title: ColonTR_133


title: ColonTR_136

status: Public on May 26 2018

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

growth_protocol: Live cells were sorted by flow cytometry from the spleen and colon lamina propria of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp

tag: Sex

value: male

tag: age (months)

tag: tissue

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: ColonTR_132


title: ColonTR_135


title: ColonTR_127


title: ColonTR_131


title: ColonTR_123


title: ColonTR_137


title: ColonTR_124


title: ColonTR_115


title: ColonTR_117


title: ColonTR_122


title: ColonTR_116


title: ColonTR_114


title: ColonTR_113


title: ColonTR_110


title: ColonTR_105


title: ColonTR_108


title: ColonTR_106


title: ColonTR_101


title: ColonTR_102


title: ColonTR_150


title: ColonTR_92


title: ColonTR_94


title: ColonTR_91


title: ColonTR_90


title: ColonTR_87


title: ColonTR_85


title: ColonTR_86


title: ColonTR_84


title: ColonTR_80


title: ColonTR_75


title: ColonTR_95


title: ColonTR_73


title: ColonTR_74


title: ColonTR_72


title: ColonTR_70


title: ColonTR_69


title: ColonTR_81


title: ColonTR_60


title: ColonTR_58


title: 607_24h_Beijing

type: RNA

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

description: Gene expression in lung tissue infected with Mtb strain Bejing

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human whole genome microarrays (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Data were processed, quantile normalized and analyzed using the R package Lima

organism: Homo sapiens

source_name: lung tissue

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was extracted from lung tissue homogenized in Trizol

treatment_protocol: Explanted human lung tissue infected with Mycobacteria tuberculosis

value: lung

tag: agent

value: Mycobacterium tuberculosis str. Beijing

tag: timepoint (weeks post vaccination)


title: 551_24h

description: Gene expression in uninfected lung tissue

value: uninfected


title: 548_24h


title: 549_24h_H37Rv

description: Gene expression in lung tissue infected with Mtb strain H37Rv

value: Mycobacterium tuberculosis str. H37Rv


title: 548_24h_H37Rv


title: 607_24h_H37Ra

description: Gene expression in lung tissue infected with Mtb strain H37Ra

value: Mycobacterium tuberculosis str. H37Ra


title: 540_24h_H37Rv


title: 550_24h


title: ColonTR_57


title: 607_24h_H37Rv


title: 550_24h_H37Rv


title: 606_24h_H37Rv


title: 606_24h_Beijing


title: ColonTR_68


title: 549_24h


title: 606_24h_H37Ra


title: ColonTR_54


title: 540_24h


title: ColonTR_53


title: ColonTR_52


title: ColonTR_50


title: 600_24h_Beijing


title: 600_24h_H37Rv


title: 606_24h


title: 597_24h_Beijing


title: 607_24h


title: 600_24h_H37Ra


title: 597_24h_H37Ra


title: 597_24h_H37Rv


title: ColonTR_44


title: ColonTR_56


title: 600_24h


title: ColonTR_33


title: ColonTR_39


title: ColonTR_34


title: ColonTR_32


title: ColonTR_42


title: ColonTR_30


title: 589b_48h


title: 595_24h


title: 592_24h_H37Rv


title: 595_24h_H37Rv


title: ColonTR_29


title: ColonTR_28


title: 589a_24h


title: 592_24h


title: 597_24h


title: 589a_24h_H37Rv


title: 588b_48h_H37Rv


title: 588b_48h


title: 589b_48h_H37Rv


title: ColonTR_26


title: ColonTR_20


title: ColonTR_22


title: 588a_24h_H37Rv


title: ColonTR_25


title: ColonTR_19


title: ColonTR_21


title: ColonTR_10


title: ColonTR_6


title: 588a_24h


title: ColonTR_4


title: ColonTR_1


title: ColonTR_3


title: P1

city: Guangzhou

first: Yi

last: Xiaochun

state: Guangdong

address: No. 107  West Road along the river, Yuexiu District

country: China

institute: Sun Yat-sen Memorial Hospital of the Sun Yat-sen University

description:
BALB/c ♀×BALB/c ♂
processed data file: processed_data.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: processed_data.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: placenta

extract_protocol:
Placentas were removed and pulverized in liquid nitrogen. Total RNA was isolated using Trizol reagent (Life Technologies) and puriﬁed with GeneJET RNA purification kit (Thermo) and RNase-free DNase set (QIAGEN) following manufacturer’s instructions. RNA electrophoresis was conducted to inspect RNA integration.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: On day 15.5 of gestation, an abdominal minilaparotomy was performed. The upper right uterine horn between the first and second sacs received injections of saline (C) or 20 mg E. coli LPS serotype O55:B5 (Sigma-Aldrich, Gillingham, UK) (P) to model preterm labor. Six hours after injections of LPS, the mice were sacrificed.

tag: genetic background

value: BALB/c female x BALB/c male

value: placenta

tag: treatment

value: pregnant day 13.5 with injections of LPS


title: P2


title: P4


title: P3


title: C3

value: pregnant day 13.5 with injections of saline


title: 584_24h_Beijing


title: 584_24h_H37Rv


title: 584_24h


title: 583_24h


title: C2


title: C1


title: 583_24h_Beijing


title: 580_24h_H37Ra


title: 580_24h


title: 579_24h_H37Rv


title: 579_24h_H37Ra


title: 583_24h_H37Rv


title: 584_24h_H37Ra


title: NMA65 PDPNlow

city: Heidelberg

first: Peter

last: Angel

address: Im Neuenheimer Feld 280

department: Signal Transduction and Growth Control

institute: German Cancer Research Center

description:
biological replicate 6
SAMPLE 11

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide)

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

label: biotin, streptavidin-Cy3

source_name: glioblastoma spheroid culture sorted for low PDPN expression

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA from input amounts of 300ng total RNA.

growth_protocol: Human glioblastoma cells were cultivated as spheroids in neurobasal medium supplemented with B27; EGF; FGF and heparin sodium salt.

extract_protocol: RNA was isolated using the RNeasy mini kit (Qiagen), including on-column DNAse treatment, quality was controled by Agilent Bioanalyzer.

treatment_protocol: Spheroids were dissociated using accutase to obtain single cell suspensions, cells were stained with the NC-08 antibody directed against PDPN and FACSorted according to their PDPN levels.

tag: tumor source

value: glioblastoma

tag: cell line

tag: genotype/variation

value: low PDPN expression


title: A375 Coculture Rep3

city: New York

first: Maomao

last: Zhang

state: NY

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
DEseq2.xlsx
HTseq.xlsx

data_processing:
Reads mapped to a concatenated human (hg19) and mouse (mm10) genome using STAR (v2.5.0a) with default parameters and the parameter "--outFilterMismatchNmax 0"
Gene counts were assessed using the "--quantMode Gene/counts" parameter in STAR with a custom gff file combining the mm10 and hg19 genomes
Subsequent count matrix was subset for human genes and used as an input for the R package DESeq2, with differentially expressed genes called using a base mean of 15, log2 fold change of +/- 1 and a FDR of 5%
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 fold changes (Results.txt) or raw or normalized counts for each sample (Results_Raw_Refseq.txt and Results_Normalized_Refseq.txt).

source_name: A375 human melanoma cells

extract_protocol:
Total RNA was isolated using the Zymo RNA kit and used for cDNA syntehsis and barcoding with Illumina adaptors
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375-GFP cells were grown in monoculture or in coculture with 3T3L1 adipocytes in ZenBio Adipocyte Maintenance Medium (Cat no. AM-1-L1) for 7 days, then FACS-isolated

tag: condition

value: Coculture with adipocytes

tag: genotype

value: BRAF V600E


title: A375 Coculture Rep2

description:
DEseq2.xlsx
HTseq.xlsx


title: 580_24h_Beijing


title: A375 Coculture Rep1

description:
DEseq2.xlsx
HTseq.xlsx


title: NMA65 PDPNhigh

description:
biological replicate 6
SAMPLE 12

source_name: glioblastoma spheroid culture sorted for high PDPN expression

value: high PDPN expression


title: 580_24h_H37Rv


title: 579_24h_Beijing


title: A375 Monoculture Rep3

description:
DEseq2.xlsx
HTseq.xlsx

value: Monoculture


title: GBM30 PDPNhigh

description:
biological replicate 3
SAMPLE 6


title: A375 Monoculture Rep2

description:
DEseq2.xlsx
HTseq.xlsx


title: NMA50 PDPNhigh

description:
biological replicate 4
SAMPLE 8


title: 579_24h


title: NMA59 PDPNhigh

description:
biological replicate 5
SAMPLE 10


title: NMA59 PDPNlow

description:
biological replicate 5
SAMPLE 9


title: A375 Monoculture Rep1

description:
DEseq2.xlsx
HTseq.xlsx


title: NMA50 PDPNlow

description:
biological replicate 4
SAMPLE 7


title: GBM10 PDPNhigh

description:
biological replicate 2
SAMPLE 4


title: GBM30 PDPNlow

description:
biological replicate 3
SAMPLE 5


title: wt_epsilon_mutant 34C Pu-seq

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description:
rNTP-pol-e-34C_S12
processed data was generated from both delta and epsilon mutant together and is linked to the corresponding delta mutant sample records.

library_source: genomic

data_processing:
library strategy: Polymerase usage sequence (Pu-seq)
The reads were mapped using bowtie2
Origin positions and efficiencies were determined using the tools published and described in detail in Daigaku et al., 2015 and Keszthelyi et al. 2015. with default variables except for the ‘percentile threshold for origins’ option was set to 0.2 = 20th percentile.
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets)
Supplementary_files_format_and_content: Bedgraph files contain the position and the efficiency of the origins.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown on 34C in YPD media to log phase. For ‘wt’ datasets two strains were used, both strains containing rnh201 deletion together with either polymerase δ (cdc6-L591G) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq. For the wee1-50, set2Δ and wee1-50 set2 Δ datasets the two strains also contained these mutations along with rnh201 and cdc6-L591G or cdc20-M630F.

extract_protocol:
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to alkali treatment (0.3 M NaOH, 2h 55°C) which digested the DNA at the positions of rNTP incorporation and also separated the double strands. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al., 2015 and Keszthelyi et al. 2015)

value: rnh201::KanMX cdc20 M603F::lox ade6-704 leu1-32 ura4-D18


title: set2_wee1-50_epsilon_mutant 34C Pu-seq

description:
rNTP-pol-e-set2-wee1-50-34C_S10
processed data was generated from both delta and epsilon mutant together and is linked to the corresponding delta mutant sample records.


title: set2_epsilon_mutant 34C Pu-seq

description:
rNTP-pol-e-set2-34C_S6
processed data was generated from both delta and epsilon mutant together and is linked to the corresponding delta mutant sample records.


title: wee1-50_delta_mutant 34C Pu-seq


title: wee1-50_epsilon_mutant 34C Pu-seq

description:
rNTP-pol-e-wee1-50-34C_S8
processed data was generated from both delta and epsilon mutant together and is linked to the corresponding delta mutant sample records.


title: set2_wee1-50_delta_mutant 34C Pu-seq

value: h-, Set2::KAN wee1-50 rnh201::HYG cdc6L591G  ade6-485 leu1-32 ura4-D18


title: wt_delta_mutant 34C Pu-seq

value: h-, rnh201::KanMX cdc6-L591G:lox ade6-704 leu1-32 ura4-D18


title: NMA7 PDPNhigh

description:
biological replicate 1
SAMPLE 2


title: GBM10 PDPNlow

description:
biological replicate 2
SAMPLE 3


title: NMA7 PDPNlow

description:
biological replicate 1
SAMPLE 1


title: Keratinocytes transfect with GapmeR WAKMAR1, biological rep1

city: Stockholm

first: Ning

last: Xu

state: Stockholm

address: CMM L8:02, Karolinska Institutet

department: Medicine

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from keratinocytes with WAKMAR1 inhibition

hyb_protocol: The samples were hybridized to a Human Gene 2.1 ST Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the RMA method

label: biotin

source_name: Human primary keratinocytes

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement at a final Ca2+ concentration of 0.06mM (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 24 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 30-50% confluence were transfected with 20nM WAKMAR1 GapmeRs or control oligos (Ambion) using Lipofectamine 2000 (Invitrogen).

tag: transfection

value: WAKMAR1 GapmeRs

value: skin


title: Keratinocytes transfect with GapmeR Ctrl, biological rep2

description: Gene expression data from keratinocytes transfected with control oligos with scrambled sequence.

value: control oligos with scrambled sequence


title: Keratinocytes transfect with GapmeR Ctrl, biological rep1


title: Keratinocytes transfect with GapmeR WAKMAR1, biological rep3


title: Keratinocytes transfect with GapmeR WAKMAR1, biological rep2


title: set2_delta_mutant 34C Pu-seq

tag: strain


title: ColonTR_46

tag: library name

tag: sample type

value: B6 Foxp3-Ires-Gfp

tag: Sex

value: male


title: Donor 3 DP spheres in Tofacitinib

first: Jane

middle: E.

last: Cerise

address: 1150 St. Nicholas Avenue

institute: Columbia University

description: Gene expression from dermal papilla cells derived from  donor 3  and treated with tofa for 48 hours

hyb_protocol: Samples were hybridized at the Columbia medical center facility

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Bioconductor/R and were GCRMA normalized.

source_name: Dermal papilla cells derived from  donor 1 and treated with Tofa for 48 hours

label_protocol: The Ovation RNA Amplification kit (Nugen) was used to generate amplified cDNA for microarray analysis

growth_protocol: Dermal papilla cells were derived by dissecting hair follicles from human scalp tissue obtained from transplantation procedures. Cells were expanded in vitro and cultured using the hanging drop method (Higgins et al., PNAS 2013)

extract_protocol: total RNA was extracted from DP spheres cultured in DMSO, ruxolitinib or tofacitinib from each of the three donors using the Qiagen RNAeasy micro kit.

treatment_protocol: DP cells were grown in spheres as previously described (31). DMSO, ruxolitinib or tofacitinib were added to the medium (400nM). Each hanging drop contained 1000 cells, which aggregated to form DP spheroids after 24 hours. 48 hours after plating, spheres wer collected and harvested for RNA

tag: donor

value: Tofa

tag: cell type

value: Dermal papilla cells


title: Donor 3 DP spheres in Ruxolitinib

description: Gene expression from dermal papilla cells derived from  donor 3  and treated with ruxo for 48 hours

source_name: Dermal papilla cells derived from  donor 1 and treated with Ruxo for 48 hours

value: Ruxo


title: ASF bacteria, Lactobacillus rhamnosus, Bilophila wadsworthia_High Fat Diet [F264]

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description:
Total bacterial RNA
Germ free mouse inoculated with altered Schaedler flora bacteria and Lactobacillus rhamnosus CNCM I-3690 and Bilophila wadsworthia 49260

data_processing:
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.10.1 (readquality), Cutadapt-1.2.1 (adaptor trimming)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to combined partical bacterial genome using bowtie2 v2.2.8 with parameters -q -p2 --very-sensitive -t -X1000
Genome_build: GCF_000364165.1, GCF_000364185.1, GCF_000364205.1, GCF_000364225.1, GCF_000364245.1, GCF_000364265.1, GCF_000487995.1, GCF_000492175.1, GCF_000701705.1
Supplementary_files_format_and_content: raw count data txt format for locus tags

organism: uncultured bacterium

source_name: Mouse cecal content

extract_protocol:
Total bacterial RNA from cecal content was extracted by mechanic bead-beating lysis method combined with phenol/choloroform RNA extraction method. Briefly, cecal content was suspended in 200 ul of RNAse free water and then 250 μl phenol (pH 4.8) / chloroform-isoamyalcohol mixture (5:1 ratio), 12.5 μl of SDS (20%), 25 μl NaAc (3M, pH 8) were added to the suspension. Cecal content suspension was then agitated on a FastPrep bead beater machine for 40s at setting 5 followed by 60s in ice for another round of bead beating for 20s at setting 5. After lysis, the upper phase of the suspension was collected after 15 min of centrifugation at 13000g (4OC).  Traces of phenol were eliminated by adding 250 μl of chloroforme-isoamylalchohol and then collecting the upper phase after 10 min of centrifugation. Bacterial RNA was then purified using High Pure RNA Isolation Kit (Roche), as per manufacturer’s instructions.
Library preparation and RNA-sequencing was performed by the High-throughput Sequencing Platform of I2BC. Total bacterial RNA were purified using RiboZero. Library was sequenced using NextSeq 500 on the single lane 75 bp paired-end mode.

treatment_protocol: For altered Schaedler flora (ASF) experiment, male C57BL/6J germ-free (GF) mice were obtained from Transgenese et Archivage Animaux Modeles (CNRS, UPS44, Orleans, France) and used after 1 week of receipt. Sterility was confirmed microscopically and by microbiological technique. ASF colonized mice were kindly provided by E. Verdu from McMaster University (Canada). Fresh cecal samples from ASF-colonized mice were suspended and diluted in pre-reduced sterile 0.9% NaCl with 15% glycerol (1 g in 10 ml) under anaerobic condition. Aliquots of ASF cecal suspension were stored at -80°C. GF mice (5 weeks of age) were inoculated via oral gavage with 200 μl of ASF cecal suspension and maintained on either HFD or CD. 3 weeks after ASF inoculation, mice were orally gavaged with B. wadsworthia or medium for 3 consecutive days. 1 week after the last B. wadsworthia inoculation, mice were gavaged daily with 109 CFU of L. rhamnosus CNCM I-3690 or vehicle for 4 weeks.

tag: mouse tissue

value: feces

tag: mouse diet

value: High Fat Diet

tag: mouse inoculations

value: altered Schaedler flora and Lactobacillus rhamnosus and Bilophila wadsoworthia


title: ASF bacteria, Lactobacillus rhamnosus, Bilophila wadsworthia_High Fat Diet [F267]


title: ASF bacteria, Bilophila wadsworthia_High Fat Diet [F263]


title: ASF bacteria, Lactobacillus rhamnosus, Bilophila wadsworthia_High Fat Diet [F266]


title: Donor 2 DP spheres in Tofacitinib

description: Gene expression from dermal papilla cells derived from  donor 2  and treated with tofa for 48 hours

source_name: Dermal papilla cells derived from  donor 2 and treated with Tofa for 48 hours


title: ASF bacteria, Bilophila wadsworthia_High Fat Diet [E262]

description:
Total bacterial RNA
Germ free mouse inoculated with altered Schaedler flora bacteria and Bilophila wadsworthia 49260

value: altered Schaedler flora and Bilophila wadsoworthia


title: Donor 3 DP spheres in DMSO

description: Gene expression from dermal papilla cells derived from  donor 3  and treated with DMSO for 48 hours

source_name: Dermal papilla cells derived from  donor 3  and treated with DMSO for 48 hours

value: DMSO


title: Keratinocytes transfect with GapmeR Ctrl, biological rep3

tag: tissue


title: ASF bacteria, Bilophila wadsworthia_High Fat Diet [E261]


title: ASF bacteria, Lactobacillus rhamnosus_High Fat Diet [D259]

description:
Total bacterial RNA
Germ free mouse inoculated with altered Schaedler flora bacteria and Lactobacillus rhamnosus CNCM I-3690

value: altered Schaedler flora and Lactobacillus rhamnosus


title: Donor 2 DP spheres in Ruxolitinib

description: Gene expression from dermal papilla cells derived from  donor 2  and treated with ruxo for 48 hours

source_name: Dermal papilla cells derived from  donor 2 and treated with Ruxo for 48 hours

tag: treatment


title: Donor 1 DP spheres inTofacitinib

description: Gene expression from dermal papilla cells derived from  donor 1 and treated with tofa for 48 hours


title: Cry toxin-exposed till 24 hour

city: Hyderabad

first: Aparna

middle: Dutta

last: Gupta

state: Telangana

address: S-41, Department of Animal Biology, School of Life Sciences, University of Hyderabad

department: Department of Animal Biology

country: India

institute: University of Hyderabad

description: Gene expression of larval mid-gut after 24hr of Cry toxin-exposure

hyb_protocol: Labeled cRNA sample were fragmented at 60 º C and hybridized on to Agilent Custom Castor semilooper Gene Expression 8X60K (AMADID: 84278) designed by Genotypic Technology Private Limited. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G25600D).

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

organism: Achaea janata

source_name: Homogenous population from laboratory

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Larvae were fed on castor leaves and maintained at 27 ± 2°, 14:10 h (light: dark) photoperiod and relative humidity of 60–70% till pupation. Pupae were transferred to the moist sand container for adult emergence. Adults were transferred to egg laying chamber and were supplemented with 10% honey. Adults laid their eggs on the leaves and the hatched neonate larvae again used for continuous culture.

extract_protocol: RNA was extracted using the Qiagen’s RNeasy minikit following the manufacturer's recommendations.

treatment_protocol: Toxin coated castor leaves were fed to the larvae in triplicates. Larvae exposed to the sub-lethal dosage of toxin (0.170 μg/cm2).  Exposed larvae were collected for mid-gut after successive 12h period.  Total six sample were used for this study (Control, non-exposed; Toxin Exposed 12h, 24h, 36h, 48h, 60h). Mid-gut RNA was isolated and used for cRNA preparation.

value: Larval mid-gut

tag: age

value: 3rd Instar


title: Cry toxin-exposed till 12 hour

description: Gene expression of larval mid-gut after 12hr of Cry toxin-exposure


title: Cry toxin-exposed till 60 hour

description: Gene expression of larval mid-gut after 60hr of Cry toxin-exposure


title: Donor 1 DP spheres in Ruxolitinb

description: Gene expression from dermal papilla cells derived from  donor 1 and treated with ruxo  for 48 hours


title: Donor 2 DP spheres in DMSO

description: Gene expression from dermal papilla cells derived from  donor 2  and treated with DMSO for 48 hours

source_name: Dermal papilla cells derived from  donor 2 and treated with DMSO for 48 hours


title: Cry toxin-exposed till 36 hour

description: Gene expression of larval mid-gut after 36hr of Cry toxin-exposure


title: Unexposed

description: Gene expression of larval mid-gut after 12hr feeding on normal castor plant


title: Cry toxin-exposed till 48 hour

description: Gene expression of larval mid-gut after 48hr of Cry toxin-exposure


title: ASF bacteria, Bilophila wadsworthia_High Fat Diet [E260]


title: ASF bacteria, Bilophila wadsworthia_High Fat Diet [E259]


title: ASF bacteria, Lactobacillus rhamnosus_High Fat Diet [D257]


title: ASF bacteria, Lactobacillus rhamnosus_High Fat Diet [D255]


title: ASF bacteria, Lactobacillus rhamnosus_High Fat Diet [D256]


title: PA23-gacS (3)

city: Winnipeg

first: Teresa

middle: R

last: de Kievit

state: Manitoba

address: 45 Chancellor's Circle

department: Microbiology

country: Canada

institute: University of Manitoba

data_processing:
Barcode adaptors from the RNA sequence reads were clipped and low quality reads were removed (read quality < 30) using the Trimmomatic software (Bolger et al., 2014).
Raw reads were then mapped to the genome via Tophat2 v.2.1.0 (Trapnell et al., 2012) in the high-sensitivity mode, with the P. chlororaphis PA23 reference annotation from NCBI.
Identification of novel transcripts was performed using cufflinks v2.2.1 (Trapnell et al., 2012) and transcript sequences were extracted from this annotation using BedTools.
Cuffquant, CuffNorm and Cuffdiff were used to generate normalized counts in FPKM and to identify differentially expressed genes (pooled dispersion method). Genes were considered significantly differentially expressed with a corrected p-value of < 0.05 (false discovery rate = 0.05).
Genome_build: NZ_CP008696.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Pseudomonas chlororaphis

source_name: lab generated strain

growth_protocol: Strains were cultured in M9 minimal media supplemented in 0.2% glucose and 1mM MgSO4. Cells were harvested at early stationary phase (OD600  1.2-1.5) by centrifugation for 10 minutes at 5000rpm

extract_protocol:
Total RNA was extracted using Fermentas plant RNA extraction kit.
cDNA libraries were constructed using the alternative HTR protocol described by Kumar et al. (2012) adapted for bacterial RNA. Ribosomal RNA was depleted using the MicrobExpress kit (Ambion, Carlsbad, USA) as per manufacturer’s instructions. Fragmentation time was reduced to 10 min and the number of cycles for final PCR amplification of the libraries was adjusted to 12 (Kumar et al., 2012). Final cDNA libraries with ligated adaptors were size-selected to fall between 250 and 500 bp using the E-Gel® electrophoresis system (Invitrogen). cDNA quantity was measured using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Thermo Fisher, Rockford, USA) with a Nanodrop 3300 (Thermo Fisher). cDNA was validated using Agilent Bioanalyser High Sensitivity DNA Chips (Agilent Technologies) at three points: i) after first and second strand cDNA synthesis; ii) after the final PCR amplification of the libraries; and iii) after size selection with the E-Gel® electrophoresis system.

treatment_protocol: cell pellets were flash frozen in liquid nitrogen and stored at -80C until RNA extraction

value: disruption in transcriptional regulator gacS


title: PA23-gacS (1)


title: PA23-gacA (3)

value: disruption in transcriptional regulator gacA


title: ASF bacteria_High Fat Diet [C253]

description:
Total bacterial RNA
Germ free mouse inoculated with altered Schaedler flora bacteria

value: altered Schaedler flora


title: PA23-gacA (2)


title: ASF bacteria_High Fat Diet [C252]


title: ASF bacteria_High Fat Diet [C251]


title: PA23-gacA (1)


title: ASF bacteria_High Fat Diet [C250]


title: ASF bacteria, Lactobacillus rhamnosus, Bilophila wadsworthia_High Fat Diet [F265]


title: PA23-gacS (2)


title: Donor 1 DP spheres in DMSO

description: Gene expression from dermal papilla cells derived from  donor 1 and treated with DMSO for 48 hours

source_name: Dermal papilla cells derived from  donor 1 and treated with DMSO for 48 hours


title: ASF bacteria, Lactobacillus rhamnosus_High Fat Diet [D254]


title: PA23-ptrA (2)

value: disruption in transcriptional regulator ptrA


title: PA23-ptrA (1)


title: ColonTR_49

value: B6 Foxp3-Ires-Gfp

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: PA23-phzR (2)

tag: genotype

value: disruption in transcriptional regulator phzR


title: ASF bacteria, Lactobacillus rhamnosus_Control Diet [B248]

description:
Total bacterial RNA
Germ free mouse inoculated with altered Schaedler flora bacteria & Lactobacillus rhamnosus CNCM I-3690

value: Control Diet


title: ASF bacteria, Lactobacillus rhamnosus_Control Diet [B246]


title: ASF bacteria, Lactobacillus rhamnosus_Control Diet [B247]


title: PA23-AHL (3)

value: pME6863 containing AHL-lactonase inserted into WT PA23

tag: strain


title: PA23-ptrA (3)


title: ASF bacteria_Control Diet [A242]


title: Human TIL Sample CD39- CD103+ [015A_11H1_21F9n3p_589RM]

city: Portland

first: Andrew

last: Weinberg

state: Oregon

address: 4805 NE Glisan St 2N35

institute: Agonox

description: Gene Expression Data from TIL

hyb_protocol: GeneChip Hybridization Oven 645: 18 hours/45°C/45rpm

scan_protocol: GeneChip Scanner with the 7G upgrade

data_processing: The image processing and expression analysis was performed using Affymetrix GeneChip Command Console v. 3.1.1 and Affymetrix Expression Console v 1.1 software, respectively. Normalization was performed with the Robust Multi-array Algorithm (RMA)

label: Biotin

source_name: CD8+ Tumor Infiltrating Lymphocytes (TIL)

label_protocol: Labeled using NuGEN Ovation Pico WTA System with Encore Biotin Module protocol (3'IVT assay)

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

value: Tumor


title: ASF bacteria, Lactobacillus rhamnosus_Control Diet [B244]

value: feces


title: Human TIL Sample CD39+ CD103+ [014A_11H1_2039p3p_589RM]

description: Gene Expression Data from TIL


title: ASF bacteria, Lactobacillus rhamnosus_Control Diet [B245]


title: Human TIL Sample CD39- CD103- [017A_11H1_2039n3n_589RM]

description: Gene Expression Data from TIL


title: ASF bacteria_Control Diet [A241]


title: PA23-phzR (3)


title: ASF bacteria_High Fat Diet [C249]

value: High Fat Diet


title: Human TIL Sample CD39- CD103+ [019A_11H1_1939n3p_589RM]

description: Gene Expression Data from TIL


title: PA23-WT (3)

source_name: soy bean rhizosphere

value: wild type


title: ASF bacteria_Control Diet [A240]


title: Human TIL Sample CD39- CD103- [013A_11H1_21R9n3n_589RM]

description: Gene Expression Data from TIL


title: PA23-phzR (1)


title: PA23-WT (2)


title: Human TIL Sample CD39- CD103- [018A_11H1_21F9n3n_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39- CD103+ [011A_11H1_21R9n3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39+ CD103+ [010A_11H1_1939p3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39+ CD103+ [016A_11H1_1839p3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39- CD103+ [012A_11H1_1839n3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39+ CD103+ [009A_11H1_21R9p3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39+ CD103+ [007A_11H1_21F9p3p_589RM]

description: Gene Expression Data from TIL


title: Human TIL Sample CD39- CD103- [008A_11H1_1839n3n_589RM]

description: Gene Expression Data from TIL


title: PA23-WT (1)


title: PA23-AHL (2)


title: Human TIL Sample CD39- CD103+ [006A_11H1_2039n3p_589RM]

description: Gene Expression Data from TIL


title: PA23-AHL (1)


title: ASF bacteria_Control Diet [A238]


title: Human TIL Sample CD39- CD103- [005A_11H1_1939n3n_589RM]

description: Gene Expression Data from TIL


title: ASF bacteria_Control Diet [A239]


title: NOB0822_NBE_p3_Hind

status: Public on May 25 2018

type: genomic

city: Washington

first: Krithika

last: Bhuvaneshwar

state: DC

address: 2115 Wisconsin Ave NW

institute: Georgetown University

description: Hind

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.

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: disease state

value: GBM

tag: provider

value: NIH NEURO-ONCOLOGY BRANCH


title: NOB0320_NBE_p2_Hind

description: Hind


title: NOB1228_NBE_p7_diff_Hind

description: Hind


title: NOB0822_NBE_p10_Hind

description: Hind


title: NOB1228_NBE_p3Side_Hind

description: Hind


title: NOB0308_NBE_R1b_Hind

description: Hind

tag: tumorgrade

value: IV


title: NOB0308_NBE_p30_IC2_Hind

description: Hind


title: NOB0211_NBE_NBE_p3_Hind

description: Hind

value: Unknown


title: MD548457_T_Hind

description: Hind

tag: analyzed with cindex?

value: yes

value: Astrocytoma

value: M. D. ANDERSON CANCER CENTER

value: III


title: MD548457_B_Hind

description:
Duplicate
Hind


title: HF1708_T_Hind

description: Hind

value: HENRY FORD HOSPITAL (RETRO)

value: II


title: MD508984_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: HF1671_T_Hind

description: Hind


title: HF1618_T_Hind

description: Hind


title: HF1608_T_Hind

description: Hind


title: HF1640_T_Hind

description: Hind


title: HF1628_T_Hind

description: Hind


title: HF1702_T_Hind

description: Hind


title: HF1667_T_Hind

description: Hind


title: HF1677_T_Hind

description: Hind


title: HF1606_T_Hind

description: Hind


title: HF1589_T_Hind

description: Hind


title: HF1588_T_Hind

description: Hind


title: HF1581_T_Hind

description: Hind


title: HF1568_T_Hind

description: Hind


title: HF1553_T_Hind

description: Hind


title: HF1560_T_Hind

description: Hind


title: NOB0308_NBE_p30_IC1_Hind

description: Hind


title: HF1585_T_Hind

description: Hind


title: HF1551_T_Hind

description: Hind


title: HF1538_T_Hind

description: Hind


title: HF1534_T_Hind

description: Hind


title: HF1613_T_Hind

description: Hind


title: HF1517_T_Hind

description: Hind


title: HF1509_T_Hind

description: Hind


title: HF1502_T_Hind

description: Hind


title: HF1493_T_Hind

description: Hind


title: HF1494_T_Hind

description: Hind


title: HF1490_T_Hind

description: Hind


title: HF1489_T_Hind

description: Hind


title: HF1540_T_Hind

description: Hind


title: HF1458_T_Hind

description: Hind


title: HF1442_T_Hind

description: Hind


title: HF1433_T_Hind

description: Hind


title: HF1463_T_Hind

description: Hind


title: HF1409_T_Hind

description: Hind


title: HF1407_T_Hind

description: Hind


title: HF1398_T_Hind

description: Hind


title: HF1382_T_Hind

description: Hind


title: HF1381_T_Hind

description: Hind


title: HF1380_T_Hind

description: Hind


title: HF1357_T_Hind

description: Hind


title: HF1366_T_Hind

description: Hind


title: HF1469_T_Hind

description: Hind


title: HF1397_T_Hind

description: Hind


title: HuMice_3

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: SAMPLE 3

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the GenomeStudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replicates.

label: Cy5 and Cy3

source_name: human cord blood 3

growth_protocol: Cord blood (CB) was obtained in accordance with the guidelines approved by the Ethics Committee of the Dresden University of Technology. Mononuclear cell enrichment was performed by density gradient centrifugation and CD34+ HPCs were enriched with CD34 MicroBeads (Miltenyi BioTec, Bergisch Gladbach, Germany). 50,000 CD34+ cells were injected intravenously into five 9 to 7 week old KIT-deficient NOD/SCID Il2rg-/-KitW41/W41 (NSGW41) mice. Flow cytometric analysis of bone marrow (BM) cells 19 weeks after transplantation revealed that 96.4% ± 1.9% of hematopoietic cells were of human origin. Subsequently hCD45+ cells were separated for further analysis of DNA methylation profiles.

extract_protocol: Genomic DNA was extracted using the QIAmp DNA Blood Mini Kit (Qiagen).

treatment_protocol: 1*10^6 human CD45+ cells were sorted from bone marrow of humanized NSGW41 mice 19 weeks after transplantation.

tag: cell type

value: hCD45+ cells from bone marrow of NSGW41 mice 19 weeks after transplantation

value: bone marrow

tag: host mouse strain

tag: humanized duration

value: 19.1 weeks

tag: primary cell type

value: CD34+ HSC

tag: primary tissue type

value: human umbilical cord blood


title: HF1326_T_Hind

description: Hind


title: HF1334_T_Hind

description: Hind


title: HF1345_T_Hind

description: Hind


title: HF1325_T_Hind

description: Hind


title: HF1511_T_Hind

description: Hind


title: HF1318_T_Hind

description: Hind


title: HuMice_4

description: SAMPLE 4

source_name: human cord blood 4

label_protocol: Standard Infinium HD Methylation Assay protocol

tag: tissue


title: HF1313_T_Hind

description: Hind


title: HF1295_T_Hind

description: Hind


title: HF1280_T_Hind

description: Hind


title: HF1297_T_Hind

description: Hind


title: HF1286_T_Hind

description: Hind


title: HF1269_T_Hind

description: Hind


title: HF1344_T_Hind

description: Hind


title: HF1264_T_Hind

description: Hind


title: HF1262_T_Hind

description: Hind


title: HuMice_2

description: SAMPLE 2

source_name: human cord blood 2


title: HF1246_T_Hind

description: Hind


title: HuMice_5

description: SAMPLE 5

source_name: human cord blood 5

value: NSGW41 IL7-


title: HF1232_T_Hind

description: Hind


title: HF1242_T_Hind

description: Hind


title: HF1235_T_Hind

description: Hind


title: HF1255_T_Hind

description: Hind


title: HF1227_T_Hind

description: Hind


title: HF1219_T_Hind

description: Hind


title: HF1220_T_Hind

description: Hind

value: GBM


title: HF1191_T_Hind

description: Hind


title: HuMice_1

description: SAMPLE 1

source_name: human cord blood 1


title: HF1186_T_Hind

description: Hind


title: HF1185_T_Hind

description: Hind


title: HF1167_T_Hind

description: Hind


title: HF1178_T_Hind

description: Hind


title: HF1150_T_Hind

description: Hind


title: HF1156_T_Hind

description: Hind


title: HF1136_T_Hind

description: Hind


title: HF1139_T_Hind

description: Hind


title: HF1137_T_Hind

description: Hind


title: HF1122_T_Hind

description: Hind


title: HF1097_T_Hind

description: Hind


title: HF1077_T_Hind

description: Hind


title: HF1058_T_Hind

description: Hind


title: HF1032_T_Hind

description: Hind


title: HF1071_T_Hind

description: Hind


title: HF1057_T_Hind

description: Hind


title: HF1000_T_Hind

description: Hind


title: HF1090_T_Hind

description: Hind


title: HF0992_T_Hind

description: Hind


title: HF0990_T_Hind

description: Hind


title: HF0986_T_Hind

description: Hind


title: HF0963_T_Hind

description: Hind


title: HF0954.2_T_Hind

description: Hind


title: HF0962_T_Hind

description: Hind


title: HF0975_T_Hind

description: Hind


title: HF0960_T_Hind

description: Hind


title: HF0936_T_Hind

description: Hind


title: HF0897_T_Hind

description: Hind


title: HF0894_T_Hind

description: Hind


title: HF0899_T_Hind

description: Hind


title: HF0850_T_Hind

description: Hind


title: HF1087_T_Hind

description: Hind


title: HF0828_T_Hind

description: Hind


title: HF1059_T_Hind

description: Hind

value: mixed


title: HF0844_T_Hind

description: Hind


title: HF0831_T_Hind

description: Hind


title: HF0822_T_Hind

description: Hind


title: HF0982_T_Hind

description: Hind


title: HF0802_T_Hind

description: Hind


title: HF0790_T_Hind

description: Hind

value: IV


title: HF0666_T_Hind

description: Hind


title: HF0757_T_Hind

description: Hind


title: HF0749_T_Hind

description: Hind


title: HF0778_T_Hind

description: Hind


title: HF0654_T_Hind

description: Hind


title: HF0652.4_T_Hind

description: Hind


title: HF0953_T_Hind

description: Hind


title: HF0608_T_Hind

description: Hind


title: HF0599_T_Hind

description: Hind


title: HF0606_T_Hind

description: Hind


title: HF0627_T_Hind

description: Hind


title: HF0583_T_Hind

description: Hind


title: HF0520_T_Hind

description: Hind


title: HF0543_T_Hind

description: Hind


title: HF0615_T_Hind

description: Hind


title: HF0855_T_Hind

description: Hind


title: HF0505_T_Hind

description: Hind


title: HF0491_T_Hind

description: Hind


title: HF0488_T_Hind

description: Hind


title: HF0445_T_Hind

description: Hind


title: HF0471_T_Hind

description: Hind


title: HF0460_T_Hind

description: Hind


title: HF0453_T_Hind

description: Hind


title: HF0450_T_Hind

description: Hind


title: HF0442.5_T_Hind

description: Hind


title: HF0435_T_Hind

description: Hind


title: HF0350_T_Hind

description: Hind


title: HF0639_T_Hind

description: Hind


title: HF0285_T_Hind

description: Hind


title: HF0434_T_Hind

description: Hind


title: HF0332_T_Hind

description: Hind


title: HF0252_T_Hind

description: Hind


title: HF0408_T_Hind

description: Hind


title: HF0212_T_Hind

description: Hind


title: HF0510_T_Hind

description: Hind


title: HF0329_T_Hind

description: Hind


title: HF0244_T_Hind

description: Hind


title: HF0152_T_Hind

description: Hind


title: HF0251_T_Hind

description: Hind


title: HF0223_T_Hind

description: Hind


title: HF0050_T_Hind

description: Hind


title: HF0022_T_Hind

description: Hind


title: HF0087_T_Hind

description: Hind


title: HF0066_T_Hind

description: Hind


title: HF0184_T_Hind

description: Hind


title: HF0180_T_Hind

description: Hind


title: HF0024_T_Hind

description: Hind


title: HF0108_T_Hind

description: Hind


title: HF0089_T_Hind

description: Hind


title: E50091_T_Hind

description: Hind

value: MSKCC/NEW YORK


title: E50091_B_Hind

description:
Duplicate
Hind


title: E50074_T_Hind

description: Hind

value: yes

value: DANA-FARBER CANCER INSTITUTE


title: E50057_T_Hind

description: Hind

value: UCLA SCHOOL OF MEDICINE


title: HF0031_T_Hind

description: Hind


title: HF0026_T_Hind

description: Hind

value: Astrocytoma


title: HF0017_T_Hind

description: Hind

value: HENRY FORD HOSPITAL (RETRO)

value: III


title: E10690_T_Hind

description: Hind

value: MIXED

value: NIH


title: E10692_T_Hind

description: Hind

value: TBD


title: E50057_B_Hind

description:
Duplicate
Hind


title: E10692_B_Hind

description:
Duplicate
Hind


title: E10691_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: E10691_B_Hind

description:
Duplicate
Hind


title: E10690_B_Hind

description:
Duplicate
Hind


title: E10662_T_Hind

description: Hind


title: E10662_B_Hind

description:
Duplicate
Hind


title: E10615_B_Hind

description:
Duplicate
Hind

value: ASTROCYTOMA


title: E10645_T_Hind

description: Hind


title: E10551_T_Hind

description: Hind


title: E10540_T_Hind

description: Hind


title: E10622_T_Hind

description: Hind


title: E10622_B_Hind

description:
Duplicate
Hind


title: E10514_T_Hind

description: Hind


title: E10514_B_Hind

description:
Duplicate
Hind


title: E10616_B_Hind

description:
Duplicate
Hind


title: E10615_T_Hind

description: Hind


title: E10595_T_Hind

description: Hind


title: E10595_B_Hind

description:
Duplicate
Hind


title: E10596_T_Hind

description: Hind


title: E10645_B_Hind

description:
Duplicate
Hind


title: E10556_B_Hind

description:
Duplicate
Hind


title: E10488_B_Hind

description:
Duplicate
Hind


title: E10556_T_Hind

description: Hind


title: HF1356_T_Hind

description: Hind


title: E10476_B_Hind

description:
Duplicate
Hind

value: Henry Ford


title: E10596_B_Hind

description:
Duplicate
Hind


title: E10362_T_Hind

description: Hind


title: E10488_T_Hind

description: Hind


title: E10540_B_Hind

description:
Duplicate
Hind


title: E10362_B_Hind

description:
Duplicate
Hind


title: E10313_T_Hind

description: Hind

value: UNIV OF PITTSBURGH


title: E10551_B_Hind

description:
Duplicate
Hind

value: GBM


title: E10616_T_Hind

description: Hind


title: E10476_T_Hind

description: Hind


title: E10306_T_Hind

description: Hind


title: E10305_T_Hind

description: Hind


title: E10306_B_Hind

description:
Duplicate
Hind


title: E10305_B_Hind

description:
Duplicate
Hind


title: E10313_B_Hind

description:
Duplicate
Hind


title: E10300_B_Hind

description:
Duplicate
Hind


title: E10300_T_Hind

description: Hind


title: E10292_T_Hind

description: Hind


title: E10290_T_Hind

description: Hind


title: E10290_B_Hind

description:
Duplicate
Hind


title: E10292_B_Hind

description:
Duplicate
Hind


title: E10287_B_Hind

description:
Duplicate
Hind

value: UCSF


title: E10287_T_Hind

description: Hind


title: E10286_T_Hind

description: Hind

value: UPMC


title: HF1348_T_Hind

description: Hind

value: II


title: E10285_T_Hind

description: Hind


title: E10286_B_Hind

description:
Duplicate
Hind


title: E10285_B_Hind

description:
Duplicate
Hind


title: E10284_T_Hind

description: Hind


title: E10278_B_Hind

description:
Duplicate
Hind


title: E10271_T_Hind

description: Hind


title: E10267_T_Hind

description: Hind

value: yes


title: E10267_B_Hind

description:
Duplicate
Hind


title: E10264_T_Hind

description: Hind


title: E10265_T_Hind

description: Hind


title: E10264_B_Hind

description:
Duplicate
Hind


title: E10265_B_Hind

description:
Duplicate
Hind


title: E10262_T_Hind

description: Hind


title: E10262_B_Hind

description:
Duplicate
Hind


title: E10258_T_Hind

description: Hind


title: E10250_T_Hind

description: Hind


title: E10253_B_Hind

description:
Duplicate
Hind


title: E10250_B_Hind

description:
Duplicate
Hind


title: E10252C_T_Hind

description: Hind


title: E10252C_Hind

description: Hind


title: E10249_B_Hind

description:
Duplicate
Hind

value: NABTT/HENRY FORD HOSPITAL


title: E10248_T_Hind

description: Hind


title: E10248_B_Hind

description:
Duplicate
Hind


title: E10227_B_Hind

description:
Duplicate
Hind


title: E10235_B_Hind

description:
Duplicate
Hind


title: E10235_T_Hind

description: Hind


title: E10278_T_Hind

description: Hind


title: E10227_T_Hind

description: Hind


title: E10226_T_Hind

description: Hind


title: E10211_T_Hind

description: Hind


title: E10211_B_Hind

description:
Duplicate
Hind


title: E10210_T_Hind

description: Hind

value: NIH NEURO-ONCOLOGY BRANCH


title: E10193_T_Hind

description: Hind

value: UCLA SCHOOL OF MEDICINE


title: E10193_B_Hind

description:
Duplicate
Hind


title: E10203_B_Hind

description:
Duplicate
Hind


title: E10192_T_Hind

description: Hind


title: E10192_B_Hind

description:
Duplicate
Hind


title: E10191_T_Hind

description: Hind


title: E10258_B_Hind

description:
Duplicate
Hind


title: E10253_T_Hind

description: Hind


title: E10252B_T_Hind

description:
second resection/operation
Hind


title: E10185_T_Hind

description: Hind


title: E10184_B_Hind

description:
Duplicate
Hind


title: E10185_B_Hind

description:
Duplicate
Hind


title: E10182_T_Hind

description: Hind


title: E10184_T_Hind

description: Hind


title: E10162_T_Hind

description: Hind


title: E10158_T_Hind

description: Hind


title: E10226_B_Hind

description:
Duplicate
Hind


title: E10144_T_Hind

description: Hind

value: IV


title: E10158_B_Hind

description:
Duplicate
Hind


title: E10141_B_Hind

description:
Duplicate
Hind


title: E10140_T_Hind

description: Hind

value: MSKCC/NEW YORK


title: E10210_B_Hind

description:
Duplicate
Hind


title: E10141_T_Hind

description: Hind


title: E10143_T_Hind

description: Hind


title: E10136_T_Hind

description: Hind

value: HENRY FORD HOSPITAL


title: E10203_T_Hind

description: Hind


title: E10136_B_Hind

description:
Duplicate
Hind


title: E10191_B_Hind

description:
Duplicate
Hind


title: E10110_T_Hind

description: Hind


title: E10103_T_Hind

description: Hind


title: E10110_B_Hind

description:
Duplicate
Hind


title: E10105_T_Hind

description: Hind

value: III


title: E10105_B_Hind

description:
Duplicate
Hind


title: E10097_B_Hind

description:
Duplicate
Hind


title: E10162_B_Hind

description:
Duplicate
Hind


title: E10080_B_Hind

description:
Duplicate
Hind

value: H. LEE MOFFITT CANCER CENTER


title: E10080_T_Hind

description: Hind


title: E10097_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: E10076_T_Hind

description: Hind

value: UNIVERSITY OF WISCONSIN


title: E10076_B_Hind

description:
Duplicate
Hind


title: E10144_B_Hind

description:
Duplicate
Hind


title: E10067_T_Hind

description: Hind

value: UNKNOWN


title: E10062_B_Hind

description:
Duplicate
Hind

value: ASTROCYTOMA


title: E10072_T_Hind

description: Hind

value: Henry Ford


title: E10062_T_Hind

description: Hind


title: E10072_B_Hind

description:
Duplicate
Hind


title: E10058_T_Hind

description: Hind


title: E10041_B_Hind

description:
Duplicate
Hind

value: GBM


title: E10054_T_Hind

description: Hind


title: E10044_B_Hind

description:
Duplicate
Hind

value: NABTT/MASSACHUSETTS GENERAL HOSPITAL


title: E10041_T_Hind

description: Hind


title: E10038_B_Hind

description:
Duplicate
Hind


title: E10038_T_Hind

description: Hind


title: E10059_T_Hind

description: Hind


title: E10036_B_Hind

description:
Duplicate
Hind


title: E10103_B_Hind

description:
Duplicate
Hind


title: E10037_B_Hind

description:
Duplicate
Hind


title: E10031_T_Hind

description: Hind


title: E10031_B_Hind

description:
Duplicate
Hind


title: E10030_B_Hind

description:
Duplicate
Hind


title: E10029_B_Hind

description:
Duplicate
Hind


title: E10027_B_Hind

description:
Duplicate
Hind


title: E10025_T_Hind

description: Hind

value: II


title: E10027_T_Hind

description: Hind

value: yes


title: E10026_T_Hind

description: Hind


title: E10029_T_Hind

description: Hind


title: E10023_B_Hind

description:
Duplicate
Hind


title: E10024_B_Hind

description:
Duplicate
Hind


title: E10022_B_Hind

description:
Duplicate
Hind


title: E10044_T_Hind

description: Hind


title: E10019_T_Hind

description: Hind


title: E10023_T_Hind

description: Hind


title: E10012_T_Hind

description: Hind


title: E10013_T_Hind

description: Hind


title: E10010_T_Hind

description: Hind

value: DANA-FARBER CANCER INSTITUTE


title: E10019_B_Hind

description:
Duplicate
Hind


title: E10011_T_Hind

description: Hind


title: E10013_B_Hind

description:
Duplicate
Hind

value: NIH NEURO-ONCOLOGY BRANCH


title: E10030_T_Hind

description: Hind

value: UCLA SCHOOL OF MEDICINE


title: E10037_T_Hind

description: Hind


title: E10009_T_Hind

description: Hind


title: E10009_B_Hind

description:
Duplicate
Hind


title: E10006_T_Hind

description: Hind


title: E10008_T_Hind

description: Hind


title: E10024_T_Hind

description: Hind


title: E10008_B_Hind

description:
Duplicate
Hind


title: E10003_T_Hind

description: Hind


title: E10003_B_Hind

description:
Duplicate
Hind


title: E10002_T_Hind

description: Hind

value: IV


title: E10002_B_Hind

description:
Duplicate
Hind


title: E10022_T_Hind

description: Hind


title: E10001_B_Hind

description:
Duplicate
Hind


title: E09993_T_Hind

description: Hind


title: E09996_T_Hind

description: Hind


title: E09994_T_Hind

description: Hind


title: E09993_B_Hind

description:
Duplicate
Hind


title: E09990_T_Hind

description: Hind


title: E09989_T_Hind

description: Hind


title: E09988_T_Hind

description: Hind


title: E09988_B_Hind

description:
Duplicate
Hind


title: E09989_B_Hind

description:
Duplicate
Hind


title: E09987_T_Hind

description: Hind


title: E09982_T_Hind

description: Hind


title: E09983_B_Hind

description:
Duplicate
Hind


title: E09982_B_Hind

description:
Duplicate
Hind


title: E09979_B_Hind

description:
Duplicate
Hind


title: E09978_B_Hind

description:
Duplicate
Hind


title: E09976_T_Hind

description: Hind


title: E09975_B_Hind

description:
Duplicate
Hind


title: E09978_T_Hind

description: Hind


title: E09976_B_Hind

description:
Duplicate
Hind


title: E09975_T_Hind

description: Hind


title: E09971_T_Hind

description: Hind


title: E09971_B_Hind

description:
Duplicate
Hind


title: E09967_T_Hind

description: Hind


title: E10001_T_Hind

description: Hind


title: E09990_B_Hind

description:
Duplicate
Hind


title: E09963_T_Hind

description: Hind


title: E09960_B_Hind

description:
Duplicate
Hind

value: UNIV OF PITTSBURGH


title: E09964_T_Hind

description: Hind


title: E09966_B_Hind

description:
Duplicate
Hind


title: E09966_T_Hind

description: Hind


title: E09965_T_Hind

description: Hind


title: E09960_T_Hind

description: Hind


title: E09958_T_Hind

description: Hind

value: HENRY FORD HOSPITAL


title: E09957_B_Hind

description:
Duplicate
Hind

value: Unknown


title: E09957_T_Hind

description: Hind


title: E09958_B_Hind

description:
Duplicate
Hind


title: E09956_T_Hind

description: Hind

value: H. LEE MOFFITT CANCER CENTER


title: E09956_B_Hind

description:
Duplicate
Hind


title: E09951_B_Hind

description:
Duplicate
Hind


title: E09948_T_Hind

description: Hind

value: III


title: E09948_B_Hind

description:
Duplicate
Hind


title: E09945_B_Hind

description:
Duplicate
Hind

value: UNIVERSITY OF WISCONSIN


title: E09945_T_Hind

description: Hind

value: UNKNOWN


title: E09937_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: E09941_T_Hind

description: Hind


title: E09938_B_Hind

description:
Duplicate
Hind


title: E09936_T_Hind

description: Hind


title: E09936_B_Hind

description:
Duplicate
Hind


title: E09932_B_Hind

description:
Duplicate
Hind

value: MIXED


title: E09967_B_Hind

description:
Duplicate
Hind

value: GBM


title: E09930_T_Hind

description: Hind


title: E09930_B_Hind

description:
Duplicate
Hind


title: E09924_T_Hind

description: Hind


title: E10021_T_Hind

description: Hind


title: E09922_B_Hind

description:
Duplicate
Hind


title: E09922_T_Hind

description: Hind


title: E09923_T_Hind

description: Hind


title: E09920_B_Hind

description:
Duplicate
Hind

value: ASTROCYTOMA


title: E09917_B_Hind

description:
Duplicate
Hind


title: E09921_T_Hind

description: Hind


title: E09920_T_Hind

description: Hind


title: E09921_B_Hind

description:
Duplicate
Hind


title: E09916_B_Hind

description:
Duplicate
Hind


title: E09914_T_Hind

description: Hind


title: E09914_B_Hind

description:
Duplicate
Hind


title: E09910_T_Hind

description: Hind


title: E09907B_T_Hind

description: Hind


title: E09907_B_Hind

description:
Duplicate
Hind


title: E09902_T_Hind

description: Hind


title: E09907_T_Hind

description: Hind


title: E09906_B_Hind

description:
Duplicate
Hind


title: E09900_B_Hind

description:
Duplicate
Hind


title: E09899_T_Hind

description: Hind


title: E09899_B_Hind

description:
Duplicate
Hind


title: E09893_T_Hind

description: Hind


title: E09892_T_Hind

description: Hind


title: E09906_T_Hind

description: Hind


title: E09917_T_Hind

description: Hind


title: E09916_T_Hind

description: Hind


title: E09888_B_Hind

description:
Duplicate
Hind


title: E09890_B_Hind

description:
Duplicate
Hind

value: II


title: E09892_B_Hind

description:
Duplicate
Hind


title: E09888_T_Hind

description: Hind

value: yes


title: E09868_B_Hind

description:
Duplicate
Hind


title: E09862_T_Hind

description: Hind


title: E09868_T_Hind

description: Hind


title: E09860_T_Hind

description: Hind


title: E09871_B_Hind

description:
Duplicate
Hind


title: E09862_B_Hind

description:
Duplicate
Hind


title: E09902_B_Hind

description:
Duplicate
Hind


title: E09900_T_Hind

description: Hind


title: E09858_B_Hind

description:
Duplicate
Hind


title: E09860_B_Hind

description:
Duplicate
Hind


title: E09858_T_Hind

description: Hind


title: E09852_T_Hind

description: Hind


title: E09848_B_Hind

description:
Duplicate
Hind


title: E09846_T_Hind

description: Hind


title: E09842_B_Hind

description:
Duplicate
Hind


title: E09835_B_Hind

description:
Duplicate
Hind


title: E09842_T_Hind

description: Hind


title: E09891_B_Hind

description:
Duplicate
Hind


title: E09835_T_Hind

description: Hind


title: E09834_T_Hind

description: Hind


title: E09833B_T_Hind

description: Hind


title: E09871_T_Hind

description: Hind


title: E09833_B_Hind

description:
Duplicate
Hind


title: E09834_B_Hind

description:
Duplicate
Hind


title: E09832_T_Hind

description: Hind


title: E09829B_T_Hind

description: Hind


title: E09832_B_Hind

description:
Duplicate
Hind


title: E09833_T_Hind

description: Hind


title: E09825_T_Hind

description: Hind


title: E09829_T_Hind

description: Hind


title: E09829_B_Hind

description:
Duplicate
Hind


title: E09819_T_Hind

description: Hind


title: E09825_B_Hind

description:
Duplicate
Hind


title: E09811_T_Hind

description: Hind


title: E09819_B_Hind

description:
Duplicate
Hind


title: E09803_B_Hind

description:
Duplicate
Hind

value: NIH


title: E09810_B_Hind

description:
Duplicate
Hind


title: E09810_T_Hind

description: Hind


title: E09857_T_Hind

description: Hind


title: E09811_B_Hind

description:
Duplicate
Hind


title: E09801_T_Hind

description: Hind


title: E09802_B_Hind

description:
Duplicate
Hind


title: E09846_B_Hind

description:
Duplicate
Hind


title: E09801_B_Hind

description:
Duplicate
Hind


title: E09800_B_Hind

description:
Duplicate
Hind


title: E09786_B_Hind

description:
Duplicate
Hind

value: NIH NEURO-ONCOLOGY BRANCH


title: E09785_B_Hind

description:
Duplicate
Hind


title: E09786_T_Hind

description: Hind


title: E09800_T_Hind

description: Hind


title: E09782_T_Hind

description: Hind

value: NABTT/JOHNS HOPKINS


title: E09759_B_Hind

description:
Duplicate
Hind

value: UWI

value: IV


title: E09756_T_Hind

description: Hind


title: E09756_B_Hind

description:
Duplicate
Hind


title: E09752_T_Hind

description: Hind


title: E09774_B_Hind

description:
Duplicate
Hind


title: E09744_B_Hind

description:
Duplicate
Hind


title: E09774_T_Hind

description: Hind


title: E09755_B_Hind

description:
Duplicate
Hind


title: E09744_T_Hind

description: Hind


title: E09755_T_Hind

description: Hind


title: E09742_T_Hind

description: Hind


title: E09730_B_Hind

description:
Duplicate
Hind


title: E09740_T_Hind

description: Hind


title: E09708_T_Hind

description: Hind


title: E09722_T_Hind

description: Hind


title: E09722_B_Hind

description:
Duplicate
Hind


title: E09708_B_Hind

description:
Duplicate
Hind


title: E09699_B_Hind

description:
Duplicate
Hind


title: E09688_T_Hind

description: Hind


title: E09688_B_Hind

description:
Duplicate
Hind


title: E09680_T_Hind

description: Hind


title: E09681_T_Hind

description: Hind


title: E09699_T_Hind

description: Hind


title: E09698_B_Hind

description:
Duplicate
Hind


title: E09698_T_Hind

description: Hind


title: E09680_B_Hind

description:
Duplicate
Hind


title: E09743_B_Hind

description:
Duplicate
Hind


title: E09743_T_Hind

description: Hind


title: E09730_T_Hind

description: Hind


title: E09657_T_Hind

description: Hind


title: E09655_T_Hind

description: Hind


title: E09670_T_Hind

description: Hind


title: E09679_T_Hind

description: Hind

value: UCLA SCHOOL OF MEDICINE


title: E09645_T_Hind

description: Hind


title: E09641_B_Hind

description:
Duplicate
Hind

value: Unknown

value: UCSF


title: E09644_B_Hind

description:
Duplicate
Hind

value: H. LEE MOFFITT CANCER CENTER


title: E09649_T_Hind

description: Hind


title: E09629_T_Hind

description: Hind

value: DANA-FARBER CANCER INSTITUTE


title: E09649_B_Hind

description:
Duplicate
Hind


title: E09624_T_Hind

description: Hind


title: E09629_B_Hind

description:
Duplicate
Hind

value: UNKNOWN


title: E09641_T_Hind

description: Hind


title: E09655_B_Hind

description:
Duplicate
Hind


title: E09622_B_Hind

description:
Duplicate
Hind


title: E09622_T_Hind

description: Hind


title: E09615_T_Hind

description: Hind


title: E09615_B_Hind

description:
Duplicate
Hind


title: E09679_B_Hind

description:
Duplicate
Hind


title: E09611B_T_Hind

description: Hind


title: E09624_B_Hind

description:
Duplicate
Hind


title: E09611_B_Hind

description:
Duplicate
Hind


title: E09657_B_Hind

description:
Duplicate
Hind


title: E10010_B_Hind

description:
Duplicate
Hind


title: E09606_T_Hind

description: Hind


title: E09610_B_Hind

description:
Duplicate
Hind


title: E09605_T_Hind

description: Hind


title: E09602_T_Hind

description: Hind

value: UNIVERSITY OF WISCONSIN


title: E09605_B_Hind

description:
Duplicate
Hind


title: E09601_B_Hind

description:
Duplicate
Hind


title: E09587_B_Hind

description:
Duplicate
Hind


title: E09587_T_Hind

description: Hind


title: E09601_T_Hind

description: Hind


title: E09595_B_Hind

description:
Duplicate
Hind


title: E09569_B_Hind

description:
Duplicate
Hind


title: E09515_T_Hind

description: Hind


title: E09535_T_Hind

description: Hind


title: E09595_T_Hind

description: Hind


title: E09531_B_Hind

description:
Duplicate
Hind

value: UNIV OF PITTSBURGH


title: E09515_B_Hind

description:
Duplicate
Hind


title: E09569_T_Hind

description: Hind

value: GBM


title: E09495_T_Hind

description: Hind


title: E09503_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: E09531_T_Hind

description: Hind

value: ASTROCYTOMA


title: E09511_B_Hind

description:
Duplicate
Hind

value: mixed

value: III


title: E09611_T_Hind

description: Hind

value: NIH NEURO-ONCOLOGY BRANCH


title: E09494_T_Hind

description: Hind

value: yes


title: E09495_B_Hind

description:
Duplicate
Hind


title: E09489_T_Hind

description: Hind


title: E09471_T_Hind

description: Hind

value: Astrocytoma

value: II


title: E09494_B_Hind

description:
Duplicate
Hind


title: E09503_B_Hind

description:
Duplicate
Hind


title: E09483_T_Hind

description: Hind

value: IV


title: E09602_B_Hind

description:
Duplicate
Hind


title: E09471_B_Hind

description:
Duplicate
Hind


title: E09454_T_Hind

description: Hind


title: E09454_B_Hind

description:
Duplicate
Hind


title: E09451_B_Hind

description:
Duplicate
Hind


title: E09449_T_Hind

description: Hind


title: E09449_B_Hind

description:
Duplicate
Hind


title: E09511_T_Hind

description: Hind


title: E09448_B_Hind

description:
Duplicate
Hind


title: E09440_T_Hind

description: Hind


title: E09419_B_Hind

description:
Duplicate
Hind


title: E09419_T_Hind

description: Hind


title: E09405_B_Hind

description:
Duplicate
Hind


title: E09489_B_Hind

description:
Duplicate
Hind


title: E09369_B_Hind

description:
Duplicate
Hind


title: E09369_T_Hind

description: Hind


title: E09398_B_Hind

description:
Duplicate
Hind


title: E09378_T_Hind

description: Hind


title: E09358_T_Hind

description: Hind


title: E09348_B_Hind

description:
Duplicate
Hind


title: E09378_B_Hind

description:
Duplicate
Hind


title: E09355_T_Hind

description: Hind


title: E09348_T_Hind

description: Hind


title: E09331_B_Hind

description:
Duplicate
Hind


title: E09278B_T_Hind

description: Hind


title: E09278_T_Hind

description: Hind


title: E09296_T_Hind

description: Hind


title: E09448_T_Hind

description: Hind


title: E09264_T_Hind

description: Hind


title: E09263B_T_Hind

description:
second resection/operation-tumor
Hind

value: Unknown


title: E09263B_NT_Hind

description:
second resection/operation - nontumor
Hind


title: E09263_B_Hind

description: Hind


title: E09440_B_Hind

description:
Duplicate
Hind

value: UCSF


title: E09264_B_Hind

description:
Duplicate
Hind


title: E09398_T_Hind

description: Hind


title: E09405_T_Hind

description: Hind


title: E09262_T_Hind

description: Hind

value: MIXED


title: E09239_T_Hind

description: Hind


title: E09355_B_Hind

description:
Duplicate
Hind

value: DANA-FARBER CANCER INSTITUTE


title: E09238_B_Hind

description:
Duplicate
Hind

value: UNKNOWN


title: E09362_T_Hind

description: Hind


title: E09358_B_Hind

description:
Duplicate
Hind


title: E09239_B_Hind

description:
Duplicate
Hind


title: E09262_B_Hind

description:
Duplicate
Hind


title: E09238_T_Hind

description: Hind


title: E09231_T_Hind

description: Hind


title: E09233_T_Hind

description: Hind


title: E09231_B_Hind

description:
Duplicate
Hind


title: E09232_B_Hind

description:
Duplicate
Hind


title: E09232_T_Hind

description: Hind


title: E09214_T_Hind

description: Hind


title: E09192_T_Hind

description: Hind


title: E09214_B_Hind

description:
Duplicate
Hind


title: E09278_B_Hind

description:
Duplicate
Hind


title: E09192_B_Hind

description:
Duplicate
Hind


title: E09176_T_Hind

description: Hind


title: E09176_B_Hind

description:
Duplicate
Hind


title: E09167_T_Hind

description: Hind


title: E09151_B_Hind

description:
Duplicate
Hind


title: E07733_T_Hind

description: Hind


title: E07733_B_Hind

description:
Duplicate
Hind


title: 88375506_T_Hind

description: Hind

value: TJU


title: 88375506_B_Hind

description:
Duplicate
Hind


title: 88295267_T_Hind

description: Hind


title: 88295267_B_Hind

description:
Duplicate
Hind


title: 81668782_T_Hind

description: Hind

value: TBD


title: E09233_B_Hind

description:
Duplicate
Hind

value: GBM


title: 860772_T_Hind

description: Hind


title: 860772_B_Hind

description:
Duplicate
Hind


title: 3525342_T_Hind

description: Hind


title: 81668782_B_Hind

description:
Duplicate
Hind


title: 3522254_T_Hind

description: Hind


title: 3523498_T_Hind

description: Hind


title: 3525342_B_Hind

description:
Duplicate
Hind


title: 3523498_B_Hind

description:
Duplicate
Hind


title: 3522254_B_Hind

description:
Duplicate
Hind


title: 3514945_B_Hind

description:
Duplicate
Hind


title: 3514945_T_Hind

description: Hind


title: 3512529_B_Hind

description:
Duplicate
Hind


title: 3513467_B_Hind

description:
Duplicate
Hind


title: 3512529_T_Hind

description: Hind


title: 3513467_T_Hind

description: Hind


title: 3506280_T_Hind

description: Hind


title: E08021_T_Hind

description: Hind

value: OLIGODENDROGLIOMA


title: 3506280_B_Hind

description:
Duplicate
Hind


title: E08021_B_Hind

description:
Duplicate
Hind


title: 3495697_B_Hind

description:
Duplicate
Hind


title: 3504050_B_Hind

description:
Duplicate
Hind


title: 3497265_B_Hind

description:
Duplicate
Hind


title: 3495697_T_Hind

description: Hind


title: 3497265_T_Hind

description: Hind


title: 3504050_T_Hind

description: Hind


title: 3473067_B_Hind

description:
Duplicate
Hind


title: 3089254_T_Hind

description: Hind


title: 3089254_B_Hind

description:
Duplicate
Hind


title: 03486876_T_Hind

description: Hind


title: 03484586_T_Hind

description: Hind


title: 03480779_B_Hind

description:
Duplicate
Hind


title: 03484586_B_Hind

description:
Duplicate
Hind


title: 03484270_B_Hind

description:
Duplicate
Hind


title: 03479212_B_Hind

description:
Duplicate
Hind


title: 03480779_T_Hind

description: Hind


title: 03479212_T_Hind

description: Hind


title: 03474525_B_Hind

description:
Duplicate
Hind


title: 03476542_T_Hind

description: Hind


title: 03476542_B_Hind

description:
Duplicate
Hind


title: 03474525_T_Hind

description: Hind


title: 03473405_T_Hind

description: Hind


title: 03473067_T_Hind

description: Hind


title: 03473405_B_Hind

description:
Duplicate
Hind


title: 03471616_B_Hind

description:
Duplicate
Hind


title: 03468400_B_Hind

description:
Duplicate
Hind


title: 03468400_T_Hind

description: Hind


title: 03465304_B_Hind

description:
Duplicate
Hind


title: 03463522_T_Hind

description: Hind


title: 03466950_T_Hind

description: Hind


title: 03463812_T_Hind

description: Hind


title: 03463812_B_Hind

description:
Duplicate
Hind


title: 03465304_T_Hind

description: Hind


title: 03463522_B_Hind

description:
Duplicate
Hind


title: 03466950_B_Hind

description:
Duplicate
Hind


title: 03461404_B_Hind

description:
Duplicate
Hind


title: 03461404_T_Hind

description: Hind


title: 03477889_B_Hind

description:
Duplicate
Hind


title: 03461078_T_Hind

description: Hind

value: ASTROCYTOMA


title: 03461078_B_Hind

description:
Duplicate
Hind


title: 03471616_T_Hind

description: Hind


title: 03460111_B_Hind

description:
Duplicate
Hind


title: 03460111_T_Hind

description: Hind


title: 03450728_T_Hind

description: Hind


title: 03448110_T_Hind

description: Hind


title: 03444255_T_Hind

description: Hind


title: 03451592_T_Hind

description: Hind


title: 03451592_B_Hind

description:
Duplicate
Hind


title: 03441740_T_Hind

description: Hind


title: 03444255_B_Hind

description:
Duplicate
Hind


title: 03448110B_T_Hind

description:
second resection/operation
Hind


title: 03442083_B_Hind

description: Hind


title: 03441358_T_Hind

description: Hind


title: 03441740_B_Hind

description:
Duplicate
Hind


title: 03441358_B_Hind

description:
Duplicate
Hind


title: 03439543_B_Hind

description:
Duplicate
Hind


title: 03437595_B_Hind

description:
Duplicate
Hind


title: 03437691_T_Hind

description: Hind


title: 03439543_T_Hind

description: Hind


title: 03437595_T_Hind

description: Hind


title: 03437691_B_Hind

description:
Duplicate
Hind


title: 03434766_T_Hind

description: Hind


title: 03434174_T_Hind

description: Hind


title: 03436958_B_Hind

description:
Duplicate
Hind


title: 03434766_B_Hind

description:
Duplicate
Hind


title: 03434174_B_Hind

description:
Duplicate
Hind


title: 03450728_B_Hind

description:
Duplicate
Hind


title: 03433293_T_Hind

description: Hind


title: 03433293_B_Hind

description:
Duplicate
Hind


title: 03431774_B_Hind

description:
Duplicate
Hind


title: 03436958_T_Hind

description: Hind


title: 03431774_T_Hind

description: Hind


title: 03448110_B_Hind

description:
Duplicate
Hind


title: 03431712_B_Hind

description:
Duplicate
Hind


title: 03425149_B_Hind

description:
Duplicate
Hind


title: 03421536_T_Hind

description: Hind

value: UNCLASSIFIED


title: 03352571_B_Hind

description:
Duplicate
Hind


title: 03352571_T_Hind

description: Hind


title: 03421899_T_Hind

description: Hind

value: III


title: 03425149_T_Hind

description: Hind


title: 03431712_T_Hind

description: Hind


title: 03272709_T_Hind

description: Hind


title: 03421899_B_Hind

description:
Duplicate
Hind


title: 03184579_T_Hind

description: Hind


title: 03272709_B_Hind

description:
Duplicate
Hind


title: 01074569_T_Hind

description: Hind


title: 00715851_T_Hind

description: Hind


title: 01113810_T_Hind

description: Hind


title: 01113810_B_Hind

description:
Duplicate
Hind


title: 00641238_T_Hind

description: Hind


title: 00715851_B_Hind

description:
Duplicate
Hind


title: HF1613_T_Xba

description: Xba

value: HENRY FORD HOSPITAL (RETRO)


title: 00518392_T_Hind

description: Hind

value: yes


title: 00518392_B_Hind

description:
Duplicate
Hind


title: HF1588_T_Xba

description: Xba

value: Astrocytoma


title: 03421536_B_Hind

description:
Duplicate
Hind


title: HF1608_T_Xba

description: Xba


title: HF1606_T_Xba

description: Xba

value: II


title: HF1585_T_Xba

description: Xba

value: IV


title: HF1551_T_Xba

description: Xba


title: HF1581_T_Xba

description: Xba


title: HF1553_T_Xba

description: Xba


title: HF1589_T_Xba

description: Xba


title: HF1560_T_Xba

description: Xba


title: HF1540_T_Xba

description: Xba


title: HF1568_T_Xba

description: Xba


title: 03184579_B_Hind

description:
Duplicate
Hind


title: HF1511_T_Xba

description: Xba


title: HF1534_T_Xba

description: Xba


title: 01074569_B_Hind

description:
Duplicate
Hind


title: HF1517_T_Xba

description: Xba


title: HF1509_T_Xba

description: Xba


title: HF1494_T_Xba

description: Xba


title: 00641238_B_Hind

description:
Duplicate
Hind


title: HF1538_T_Xba

description: Xba


title: HF1469_T_Xba

description: Xba


title: HF1490_T_Xba

description: Xba


title: HF1433_T_Xba

description: Xba


title: HF1502_T_Xba

description: Xba


title: HF1489_T_Xba

description: Xba


title: HF1487_T_Xba

description: Xba


title: HF1458_T_Xba

description: Xba


title: HF1409_T_Xba

description: Xba


title: HF1356_T_Xba

description: Xba


title: HF1442_T_Xba

description: Xba


title: HF1463_T_Xba

description: Xba


title: HF1348_T_Xba

description: Xba


title: HF1357_T_Xba

description: Xba


title: HF1381_T_Xba

description: Xba


title: HF1398_T_Xba

description: Xba


title: HF1397_T_Xba

description: Xba


title: HF1345_T_Xba

description: Xba


title: HF1382_T_Xba

description: Xba


title: HF1325_T_Xba

description: Xba


title: HF1326_T_Xba

description: Xba


title: HF1297_T_Xba

description: Xba


title: HF1313_T_Xba

description: Xba


title: HF1338_T_Xba

description: Xba


title: HF1295_T_Xba

description: Xba


title: HF1280_T_Xba

description: Xba


title: HF1255_T_Xba

description: Xba


title: HF1334_T_Xba

description: Xba


title: HF1269_T_Xba

description: Xba


title: HF1246_T_Xba

description: Xba


title: HF1318_T_Xba

description: Xba


title: HF1493_T_Xba

description: Xba


title: HF1286_T_Xba

description: Xba


title: HF1235_T_Xba

description: Xba


title: HF1264_T_Xba

description: Xba


title: HF1366_T_Xba

description: Xba


title: HF1262_T_Xba

description: Xba


title: HF1185_T_Xba

description: Xba


title: HF1242_T_Xba

description: Xba


title: HF1344_T_Xba

description: Xba


title: HF1156_T_Xba

description: Xba


title: HF1232_T_Xba

description: Xba


title: HF1227_T_Xba

description: Xba


title: HF1220_T_Xba

description: Xba


title: HF1219_T_Xba

description: Xba


title: HF1186_T_Xba

description: Xba


title: HF1178_T_Xba

description: Xba


title: HF1167_T_Xba

description: Xba


title: HF1191_T_Xba

description: Xba


title: HF1122_T_Xba

description: Xba


title: HF1150_T_Xba

description: Xba


title: HF1139_T_Xba

description: Xba


title: HF1059_T_Xba

description: Xba

value: mixed


title: HF1057_T_Xba

description: Xba


title: HF1136_T_Xba

description: Xba


title: HF1032_T_Xba

description: Xba


title: HF1137_T_Xba

description: Xba


title: HF1097_T_Xba

description: Xba


title: HF1087_T_Xba

description: Xba


title: HF1090_T_Xba

description: Xba


title: HF1071_T_Xba

description: Xba


title: HF0963_T_Xba

description: Xba


title: HF1000_T_Xba

description: Xba


title: HF0960_T_Xba

description: Xba


title: HF0992_T_Xba

description: Xba


title: HF0990_T_Xba

description: Xba


title: HF0897_T_Xba

description: Xba


title: HF0894_T_Xba

description: Xba


title: HF0986_T_Xba

description: Xba


title: HF1077_T_Xba

description: Xba


title: HF0855_T_Xba

description: Xba


title: HF0962_T_Xba

description: Xba


title: HF0954.2_T_Xba

description: Xba


title: HF0982_T_Xba

description: Xba


title: HF0953_T_Xba

description: Xba


title: HF0828_T_Xba

description: Xba


title: HF1058_T_Xba

description: Xba


title: HF0802_T_Xba

description: Xba


title: HF0790_T_Xba

description: Xba


title: HF0931_T_Xba

description: Xba


title: HF0778_T_Xba

description: Xba


title: HF0936_T_Xba

description: Xba


title: HF0757_T_Xba

description: Xba


title: HF0702_T_Xba

description: Xba


title: HF0899_T_Xba

description: Xba


title: HF0850_T_Xba

description: Xba


title: HF0666_T_Xba

description: Xba


title: HF0822_T_Xba

description: Xba


title: HF0831_T_Xba

description: Xba


title: HF0639_T_Xba

description: Xba


title: HF0749_T_Xba

description: Xba


title: HF0844_T_Xba

description: Xba


title: HF0510_T_Xba

description: Xba


title: HF0599_T_Xba

description: Xba


title: HF0816_T_Xba

description: Xba


title: HF0652.4_T_Xba

description: Xba


title: HF0488_T_Xba

description: Xba


title: HF0627_T_Xba

description: Xba


title: HF0654_T_Xba

description: Xba


title: HF0615_T_Xba

description: Xba


title: HF0606_T_Xba

description: Xba


title: HF0471_T_Xba

description: Xba


title: HF0583_T_Xba

description: Xba


title: HF0445_T_Xba

description: Xba


title: HF0543_T_Xba

description: Xba


title: HF0329_T_Xba

description: Xba


title: HF0520_T_Xba

description: Xba


title: HF0332_T_Xba

description: Xba


title: HF0505_T_Xba

description: Xba


title: HF0291_T_Xba

description: Xba


title: HF0491_T_Xba

description: Xba


title: HF0453_T_Xba

description: Xba


title: HF0450_T_Xba

description: Xba


title: HF0434_T_Xba

description: Xba


title: HF0251_T_Xba

description: Xba


title: HF0252_T_Xba

description: Xba


title: HF0442.5_T_Xba

description: Xba


title: HF0223_T_Xba

description: Xba


title: HF0212_T_Xba

description: Xba


title: HF0189_T_Xba

description: Xba


title: HF0350_T_Xba

description: Xba


title: HF0460_T_Xba

description: Xba


title: HF0608_T_Xba

description: Xba


title: HF0184_T_Xba

description: Xba


title: HF0244_T_Xba

description: Xba


title: HF0218_T_Xba

description: Xba


title: HF0180_T_Xba

description: Xba


title: HF0152_T_Xba

description: Xba


title: HF0138_T_Xba

description: Xba


title: HF0108_T_Xba

description: Xba


title: HF0050_T_Xba

description: Xba


title: HF0031_T_Xba

description: Xba


title: HF0089_T_Xba

description: Xba


title: HF0087_T_Xba

description: Xba


title: E50057_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E50057_B_Xba

description:
Duplicate
Xba


title: HF0408_T_Xba

description: Xba


title: HF0066_T_Xba

description: Xba


title: HF0026_T_Xba

description: Xba


title: E10691_B_Xba

description:
Duplicate
Xba

value: NIH


title: HF0022_T_Xba

description: Xba


title: E50074_T_Xba

description: Xba

value: DANA-FARBER CANCER INSTITUTE


title: E10662_T_Xba

description: Xba


title: E10662_B_Xba

description:
Duplicate
Xba


title: E50074_B_Xba

description:
Duplicate
Xba


title: E10690_B_Xba

description:
Duplicate
Xba

value: MIXED


title: E10622_T_Xba

description: Xba


title: E10645_T_Xba

description: Xba


title: E10622_B_Xba

description:
Duplicate
Xba


title: E10616_T_Xba

description: Xba


title: HF0024_T_Xba

description: Xba


title: E10615_T_Xba

description: Xba


title: E10615_B_Xba

description:
Duplicate
Xba


title: E50091_B_Xba

description:
Duplicate
Xba

value: MSKCC/NEW YORK


title: E10596_B_Xba

description:
Duplicate
Xba


title: E10595_B_Xba

description:
Duplicate
Xba

value: TBD


title: E50091_T_Xba

description: Xba

value: GBM


title: E10595_T_Xba

description: Xba


title: E10556_T_Xba

description: Xba


title: E10692_B_Xba

description:
Duplicate
Xba


title: E10692_T_Xba

description: Xba


title: E10690_T_Xba

description: Xba


title: E10556_B_Xba

description:
Duplicate
Xba


title: E10551_T_Xba

description: Xba


title: E10551_B_Xba

description:
Duplicate
Xba


title: E10540_B_Xba

description:
Duplicate
Xba


title: E10514_B_Xba

description:
Duplicate
Xba


title: E10540_T_Xba

description: Xba


title: E10476_T_Xba

description: Xba

value: Henry Ford


title: E10362_T_Xba

description: Xba

value: ASTROCYTOMA


title: E10476_B_Xba

description:
Duplicate
Xba


title: E10488_T_Xba

description: Xba


title: E10362_B_Xba

description:
Duplicate
Xba


title: E10313_T_Xba

description: Xba

value: UNIV OF PITTSBURGH


title: E10313_B_Xba

description:
Duplicate
Xba


title: E10596_T_Xba

description: Xba


title: E10306_B_Xba

description:
Duplicate
Xba


title: E10305_T_Xba

description: Xba


title: E10306_T_Xba

description: Xba


title: E10305_B_Xba

description:
Duplicate
Xba


title: E10300_B_Xba

description:
Duplicate
Xba


title: E10300_T_Xba

description: Xba


title: E10292_B_Xba

description:
Duplicate
Xba


title: E10290_T_Xba

description: Xba


title: E10292_T_Xba

description: Xba


title: E10287_T_Xba

description: Xba

value: UCSF


title: E10286_B_Xba

description:
Duplicate
Xba

value: UPMC


title: E10286_T_Xba

description: Xba

value: yes


title: E10290_B_Xba

description:
Duplicate
Xba


title: E10285_T_Xba

description: Xba

value: Astrocytoma


title: E10284_B_Xba

description:
Duplicate
Xba


title: E10287_B_Xba

description:
Duplicate
Xba


title: E10514_T_Xba

description: Xba


title: E10488_B_Xba

description:
Duplicate
Xba


title: E10278_B_Xba

description:
Duplicate
Xba

value: OLIGODENDROGLIOMA


title: E10271_B_Xba

description:
Duplicate
Xba


title: E10267_B_Xba

description:
Duplicate
Xba


title: E10265_T_Xba

description: Xba


title: E10267_T_Xba

description: Xba


title: E10271_T_Xba

description: Xba


title: E10264_T_Xba

description: Xba


title: E10265_B_Xba

description:
Duplicate
Xba


title: E10262_T_Xba

description: Xba


title: E10262_B_Xba

description:
Duplicate
Xba


title: E10264_B_Xba

description:
Duplicate
Xba


title: E10258_B_Xba

description:
Duplicate
Xba


title: E10252C_T_Xba

description: Xba


title: E10258B_T_Xba

description: Xba


title: E10250_T_Xba

description: Xba


title: E10285_B_Xba

description:
Duplicate
Xba


title: E10258_T_Xba

description: Xba


title: E10249_B_Xba

description:
Duplicate
Xba

value: NABTT/HENRY FORD HOSPITAL


title: E10248_T_Xba

description: Xba


title: E10235_T_Xba

description: Xba


title: E10248_B_Xba

description:
Duplicate
Xba


title: E10278_T_Xba

description: Xba


title: E10235_B_Xba

description:
Duplicate
Xba


title: E10252C_Xba

description: Xba


title: E10226_B_Xba

description:
Duplicate
Xba


title: E10203_B_Xba

description:
Duplicate
Xba


title: E10210_T_Xba

description: Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: E10203_T_Xba

description: Xba


title: E10250_B_Xba

description:
Duplicate
Xba


title: E10192_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E10210_B_Xba

description:
Duplicate
Xba


title: E10192_B_Xba

description:
Duplicate
Xba


title: E10227_B_Xba

description:
Duplicate
Xba


title: E10191_T_Xba

description: Xba


title: E10185_T_Xba

description: Xba


title: E10184_B_Xba

description:
Duplicate
Xba


title: E10193_T_Xba

description: Xba


title: E10182_T_Xba

description: Xba


title: E10185_B_Xba

description:
Duplicate
Xba


title: E10184_T_Xba

description: Xba


title: E10249_T_Xba

description: Xba


title: E10226_T_Xba

description: Xba


title: E10162_T_Xba

description: Xba

value: III


title: E10191_B_Xba

description:
Duplicate
Xba


title: E10227_T_Xba

description: Xba


title: E10162_B_Xba

description:
Duplicate
Xba


title: E10158_B_Xba

description:
Duplicate
Xba


title: E10144_T_Xba

description: Xba

value: IV


title: E10144_B_Xba

description:
Duplicate
Xba


title: E10158_T_Xba

description: Xba


title: E10141_T_Xba

description: Xba


title: E10141_B_Xba

description:
Duplicate
Xba


title: E10211_T_Xba

description: Xba


title: E10140_T_Xba

description: Xba


title: E10140_B_Xba

description:
Duplicate
Xba


title: E10110_T_Xba

description: Xba


title: E10136_B_Xba

description:
Duplicate
Xba

value: HENRY FORD HOSPITAL


title: E10136_T_Xba

description: Xba


title: E10110_B_Xba

description:
Duplicate
Xba


title: E10105_B_Xba

description:
Duplicate
Xba


title: E10105_T_Xba

description: Xba


title: E10097_T_Xba

description: Xba


title: E10103_B_Xba

description:
Duplicate
Xba


title: E10080_B_Xba

description:
Duplicate
Xba

value: H. LEE MOFFITT CANCER CENTER


title: E10080_T_Xba

description: Xba


title: E10072_T_Xba

description: Xba


title: E10076_T_Xba

description: Xba

value: UNIVERSITY OF WISCONSIN


title: E10072_B_Xba

description:
Duplicate
Xba


title: E10062_T_Xba

description: Xba


title: E10062_B_Xba

description:
Duplicate
Xba


title: E10059_T_Xba

description: Xba

value: UNKNOWN

value: NABTT/MASSACHUSETTS GENERAL HOSPITAL


title: E10067_T_Xba

description: Xba


title: E10059_B_Xba

description:
Duplicate
Xba


title: E10054_B_Xba

description:
Duplicate
Xba

value: II


title: E10054_T_Xba

description: Xba


title: E10041_T_Xba

description: Xba

value: GBM


title: E10041_B_Xba

description:
Duplicate
Xba


title: E10038_B_Xba

description:
Duplicate
Xba


title: E10044_T_Xba

description: Xba


title: E10044_B_Xba

description:
Duplicate
Xba


title: E10038_T_Xba

description: Xba


title: E10103_T_Xba

description: Xba

value: ASTROCYTOMA

value: Henry Ford


title: E10037_B_Xba

description:
Duplicate
Xba


title: E10036_B_Xba

description:
Duplicate
Xba


title: E10031_T_Xba

description: Xba

value: yes


title: E10037_T_Xba

description: Xba


title: E10031_B_Xba

description:
Duplicate
Xba


title: E10030_T_Xba

description: Xba


title: E10030_B_Xba

description:
Duplicate
Xba


title: E10029_T_Xba

description: Xba


title: E10097_B_Xba

description:
Duplicate
Xba


title: E10029_B_Xba

description:
Duplicate
Xba


title: WT-ATRA rep2

first: Kristian

last: Laursen

address: 1300 York Ave.

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
The sequencing reads were cleaned by trimming adapter sequences and low quality bases, and were aligned to the mouse reference genome (GRCm38) using STAR.
Cufflinks was used to measure transcript abundances in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: .xls containing abundance measurements and differential expression data

source_name: Embryonic stem cells

growth_protocol: The cells were propagated on gelatinized plates in LIF-supplemented ES media

extract_protocol:
RNA was extracted using an RNeasy kit (Qiagen)
The cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced with single-end 51 bps on HiSeq4000 sequencer.

treatment_protocol: Murine Embryonic Stem Cells (WT and RAR-deficient TKO cells) were treated with vehicle (ETOH) or all-trans retinoic acid (ATRA, 1uM) for a duration of 24 hrs.

value: wild type

value: Embryonic stem cells


title: TKO-ETOH rep3

description: genotype: RARα-/-, RARβ-/-, RARγ-/-

value: RARalpha-/-, RARbeta-/-, RARgamma-/-


title: TKO-ATRA rep3

description: genotype: RARα-/-, RARβ-/-, RARγ-/-


title: TKO-ETOH rep2

description: genotype: RARα-/-, RARβ-/-, RARγ-/-


title: E10026_T_Xba

description: Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: WT-ATRA rep3


title: TKO-ETOH rep1

description: genotype: RARα-/-, RARβ-/-, RARγ-/-


title: TKO-ATRA rep2

description: genotype: RARα-/-, RARβ-/-, RARγ-/-


title: TKO-ATRA rep1

description: genotype: RARα-/-, RARβ-/-, RARγ-/-


title: Sample66_BALB.c_SNI_F

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

institute: Oxford University

description:
Ribozero RNA
BALB.c_SNI

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version 3.3.52 and Illumina HiSeq2000 analysis software version 2.0.12.0
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14 and BcltoFastq 1.8.4
Reads were mapped to mm10 genome (Mus_musculus.GRCm38.dna.primary_assembly.fa, Mus_musculus.GRCm38.87.chr.gtf) or rn6 genome (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa, Rattus_norvegicus.Rnor_6.0.90.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with Intersection not empty strategy
All reads overlapping annotations:  RefSeq (Pruitt et al., 2014), XenoRefSeq, ENSEMBL genes (Harrow et al., 2012) were discarded. We then used the remaining subset of RNA-seq reads in order to identify islands of expression outside known gene models (continuously expressed regions) using a coverage window approach. Workflow generally described in (Cabili et al., 2011; Gerstein et al., 2014; Ilott and Ponting, 2013) with modifications to produce annotations at the gene level. Doing this we get a non-redundant annotation of unique genes of LncRNAs suitable for count based DE analysis (Anders et al., 2015; Love et al., 2014). The concept of islands of expression (I.o.E) is described in (Gerstein et al., 2014). Coverage cut-off has been set as in (Cabili et al., 2011)  Only properly paired and uniquely mapped reads were selected. We selected splicing junctions covered with > 2 reads. We discarded all reads overlapping know gene models. We then used the remaining subset of RNA-seq reads to identify I.o.E outside known gene models using a coverage window approach.  We selected continuous regions above the coverage threshold of more than a read-mate length to ensure that overlapping read-mates would not artificially increase coverage. I.o.E were collapsed and clustered as co-overlapping features connected by splicing junctions. In each cluster consensus introns were calculated by the relative frequency of each discrete segment of a set of splicing junctions. We then subtracted the genomic intervals of these consensus introns from the genomic intervals of the grouped (I.o.E) to reconstruct full length putative LncRNAs.   We included putative LncRNAs in this novel annotation only if they were present in all replicates a biological condition or strain. Annotations were exported in the Gene Transfer Format (GTF). Subsequently we filtered out transcripts with length < 200 bp and we used CPAT (Wang et al., 2013) to assess coding potential. The pipeline was scripted in R using bioconductor (Gentleman et al., 2004) packages and custom scripts.
Genome_build: mm10 for mouse, rn6 for rat
Supplementary_files_format_and_content: CSV files res_sni_vs_sham_BALB.c.csv, res_sni_vs_sham_B10.D2.csv, res_snt_vs_sham.csv include DESeq2 results for both ENSEMBL genes and novel LncRNAs. CSV files *toc*.csv include read-pairs counts calculated using HTSeq. GTF files Novel_LncRNAs_*.gtf included gene models of novel LncRNAs.

source_name: DRG L3 and L4

extract_protocol:
RNA was extracted according to the hybrid method of combined phenol extraction (TriPure, Roche) and column purification (High Pure RNA tissue Kit, Roche) (Bartus et al., 2016). The concentration of RNA in the samples was measured using a nanodrop and proved sufficient for sequencing. According to the hybrid method, DRG tissue was first homogenized in TriPure and then mixed with chloroform, following the phenol extraction method. After centrifuging the aqueous liquid, which stays on the top of the tube and contains the nucleic acids, was removed. This solution was then subjected to the column purification method. Following this protocol, the clear aqueous liquid was placed in Roche High Pure RNA tissue Kit columns and washed several times in order to purify the RNA. RNA was then extracted with the mRNeasy kit and all samples were subjected to on-column DNAse digestion in order to prevent genomic contamination i.e. presence of DNA in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols. Second strand cDNA  synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing over eight lanes of a flow cell.

tag: pooled

value: NO

tag: genome build

value: BALB/c

tag: Sex

value: Female

tag: condition

value: SNI surgery


title: WT-ATRA rep1

tag: genotype


title: E10025_T_Xba

description: Xba

value: H. LEE MOFFITT CANCER CENTER


title: WT-ETOH rep2

tag: strain


title: WT-ETOH rep1


title: E10024_B_Xba

description:
Duplicate
Xba

tag: patient id

value: HENRY FORD HOSPITAL


title: E10025_B_Xba

description:
Duplicate
Xba

tag: disease state


title: E10024_T_Xba

description: Xba

value: UNKNOWN

tag: provider


title: E10022_T_Xba

description: Xba


title: E10021_B_Xba

description:
Duplicate
Xba

value: OLIGODENDROGLIOMA

tag: tumorgrade


title: E10022_B_Xba

description:
Duplicate
Xba


title: Sample59_B10.D2_SHAM_M

description:
Ribozero RNA
B10.D2_SHAM

value: Male

value: Sham surgery


title: E10023_T_Xba

description: Xba

tag: analyzed with cindex?


title: E10019_T_Xba

description: Xba


title: E10019_B_Xba

description:
Duplicate
Xba


title: E10013_B_Xba

description:
Duplicate
Xba

value: GBM


title: E10012_T_Xba

description: Xba

value: IV


title: E10012_B_Xba

description:
Duplicate
Xba


title: E10011_T_Xba

description: Xba

value: yes

value: II


title: E10009_T_Xba

description: Xba


title: E10008_T_Xba

description: Xba


title: E10011_B_Xba

description:
Duplicate
Xba


title: E10009_B_Xba

description:
Duplicate
Xba


title: WT-ETOH rep3

value: wild type

value: Embryonic stem cells


title: E10008_B_Xba

description:
Duplicate
Xba


title: E10006_T_Xba

description: Xba

value: UCLA SCHOOL OF MEDICINE


title: E10003_B_Xba

description:
Duplicate
Xba


title: E10001_T_Xba

description: Xba

value: III


title: E10001_B_Xba

description:
Duplicate
Xba


title: E10023_B_Xba

description:
Duplicate
Xba


title: E09994_B_Xba

description:
Duplicate
Xba


title: E09996_T_Xba

description: Xba


title: E10013_T_Xba

description: Xba

value: NIH NEURO-ONCOLOGY BRANCH


title: E09993_T_Xba

description: Xba


title: E09993_B_Xba

description:
Duplicate
Xba


title: YAP_KO_LPA_Rep1

city: La Jolla

first: Bing

last: Ren

state: CA

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

institute: University of California, San Diego School of Medicine

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

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.

value: YAP-KO

value: LPA