title: Blood_post_XD0014_rep1

description: QC ok


title: Glioblastoma_W31

status: Public on Feb 01 2017

type: RNA

city: Hanover

first: Robert

last: Allaway

state: New Hampshire

address: Vail 501A, 72 College St

department: Department of Molecular and Systems Biology

country: USA

institute: Geisel School of Medicine

description: Human glioblastoma samples were retained from pathological samples, flash frozen, stored, and obtained from the MMC BioBank, a core facility of Maine Medical Center Research Institute

hyb_protocol: Hybridization was performed using the WT Plus kit standard operating protocol for these arrays.

scan_protocol: Before scanning, washing and staining was performed with the WT Plus kit following the standard operating protocol for this array, on a GeneChip Fluidics 450. Scanning was performed on a GeneChip Scanner 3000.

data_processing:
Probe set intensites were summarized using robust multi-array analysis. Guided principle components analysis determeind wthat batch normalization was unnecessary. Probesets were collapsed into gene level measurements using the 'collapseRows()' function with the maxmean method from the R package WGCNA. R version: 3.2.3.
HTA-2.0.r1.Psrs.mps

label: Affymetrix Proprietary DNA Label linked to Biotin

molecule: total RNA

organism: Homo sapiens

source_name: flash-frozen globlastoma pathological sample

label_protocol: Samples were labeled with a WT Plus kit from Affymetrix, which was purchased with the arrays. PolyA controls were used.

extract_protocol: To isolate RNA, -80 C tumor fragments were placed in 5-10 volumes of RNAlater-ICE Frozen Tissue Transition Solution (Ambion) and placed at -20°C until RNA extraction with a mirVana miRNA isolation kit, without phenol, following the standard operating protocol (Thermo Scientific). RNA concentration and quality was determined using a Qubit Fluorometer (Thermo Scientific) and a Fragment Analyzer (Advanced Analytical Technologies).

tag: tissue

value: glioblastoma tumor tissue

tag: tumor stage

value: WHO IV

tag: gender

value: F

tag: patient age


title: MEDGP3_ID00401_1; reanalysis of GSM2306172

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: reanalysis of GSM2306172

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values.

label: biotin

source_name: brain tumor (medulloblastoma group 3)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy or Allprep (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor

tag: disease state

value: medulloblastoma group 3


title: GG_ID01152_1_AMBION; analysis of ganglioglioma surgical sample

source_name: brain tumor (ganglioglioma)

value: ganglioglioma


title: GG_XX00001_1; analysis of ganglioglioma surgical sample


title: MEDGP3_ID00676_1_AMBION; reanalysis of GSM2306173

description: reanalysis of GSM2306173


title: GG_ID01116_1_AMBION; analysis of ganglioglioma surgical sample


title: Blood_post_XD0010_rep1

city: London

first: Thalia

last: Eley

address: DeCrespigny Park, Denmark Hill

department: SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience

country: United Kingdom

institute: King's College London

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Stringent quality control processing of the data was conducted using standardised procedures from internal pipelines (available at https://github.com/snewhouse/BRC_MH_Bioinformatics). Expression data was background corrected using Module-based Background Correction for Beadarray (Ding et al., 2008). Probes were then filtered by selecting probes with expression levels >2SD greater than the mean intensity of the negative control (background) beads. Reported gender was compared to XIST gene expression (female specific) and Y chromosome gene expression (male specific). Each probe was then transformed and normalised using log2 transformation and Robust-Spline Normalisation (Schmid et al., 2010, Du et al., 2008). Sample relationships within the co-expression network were assessed and outliers were removed (Oldham et al., 2012).

source_name: Human, Whole Blood, post-therapy

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina Sentrix Arrays.

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

value: FEMALE

value: Blood

tag: timepoint

value: post


title: Blood_fu_XD0007_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: Blood_pre_XD0010_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy

value: pre


title: Blood_post_XD0007_rep1

description: QC ok


title: Blood_pre_XD0007_rep1

description: QC ok


title: Blood_fu_XD0005_rep1

description: QC ok

value: MALE


title: Blood_fu_XD0003_rep1

description: QC ok


title: Blood_post_XD0003_rep1

description: QC ok


title: Blood_pre_XD0005_rep1

description: QC ok


title: GG_ID00713_1; analysis of ganglioglioma surgical sample


title: Blood_post_XD0005_rep1

description: QC ok


title: GG_ID00763_1; analysis of ganglioglioma surgical sample


title: Blood_pre_XD0003_rep1

description: QC ok


title: GG_ID00683_1; analysis of ganglioglioma surgical sample


title: MEDGP3_ID00231_1; reanalysis of GSM2306169

description: reanalysis of GSM2306169


title: GG_ID00487_1; analysis of ganglioglioma surgical sample


title: GG_ID00380_1; analysis of ganglioglioma surgical sample


title: GG_ID00749_1; analysis of ganglioglioma surgical sample


title: Blood_pre_XB0061_rep1

description: QC ok


title: Blood_post_XB0061_rep1

description: QC ok


title: GBM_ID00637_1; reanalysis of GSM2306163

description: reanalysis of GSM2306163

source_name: brain tumor (glioblastoma)

value: glioblastoma


title: Blood_fu_XB0052_rep2

description: QC ok


title: GG_ID00199_AMBION; analysis of ganglioglioma surgical sample


title: GBM_ID00434_1; reanalysis of GSM2306162

description: reanalysis of GSM2306162


title: Blood_fu_XB0061_rep1

description: QC ok


title: GBM_ID00309_1; reanalysis of GSM2306160

description: reanalysis of GSM2306160


title: GG_ID00484_1; analysis of ganglioglioma surgical sample


title: GBM_ID00391_1; reanalysis of GSM2306161

description: reanalysis of GSM2306161


title: 557216A12 - 39Ox_without_Fe_3 vs. WT_without_Fe_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Differential gene expression between 39Ox and WT at +Fe and -Fe.

hyb_protocol: WT_without_Fe_3 Cy5 / 39Ox_without_Fe_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:532nm,pmt voltage 480V, laser power 35%, Cy5:635nm,pmt voltage 480V, laser power 30%.

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media: Hoagland agar medium +Fe or -Fe. Temperature: 21°C. Light: 110-150 µmol.m-2s-1.

treatment_protocol: Name: Without FE_treatment - compound based treatment - abiotic stress, fe -:quantity 0uM time 6day. Seeds were surface sterilized and grown for 6 days directly on +Fe.

tag: ecotype

tag: genotype/variation

value: WT

value: whole seedlings

tag: age

value: 6 days

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:1.00

tag: treatment

value: -Fe

growth_protocol: whole plant - Media: Hoagland agar medium +Fe or -Fe. Temperature: 21°C. Light: 110-150 µmol.m-2s-1.


title: 557216A11 - WT_without_Fe_3 vs. 39Ox_without_Fe_3

hyb_protocol: 39Ox_without_Fe_3 Cy5 / WT_without_Fe_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 557216A10 - 39Ox_without_Fe_2 vs. WT_without_Fe_2

hyb_protocol: WT_without_Fe_2 Cy5 / 39Ox_without_Fe_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Blood_post_XB0052_rep2

description: QC ok


title: GBM_ID00271_1; reanalysis of GSM2306158

description: reanalysis of GSM2306158


title: Blood_pre_XB0052_rep2

description: QC ok


title: Blood_fu_XB0032_rep2

description: QC ok


title: Blood_fu_XB0029_rep1

description: QC ok


title: Blood_post_XB0032_rep2

description: QC ok


title: Blood_pre_XB0029_rep1

description: QC ok


title: Blood_pre_XB0032_rep2

description: QC ok


title: GBM_ID00089_1_AMBION; reanalysis of GSM2306156

description: reanalysis of GSM2306156


title: GBM_ID00281_1; reanalysis of GSM2306159

description: reanalysis of GSM2306159


title: GBM_ID00000_1; reanalysis of GSM2306154

description: reanalysis of GSM2306154


title: 557216A08 - 39Ox_without_Fe_1 vs. WT_without_Fe_1

hyb_protocol: WT_without_Fe_1 Cy5 / 39Ox_without_Fe_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: EPNST_ID00416_1; reanalysis of GSM2306149

description: reanalysis of GSM2306149

source_name: brain tumor (ST ependymoma)

value: ST ependymoma


title: GBM_ID00098_1; reanalysis of GSM2306157

description: reanalysis of GSM2306157


title: EPNST_ID00333_1; reanalysis of GSM2306147

description: reanalysis of GSM2306147


title: 557216A05 - WT_with_Fe_3 vs. 39Ox_with_Fe_3

hyb_protocol: 39Ox_with_Fe_3 Cy5 / WT_with_Fe_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name: FE_treatment - compound based treatment - abiotic stress, fe +:quantity 50uM time 6day. Seeds were surface sterilized and grown for 6 days directly on +Fe.

value: +Fe


title: GG_ID00212_1; analysis of ganglioglioma surgical sample

value: brain tumor


title: GBM_ID00057_1; reanalysis of GSM2306155

description: reanalysis of GSM2306155


title: Blood_post_XB0029_rep1

description: QC ok


title: 557216A07 - WT_without_Fe_1 vs. 39Ox_without_Fe_1

hyb_protocol: 39Ox_without_Fe_1 Cy5 / WT_without_Fe_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 557216A06 - 39Ox_with_Fe_3 vs. WT_with_Fe_3

hyb_protocol: WT_with_Fe_3 Cy5 / 39Ox_with_Fe_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Blood_post_XB0026_rep1

description: QC ok


title: Blood_pre_XB0026_rep1

description: QC ok


title: Blood_fu_XB0015_rep1

description: QC ok


title: Blood_pre_XB0015_rep1

description: QC ok


title: Blood_post_XB0011_rep1

description: QC ok


title: EPNST_ID00135_1; reanalysis of GSM2306145

description: reanalysis of GSM2306145


title: EPNST_ID00388_1; reanalysis of GSM2306148

description: reanalysis of GSM2306148


title: GG_ID00932_2_AMBION; analysis of ganglioglioma surgical sample


title: Blood_post_XB0015_rep1

description: QC ok


title: 557216A04 - 39Ox_with_Fe_2 vs. WT_with_Fe_2

hyb_protocol: WT_with_Fe_2 Cy5 / 39Ox_with_Fe_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 557216A02 - 39Ox_with_Fe_1 vs. WT_with_Fe_1

hyb_protocol: WT_with_Fe_1 Cy5 / 39Ox_with_Fe_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 557216A03 - WT_with_Fe_2 vs. 39Ox_with_Fe_2

hyb_protocol: 39Ox_with_Fe_2 Cy5 / WT_with_Fe_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: EPNST_ID00285_1; reanalysis of GSM2306146

description: reanalysis of GSM2306146


title: Blood_pre_XB0011_rep1

description: QC ok


title: EPNPFB_ID00811_5_AMBION; reanalysis of GSM2306144

description: reanalysis of GSM2306144

source_name: brain tumor (PFB ependymoma)

value: PFB ependymoma


title: EPNPFB_ID00811_4_AMBION; reanalysis of GSM2306143

description: reanalysis of GSM2306143


title: 557216A01 - WT_with_Fe_1 vs. 39Ox_with_Fe_1

hyb_protocol: 39Ox_with_Fe_1 Cy5 / WT_with_Fe_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Blood_fu_XB0010_rep1

description: QC ok


title: Blood_post_XB0010_rep1

description: QC ok


title: Blood_fu_XB0009_rep1

description: QC ok


title: Blood_post_XB0009_rep1

description: QC ok


title: EPNPFB_ID00723_1; reanalysis of GSM2306141

description: reanalysis of GSM2306141


title: Blood_pre_XB0009_rep1

description: QC ok


title: EPNPFB_ID00811_1_AMBION; reanalysis of GSM2306142

description: reanalysis of GSM2306142


title: Blood_fu_XB0005_rep1

description: QC ok


title: EPNPFB_ID00364_1; reanalysis of GSM2306136

description: reanalysis of GSM2306136


title: EPNPFB_ID00419_1; reanalysis of GSM2306138

description: reanalysis of GSM2306138


title: EPNPFB_ID00483_1; reanalysis of GSM2306139

description: reanalysis of GSM2306139


title: EPNPFB_ID00080_1; reanalysis of GSM2306133

description: reanalysis of GSM2306133


title: EPNPFB_ID00700_1; reanalysis of GSM2306140

description: reanalysis of GSM2306140


title: EPNPFB_ID00392_1; reanalysis of GSM2306137

description: reanalysis of GSM2306137


title: Blood_fu_XB0004_rep1

description: QC ok


title: Blood_post_XB0005_rep1

description: QC ok


title: EPNPFB_ID00246_1; reanalysis of GSM2306135

description: reanalysis of GSM2306135


title: EPNPFB_ID00110_1; reanalysis of GSM2306134

description: reanalysis of GSM2306134


title: EPNPFA_ID00928_3_AMBION; reanalysis of GSM2306131

description: reanalysis of GSM2306131

source_name: brain tumor (PFA ependymoma)

value: PFA ependymoma


title: Blood_post_XB0004_rep1

description: QC ok

value: FEMALE


title: EPNPFA_ID00928_4 _AMBION; reanalysis of GSM2306132

description: reanalysis of GSM2306132


title: Blood_pre_XB0004_rep1

description: QC ok

value: Blood


title: EPNPFA_ID00859_1_AMBION; reanalysis of GSM2306129

description: reanalysis of GSM2306129


title: Blood_pre_XB0005_rep1

description: QC ok


title: EPNPFA_ID00928_1_AMBION; reanalysis of GSM2306130

description: reanalysis of GSM2306130


title: EPNPFA_ID00839_1_AMBION; reanalysis of GSM2306128

description: reanalysis of GSM2306128


title: shControl sample 20

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

institute: Stem Cell and Brain Research Institute

description: replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Neurons

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

growth_protocol: NPC differentiation of ESCs and iPSCs was done based on established protocols. Cells were first plated in clumps on matrigel-coated 6 well-plates using mTESR1 media. The following day, the media was changed with NPC media composed of DMEM-F12/Neurobasal media (1:1) supplemented with N2 and B27 without vitamin A supplements and CHIR99021 (4µM), SB431245 (3µM), CompoundE (0.1µM) and human LIF (10ng/ml). After 7 days, cells were passaged using accutase and grown in the same media using CHIR99021 (3µM) and SB431245 (2µM) together with LIF (10ng/ml), EGF and bFGF (20ng/ml).  For neuronal differentiation NPCs were plated at a density of 200,000 cells per 6 well and grown in DMEM-F12/Neurobasal media (1:1) supplemented with N2 and B27 supplements together with GDNF (20ng/ml), BDNF (20ng/ml), dibutyryl-cyclic AMP (1mM) and Acid ascorbic (200nM) for at least 4 weeks.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Except for the differentiation protocols, no treatment has been done on the cells.

value: shControl


title: shControl sample 19

description: replicate 1


title: EPNPFA_ID00691_1a; reanalysis of GSM2306126

description: reanalysis of GSM2306126


title: EPNPFA_ID00507_1; reanalysis of GSM2306125

description: reanalysis of GSM2306125


title: shGTDC1 #1 sample 15

description: replicate 1


title: shControl sample 13

description: replicate 1

source_name: NPCs


title: shGTDC1 #1 sample 16

description: replicate 2


title: EPNPFA_ID00064_1; reanalysis of GSM2306121

description: reanalysis of GSM2306121


title: shGTDC1 #3 sample 18

description: replicate 2


title: shGTDC1 #3 sample 17

description: replicate 1


title: EPNPFA_ID00393_1; reanalysis of GSM2306123

description: reanalysis of GSM2306123


title: EPNPFA_ID00195_1; reanalysis of GSM2306122

description: reanalysis of GSM2306122


title: shControl sample 14

description: replicate 2


title: 557216A09 - WT_without_Fe_2 vs. 39Ox_without_Fe_2

hyb_protocol: 39Ox_without_Fe_2 Cy5 / WT_without_Fe_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: shGTDC1 #3 sample 12

description: replicate 2


title: EPNPFA_ID00492_1; reanalysis of GSM2306124

description: reanalysis of GSM2306124


title: EPNM_ID00685_1; analysis of myxopapillary ependymoma surgical sample

source_name: brain tumor (myxopapillary ependymoma)

value: myxopapillary ependymoma


title: EPNM_ID00511_1; analysis of myxopapillary ependymoma surgical sample


title: EPNM_ID00656_1; analysis of myxopapillary ependymoma surgical sample


title: CPP_ID00814_1_AMBION; reanalysis of GSM1661004

description: reanalysis of GSM1661004

source_name: brain tumor (choroid plexus papilloma)

value: choroid plexus papilloma


title: shGTDC1 #3 sample 11

description: replicate 1


title: CPP_ID00420_1; reanalysis of GSM1661002

description: reanalysis of GSM1661002


title: EPNM_ID00260_1; analysis of myxopapillary ependymoma surgical sample


title: Control iPSCs #1 sample 6

description: replicate 1

value: control


title: EPNM_ID00085_1; analysis of myxopapillary ependymoma surgical sample


title: shGTDC1 #1 sample 9

description: replicate 1


title: shGTDC1 #1 sample 10

description: replicate 2


title: Control iPSCs #2 sample 8

description: replicate 1


title: CPP_ID00451_1; reanalysis of GSM1661003

description: reanalysis of GSM1661003


title: Control iPSCs #2 sample 7

description: replicate 2


title: ATRT_ID00737_1; reanalysis of GSM2306110

description: reanalysis of GSM2306110

source_name: brain tumor (atypical teratoid/rhabdoid tumor)

value: atypical teratoid/rhabdoid tumor


title: CPP_ID00284_1; reanalysis of GSM1661001

description: reanalysis of GSM1661001


title: CPP_ID00037_1; reanalysis of GSM1661000

description: reanalysis of GSM1661000


title: CD6 #15 sample 4

description: replicate 1


title: CD6 #5 sample 2

description: replicate 1


title: ATRT_ID00413_1; reanalysis of GSM2306106

description: reanalysis of GSM2306106


title: CD6 #15 sample 3

description: replicate 2


title: ATRT_ID00517_1; reanalysis of GSM2306109

description: reanalysis of GSM2306109


title: CD6 #5 sample 1

description: replicate 3


title: ATRT_ID00370_1; reanalysis of GSM2306104

description: reanalysis of GSM2306104


title: ATRT_ID00404_1; reanalysis of GSM2306105

description: reanalysis of GSM2306105


title: FS1_DMSO_24h

city: Bonn

first: Sina

last: Jostes

address: Venusberg Campus 1

department: Department of Developmental Pathology

country: Germany

institute: Institute of Pathology

description: replicate 1

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

source_name: Sertoli cell line

growth_protocol: TCam-2 cells were cultured in RPMI medium (Life Technologies, Darmstadt, Germany). NT2/D1(-R), 2102EP(-R) and NCCIT(-R) cells were cultured in DMEM medium (Life Technologies). Both media were supplemented with 10% FBS (Life Technologies), 1% penicillin / streptomycin (PAN, Aidenbach, Germany) and 200 mM L-glutamine (PAN). Human adult fibroblast cells (MPAF) were grown in DMEM medium, supplemented with 10% FBS, 1% non-essential amino acids (NEAA) (PAN), 1% penicillin / streptomycin and 200 mM L-glutamine. Human Sertoli cells (FS1) were cultured in DMEM medium, supplemented with 20% FBS, 1% NEAA, 1% penicillin / streptomycin and 200 mM L-glutamine.

extract_protocol: For RNA and protein isolation, cells were seeded out at a density of 1 x 10^5 cells / well in a 6-well plate prior to initial JQ1 treatment. RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: The cells were treated with 100 nM JQ1 inhibitor (kindly provided by Jay Bradner, Dana-Farber Cancer Institute, Boston, MA, USA) every 48 hours. As a negative control, the cells were treated with equal amounts of reconstitution solution (DMSO) only.

tag: cell line

tag: cell type

value: Sertoli cell line

tag: treated with

value: DMSO

tag: time point

value: 24hr after treatment


title: ATRT_ID00514_1; reanalysis of GSM2306108

description: reanalysis of GSM2306108


title: ATRT_ID00504_1; reanalysis of GSM2306107

description: reanalysis of GSM2306107


title: ATRT_ID00343_1; reanalysis of GSM2306103

description: reanalysis of GSM2306103


title: MPAF_DMSO_72h

description: replicate 1

source_name: adult primary fibroblasts

value: MPAF

value: adult primary fibroblasts

value: 72hr after treatment


title: FS1_DMSO_72h

description: replicate 1


title: FS1_JQ1_24h

description: replicate 1

value: 100 nM JQ1


title: ATRT_ID00119_1; reanalysis of GSM2306102

description: reanalysis of GSM2306102

value: brain tumor


title: FS1_JQ1_72h

description: replicate 1


title: MPAF_DMSO_24h

description: replicate 1


title: Control iPSCs #1 sample 5

description: replicate 2


title: ACP_TK00077_AMBION; analysis of craniopharyngioma surgical sample

source_name: brain tumor (adamantinomatous craniopharyngioma)

value: adamantinomatous craniopharyngioma


title: ATRT_ID00003_1; reanalysis of GSM2306101

description: reanalysis of GSM2306101


title: MPAF_JQ1_72h

description: replicate 1


title: ACP_TK00756_AMBION; analysis of craniopharyngioma surgical sample


title: MPAF_JQ1_24h

description: replicate 1


title: NCCIT_JQ1_72h

description: replicate 1

source_name: Embryonal carcinoma-like cell line

value: NCCIT

value: Embryonal carcinoma-like cell line


title: TCam-2_DMSO_72h

description: replicate 1

source_name: Seminoma like cell line

value: Seminoma like cell line


title: NCCIT_DMSO_72h

description: replicate 1


title: NCCIT_DMSO_24h

description: replicate 1


title: NCCIT_JQ1_24h

description: replicate 1


title: ACP_TK00034_AMBION; analysis of craniopharyngioma surgical sample


title: ACP_R000011_1_AMBION; analysis of craniopharyngioma surgical sample


title: TCam-2_JQ1_24h

description: replicate 1


title: ACP_R000005_1_AMBION; analysis of craniopharyngioma surgical sample


title: ACP_R000003_1_AMBION; analysis of craniopharyngioma surgical sample


title: ACP_PC00002_AMBION; reanalysis of GSM1660999

description: reanalysis of GSM1660999


title: TCam-2_JQ1_72h

description: replicate 1


title: TCam-2_DMSO_24h

description: replicate 1


title: ACP_ID01000_1_AMBION; reanalysis of GSM1660998

description: reanalysis of GSM1660998


title: ACP_ID01036_1_AMBION; analysis of craniopharyngioma surgical sample


title: WD2

hyb_protocol: RNA was hybridized to an HT12v4 microarray overnight in an Illumina hybridization oven.

scan_protocol: Arrays were scanned with the iScan microarray scanner.

data_processing: Analyses were performed using BRB-Array Tools Version 4.2.1.  BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data which was developed by the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute under the direction of Dr. Richard Simon. Variance stabilizing transformation was applied to raw intensity data which was then normalized using robust spline normalization and filtered to remove non-detected spots as determined by Illumina BeadStudio Software.  Differentially expressed genes were identified using a random-variance t-test with a p-value cutoff of 0.05. Multiple testing correction was performed using the method of Benjamini and Hochberg.

source_name: IMECs treated with DMSO

label_protocol: 300 ng RNA/sample was labeled with the TargetAmp Nano kit (Epicentre Bio, Madison, WI)

growth_protocol: Cells were plated at 400,000 cells/well in a six well plate and allowed to adhere overnight.

extract_protocol: RNA isolation was perfomed with the Norgen Biotek DNA/RNA/Protein plus kit, following the standard operating protocol.

treatment_protocol: Cells were treated for 8 hours with 1 micromolar Y100 in DMEM+10% fetal bovine serum, or an equivalent amount of DMSO in DMEM+10% fetal bovine serum.

value: immortalized mammary epithelial cells (IMECs)

tag: agent


title: ACP_ID01086_1_AMBION; analysis of craniopharyngioma surgical sample


title: WY1

source_name: IMECs treated with Y100


title: EPNPFA_ID00812_1a; reanalysis of GSM2306127

description: reanalysis of GSM2306127

value: PFA ependymoma


title: ACP_ID00980_1_AMBION; reanalysis of GSM1660997

description: reanalysis of GSM1660997


title: WY2


title: ACP_ID00802_1_AMBION; reanalysis of GSM1660994

description: reanalysis of GSM1660994


title: ACP_ID00956_1_AMBION; reanalysis of GSM1660996

description: reanalysis of GSM1660996


title: EVT_HLA-G+ _Wk8_Tr1_P720_776.2435.1.1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

description: SAMPLE 11

data_processing: The data were filtered for detection pValue < 0.01 and normalised using Robust Spline Normalisation with lumi in R v3.2.1

label: Biotin

source_name: first trimester placenta

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

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 v4 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: First trimester trophoblasts were isolated using serial enzymatic digestion and Percoll gradient from 6-8 week gestational age human placentas. Freshly isolated cells were stained with PE-conjugated mouse anti-HLA-G (87G, Biolegend) and APC-conjugated mouse anti-EGFR (BioLegend) and sorted using a BD Influx instrument (BD Biosciences) to obtain separate populations of EGFR+ vCTB and HLA-G+ pcEVT.

tag: origin

value: Placenta


title: EVT_HLA-G+ _Wk7.5_Tr1_P716_776.2431.1.1

description: SAMPLE 10


title: ACP_ID00740_1_AMBION; reanalysis of GSM1660993

description: reanalysis of GSM1660993

tag: tissue


title: WD1


title: WD3


title: ACP_ID00883_2_AMBION; reanalysis of GSM1660995

description: reanalysis of GSM1660995


title: ACP_ID01206_1_AMBION; analysis of craniopharyngioma surgical sample


title: EVT_HLA-G+ _Wk7.2_Tr1_P723_776.2438.1.1

description: SAMPLE 9


title: EVT_HLA-G+ _Wk6.3_Tr1_P718_776.2433.1.1

description: SAMPLE 8


title: ACP_ID00673_2_AMBION; reanalysis of GSM1660992

description: reanalysis of GSM1660992


title: CTB_EGFR+ _Wk8_Tr1_P720_581.2435.1.1 (2)

description: SAMPLE 7


title: ACP_ID00598_1_AMBION; reanalysis of GSM1660990

description: reanalysis of GSM1660990


title: ACP_ID00463_2_AMBION; reanalysis of GSM1660989

description: reanalysis of GSM1660989


title: ACP_ID00411_2_AMBION; reanalysis of GSM1660988

description: reanalysis of GSM1660988


title: ACP_ID00646_1_AMBION; reanalysis of GSM1660991

description: reanalysis of GSM1660991


title: CTB_EGFR+ _Wk7.2_Tr1_P723_581.2438.1.1 (2)

description: SAMPLE 5


title: CTB_EGFR+ _Wk7.5_Tr1_P716_581.2431.1.1 (2)

description: SAMPLE 6


title: ACP_CB00001_AMBION; reanalysis of GSM1660986

description: reanalysis of GSM1660986


title: ACP_CB00002_AMBION; reanalysis of GSM1660987

description: reanalysis of GSM1660987


title: CTB_EGFR+ _Wk7_Tr1_P719_581.2434.1.1 (2)

description: SAMPLE 3


title: CTB_EGFR+ _Wk7.1_Tr1_P721_581.2436.1.1

description: SAMPLE 4


title: CTB_shARNT_HYPOX_641P_581_2514_1_1

description: SAMPLE 22

growth_protocol: First trimester cytotrophoblast were isolated using serial enzymatic digestion and Percoll gradient. Cells were grown in media containing DMEM/F12 (Gibco), 10% fetal bovine serum (FBS, Sigma-Aldrich), containing penicillin-streptomycin (Thermo Fisher Scientific) and  gentamicin (Gibco) and cultured for 4 days. Media was changed at day 1 and day 3.

treatment_protocol: Cells were infected with Scramble (control) or ARNT-specific shRNA lentivirus. For hypoxic culture (2% oxygen), cells were incubated for 4 days, media was changed at day 1 and day 3 and cells were lysed in an XVIVO system (Biospherix, Parish, NY). For normoxic culture (20% oxygen), cells were incubated for 4 days, and media was changed at day 1 and day 3 in a standard 5% CO2 incubator.

value: shARNT

tag: oxygen

value: Hypoxia (2% O2)


title: CTB_shARNT_HYPOX_634P_581_2504_1_1

description: SAMPLE 12


title: CTB_Isolated_641P_581_2512_1_1

description: SAMPLE 20

value: untreated

value: Normoxia (20% O2)


title: CTB_Scramble_HYPOX_641P_581_2513_1_1

description: SAMPLE 21

value: shScramble


title: CTB_Scramble_NORMOX_641P_581_2515_1_1

description: SAMPLE 23


title: CTB_shARNT_NORMOX_641P_581_2516_1_1

description: SAMPLE 24


title: CTB_shARNT_NORMOX_636P_581_2511_1_1

description: SAMPLE 19


title: CTB_EGFR+ _Wk6.4_Tr1_P722_581.2437.1.1 (2)

description: SAMPLE 2


title: CTB_EGFR+ _Wk6.3_Tr1_P718_581.2433.1.1 (2)

description: SAMPLE 1


title: CTB_Scramble_NORMOX_634P_581_2505_1_1

description: SAMPLE 13


title: CTB_Scramble_NORMOX_636P_581_2510_1_1

description: SAMPLE 18


title: CTB_shARNT_NORMOX_634P_581_2506_1_1

description: SAMPLE 14


title: CTB_Scramble_HYPOX_636P_581_2508_1_1

description: SAMPLE 16


title: CTB_shARNT_HYPOX_636P_581_2509_1_1

description: SAMPLE 17


title: CTB_shARNT_NORMOX_630P_581_2501_1_1

description: SAMPLE 9


title: CTB_Scramble_HYPOX_634P_581_2503_1_1

description: SAMPLE 11


title: CTB_Isolated_634P_581_2507_1_1

description: SAMPLE 15


title: ACP_AB00009_1_AMBION; reanalysis of GSM1660985

description: reanalysis of GSM1660985


title: CTB_shARNT_HYPOX_630P_581_2502_1_1

description: SAMPLE 10


title: CTB_Isolated_630P_581_2498_1_1

description: SAMPLE 6


title: CTB_shARNT_NORMOX_618P_581_2497_1_1

description: SAMPLE 5


title: CTB_Scramble_HYPOX_630P_581_2499_1_1

description: SAMPLE 7


title: CTB_Scramble_NORMOX_618P_581_2496_1_1

description: SAMPLE 4


title: CTB_Scramble_NORMOX_630P_581_2500_1_1

description: SAMPLE 8


title: CTB_Isolated_618P_581_2493_1_1

description: SAMPLE 1


title: CTB_Scramble_HYPOX_618P_581_2494_1_1

description: SAMPLE 2


title: Meningial Cells [gene]

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description:
Sample name: 15
Gene expression data from human meningial cells grown under normal conditions.

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strips were washed and stained in the GeneAtlas Fluidics station (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner.

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software.

source_name: Meningial cells grown under normal conditions

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA.

growth_protocol: Meningial cells were cultured in T75 cell culture flasks in Meningeal Cell Medium.

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

treatment_protocol: Not Applicable.

value: Meningial cell line


title: HCV patient C09

city: san diego

first: mario

last: chojkier

state: ca

address: 3350 la jolla village drive

department: Medicine

institute: UCSD

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, RPLP0, GAPDH, HGDC,HPRT1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: blood from HCV-infected patient with Child B cirrhosis

label_protocol: PCR assays were performed using the BioRad CFX 96 Real Time System - and PCR Array   Cat.#PASH-062 ZD(SA Biosciences/Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 1 ug total RNA using the RT2 First Strand Kit (SA Biosciences). Real-time PCR were performed  with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with Trizol (Thermo Fisher Scientific)  followed by DNase I treatment

value: Buffy Coat

tag: disease status

value: HCV infection


title: HCV patient C05

description: Test


title: HCV patient C07

description: Test


title: HCV patient C04

description: Test


title: HCV patient C06

description: Test


title: HCV patient C03

description: Test


title: HCV patient C02

description: Test


title: Meningioma 11 [gene]

description:
Sample name: 11
Gene expression data from fresh-frozen meningioma tumor sample.

source_name: Fresh-frozen meningioma tumor sample

value: Meningioma tumor

tag: location

value: Right parietal convexity Meningioma

tag: gender

value: Female


title: Healthy patient H10

description: Control

source_name: blood from healthy patient

value: healthy


title: Meningioma 14 [gene]

description:
Sample name: 14
Gene expression data from fresh-frozen meningioma tumor sample.

value: Tuberculum Sella meningioma

value: Male


title: HCV patient C01

description: Test


title: Meningioma 8 [gene]

description:
Sample name: 8
Gene expression data from fresh-frozen meningioma tumor sample.


title: Meningioma 4 [gene]

description:
Sample name: 4
Gene expression data from fresh-frozen meningioma tumor sample.

value: Petrous Meningioma


title: Meningioma 13 [gene]

description:
Sample name: 13
Gene expression data from fresh-frozen meningioma tumor sample.

value: Left Parietal Parasagital Meningioma


title: Healthy patient H09

description: Control


title: Meningioma 10 [gene]

description:
Sample name: 10
Gene expression data from fresh-frozen meningioma tumor sample.

value: Left sphenoid wing Meningioma


title: Meningioma 6 [gene]

description:
Sample name: 6
Gene expression data from fresh-frozen meningioma tumor sample.

value: Parietal Parasagital Meningioma


title: Meningioma 12 [gene]

description:
Sample name: 12
Gene expression data from fresh-frozen meningioma tumor sample.

value: Left Clinoidal Meningioma


title: Meningioma 9 [gene]

description:
Sample name: 9
Gene expression data from fresh-frozen meningioma tumor sample.

value: Right frontobasal Meningioma


title: Meningioma 3 [gene]

description:
Sample name: 3
Gene expression data from fresh-frozen meningioma tumor sample.

value: Parietal Convexity Meningioma


title: Meningioma 1 [gene]

description:
Sample name: 1
Gene expression data from fresh-frozen meningioma tumor sample.

value: Olfactor Groove Meningioma


title: HCV patient C08

description: Test


title: Healthy patient H08

description: Control


title: Healthy patient H07

description: Control


title: Meningioma 7 [gene]

description:
Sample name: 7
Gene expression data from fresh-frozen meningioma tumor sample.

value: Left cavernous Sinus Meningioma


title: Meningioma 5 [gene]

description:
Sample name: 5
Gene expression data from fresh-frozen meningioma tumor sample.

value: Petroclival Meningioma


title: Healthy patient H06

description: Control

value: Buffy Coat


title: Healthy patient H03

description: Control


title: Healthy patient H02

description: Control


title: Healthy patient H04

description: Control


title: Healthy patient H01

description: Control


title: wound_control_rep4

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from skin wound treated with control mimics.

hyb_protocol: The samples were hybridized to a mouse Clariom™ D assay plate (previously known as GeneChip® Mouse Transcriptome Assay 1.0) according to standard protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneChip Scanner 3000.

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

organism: Mus musculus

source_name: Mouse skin wound treated with control mimics

label_protocol: 150ng of total RNA were used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol.

growth_protocol: Eleven-week-old male diabetic db/db [BKS(D)-Leprdb/JOrlRj)] mice on the C57Bl/6J background (Janvier Labs) were caged individually for one week, handled daily, and then wounded. General anesthesia was performed with 3% isoflurane (Abbott). The hair on the back was shaved with an electronic hair remover followed by Veet® hair removal cream. The skin was rinsed with PBS and two full-thickness wounds extending through the panniculus carnosus were made on the dorsum on each side of midline, using a 4 mm biopsy punch.

extract_protocol: The mice were sacrificed 6 days after injury and the total RNA was extracted from wound-edge biopsies using miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 0.5 nmol miR-132 mimics or control mimics (ThermoFisher Scientific) were mixed with MaxSuppressor™ In Vivo RNA-LANCEr II (Bioo Scientific) in a total volume of 100 μl for each wound and injected intradermally into 4 points around the wound edges in the mice immediately after wounding. Following the surgical procedure, the animals were individually caged. During the first 2 days, the animals received s.c. buprenorphine (0.03 mg/kg) twice a day for relief of any possible distress caused by the procedure.

value: skin

tag: genotype

value: db/db [BKS(D)-Leprdb/JOrlRj)]

tag: strain background

value: male


title: wound_control_rep2


title: wound_control_rep1


title: wound_miR-132_rep4

description: Gene expression data from skin wound treated with miR-132 mimics.

source_name: Mouse skin wound treated with miR-132 mimics


title: wound_miR-132_rep2


title: wound_miR-132_rep5


title: wound_control_rep5


title: wound_control_rep3


title: CC 4h IVM with DMSO, replicate 1

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

institute: INRA

description: Gene expression after 4hr IVM in bovine cumuls cells

hyb_protocol: Hybridization was performed using 600 ng of Cy3-labeled cRNA with specific activity > 6.0 pmol of Cy3/μg of cRNA during 17 hours at 65°C, following the manufacturer’s protocol (http://crb-gadie.inra.fr/).

scan_protocol: The slides were scanned immediately after washing using a G2565CA Scanner System with one color scan setting for 8×60k array slides (Agilent Technologies)

data_processing: The resulting images were analysed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies).

organism: Bos taurus

source_name: Bovine cumulus cells, 4h IVM, control, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared with 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit following the recommended protocol (Agilent Technologies, SantaClara, CA, USA)

growth_protocol: Cumulus-oocyte complexes were punctioned from bovine ovaries after slaughting.

extract_protocol: Total RNA was extracted using Trizol Reagent(Invitrogen, Cergy Pontoise, France)  and then and treated using RQ1 DNAse (Promega, Frace) according to manufacturer's instructions.

treatment_protocol: 1µM DHA dissovled in DMSO or only DMSO was  added to COCs in the beginning of in vitro maturation (IVM) culture. IVM was performed during 4 hours, the CC were detached, washed in cold PBS and put into Trizol reagent, kept at -80°C

value: ovarian cumulus cells

value: DMSO


title: CC 4h IVM with DHA, replicate 1

source_name: Bovine cumulus cells, 4h IVM, DHA 1µM, rep1

value: DHA


title: CC 4h IVM with DHA, replicate 3

source_name: Bovine cumulus cells, 4h IVM, DHA 1µM, rep3


title: CC 4h IVM with DMSO, replicate 3

source_name: Bovine cumulus cells, 4h IVM, control, rep3


title: CC 4h IVM with DHA, replicate 4

source_name: Bovine cumulus cells, 4h IVM, DHA 1µM, rep4


title: WT DT40 B cells rep1

status: Public on Jan 01 2017

city: Turku

first: Paulina

last: Budzynska

address: Kiinamyllynkatu 13

country: Finland

institute: University of Turku

hyb_protocol: 1.65 ug of Cy-3 labeled sample was hybridized onto Agilent’s 4x44K Chicken V2 array (Design ID 026441) at 65 °C overnight using Agilent’s GE Hybridization Kit (Product number 5188-5242) following manufacturer's instructions.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA. Scan Profile:  AgilentHD_GX_1Color.

data_processing: gProcessedSignal column in the Agilent raw data files was used as the input for the analysis. The data were normalised using quantile normalisation with limma package in R/Bioconductor tool (Bioconductor version 2.7, R version 2.12.0)

organism: Gallus gallus

source_name: WT DT40 B cells

label_protocol: Cy3-labeled with Agilent’s one-color Low Input Quick Amp Labeling kit, one-color according to manufacturer's instructions.

extract_protocol: Total RNA was prepared from 5x10^6 cells of three independent cultures of WT and IRF4KO cells with RNeasy Mini Kit (Qiagen) with RNase- Free DNase treatment according to manufacturer’s instructions.

tag: genotype/variation

value: wild type


title: CC 4h IVM with DHA, replicate 2

source_name: Bovine cumulus cells, 4h IVM, DHA 1µM, rep2


title: CC 4h IVM with DMSO, replicate 4

source_name: Bovine cumulus cells, 4h IVM, control, rep4


title: WT DT40 B cells rep3


title: wound_miR-132_rep1


title: WT DT40 B cells rep2


title: wound_miR-132_rep3


title: CC 4h IVM with DMSO, replicate 2

source_name: Bovine cumulus cells, 4h IVM, control, rep2


title: 095_24h

status: Public on Dec 31 2016

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

hyb_protocol: mRNA was hybridized on Affymetrix Human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA) which contain approximately 1.4 M probesets. The hybridization was carried out as follows: target synthesis was led starting from 350ng globin free totoal RNA using the WT expression kit (Ambion) following the standard recommendations, except that 12 µg cRNA was used instead of 10 µg for entering the second reverse transcription.

scan_protocol: GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G

data_processing: DAT images and CEL files of the microarrays were generated using  Affymetrix GeneChip Command Control 3.0.0.1214. The exon level probesets were pre-processed, quality checked and normalized using the RMA procedure. Only exonic probesets were kept for our analysis (intronic, inter-genic and unreliable probesets were excluded).

source_name: Peripheral blood

label_protocol: Biotin. Fragmentation and labelling of cDNA were performed using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Peripheral blood was taken at baseline and 24h after the start of the treatment and stored in PaxGenes

extract_protocol: Circulating RNA from pheripheral blood was extracted using the PAXgene Blood RNA Kit (Qiagen) followed by further purification on Qiagen Rneasy MinElute Cleanup Kit (Qiagen), and the depletion of Alpha and Beta Globins using the GlobinClear Human Kit (Ambion) according to the standard recommendations with the following exception: 5µg RNA Cleanup kit (Zymo) was used for cleaning the depeted RNA instead of the magnetic beads provided in the Ambion kit, which significantly increased the recovery of RNA and provided sufficient quality for microarray hybridization. Total RNA were quantified using a NanoDrop ND-1000 and purity was assessed by determining the 260/280 ratio. Total RNA was monitored using the RNA Nano 6000 Chip on 2100 Bioanalyzer (Agilent) and RNA integrity number (RIN) was assessed for each sample.

treatment_protocol: Patients received the combine targeted therapy bevacizumab-erlotinib until progression or toxicity followed by chemotherapy cisplatine + gemcitabine

tag: overall survival time (months)

tag: overall survival event (0

value: alive, 1:dead):1

value: peripheral blood

tag: upn

tag: age

value: M

tag: Stage

value: IV

tag: time

tag: responder

value: Responder


title: 098_24h

value: alive, 1:dead):0

value: F


title: 103_24h


title: 096_24h

value: Non-responder


title: CTB_shARNT_HYPOX_618P_581_2495_1_1

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

source_name: first trimester placenta

value: Placenta

tag: treatment

value: shARNT

value: Hypoxia (2% O2)


title: Meningioma 2 [gene]

description:
Sample name: 2
Gene expression data from fresh-frozen meningioma tumor sample.

value: Meningioma tumor

value: Sphennopetroclival Meningioma

value: Female


title: 099_24h


title: 101_24h


title: 094_24h


title: 093_24h


title: 102_24h


title: 091_24h


title: 089_24h


title: 074_24h


title: 081_24h


title: 080_24h


title: 083_24h


title: 084_24h


title: 090_24h


title: 073_24h


title: 088_24h


title: 077_24h


title: 065_24h


title: 070_24h


title: 069_24h

value: IIIB


title: 075_24h


title: 068_24h


title: 072_24h


title: 067_24h


title: 058_24h


title: 078_24h


title: 063_24h


title: 064_24h


title: 061_24h


title: 060_24h


title: 056_24h


title: 057_24h


title: 082_24h


title: 087_24h


title: 002_24h


title: 049_24h


title: 094_Baseline

value: Baseline


title: 095_Baseline


title: 055_24h


title: 038_24h


title: 101_Baseline


title: 096_Baseline


title: 099_Baseline


title: 098_Baseline


title: 093_Baseline


title: 023_24h


title: 051_24h


title: 091_Baseline


title: 083_Baseline


title: 084_Baseline


title: 078_Baseline


title: 087_Baseline


title: 089_Baseline


title: 075_Baseline


title: 103_Baseline


title: 081_Baseline


title: 082_Baseline


title: 074_Baseline


title: 077_Baseline


title: 067_Baseline


title: 070_Baseline


title: 102_Baseline


title: 069_Baseline


title: 072_Baseline


title: 073_Baseline


title: 068_Baseline


title: LncKdm2b KO

status: Public on Dec 24 2016

city: Beijing

first: Buqing

last: Ye

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: This sample  is of lncKdm2b-deficient emrbyonic stem cells

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing:
 Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
High quality expression values (for example, where at least 1 out of 2 samples have values within cut-off, cut-off =100) will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups. Hierarchical clustering was performed using R scripts. GO analysis and Pathway analysis were performed using the standard enrichment computation methods.

source_name: lncKdm2b knockout ES cells

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Mouse ESCs were grown on CF-1 mouse MEFs treated with mitomycin C. mESCs were cultured in DMEM supplemented with 15% FBS (Invitrogen, USA), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM nucleotide, 0.1 mM non-essential amino acids and 103 units/ml mouse leukemia inhibitory factor (LIF).

extract_protocol: Total RNA was extracted using the TRIZOL reagent (TRIzol Plus RNA Purification Kit, Invitrogen life technologies) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

value: lncKdm2b deletion

tag: cell type

value: embryonic stem cells (ES cells)


title: 080_Baseline

value: alive, 1:dead):1

tag: tissue

value: peripheral blood


title: 065_Baseline

value: IV


title: L37, human CP tissue

status: Public on Dec 09 2016

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

description: Gene expreesion data

hyb_protocol: Labeled RNA was hybridized to a Agilent human geneexpression microarray according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Agilent G2565CA manufacturer's instructions.

data_processing: Probe intensities were extracted using FeatureExtraction software (Agilent). Value definition Probe intensities were background corrected and normalized (quantile normalization) using the LIMMA package in R.

source_name: Chronic Pancreatitis tissue

label_protocol: Total RNA (100 ng)Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA of normal pancreatic specimens were purchased commercially. Trizol extraction of total RNA was performed on PDAC and adjacent benign specimens according to the manufacturer's instructions.

value: Pancreas

tag: disease state

value: Chronic Pancreatitis


title: 090_Baseline

value: F

value: Responder


title: 058_Baseline

value: Non-responder


title: 063_Baseline


title: 061_Baseline


title: 049_Baseline

value: M


title: 088_Baseline


title: 023_Baseline


title: 057_Baseline


title: 060_Baseline

value: alive, 1:dead):0


title: 055_Baseline


title: 051_Baseline


title: 038_Baseline


title: 056_Baseline


title: L34, human CP tissue

description: Gene expreesion data


title: 064_Baseline


title: 002_Baseline


title: matched normal blood_#854 vs. normal Coriell Sample (Coriell_NA12878)-European_Female

status: Public on Dec 27 2016

type: genomic

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

description:
matched normal blood_#854 vs. normal Coriell Sample
5N_Cy5 vs. Coriell_NA12878*13_Cy3

hyb_protocol: Equal amount of labeled Test & Control DNA sample was added into a fresh tube containing 25 µl of Human Cot-1 DNA (1mg/ml),  26ul of Agilent 10X blocking agent and 130ul Agilent 2X hybridization buffer. The total hybridization volume was 45ul. The above hybridization mix was denatured at 95°C for 3 minutes and incubated the microfuge tubes at 37°C for 30 minutes.  The samples were hybridized at 65°C for 40 hours in the hybridization chamber. After hybridization, the slides were washed using aCGH Wash Buffer1 (Agilent Technologies, Part Number 5188-5221) at room temperature for 5 minutes and aCGH Wash Buffer 2 (Agilent Technologies, Part Number 5188-5222) at 37°C for 1 minutes. The slides were then washed with Acetonitrile for 10 seconds.

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images were quantified using Agilent Feature Extraction Software . Feature extracted raw data was normalized using Lowes normalization and analyzed Agilent CytoGenomics 2.7 SoftwarE.

molecule: genomic DNA

source_name: matched normal blood_#854

label_protocol: Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that,  the  control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.

growth_protocol: Primary uterine cervical lesions and corresponding peripheral blood lymphocytes (PBL) were collected from the hospital section of Chittaranjan National Cancer Institute, Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients were taken.

extract_protocol: Genomic DNA from cryosections (5µm) of tumor tissue specimen and PBL were isolated by standard phenol/chloroform method.

tag: subject status

value: Indian CACX (cancer of the uterine cervix) patient

tag: subject id

value: Stage IIIB

tag: tissue/cell type

label: Normal  Coriell_Cy3

source_name: European_Female_cell line

tag: cell line

value: Coriell NA12878


title: Colorectal cancer liver metastasis t99-3_run2

status: Public on Jul 11 2016

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array

hyb_protocol: Samples were hybridized onto the Affymetrix Genome-Wide Human SNP 6.0 Array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000, according to the manufacturer's instructions.

data_processing:
Raw probe intensity data from scanned images of the arrays were stored in CEL files by the Affymetrix Gene Chip Command Console software. CEL file signal extraction, quantile normalization, median polishing, and signal intensity generation was performed using the Affymetrix Power Tools software and the GenomeWideSNP_6.cdf annotation file. Calculation of total signal intensity values (log R ratio) per marker and GC-adjustment to account for genomic waves in signal intensities were performed according to the PennCNV protocol adapted for Affymetrix genotyping arrays (PennCNV-Affy), using the PennCNV-Affy affygw6.hg18.pfb annotation file. As an integrated part of the PennCNV-Affy pipeline, HapMap samples were used as reference for normalization (using the hapmap.quant-norm.normalization-target.txt file) and log R ratio calculation (using the hapmap.genocluster file).
Total signal intensity value (log R ratio) per marker and sample. Genomic positions are given according to the NCBI 36 (hg18) human genome assembly.

source_name: Colorectal cancer patient

label_protocol: 500 ng genomic DNA per sample was processed according to the Affymetrix SNP 6.0 Cytogenetics Copy Number Assay.

extract_protocol: Genomic DNA was extracted from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen), according to the manufacturer's instructions.

value: Biopsy from liver metastasis

tag: patient no.


title: Colorectal cancer liver metastasis t99-2


title: Colorectal cancer liver metastasis t96-1


title: Colorectal cancer liver metastasis t97-2


title: Colorectal cancer liver metastasis t98B-2


title: Colorectal cancer liver metastasis t96-5


title: Colorectal cancer liver metastasis t97-1


title: Colorectal cancer liver metastasis t98B-1


title: Colorectal cancer liver metastasis t85-1


title: Colorectal cancer liver metastasis t98-1


title: Colorectal cancer liver metastasis t96-4


title: Colorectal cancer liver metastasis t9-3


title: Colorectal cancer liver metastasis t99-1


title: Colorectal cancer liver metastasis t85-3


title: Colorectal cancer liver metastasis t85-6


title: Colorectal cancer liver metastasis t85-7


title: Primary colorectal cancer t93-0

value: Biopsy from primary colorectal cancer


title: Colorectal cancer liver metastasis t99-4


title: Colorectal cancer liver metastasis t98-2


title: Colorectal cancer liver metastasis t93-3


title: Colorectal cancer liver metastasis t85-5


title: Colorectal cancer liver metastasis t85-2


title: Colorectal cancer liver metastasis t85-4


title: Colorectal cancer liver metastasis t96-2


title: Colorectal cancer liver metastasis t96-3


title: Colorectal cancer liver metastasis t9-2


title: Colorectal cancer liver metastasis t93-1


title: Colorectal cancer liver metastasis t96-6


title: Colorectal cancer liver metastasis t93-2


title: Colorectal cancer liver metastasis t9-1_P20


title: Colorectal cancer liver metastasis t84B-1


title: Colorectal cancer liver metastasis t84-3_P214


title: Primary colorectal cancer t84-0


title: Colorectal cancer liver metastasis t84-2_P213


title: Colorectal cancer liver metastasis t74-2_P192


title: Colorectal cancer liver metastasis t73-5_run2


title: Colorectal cancer liver metastasis t81-1


title: Colorectal cancer liver metastasis t74-1_P191


title: Colorectal cancer liver metastasis t73-6


title: Colorectal cancer liver metastasis t67-5


title: Colorectal cancer liver metastasis t73-3


title: Colorectal cancer liver metastasis t74-3_193


title: Colorectal cancer liver metastasis t7-1_P13


title: Colorectal cancer liver metastasis t73B-1


title: Colorectal cancer liver metastasis t73-1


title: Colorectal cancer liver metastasis t73-4


title: Colorectal cancer liver metastasis t82-2


title: Colorectal cancer liver metastasis t7-4_P16


title: Colorectal cancer liver metastasis t67-6


title: Colorectal cancer liver metastasis t67-4


title: Colorectal cancer liver metastasis t73-2


title: Colorectal cancer liver metastasis t71-1_P182


title: Colorectal cancer liver metastasis t81-2


title: Colorectal cancer liver metastasis t70-2_P181


title: Colorectal cancer liver metastasis t82-1


title: Colorectal cancer liver metastasis t67-1


title: Colorectal cancer liver metastasis t71-2_P183


title: Colorectal cancer liver metastasis t64B-4


title: Colorectal cancer liver metastasis t70-1_P180


title: Colorectal cancer liver metastasis t64B-3


title: Colorectal cancer liver metastasis t65-1


title: Colorectal cancer liver metastasis t65-2


title: Colorectal cancer liver metastasis t67-2


title: Colorectal cancer liver metastasis t65-3


title: Primary colorectal cancer t73-0


title: Colorectal cancer liver metastasis t64-4


title: Colorectal cancer liver metastasis t64-5


title: Colorectal cancer liver metastasis t64-2_run2


title: Colorectal cancer liver metastasis t45-2_P105_scan2


title: Colorectal cancer liver metastasis t64-1


title: Colorectal cancer liver metastasis t39-1_run2


title: Colorectal cancer liver metastasis t49-1_P107


title: Colorectal cancer liver metastasis t4B-1


title: Colorectal cancer liver metastasis t39-3


title: Colorectal cancer liver metastasis t39-2


title: Colorectal cancer liver metastasis T42-1


title: Colorectal cancer liver metastasis t49-2_P108


title: Colorectal cancer liver metastasis t45-1_P104


title: Colorectal cancer liver metastasis T30-1


title: Colorectal cancer liver metastasis T29-4


title: Colorectal cancer liver metastasis t64B-1


title: Colorectal cancer liver metastasis t42-2_P101


title: Colorectal cancer liver metastasis T29-3


title: Colorectal cancer liver metastasis t42-3_P102


title: Colorectal cancer liver metastasis T29-2


title: Colorectal cancer liver metastasis t4-2_P7


title: Colorectal cancer liver metastasis T29-1


title: Colorectal cancer liver metastasis t25-5


title: Colorectal cancer liver metastasis t25-3


title: Colorectal cancer liver metastasis t19-1_P53


title: Colorectal cancer liver metastasis t25-1


title: Colorectal cancer liver metastasis t19-2_P54


title: Colorectal cancer liver metastasis T30-2


title: Colorectal cancer liver metastasis t15-1_P40


title: Colorectal cancer liver metastasis t141-1


title: Colorectal cancer liver metastasis t15-2_P41


title: Colorectal cancer liver metastasis t25-2


title: Colorectal cancer liver metastasis t141-2


title: Colorectal cancer liver metastasis t137-1


title: Colorectal cancer liver metastasis t15-3_P42


title: Colorectal cancer liver metastasis t14-2_P39


title: Colorectal cancer liver metastasis t25-4


title: Colorectal cancer liver metastasis t14-1


title: Colorectal cancer liver metastasis t128-1


title: Colorectal cancer liver metastasis t12-3_P32


title: Colorectal cancer liver metastasis t129B-1


title: Colorectal cancer liver metastasis t128-2


title: Colorectal cancer liver metastasis t143-1_run2


title: Colorectal cancer liver metastasis t128-3


title: Colorectal cancer liver metastasis t143-2_run2


title: Primary colorectal cancer t129-0


title: Colorectal cancer liver metastasis t12-1_P30


title: Colorectal cancer liver metastasis t132-1


title: Colorectal cancer liver metastasis t137-2_run2


title: Colorectal cancer liver metastasis t135-3


title: Colorectal cancer liver metastasis t118-3


title: Colorectal cancer liver metastasis t118-1


title: Colorectal cancer liver metastasis t12-2_P31


title: Colorectal cancer liver metastasis t113-1


title: Colorectal cancer liver metastasis t135-1


title: CLL-blood (JB2009091026)

status: Public on Dec 01 2015

city: Boston

first: Jennifer

middle: R.

last: Brown

state: MA

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description: CLL-blood

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: All expression profiles were processed using MAS 5.0, and Combat implemented by the PreprocessDataset module in GenePattern

source_name: leukemia cells

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog

growth_protocol: No growth, freshly isolated from peripheral blood, or after thawing.

extract_protocol: RNA were extracted using Trizol and further purified by RNeasy kit from Qiagen

treatment_protocol: Cells were not treated but rather thawed and processed immediately

tag: phenotype

value: chronic lymphocytic leukemia

value: blood


title: Colorectal cancer liver metastasis t118-2


title: normal B cells (JB2009091030)

description: normal B cells

source_name: Normal B cells

value: healthy donor

value: sorted CD19pos B cells


title: Colorectal cancer liver metastasis t11-1


title: Colorectal cancer liver metastasis t132-2


title: normal B cells (JB2009091031)

description: normal B cells


title: CLL-blood (JB2009091027)

description: CLL-blood


title: CLL-blood (JB2009091029)

description: CLL-blood


title: CLL-blood (JB2009091028)

description: CLL-blood


title: CLL-blood (JB2009091025)

description: CLL-blood


title: Primary colorectal cancer t110-0


title: CLL-blood (JB2009091019)

description: CLL-blood


title: CLL-blood (JB2009091020)

description: CLL-blood


title: Primary colorectal cancer t113-0


title: CLL-blood (JB2009091018)

description: CLL-blood


title: CLL-blood (JB2009091021)

description: CLL-blood


title: CLL-blood (JB2009091023)

description: CLL-blood


title: CLL-blood (JB2009091015)

description: CLL-blood


title: CLL-blood (JB2009091017)

description: CLL-blood


title: CLL-blood (JB2009091024)

description: CLL-blood


title: CLL-blood (JB2009091016)

description: CLL-blood


title: CLL-blood (JB2009091014)

description: CLL-blood


title: CLL-blood (JB2009091011)

description: CLL-blood


title: CLL-blood (JB2009091013)

description: CLL-blood


title: Colorectal cancer liver metastasis t110-1


title: CLL-blood (JB2009091012)

description: CLL-blood


title: CLL-blood (JB2009091007)

description: CLL-blood


title: CLL-blood (JB2009091008)

description: CLL-blood


title: CLL-blood (JB2009091009)

description: CLL-blood


title: CLL-blood (JB2009091006)

description: CLL-blood


title: Colorectal cancer liver metastasis t109-2


title: CLL-blood (JB2009091005)

description: CLL-blood


title: CLL-blood (JB2009091010)

description: CLL-blood


title: Colorectal cancer liver metastasis t108-1


title: CLL-blood (JB2009091004)

description: CLL-blood


title: CLL-blood (JB2009091003)

description: CLL-blood


title: CLL-blood (JB2009071049)

description: CLL-blood


title: Colorectal cancer liver metastasis t105B-1


title: CLL-blood (JB2009091002)

description: CLL-blood


title: CLL-blood (JB2009071050)

description: CLL-blood


title: Colorectal cancer liver metastasis t109-1


title: normal B cells (JB2009071052)

description: normal B cells


title: CLL-blood (JB2009091001)

description: CLL-blood


title: Colorectal cancer liver metastasis t108B-1


title: CLL-blood (JB2009071051)

description: CLL-blood


title: Colorectal cancer liver metastasis t105-1


title: CLL-blood (JB2009071042)

description: CLL-blood


title: Colorectal cancer liver metastasis t109-3


title: CLL-blood (JB2009071045)

description: CLL-blood


title: Colorectal cancer liver metastasis t104-2


title: CLL-blood (JB2009091022)

description: CLL-blood


title: Colorectal cancer liver metastasis t129-1


title: CLL-blood (JB2009071039)

description: CLL-blood


title: CLL-blood (JB2009071048)

description: CLL-blood


title: CLL-blood (JB2009071044)

description: CLL-blood


title: CLL-blood (JB2009071043)

description: CLL-blood


title: CLL-blood (JB2009071046)

description: CLL-blood


title: CLL-blood (JB2009071040)

description: CLL-blood


title: Colorectal cancer liver metastasis t108-2


title: CLL-blood (JB2009071047)

description: CLL-blood


title: Colorectal cancer liver metastasis t105-2


title: CLL-blood (JB2009071035)

description: CLL-blood


title: CLL-blood (JB2009071038)

description: CLL-blood


title: CLL-blood (JB2009071034)

description: CLL-blood


title: CLL-blood (JB2009071030)

description: CLL-blood


title: CLL-blood (JB2009071029)

description: CLL-blood


title: CLL-blood (JB2009071027)

description: CLL-blood


title: CLL-blood (JB2009071033)

description: CLL-blood


title: CLL-blood (JB2009071021)

description: CLL-blood


title: Colorectal cancer liver metastasis t11-2_P29


title: CLL-blood (JB2009071031)

description: CLL-blood


title: CLL-blood (JB2009071028)

description: CLL-blood


title: CLL-blood (JB2009071037)

description: CLL-blood


title: CLL-blood (JB2009071026)

description: CLL-blood


title: CLL-blood (JB2009071020)

description: CLL-blood


title: CLL-blood (JB2009071023)

description: CLL-blood


title: CLL-blood (JB2009071022)

description: CLL-blood


title: CLL-blood (JB2009071019)

description: CLL-blood


title: CLL-blood (JB2009071024)

description: CLL-blood


title: CLL-blood (JB2009071016)

description: CLL-blood


title: CLL-blood (JB2009071036)

description: CLL-blood


title: normal B cells (JB2009071053)

description: normal B cells


title: CLL-blood (JB2009071025)

description: CLL-blood


title: CLL-blood (JB2009071018)

description: CLL-blood


title: CLL-blood (JB2009071013)

description: CLL-blood


title: CLL-blood (JB2009071015)

description: CLL-blood


title: CLL-blood (JB2009071014)

description: CLL-blood


title: CLL-blood (JB2009071012)

description: CLL-blood


title: Colorectal cancer liver metastasis t104-1


title: Colorectal cancer liver metastasis t108-3


title: CLL-blood (JB2009071011)

description: CLL-blood


title: CLL-blood (JB2009071010)

description: CLL-blood


title: CLL-blood (JB2009071005)

description: CLL-blood


title: CLL-blood (JB2009071006)

description: CLL-blood


title: CLL-blood (JB2009071004)

description: CLL-blood


title: CLL-blood (JB2009052251)

description: CLL-blood


title: CLL-blood (JB2009052249)

description: CLL-blood


title: CLL-blood (JB2009052254)

description: CLL-blood


title: CLL-blood (JB2009052248)

description: CLL-blood


title: CLL-blood (JB2009052256)

description: CLL-blood


title: CLL-blood (JB2009071017)

description: CLL-blood


title: CLL-blood (JB2009071008)

description: CLL-blood


title: CLL-blood (JB2009071041)

description: CLL-blood


title: CLL-blood (JB2009071002)

description: CLL-blood


title: CLL-blood (JB2009071003)

description: CLL-blood


title: CLL-blood (JB2009052253)

description: CLL-blood


title: CLL-blood (JB2009052252)

description: CLL-blood


title: CLL-blood (JB2009071009)

description: CLL-blood


title: CLL-blood (JB2009052244)

description: CLL-blood


title: CLL-blood (JB2009071001)

description: CLL-blood


title: CLL-blood (JB2009052241)

description: CLL-blood


title: CLL-blood (JB2009052250)

description: CLL-blood


title: CLL-blood (JB2009052255)

description: CLL-blood


title: CLL-blood (JB2009052246)

description: CLL-blood


title: CLL-blood (JB2009052247)

description: CLL-blood


title: CLL-blood (JB2009052245)

description: CLL-blood


title: CLL-blood (JB2009052243)

description: CLL-blood


title: CLL-blood (JB2009052240)

description: CLL-blood


title: CLL-blood (JB2009052235)

description: CLL-blood


title: CLL-blood (JB2009052233)

description: CLL-blood


title: CLL-blood (JB2009052229)

description: CLL-blood


title: CLL-blood (JB2009052231)

description: CLL-blood


title: CLL-blood (JB2009052239)

description: CLL-blood


title: CLL-blood (JB2009052228)

description: CLL-blood


title: CLL-blood (JB2009052242)

description: CLL-blood


title: CLL-blood (JB2009052238)

description: CLL-blood


title: CLL-blood (JB2009052236)

description: CLL-blood


title: CLL-blood (JB2009052234)

description: CLL-blood


title: CLL-blood (JB2009052225)

description: CLL-blood


title: CLL-blood (JB2009052222)

description: CLL-blood


title: CLL-blood (JB2009052221)

description: CLL-blood


title: CLL-blood (JB2009052226)

description: CLL-blood


title: CLL-blood (JB2009052223)

description: CLL-blood


title: CLL-blood (JB2009052227)

description: CLL-blood


title: CLL-blood (JB2009052224)

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title: CLL-blood (JB2009052218)

description: CLL-blood


title: CLL-blood (JB2009052232)

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title: CLL-blood (JB2009052237)

description: CLL-blood


title: CLL-blood (JB2009052230)

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title: CLL-blood (JB2009052217)

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title: CLL-blood (JB2009052214)

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title: CLL-blood (JB2009052212)

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title: CLL-blood (JB2009052213)

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title: CLL-blood (JB2009052216)

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title: CLL-blood (JB2009052215)

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title: CLL-blood (JB2009052219)

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title: CLL-blood (JB2009052211)

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title: CLL-blood (JB2009052201)

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title: CLL-blood (JB2009052207)

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title: CLL-blood (JB2009052208)

description: CLL-blood


title: CLL-blood (JB2009021974)

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title: CLL-blood (JB2009021973)

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title: CLL-blood (JB2009021970)

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title: CLL-blood (JB2009052210)

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title: CLL-blood (JB2009071007)

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title: CLL-blood (JB2009021969)

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description: normal B cells


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title: normal B cells (CW2011052703)

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title: CLL-blood (CW2011052720)

description: CLL-blood


title: CLL-blood (CW2011052722)

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description: CLL-blood


title: CLL-blood (CW2011031036)

description: CLL-blood


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title: CLL-blood (CW2011052712)

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title: normal B cells (CW2010051810)

description: normal B cells


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description: normal B cells


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description: normal B cells


title: normal B cells (CW2010051805)

description: normal B cells


title: CLL-blood (CW2009091602)

description: CLL-blood


title: CLL-blood (CW2009091601)

description: CLL-blood


title: CLL-blood (CW2009081158)

description: CLL-blood


title: normal B cells (CW2009081153)

description: normal B cells


title: normal B cells (CW2009081152)

description: normal B cells


title: CLL-blood (CW2009081157)

description: CLL-blood


title: B2_TubAffyAnnot_FSGS_27

status: Public on Jul 15 2015

city: Ann Arbor

first: Matthew

middle: Gordon

last: Sampson

state: MI

address: 8220DMSRB3 1150 West Medical Center Drive

institute: University of Michigan School of Medicine

description:
Gene expression from tubulointerstitium
Batch 1 and 2 normalizations are available on the series record. The batch-corrected normalized data are available in the sample tables.

hyb_protocol: not provided

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: Preprocessing, normalization with RMA, background correction performed with affymetrix powertools

source_name: Kidney Biopsy from NEPTUNE subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol

value: kidney

tag: compartment

value: tubulointerstitium

tag: histopath

value: FSGS

tag: apol1 risk status

value: High-Risk

tag: patient age


title: B1_TubAffyAnnot_Other_17

value: Other

value: Low-Risk


title: JJ-34, human Chronic Pancreatitis tissue

status: Public on Aug 13 2015

description: Gene expression data from human CP tisssue

hyb_protocol: Labeled cRNA targets were hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0array for 16 h at 45 °C rotating at 60rpm.  The arrays were washed and stained using the Fluidics Station 450

scan_protocol: GeneChips were scanned using the the Affymetrix GeneChip Scanner 3000.

data_processing:
Gene expression raw data from Affymetric microarrays were processed and normalized using  'affy' R package (v.2.0.0) from Bioconductor (PMID:14960456). Normalization was done using RMA algorithm (PMID:12925520).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: Tissue from CP patients

label_protocol: A 2ug aliquot of total RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences).  Then, 15ug of labeled cRNA was frageneted following the manufacturer's instructions.

extract_protocol: RNA of normal pancreatic specimens were purchased commercially. Trizol extraction of total RNA was performed on PDAC specimens according to the manufacturer's instructions.

value: Chronic Pancreatitis

value: pancrea

tag: tissue subtype

value: CP


title: B2_TubAffyAnnot_Other_44


title: B1_TubAffyAnnot_FSGS_5


title: B1_TubAffyAnnot_Other_18

value: MCD


title: B1_TubAffyAnnot_MN_15

value: MN


title: B2_TubAffyAnnot_FSGS_29


title: B2_TubAffyAnnot_FSGS_28


title: B2_TubAffyAnnot_Other_45


title: B2_TubAffyAnnot_FSGS_31


title: B2_TubAffyAnnot_FSGS_25


title: B1_TubAffyAnnot_Other_57


title: B1_TubAffyAnnot_MN_14


title: B1_TubAffyAnnot_FSGS_52


title: B2_TubAffyAnnot_FSGS_30


title: B2_TubAffyAnnot_Other_46


title: B1_TubAffyAnnot_MN_13


title: B1_TubAffyAnnot_FSGS_4


title: B2_TubAffyAnnot_FSGS_26


title: B1_TubAffyAnnot_FSGS_47


title: B2_TubAffyAnnot_MN_40


title: B1_TubAffyAnnot_MCD_54


title: B2_TubAffyAnnot_FSGS_24


title: B1_TubAffyAnnot_MN_12


title: B1_TubAffyAnnot_FSGS_3


title: B1_TubAffyAnnot_FSGS_2


title: B2_TubAffyAnnot_MCD_35


title: B1_TubAffyAnnot_FSGS_50


title: B1_TubAffyAnnot_MCD_10


title: B2_TubAffyAnnot_FSGS_23


title: B2_TubAffyAnnot_MCD_32


title: B1_TubAffyAnnot_Other_56


title: B2_TubAffyAnnot_MCD_55


title: B2_TubAffyAnnot_Other_43


title: B2_TubAffyAnnot_MN_39


title: B1_TubAffyAnnot_FSGS_51


title: B1_TubAffyAnnot_MCD_9


title: B2_TubAffyAnnot_MN_36


title: B2_TubAffyAnnot_MCD_34


title: B1_TubAffyAnnot_MCD_8


title: B2_TubAffyAnnot_MN_38


title: B2_TubAffyAnnot_MCD_33


title: B1_TubAffyAnnot_Other_16


title: B2_TubAffyAnnot_FSGS_21


title: B1_TubAffyAnnot_MCD_7


title: B2_TubAffyAnnot_FSGS_53


title: B2_GlomAffyAnnot_FSGS_31

description:
Gene expression from glomerulus
Batch 1 and 2 normalizations are available on the series record. The batch-corrected normalized data are available in the sample tables.

value: glomerulus


title: B2_TubAffyAnnot_FSGS_22


title: B1_TubAffyAnnot_MCD_6


title: B2_TubAffyAnnot_FSGS_19


title: B2_TubAffyAnnot_Other_41


title: B1_TubAffyAnnot_FSGS_49


title: B2_TubAffyAnnot_Other_42


title: B2_TubAffyAnnot_FSGS_20


title: B1_TubAffyAnnot_FSGS_48


title: B2_GlomAffyAnnot_Other_46


title: B2_TubAffyAnnot_MN_37


title: B2_GlomAffyAnnot_FSGS_30


title: B2_GlomAffyAnnot_Other_45


title: B1_GlomAffyAnnot_FSGS_5


title: B2_GlomAffyAnnot_FSGS_28


title: B1_GlomAffyAnnot_MN_14


title: B2_GlomAffyAnnot_MN_40


title: B2_GlomAffyAnnot_FSGS_29


title: B1_GlomAffyAnnot_FSGS_4


title: B1_GlomAffyAnnot_Other_18


title: B2_GlomAffyAnnot_FSGS_25


title: B1_GlomAffyAnnot_Other_17


title: B2_GlomAffyAnnot_FSGS_27


title: B1_GlomAffyAnnot_Other_16


title: B1_GlomAffyAnnot_MN_15


title: B2_GlomAffyAnnot_FSGS_23


title: B2_GlomAffyAnnot_MCD_34


title: B2_GlomAffyAnnot_FSGS_24


title: B1_GlomAffyAnnot_MN_13


title: B2_GlomAffyAnnot_FSGS_22


title: B2_GlomAffyAnnot_FSGS_26


title: B1_GlomAffyAnnot_MN_12


title: B1_GlomAffyAnnot_MCD_9


title: B1_GlomAffyAnnot_FSGS_2


title: B2_GlomAffyAnnot_MCD_33


title: B2_GlomAffyAnnot_Other_43


title: B2_GlomAffyAnnot_Other_44


title: B1_GlomAffyAnnot_FSGS_3


title: B2_GlomAffyAnnot_MN_39


title: B2_GlomAffyAnnot_MCD_32


title: B1_GlomAffyAnnot_MCD_10


title: B2_GlomAffyAnnot_MCD_35


title: B1_GlomAffyAnnot_MCD_8


title: B2_GlomAffyAnnot_MN_38


title: B1_GlomAffyAnnot_MCD_7


title: B2_GlomAffyAnnot_FSGS_21


title: B2_GlomAffyAnnot_FSGS_19


title: B2_GlomAffyAnnot_Other_41


title: SEQC_NB496 [2]

status: Public on Oct 22 2014

type: SRA

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for Illumina basecalling.
Reads were aligned with Novoalign and quantified with in-house program
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPM for each transcript

source_name: neuroblastoma

extract_protocol: Illumina libraries were prepared using standard Illumina TruSeq RNA-Seq protocols

tag: training/validation

value: Validation

tag: Sex

value: M

tag: age

tag: efs day

tag: efs bin

tag: os day

tag: os bin

value: neuroblastoma


title: SEQC_NB490 [2]

value: F

tag: high risk

value: HR

tag: tissue


title: SEQC_NB489 [2]

value: Training


title: SEQC_NB491 [2]


title: SEQC_NB497 [2]


title: SEQC_NB488 [2]