: MM34_34


title: MM34_28


title: MM34_45


title: MM34_43


title: MM34_62


title: MM34_33


title: MM34_32


title: MM34_25


title: MM34_42


title: MM34_11


title: MM34_12


title: MM34_1


title: MM34_13


title: MM34_3


title: MM16R_9

value: I


title: MM34_15


title: MM34_69


title: MM34_10


title: MM16R_87


title: MM16R_56


title: MM16R_70


title: MM16R_60


title: MM16R_65


title: MM16R_59


title: MM16R_51


title: MM16R_44


title: MM16R_41


title: MM34_21


title: MM16R_93


title: 10962X2

value: Index 10 TAGCTT

value: HCI001 P7


title: MM16R_16

value: CD138 positive

value: kappa


title: MM16R_07


title: MM16R_21


title: MM16R_30


title: MM16R_34


title: MM16R_02


title: MM16R_01


title: MM16R_23


title: MM16_9


title: MM16_74


title: MM16_83


title: MM16R_38


title: MM16_63


title: MM16R_39


title: MM16_57


title: MM16_61


title: MM16_6


title: MM16_54


title: MM34_22

value: III


title: MM16_52


title: MM16R_32


title: MM16_8


title: MM16_3


title: MM16_21


title: MM16_24


title: MM16_17


title: MM16_31


title: MM16_5


title: MM16_35


title: MM16_10


title: MM16_16


title: MM16_12


title: MM16_69


title: MM16_15


title: MM16_1


title: ILC1 WT_3

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

data_processing:
mapping to GRCm38 using Hisat2 (default parameters)
quantification of gene expression measures with featureCounts v1.5.2 using Mus_musculus.GRCm38.85 annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: table of counts (From featureCounts)

source_name: ILC1 WT

extract_protocol:
Cells were sorted directly in RLT lysis buffer (Qiagen). Total RNA was prepared from purified ILC populations with an RNeasy Micro Kit (Qiagen).
Preamplification was performed with the SMART-Seq® v4 Ultra® Low-Input RNA Kit (Clontech). The DNA libraries were generated by double-indexing with the Nextera XT DNA Kit (Illumina) and RNA sequencing was performed with a NextSeq 500 (Illumina; paired-end reads 2x75 with 30 M reads per sample).

tag: strain background

tag: genotype/variation

value: wild type

tag: Sex

value: female

value: liver

value: innate lymphoid cells (ILCs)


title: NK liver GRNcr1-iCre_1

source_name: NK liver GRNcr1-iCre

tag: tissue

value: NK cells


title: ILC1 GRNcr1-iCre_2

source_name: ILC1 GRNcr1-iCre


title: NK liver WT_3

source_name: NK liver WT


title: NK liver WT_2


title: ILC1 WT_2


title: ILC1 WT_1


title: NK spleen GRNcr1-iCre_1

source_name: NK spleen GRNcr1-iCre

value: spleen


title: NK spleen WT_3

source_name: NK spleen WT


title: NK spleen GRNcr1-iCre_2


title: NK spleen WT_2


title: NK liver GRNcr1-iCre_2


title: ILC1 GRNcr1-iCre_1


title: NK liver WT_1


title: NK spleen WT_1


title: NK spleen GRNcr1-iCre_3


title: MM34_27


title: NK liver GRNcr1-iCre_3