title: B2-3_SFTPC-pos-P3_Ctrl_rep2

description: P3 SFTPC+ cells treated with vehicle control for 10 days.

source_name: SFTPC-positive cells derived from B2-3 hiPSCs, P3, DMSO

value: Vehicle control


title: B2-3_SFTPC-pos-P3_Amiodarone_rep1

status: Public on Oct 02 2017

type: RNA

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: P3 SFTPC+ cells treated with 10µM of amiodarone for 10 days.

hyb_protocol: 0.6 μg of labeled-cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent. Fragmented samples were then hybridized to SurePrint G3 Human Gene Expression 8x60K v2 microarrays (Agilent Technologies) for 17 hours at 65°C.

scan_protocol: The array slides were scanned using a microarray scanner (Agilent Technologies, G2600D) with one color scan setting for 8x60k array slides.

data_processing:
To obtain expression level, the scanned images were processed with Feature Extraction Software (Agilent Technologies).
Normalized signal intensity with baseline correction to mean of the control samples using GeneSpring software GX13.0.

molecule: total RNA

organism: Homo sapiens

source_name: SFTPC-positive cells derived from B2-3 hiPSCs, P3, amiodarone

label_protocol: Cy3-labeled cRNA were generated from 0.1 µg of total RNA using the Low Input Quick Amp Labeling Kit (Agilent technologies) and purified by RNeasy column (Qiagen) according to the manufacturer's protocol.

growth_protocol: CPMhigh progenitor cells were induced from iPSCs via ventralized anterior foregut andodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days; Step 2: SB431542 and Noggin for 4 days; Step 3: CHIR99021, BMP4 and ATRA; and Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days. P0 SFTPC+ cells were induced from CPMhigh progenitor cells by forming AO in three-dimensional coculture with human fetal lung fibroblasts. P3 SFTPC+ cells were obtained from three-times passaged AO.

extract_protocol: Total RNA was extracted by using the PureLink RNA Mini Kit (Life Technologies) according to manufacturer's protocol. To digest genomic DNA, extracts were cleaned up by using the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel).

treatment_protocol: After passaged three times every two weeks, AO were treated with 5 µM of GNE7915, 10 µM of amiodarone, or vehicle control (DMSO) for 10 days.

tag: originating cell line

value: B2-3 hiPSCs

tag: cell type

value: SFTPC-positive cells

tag: drug

value: Amiodarone


title: Organoid4_cyst_73day_rep4

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

country: Canada

institute: University of Toronto

hyb_protocol: Fragmented and biotin-labelled ss-cDNAs were then hybridized to GeneChip Human Gene 2.0 ST Arrays for 16 hours at 45ºC. Hybridized arrays were then stained and washed in the Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The (.DAT) image files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.3 to generate cell intensity (.CEL) files. The (.CEL) files were uploaded to the Affymetrix Expression Console software v1.4.1 for further processing and quality control. The probe set's signal intensities were then extracted and normalized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software. The downstream paired sample t-test was carried out via Partek Genomics Suite 6.6 (Partek Inc.) to determine differentially expressed genes between cysts and tubules. Gene set enrichment analysis (GSEA) was used as the primary tool to identify potential gene pathways or gene sets that may modulate kidney organoid cyst growth.

label: biotin

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 73 days of culture

label_protocol: Biotin-labelled ss-cDNAs were prepared by using the GeneChip WT Pico Reagent Kit according to the standard Affymetrix protocol for 10 ng of total RNA.

growth_protocol: Kidney organoids with biallelic PKD mutations were cultured under conditions promoting cyst formation, without stimulation of cyclic AMP signaling. The cyst-like structures were microdissected from organoids after being cultured for 71-87 days. Seven paired samples (cyst-like structures and remnant tubular organoids) were used for the microarray study.

extract_protocol: The total RNA was extracted using RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA sample was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the RNA integrity number (RIN) was greater than 7.

treatment_protocol: All tissues were washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80°C freezer.

tag: organoid

value: kidney organoid with CRISPR-induced PKD1 mutation

tag: organoid id

tag: tissue

value: Cyst from PKD1 mutant kidney organoid


title: Organoid6_cyst_71day_rep6

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 71 days of culture


title: 233_Nasal (expr)

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

description: expression from fresh patient cellls

hyb_protocol: Agilent standard protocol for gene expression array

scan_protocol: Nimblegen scanner for gene expression array

data_processing: Quantile normalization and log2-transformation for expression arrays

growth_protocol: NA, these are fresh patient cells so no culture

extract_protocol: DNA and RNA extracted using the AllPrep kit from Qiagen from freshly collected cells

treatment_protocol: NA, no treatment

tag: sample id

value: nasal epithelia

tag: disease state

value: Normal

tag: subarray

tag: age

tag: gender

value: M


title: 223_bronch (expr)

description: expression from fresh patient cellls

label_protocol: Agilent standard protocol for gene expression array

value: bronchial epithelia


title: 224_bronch (expr)

description: expression from fresh patient cellls

value: F


title: Organoid3_cyst_87day_rep3

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 87 days of culture


title: B2-3_SFTPC-pos-P3_Amiodarone_rep2


title: 230_Nasal (expr)

description: expression from fresh patient cellls

value: Asthma


title: 233_bronch (expr)

description: expression from fresh patient cellls


title: B2-3_SFTPC-pos-P3_GNE7915_rep3

description: P3 SFTPC+ cells treated with 5µM of GNE7915 for 10 days.

source_name: SFTPC-positive cells derived from B2-3 hiPSCs, P3, GNE7915


title: 232_Nasal (expr)

description: expression from fresh patient cellls


title: 231_Nasal (expr)

description: expression from fresh patient cellls


title: 230_bronch (expr)

description: expression from fresh patient cellls


title: 231_PBMC (expr)

description: expression from fresh patient cellls

value: PBMC


title: B2-3_SFTPC-pos-P3_Ctrl_rep3


title: 228_PBMC (expr)

description: expression from fresh patient cellls


title: 226_PBMC (expr)

description: expression from fresh patient cellls


title: 224_PBMC (expr)

description: expression from fresh patient cellls


title: 223_PBMC (expr)

description: expression from fresh patient cellls


title: 232_bronch (expr)

description: expression from fresh patient cellls


title: 228_Nasal (expr)

description: expression from fresh patient cellls


title: B2-3_SFTPC-pos-P3_Ctrl_rep1


title: 226_bronch (expr)

description: expression from fresh patient cellls


title: 231_bronch (expr)

description: expression from fresh patient cellls


title: 217_Nasal (expr)

description: expression from fresh patient cellls


title: 233_PBMC (expr)

description: expression from fresh patient cellls


title: 221_bronch (meth)

description: methylation from fresh patient cells

hyb_protocol: Illumina standard protocol for 450k methylation array

scan_protocol: iScan for 450k methylation array

data_processing: SWAN normalization and logit transformation for methylation arrays

label: Cy3, Cy5


title: 221_Nasal (expr)

description: expression from fresh patient cellls


title: 220_bronch (meth)

description: methylation from fresh patient cells

label_protocol: Illumina standard protocol for 450k methylation array


title: 228_bronch (meth)

description: methylation from fresh patient cells


title: 233_bronch (meth)

description: methylation from fresh patient cells


title: 223_bronch (meth)

description: methylation from fresh patient cells


title: 224_Nasal (expr)

description: expression from fresh patient cellls


title: 232_PBMC (expr)

description: expression from fresh patient cellls


title: 230_bronch (meth)

description: methylation from fresh patient cells


title: 224_bronch (meth)

description: methylation from fresh patient cells


title: 216_Nasal (expr)

description: expression from fresh patient cellls


title: 220_Nasal (expr)

description: expression from fresh patient cellls


title: 231_bronch (meth)

description: methylation from fresh patient cells


title: 223_Nasal (expr)

description: expression from fresh patient cellls


title: 226_Nasal (expr)

description: expression from fresh patient cellls


title: 219_Nasal (expr)

description: expression from fresh patient cellls


title: 214_Nasal (expr)

description: expression from fresh patient cellls


title: 230_PBMC (expr)

description: expression from fresh patient cellls


title: 212_Nasal (expr)

description: expression from fresh patient cellls


title: 228_bronch (expr)

description: expression from fresh patient cellls


title: 217_bronch (meth)

description: methylation from fresh patient cells


title: 226_bronch (meth)

description: methylation from fresh patient cells


title: 219_bronch (meth)

description: methylation from fresh patient cells


title: B2-3_SFTPC-pos-P3_GNE7915_rep1


title: 218_Nasal (expr)

description: expression from fresh patient cellls


title: 214_PBMC (expr)

description: expression from fresh patient cellls


title: 218_bronch (meth)

description: methylation from fresh patient cells


title: 232_bronch (meth)

description: methylation from fresh patient cells


title: 215_bronch (meth)

description: methylation from fresh patient cells


title: 217_PBMC (expr)

description: expression from fresh patient cellls


title: 209_bronch (meth)

description: methylation from fresh patient cells


title: 220_PBMC (expr)

description: expression from fresh patient cellls


title: 212_PBMC (expr)

description: expression from fresh patient cellls


title: 206_bronch (meth)

description: methylation from fresh patient cells


title: 201_bronch (expr)

description: expression from fresh patient cellls


title: 221_PBMC (expr)

description: expression from fresh patient cellls


title: 218_PBMC (expr)

description: expression from fresh patient cellls


title: 219_PBMC (expr)

description: expression from fresh patient cellls


title: 216_PBMC (expr)

description: expression from fresh patient cellls


title: 216_bronch (meth)

description: methylation from fresh patient cells


title: 204_bronch (meth)

description: methylation from fresh patient cells


title: 204_bronch (expr)

description: expression from fresh patient cellls


title: 213_bronch (meth)

description: methylation from fresh patient cells


title: 207_bronch (meth)

description: methylation from fresh patient cells


title: 201_bronch (meth)

description: methylation from fresh patient cells


title: 213_bronch (expr)

description: expression from fresh patient cellls


title: 202_bronch (meth)

description: methylation from fresh patient cells


title: 215_bronch (expr)

description: expression from fresh patient cellls


title: 206_bronch (expr)

description: expression from fresh patient cellls


title: 233_Nasal (meth)

description: methylation from fresh patient cells


title: 232_Nasal (meth)

description: methylation from fresh patient cells


title: 214_bronch (meth)

description: methylation from fresh patient cells


title: 207_bronch (expr)

description: expression from fresh patient cellls


title: 201_Nasal (expr)

description: expression from fresh patient cellls


title: 221_Nasal (meth)

description: methylation from fresh patient cells


title: 209_bronch (expr)

description: expression from fresh patient cellls


title: 231_Nasal (meth)

description: methylation from fresh patient cells


title: 230_Nasal (meth)

description: methylation from fresh patient cells


title: 220_Nasal (meth)

description: methylation from fresh patient cells


title: 202_bronch (expr)

description: expression from fresh patient cellls


title: 223_Nasal (meth)

description: methylation from fresh patient cells


title: 204_Nasal (expr)

description: expression from fresh patient cellls


title: 206_Nasal (expr)

description: expression from fresh patient cellls


title: 224_Nasal (meth)

description: methylation from fresh patient cells


title: 228_Nasal (meth)

description: methylation from fresh patient cells


title: 218_Nasal (meth)

description: methylation from fresh patient cells


title: 226_Nasal (meth)

description: methylation from fresh patient cells


title: 209_Nasal (expr)

description: expression from fresh patient cellls


title: 213_Nasal (expr)

description: expression from fresh patient cellls


title: 202_Nasal (expr)

description: expression from fresh patient cellls


title: 212_bronch (meth)

description: methylation from fresh patient cells


title: 209_Nasal (meth)

description: methylation from fresh patient cells


title: 217_Nasal (meth)

description: methylation from fresh patient cells


title: 201_PBMC (expr)

description: expression from fresh patient cellls


title: 206_PBMC (expr)

description: expression from fresh patient cellls


title: 207_Nasal (expr)

description: expression from fresh patient cellls


title: 215_PBMC (expr)

description: expression from fresh patient cellls


title: 214_Nasal (meth)

description: methylation from fresh patient cells


title: 204_PBMC (expr)

description: expression from fresh patient cellls


title: 213_PBMC (expr)

description: expression from fresh patient cellls


title: 209_PBMC (expr)

description: expression from fresh patient cellls


title: 215_Nasal (meth)

description: methylation from fresh patient cells


title: 202_PBMC (expr)

description: expression from fresh patient cellls


title: 207_PBMC (expr)

description: expression from fresh patient cellls


title: 207_Nasal (meth)

description: methylation from fresh patient cells


title: 219_Nasal (meth)

description: methylation from fresh patient cells


title: 206_Nasal (meth)

description: methylation from fresh patient cells


title: 215_Nasal (expr)

description: expression from fresh patient cellls


title: 216_Nasal (meth)

description: methylation from fresh patient cells


title: 202_Nasal (meth)

description: methylation from fresh patient cells


title: 204_Nasal (meth)

description: methylation from fresh patient cells


title: 217_bronch (expr)

description: expression from fresh patient cellls


title: 213_Nasal (meth)

description: methylation from fresh patient cells


title: 214_bronch (expr)

description: expression from fresh patient cellls


title: 201_Nasal (meth)

description: methylation from fresh patient cells


title: 219_bronch (expr)

description: expression from fresh patient cellls


title: 233_PBMC (meth)

description: methylation from fresh patient cells


title: 220_bronch (expr)

description: expression from fresh patient cellls


title: 221_bronch (expr)

description: expression from fresh patient cellls


title: 216_bronch (expr)

description: expression from fresh patient cellls


title: 212_bronch (expr)

description: expression from fresh patient cellls


title: 218_bronch (expr)

description: expression from fresh patient cellls


title: 212_Nasal (meth)

description: methylation from fresh patient cells


title: 224_PBMC (meth)

description: methylation from fresh patient cells


title: 232_PBMC (meth)

description: methylation from fresh patient cells


title: 223_PBMC (meth)

description: methylation from fresh patient cells


title: 221_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17M_1

city: Ulm

first: Kevin

last: Mellert

address: Albert-Einstein-Allee 23

department: Institute of Pathology

country: Germany

institute: University Hospital Ulm

hyb_protocol: 100 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human 4x44K Whole Genome Microarray (G412F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.1.1(Agilent) using Default Parameters (protocol GE1_1200_Jun14 and grid: 014850_D_F_20080627) to obtain Background subtracted and spatially detrended processed signal intensities.

source_name: Soft tissue metastasis derived cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: The cell lines were cultured in Iscove’s Modified Dulbecco’s Medium/RPMI 1640 (4:1; Lonza, Basel, Switzerland) with 10 % fetal bovine serum (Biochrom AG, Berlin, Germany), 2 mM glutamine, and penicillin/streptomycin

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The cell lines were not treated with any reagents.

tag: cell line

value: stable chordoma cell line

tag: cell type source

value: Soft tissue metastasis


title: 228_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17M_3


title: 220_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17M_2


title: U-CH17S_2

source_name: Skin metastasis derived cell line

value: Skin metastasis


title: U-CH17S_3


title: 231_PBMC (meth)

description: methylation from fresh patient cells


title: 219_PBMC (meth)

description: methylation from fresh patient cells


title: 218_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17S_1


title: 226_PBMC (meth)

description: methylation from fresh patient cells


title: 217_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17P_1

source_name: primary tumour derived cell line

value: Primary tumour


title: 215_PBMC (meth)

description: methylation from fresh patient cells


title: 207_PBMC (meth)

description: methylation from fresh patient cells


title: 216_PBMC (meth)

description: methylation from fresh patient cells


title: 209_PBMC (meth)

description: methylation from fresh patient cells


title: 213_PBMC (meth)

description: methylation from fresh patient cells


title: 204_PBMC (meth)

description: methylation from fresh patient cells


title: 201_PBMC (meth)

description: methylation from fresh patient cells


title: 202_PBMC (meth)

description: methylation from fresh patient cells


title: 206_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17P_3


title: 212_PBMC (meth)

description: methylation from fresh patient cells


title: case50 primary tumor

status: Public on Oct 01 2017

type: genomic

city: Duesseldorf

first: Valentin

last: Rausch

address: Moorenstr. 5

department: Department of General, Visceral, and Pediatric Surgery

institute: Heinrich-Heine-University and University Hospital

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: pancreatic ductal adenocarcinoma

label_protocol: Protocol Version 3.2, Oct 2010, Agilent. Reference DNA was extracted from a healthy lymph node of the respective patient.

extract_protocol: QIAamp DNA FFPE Tissue Handbook, April 2010, Qiagen. Genomic DNA was isolated from formalin-fixated paraffin embedded metastasis/tumor samples. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: m

source_name: control DNA

tag: reference

value: control DNA


title: case50 lymph node metastasis 3

hyb_protocol: Protocol Version 3.2, Oct 2010, Agilent.

source_name: lymph node metastasis


title: case49 primary tumor


title: case50 lymph node metastasis 1


title: 214_PBMC (meth)

description: methylation from fresh patient cells


title: 230_PBMC (meth)

description: methylation from fresh patient cells


title: U-CH17P_2


title: case49 organ metastasis 2

source_name: liver metastasis


title: case49 organ metastasis 1


title: case50 organ metastasis 1


title: Individual 59. Fulani. Uninfected, Monocyte. DNA-methylation

city: Stockholm

first: Ann-Kristin

last: Östlund-Farrants

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard manufacturers protocol

scan_protocol: Illumina GenomeStudio Default Protocol

data_processing: IDAT files were processed by minfi Package and quantile normalized by shinyMethyl package in R

source_name: Peripheral blood mononuclear cells from 18ml venous whole blood

label_protocol: standard manufacturers protocol for Illumina Infinium HumanMethylation450 BeadChip

extract_protocol: Venous whole blood (approximately 18ml) was collected from study participants, and peripheral blood mononuclear cells (PBMCs) were purified by Ficoll-Paque density centrifugation. CD14+ monocytes were isolated with EasySep CD14 positive selection kit according to manufacturer’s instructions (Stem Cell Technologies) CD14+ monocytes and the remaining CD14- cells (lymphocytes) were stored in RNAprotect Cell Reagent (Qiagen) at -80C. Total DNA and RNA were extracted from CD14+ and CD14- cells with AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions .

tag: ethnic group

value: Fulani

tag: individual

tag: infection

value: Uninfected

tag: cell population

value: CD14+ monocyte


title: case49 lymph node metastasis 1


title: case33 organ metastasis 1

value: f


title: Individual 53. Fulani. Infected, Monocyte. DNA-methylation

value: Infected

tag: cell type


title: case33 lymph node metastasis 2


title: case33 lymph node metastasis 1


title: case24 primary tumor


title: case24 lymph node metastasis 2


title: case8 primary tumor


title: Individual 8. Mossi. Uninfected. Monocyte. DNA-methylation

value: Mossi


title: case8 lymph node metastasis 4


title: Individual 54. Fulani. Infected, Monocyte. DNA-methylation


title: case8 lymph node metastasis 2


title: Individual 49. Fulani. Uninfected, Monocyte. DNA-methylation


title: case24 lymph node metastasis 1


title: Individual 24. Mossi. Infected. Monocyte. DNA-methylation


title: Individual 43. Fulani. Uninfected, Monocyte. DNA-methylation


title: case54 primary tumor


title: Individual 7. Mossi. Uninfected. Monocyte. DNA-methylation


title: case8 lymph node metastasis 3


title: case49 lymph node metastasis 2


title: Individual 5. Mossi. Infected. Monocyte. DNA-methylation


title: Individual 47. Fulani. Infected, Monocyte. DNA-methylation


title: case53 lymph node metastasis 1


title: case54 lymph node metastasis 3


title: case33 primary tumor


title: case52 primary tumor


title: Individual 39. Mossi. Infected. Monocyte. DNA-methylation


title: case51 primary tumor


title: case52 lymph node metastasis 1


title: case51 lymph node metastasis 1


title: case54 lymph node metastasis 2


title: case53 lymph node metastasis 2


title: case47 lymph node metastasis 3


title: case47 lymph node metastasis 1


title: case53 primary tumor


title: case45 primary tumor


title: case47 lymph node metastasis 2


title: case48 primary tumor


title: case47 primary tumor


title: case45 lymph node metastasis 1


title: case48 lymph node metastasis 1


title: case24 organ metastasis 1


title: case51 lymph node metastasis 2


title: case45 lymph node metastasis 2


title: case44 lymph node metastasis 1


title: case48 lymph node metastasis 2


title: case42 lymph node metastasis 1


title: case44 lymph node metastasis 3


title: case44 primary tumor


title: case42 primary tumor


title: case41 primary tumor


title: case42 lymph node metastasis 2


title: case2 lymph node metastasis 2


title: case44 lymph node metastasis 2


title: case41 lymph node metastasis 1


title: case2 primary tumor


title: case52 lymph node metastasis 2


title: case28 lymph node metastasis 2


title: case19 lymph node metastasis 2


title: case53 lymph node metastasis 3


title: MatOb F3 replicate 4

city: Darlinghurst

first: Paul

middle: E

last: Young

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

description:
M12
gene expression data from F3 sons of an obese mother

hyb_protocol: 5.2 ug of fragmented, labeled cDNA (final concentration in hyb cocktail of 23 ng/ul) was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner as per manufacturer’s protocol.

data_processing:
Affymetrix Transcription analysis console v3
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

organism: Mus musculus

source_name: MatOb F3

label_protocol: Affymetrix GeneChip WT Plus Reagent Kit for Manual Target Preparation for GeneChip Whole Transcript Expression Arrays. An input of 100 ng of total RNA was used

growth_protocol: 12 week old male mice

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

treatment_protocol: mice were either the F2 or F3 sons of lean control females or obese Avy/a females

tag: strain

value: 12 weeks

value: male

tag: mouse status

value: F3 son of an obese mother

value: liver


title: case28 lymph node metastasis 1


title: MatOb F2 replicate 4

description:
M8
gene expression data from F2 sons of an obese mother

source_name: MatOb F2

value: F2 son of an obese mother


title: MatOb F3 replicate 2

description:
M10
gene expression data from F3 sons of an obese mother


title: MatOb F2 replicate 3

description:
M7
gene expression data from F2 sons of an obese mother


title: control replicate 4

description:
M4
gene expression data from  males with lean control parents

source_name: control

value: control mouse with lean control parents


title: case19 primary tumor


title: case2 lymph node metastasis 1


title: case28 primary tumor


title: MatOb F3 replicate 3

description:
M11
gene expression data from F3 sons of an obese mother


title: MatOb F2 replicate 2

description:
M6
gene expression data from F2 sons of an obese mother


title: MatOb F3 replicate 1

description:
M9
gene expression data from F3 sons of an obese mother


title: case19 lymph node metastasis 1


title: control replicate 3

description:
M3
gene expression data from  males with lean control parents


title: control replicate 1

description:
M1
gene expression data from  males with lean control parents


title: MatOb F2 replicate 1

description:
M5
gene expression data from F2 sons of an obese mother


title: control replicate 2

description:
M2
gene expression data from  males with lean control parents


title: Individual 2. Mossi. Uninfected. Monocyte. DNA-methylation

value: PBMC


title: Nacl_1

city: Copenhagen

first: Joshua

last: Brickman

address: 3B Blegdamsvej

country: Denmark

institute: DanStem

description: Gene expression in stable culture of ESCs in NACL

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4x44k (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried and scanned.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ESCs adapted to NACL culture for a minimum of 3 passages replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: ESCs were cultured in 2i/L. EpiSCs were cultured in standard EpiSC conditons. Diff and nEnd cultures were passaged in nEnd medium. NACL were grown in N2B27 with Activin, Chiron and LIF.

extract_protocol: RNA was prepared using the Qiagen RNeasy (74104) kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop 2000 spectrophotometer and with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were cultures in 6 well plates, and lysed directly on the plate for RNA.

value: Male

tag: cell line source

value: HVMC

value: stable culture of ESCs in NACL


title: ADE_1

description: Gene expression in EpiSCs differentiated to ADE

source_name: Epiblast stem cells differentiated to ADE for 4 days

value: HRHNG

value: EpiSCs differentiated to ADE


title: Nacl_3

source_name: ESCs adapted to NACL culture for a minimum of 3 passages replicate 3


title: T7A1

city: Istanbul

first: mehmet

last: baysan

address: Kuşbakışı Caddesi No: 27 34662 Altunizade – Üsküdar – İstanbul Office: East Campus 108

department: Department of Computer Science

country: Turkey

institute: Istanbul Sehir university

description:
Hybridized to CytoScan HD
CytoScan HD

hyb_protocol: Purified DNA was hybridized onto arrays according to the manufacturer's recommendations (Affymetrix Human SNP array 6.0 and CytoScan® HD array).

scan_protocol: After hybridization, the arrays were stained on the Affymetrix GeneChip® fluidics station 450 and scanned at high resolution using the GeneChip® Scanner 3000 7G.

data_processing: CEL files are imported into Partek Genomics Suite 6.6 and matrix file generated. Copy number

label_protocol: QIAamp® DNA kit (Qiagen, Germany) was used to prepare genomic DNA from patient tumor-derived cultured GSCs. QIAamp® DNA Blood Mini Kit (Qiagen, Germany) was used to prepare DNA from patient reference blood.

extract_protocol: none provided by the submitter

tag: sample type

value: xenograft tumor

tag: tumor type

value: recurrent GBM

value: GBM


title: T6p2

description:
Hybridized to CytoScan HD
CytoScan HD

value: polyclonal GBM cell line


title: T7T

description:
Hybridized to CytoScan HD
CytoScan HD

value: patient tumor


title: T6T

description:
Hybridized to CytoScan HD
CytoScan HD


title: T7p2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T7A2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T6MC23

description:
Hybridized to CytoScan HD
CytoScan HD

value: monoclonal GBM cell line


title: Epi_1

description: Gene expression in stable culture of EpiSCs

source_name: ESCs Differentiated to Epiblast Stem Cells and maintained as a stable culture Replicate 1

value: stable culture of EpiSCs


title: Nacl_2

source_name: ESCs adapted to NACL culture for a minimum of 3 passages replicate 2


title: ADE_2


title: Epi_2

source_name: ESCs Differentiated to Epiblast Stem Cells and maintained as a stable culture Replicate 2


title: ADE_3


title: Nacl_4

source_name: ESCs adapted to NACL culture for a minimum of 3 passages replicate 4


title: Epi_3

source_name: ESCs Differentiated to Epiblast Stem Cells and maintained as a stable culture Replicate 3


title: T6MC21

description:
Hybridized to CytoScan HD
CytoScan HD


title: MV4-11_sh_Rx1_profound_#1_rep1

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

description: Gene expression data from RUNX2 knockdown cells

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48°C on Human Gene ST Array Strip. Strip was washed and stained in the Fluidics Station of GeneAtlas System.

scan_protocol: Strip was scanned using the Imaging Station.

data_processing: The data were analyzed with Expression Console 1.3.1 and Transcriptome Analysis Console 1.0 using RMA.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: MV4-11 from ATCC was cultured in RPMI1640 medium supplemented with 10% FBS and 1% PS at 37°C, 5% CO2

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were transduced with each shRNA and subsequently incubated with 3 µM of doxycycline for 24 hours.

value: Acute Myeloid Leukemia (AML) cell line MV4-11

tag: genotype

value: RUNX1 knockdown (Profound #1)

tag: time

value: 24 hours


title: T6MC11

description:
Hybridized to CytoScan HD
CytoScan HD


title: MV4-11_sh_Rx1_profound_#2_rep1

description: Gene expression data from RUNX3 knockdown cells

value: RUNX1 knockdown (Profound #2)


title: MV4-11_sh_Rx1_moderate_rep1

description: Gene expression data from RUNX1 knockdown cells

value: RUNX1 knockdown (Moderate)


title: ADE_4

value: Male


title: x2iL_2

description: Gene expression in undifferentiated ESCs

source_name: ESCs adapted to 2i:lif conditions for at least 3 passages Replicate 2

value: undifferentiated ESCs


title: x2iL_1

source_name: ESCs adapted to 2i:lif conditions for at least 3 passages Replicate 1

value: HVMC


title: MV4-11_sh_Luc_rep1

description: Gene expression data from knockdown control cells (sh Luc)

value: Control shRNA


title: XEN_rep3 23

description: Gene expression in standard XEN cells

source_name: XEN cell controls cultured in standard XEN medium replicate 3

value: Xen

value: standard XEN cells


title: x2iL_3

source_name: ESCs adapted to 2i:lif conditions for at least 3 passages Replicate 3


title: XEN_rep2 O

description: Gene expression in standard XEN cells

source_name: XEN cell controls cultured in standard XEN medium replicate 2


title: T6MC07

description:
Hybridized to CytoScan HD
CytoScan HD

value: recurrent GBM


title: T6A2

description:
Hybridized to CytoScan HD
CytoScan HD

value: xenograft tumor

value: GBM


title: T5T

description:
Hybridized to CytoScan HD
CytoScan HD

value: patient tumor


title: T5A5

description:
Hybridized to CytoScan HD
CytoScan HD


title: T5MC01

description:
Hybridized to CytoScan HD
CytoScan HD

value: monoclonal GBM cell line


title: T5p2

description:
Hybridized to CytoScan HD
CytoScan HD

value: polyclonal GBM cell line


title: T5MC06

description:
Hybridized to CytoScan HD
CytoScan HD


title: T5A2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T4p2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T4MC14

description:
Hybridized to CytoScan HD
CytoScan HD


title: T4MC03

description:
Hybridized to CytoScan HD
CytoScan HD


title: T6A1

description:
Hybridized to CytoScan HD
CytoScan HD


title: T4A2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T3T

description:
Hybridized to CytoScan HD
CytoScan HD


title: T4A4

description:
Hybridized to CytoScan HD
CytoScan HD


title: XEN_rep1 P

description: Gene expression in standard XEN cells

source_name: XEN cell controls cultured in standard XEN medium replicate 1


title: T3MC20SC5

description:
Hybridized to CytoScan HD
CytoScan HD


title: T3p2

description:
Hybridized to CytoScan HD
CytoScan HD


title: T3MC20

description:
Hybridized to CytoScan HD
CytoScan HD


title: T3MC20SC7

description:
Hybridized to CytoScan HD
CytoScan HD


title: T3A2

description:
Hybridized to CytoScan HD
CytoScan HD


title: Late_rep1 19

description: Gene expression in late passage nEnd cultures

source_name: Late passage HRHnG nEnd cultures replicate 1

value: HRHnG

value: late passage nEnd cultures


title: Mid_rep3 16

description: Gene expression in mid passage nEnd cultures

source_name: Mid passage HRHnG nEnd cultures replicate 3

value: mid passage nEnd cultures


title: T3A4

description:
Hybridized to CytoScan HD
CytoScan HD


title: Diff_rep3 M

description: Gene expression in dESCs differentiated to PrE

source_name: HRHnG ESCs differentiated in Act/CHI/LIF for 7-8 days to primtiive endoderm replicate 3

value: dESCs differentiated to PrE


title: T2A1

description:
Hybridized to CytoScan HD
CytoScan HD


title: Mid_rep2 K

source_name: Mid passage HRHnG nEnd cultures replicate 2


title: Late_rep2 21

source_name: Late passage HRHnG nEnd cultures replicate 2


title: T1T

description:
Hybridized to CytoScan HD
CytoScan HD


title: Mid_rep1 J

source_name: Mid passage HRHnG nEnd cultures replicate 1


title: T2T

description:
Hybridized to CytoScan HD
CytoScan HD


title: Late_rep3 20

source_name: Late passage HRHnG nEnd cultures replicate 3


title: Diff_rep2 C

source_name: HRHnG ESCs differentiated in Act/CHI/LIF for 7-8 days to primtiive endoderm replicate 2


title: T2p2

description:
Hybridized to CytoScan HD
CytoScan HD


title: 203MC02

description:
Hybridized to CytoScan HD
CytoScan HD

value: primary GBM


title: T2MC09

description:
Hybridized to CytoScan HD
CytoScan HD


title: 203-PT

description:
Hybridized to CytoScan HD
CytoScan HD


title: T2MC02

description:
Hybridized to CytoScan HD
CytoScan HD


title: T2MC05

description:
Hybridized to CytoScan HD
CytoScan HD


title: T2A4

description:
Hybridized to CytoScan HD
CytoScan HD


title: NCT

description:
Hybridized to CytoScan HD
CytoScan HD

source_name: NCT

value: non-tumor brain

value: Normal Brain


title: 203MC15

description:
Hybridized to CytoScan HD
CytoScan HD


title: 203A4

description:
Hybridized to CytoScan HD
CytoScan HD


title: 203-blood

description:
Hybridized to CytoScan HD
CytoScan HD

value: blood

value: Blood


title: 203A2

description:
Hybridized to CytoScan HD
CytoScan HD


title: 203p5

description:
Hybridized to CytoScan HD
CytoScan HD


title: Diff_rep1 D

source_name: HRHnG ESCs differentiated in Act/CHI/LIF for 7-8 days to primtiive endoderm replicate 1

value: Male


title: ESC_rep2 H

source_name: Mouse embryonic HRHnG stem cells in 2i/LIF replicate 2

value: undifferentiated ESCs


title: ESC_rep3 F

source_name: Mouse embryonic HRHnG stem cells in 2i/LIF replicate 3


title: Kidney_sham_day7_3

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

description: Gene expression data from kidneys of sham-treated C57BL/6J mice age 10-16 weeks.

hyb_protocol: Fragmented cDNA was hybridized to GeneChipTM Mouse Gene 2.0 ST Arrays using the Hybridization, Wash and Stain Kit according to Affymetrix recommendations in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were pre-processed with Robust Multi-array Average (RMA) algorithm and Background Correction using R statistics software and Bioconductor packages.

source_name: kidney, sham, day 7

label_protocol: cDNA was synthesized from ~200 ng total RNA according to the standard Affymetrix protocols. ss-cDNA was fragmented and biotin-labelled according to Affymetrix recommendations.

growth_protocol: C57BL/6J wild type mice (age 10-16 weeks, weight 20-30 g) were kept under standard laboratory conditions with food and water ad libitum after approval of the local ethics committee.

extract_protocol:
After euthanasia, mice were perfused with PBS, kidneys were removed, snap frozen in liquid nitrogen and stored at -80 °C until RNA extraction.
Total RNA was extracted from approx. 30 mg of homogenized kidney tissue using RNeasy Mini Kit (QIAGEN) and QIAcube (QIAGEN) according to manufacturer's protocol.

treatment_protocol: Two different Stx2 regimes combined with volume resuscitation.

tag: strain/background

tag: genotype/variation

value: wild type

tag: Sex

value: male

tag: tissue

value: kidney

tag: treatment

value: vehicle i.v.; volume resuscitation

tag: time point

value: day 7


title: Kidney_Stx2_day7_1

description: Gene expression data from kidneys of Stx2-challenged C57BL/6J mice age 10-16 weeks 7 days after Stx2 injection.

source_name: kidney, Stx2, day 7

value: triple lower dose Stx2 i.v.; volume resuscitation


title: Kidney_sham_day7_2


title: Kidney_sham_day3_3

source_name: kidney, sham, day 3

value: day 3


title: Kidney_sham_day7_1


title: Kidney_Stx2_day7_3


title: Kidney_sham_day7_4


title: Kidney_Stx2_day3_4

description: Gene expression data from kidneys of Stx2-challenged C57BL/6J mice age 10-16 weeks 3 days after Stx2 injection.

source_name: kidney, Stx2, day 3

value: single higher dose Stx2 i.v.; volume resuscitation


title: 2003P_SRD5A2_unmethylated

city: Boston

first: Keyan

last: Salari

state: MA

address: Gray/Bigelow Rm 1102, 55 Fruit Street

institute: Massachusetts General Hospital

description: replicate 1

hyb_protocol: 750 ng of cRNA were hybridized for 16 hr at 58C on Illumina Human HT-12 v4 Array in an Illumina Hybridization Oven (Illumina SE-901-1001) per standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using the Illumina iScan Scanner running Illumina iSCAN control software v 3.3.28 per standard Illumina scanning protocol

data_processing: The data were normalized by background subtraction with IlluminaExpressionFileCreator in GenePattern, followed by log2 transformation, and batch correction using ComBat

source_name: Human prostatic transitional zone

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

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit in accordance with the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: prostate

tag: srd5a2 methylation

value: unmethylated


title: Kidney_Stx2_day3_3


title: Kidney_Stx2_day7_4


title: Kidney_Stx2_day3_1


title: Kidney_sham_day3_2


title: Kidney_sham_day3_4


title: ESC_rep1 G

source_name: Mouse embryonic HRHnG stem cells in 2i/LIF replicate 1

value: HRHnG


title: Kidney_sham_day3_1


title: Kidney_Stx2_day3_2


title: Kidney_Stx2_day7_2


title: 2003O_SRD5A2_methylated

description: replicate 1

value: methylated


title: 2003R_SRD5A2_unmethylated

description: replicate 1


title: 2003S_SRD5A2_methylated

description: replicate 1


title: 2003T_SRD5A2_methylated

description: replicate 1


title: 2003Q_SRD5A2_unmethylated

description: replicate 1


title: 2015C_SRD5A2_methylated

description: replicate 1


title: 2015D_SRD5A2_unmethylated

description: replicate 1


title: 2003U_SRD5A2_unmethylated

description: replicate 1


title: 2015B_SRD5A2_methylated

description: replicate 1


title: 2003N_SRD5A2_methylated

description: replicate 1


title: 2003L_SRD5A2_unmethylated

description: replicate 1


title: 2003J_SRD5A2_unmethylated

description: replicate 1


title: 2003K_SRD5A2_unmethylated

description: replicate 1


title: 2003I_SRD5A2_unmethylated

description: replicate 1


title: 2003D_SRD5A2_methylated

description: replicate 1


title: 2003C_SRD5A2_methylated

description: replicate 1


title: 2003F_SRD5A2_methylated

description: replicate 1


title: 2003G_SRD5A2_methylated

description: replicate 1


title: 2003B_SRD5A2_methylated

description: replicate 1


title: T7poly

hyb_protocol: Purified DNA was hybridized onto arrays according to the manufacturer's recommendations

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) was used to create raw mRNA expression data (CEL files) from HGU133PLUS2.0 chips

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated and purified from cell pellets and fresh frozen tumor tissue using TRIZOL (Life Technologies) and PureLink® RNA Mini Kit (Life Technologies).

value: polyclonal GBM cell line

value: recurrent GBM

value: GBM cell line


title: T6poly


title: T6MC23-2

value: monoclonal GBM cell line


title: T7MC20-2


title: T6MC23


title: T7MC11-2


title: T6poly-2


title: 2003A_SRD5A2_unmethylated

description: replicate 1


title: T7poly-2


title: T7MC11


title: 2003E_SRD5A2_methylated

description: replicate 1


title: T6MC07


title: T6MC07-2


title: T7MC12-2


title: T6MC21-2


title: T6MC11-2


title: T6MC21


title: T6MC11


title: T7MC12


title: T5MC01-2


title: T7MC20


title: T5MC06-2


title: T4poly


title: T5poly-2


title: T5MC01


title: T5MC06


title: T5poly


title: T4poly-2


title: T4MC03-2


title: T4MC14


title: T4MC14-2


title: T3poly


title: T3MC20-2


title: T4MC03


title: T3MC18-2


title: T3MC04-2


title: T2poly


title: T2MC09


title: T3MC18


title: T2MC09-2


title: 203poly-2

value: primary GBM


title: T3poly-2


title: T2MC05-2


title: T2poly-2


title: 203MC12-2


title: 203MC15


title: T2MC02


title: 203MC15-2


title: 203poly


title: T3MC04


title: T2MC05


title: 203MC09-2


title: 203MC12


title: T3MC20


title: 203MC09


title: 203MC02


title: Sperm from participant 48_S48

city: Amherst

first: Haotian

last: Wu

address: 686 N. Pleasant Street Room 128

institute: UMass Amherst

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
All processing done in R
minfi package - correct for technical variatio nin background (noob), remove probes below background, adjust for Type I/II probes
sva package - ComBat correction for batch
DMRcate package - remove cross-hybridizing and sex chromosome probes.
At the end, we kept both M-vals and Beta-vals in separate documents. Both were analyzed, DMRs were identified with M-vals (provided in the Series supplementary file 'mval_clean.csv') and Beta-vals (included in the sample table) were then used to estimate the magnitude of change/effect.

source_name: Sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Motile fraction enriched via 90% gradient, genomic DNA was extracted and purified from QiaAMP DNA kit

value: Sperm

tag: tissue subtype

value: Enriched motile fraction


title: 203MC02-2

tag: cell type


title: Sperm from participant 47_S47

value: male


title: Sperm from participant 46_S46


title: Sperm from participant 44_S44


title: T2MC02-2


title: Sperm from participant 38_S38


title: Sperm from participant 42_S42


title: Sperm from participant 34_S34


title: Sperm from participant 40_S40


title: Sperm from participant 41_S41


title: Sperm from participant 37_S37


title: Sperm from participant 45_S45


title: Sperm from participant 33_S33


title: Sperm from participant 31_S31


title: Sperm from participant 39_S39


title: Sperm from participant 28_S28


title: Sperm from participant 29_S29


title: Sperm from participant 43_S43


title: Sperm from participant 35_S35


title: Sperm from participant 27_S27


title: Sperm from participant 36_S36


title: Sperm from participant 30_S30


title: Sperm from participant 23_S23


title: Sperm from participant 24_S24


title: Sperm from participant 26_S26


title: Sperm from participant 22_S22


title: Sperm from participant 21_S21


title: Sperm from participant 25_S25


title: Sperm from participant 18_S18


title: Sperm from participant 20_S20


title: SW480_TSA_rep6

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

hyb_protocol: Hybridization was performed over night on Human GE 4x44K v2 Microarrays (Agilent) according to the manufacturer’s protocol version 6.5.

scan_protocol: Slides were scanned with a microarray scanner G2565BA (Agilent) at 5-micron resolution.

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol. Probes with intensity no less than 50 in at least one sample were kept for analysis.

source_name: SW480 Dukes' type B, colorectal adenocarcinoma cell line

label_protocol: One µg RNA from each cell line was amplified and labeled with Cy3 using the Quick Amp Labeling Kit, one-color (Agilent), according to manufacturer's instructions.

growth_protocol: Human colon adenocarcinoma cell lines DLD-1 and SW480 were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured in 10% fetal bovine serum (FBS) (Gibco, Thermofisher Scientific, Waltham, MA. USA) supplemented RPMI (Gibco) or DMEM (Gibco) medium, respectively. DLD-1 cells harboring an extra copy of chromosome 7 (DLD-1+7) were previously described (Upender et al. 2004) and maintained in 10% FBS supplemented RPMI medium with 100 µg/ml geneticin (G418) (Thermofisher).

extract_protocol: Total RNA was isolated from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNA integrity (RIN) was assessed with an RNA 6000 Nano LabChip Kit using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with a RIN number >8.0 were included, and five replicates per condition were used.

treatment_protocol: Cells were seeded 24h prior to treatment in a 96-well flat clear bottom black plate (Corning, Corning NY, USA), after which they were treated with 160 nM Trichostatin A (TSA) (Sigma-Aldrich, St. Louis, MO) for 24 hours. DMSO (Sigma-Aldrich) was used as vehicle control.

tag: cell line

value: colorectal adenocarcinoma cell line

tag: tsa treated

value: 160 nM TSA for 24 hours


title: SW480_TSA_rep3


title: SW480_TSA_rep4


title: SW480_Control_rep3


title: SW480_TSA_rep5


title: SW480_TSA_rep2


title: SW480_TSA_rep1


title: Sperm from participant 19_S19


title: SW480_Control_rep2


title: Sperm from participant 17_S17


title: SW480_Control_rep1


title: DLD1+chr7_TSA_rep5


title: Sperm from participant 11_S11


title: DLD1+chr7_TSA_rep2

source_name: DLD1 Dukes' type C, colorectal adenocarcinoma cell line


title: DLD1+chr7_TSA_rep3


title: DLD1+chr7_TSA_rep4


title: DLD1+chr7_Control_rep4


title: Sperm from participant 13_S13


title: Sperm from participant 6_S6


title: Sperm from participant 7_S7


title: Sperm from participant 16_S16


title: DLD1_TSA_rep4


title: DLD1+chr7_Control_rep1


title: Sperm from participant 10_S10


title: DLD1+chr7_Control_rep2


title: Sperm from participant 4_S4


title: Sperm from participant 3_S3


title: Sperm from participant 9_S9


title: DLD1+chr7_TSA_rep1


title: Sperm from participant 8_S8


title: DLD1_TSA_rep5


title: Sperm from participant 1_S1


title: Sperm from participant 5_S5


title: DLD1_TSA_rep2


title: DLD1_TSA_rep1


title: Sperm from participant 32_S32


title: DLD1_TSA_rep3


title: DLD1+chr7_Control_rep3


title: Sperm from participant 14_S14


title: DLD1_Control_rep3


title: DLD1_Control_rep1


title: DLD1_Control_rep2


title: Sperm from participant 2_S2


title: Sperm from participant 15_S15


title: BMDC, si-NR4A3, LPS(-)

city: Tokyo

first: Chiharu

last: Nishiyama

address: 6-3-1 Niijuku, Katsushika-ku

department: Biological Science and Technology

institute: Tokyo University of Science

description: RMA16 （with quantile-normalization) expression values

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned with GeneChip® Scannar 3000 7G at the Juntendo Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Sample quality, hybridization quality, and labeling quality were evaluated with Expression console version 1.1 (Affymetrix). Raw data were processed with GeneSpring　13.1 software (Agilent Technologies). CEL files were summarized using RMA16 algorithm, and normalized by quantile normalization. Bottom 20% values were considered as background signals and thus excluded from analysis.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Bone-marrow derived dendritic cells

label_protocol: Quality of total RNA was assessed with 2200 Tape Station (Agilent Technologies). Single-stranded cDNA was generated from total RNA with the Ambion WT Expression Kit (Applied Bioscience) and then fragmented and labeled with GeneChip® WT Terminal Labeling and Control Kit (Affymetrix).

growth_protocol: Whole bone marrow cells of BALB/c mice were cultured in RPMI1640 supplemented with 10% heat-inactivated fetal calf serum, antibiotics, and 20 ng/mL of murine GM-CSF for 10 days to generate dendritic cells.

extract_protocol: The extract of total RNA was performed using a ReliaPrep RNA Cell Miniprep System.

treatment_protocol: Short interfering RNA (siRNA) was introduced into bone marrow-derived dendritic cells with Nucleofector II using a Mouse Dendritic Cell Nucleofector kit on day 10. At 24 hours after siRNA transfection, 100 ng/mL of LPS was added into culture medium to stimulate cells. Cells were harvested at 24 hours after LPS-stimulation.

tag: sirna

tag: strain

tag: protocol

value: unstimulated

value: Bone-marrow derived dendritic cells


title: BMDC, si-Ctrl, LPS(-)

value: si-Ctrl


title: BMDC, si-Ctrl, LPS(+)

value: LPS-stimulated


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ BFA] 3

city: Lebanon

first: Damian

middle: A

last: Almiron Bonnin

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth College

hyb_protocol: GeneChipTM Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: GeneChipTM Scanner 3000

data_processing: Raw data generated from Clariom S Mouse Arrays was processed using Affymetrix Expression Console Software.  CEL files containing feature intensity values were converted into summarized expression values using a robust multichip analysis (RMA) which consists of background adjustment, quantile normalization and summarization across all chips.

source_name: S100β-v-erbB/p53-/- cells culture

label_protocol: WTPLus kit (by Affymetrix)

growth_protocol: Cell cultures were grown in DMEM F-12 50-50 media supplemented with B27.

extract_protocol: Trizol mRNA extraction

treatment_protocol: Cell cultures were treated with either DMSO control, BFA (1uM), or EHT-1864 (1uM) grown in hypoxia or normoxia (16h).

value: FVB-NJ

tag: agent

value: Hypoxia+ BFA


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ BFA] 1


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ DMSO] 1

value: Hypoxia+ DMSO


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ EHT] 1

value: Hypoxia+ EHT


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ EHT] 3


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ EHT] 2


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Normoxia+ DMSO] 3

value: Normoxia+ DMSO


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ BFA] 2


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ DMSO] 2


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Hypoxia+ DMSO] 3


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Normoxia+ DMSO] 1


title: [S100β-v-erbB/p53-/- TSC1 cell]-[Normoxia+ DMSO] 2


title: Sperm from participant 12_S12


title: BMDC, si-NR4A3, LPS(+)


title: NHA-B82_ATXN1L-KO_rep2

status: Public on Sep 30 2017

city: Vancouver

first: Derek

last: Wong

state: British Columbia

address: 675 W 10th Ave

department: Molecular Oncology

institute: University of British Columbia

description:
B82 2
Adult brain

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: Expression Console

label: Biotin Allonamide Triphosphate

source_name: Normal human astrocytes, CRISPR ATXN1L-KO, isogenic

label_protocol: Biotin Allonamide Triphosphate.

growth_protocol: DMEM supplemented with 10% FBS. 37'C, 5% CO2 incubator.

extract_protocol: Qiagen miRNeasy kit.

treatment_protocol: CRISPR treated, selected in puromycin then isolated into single colonies.

value: NHA

value: astrocytes

value: CRISPR ATXN1L-KO


title: pka1

first: Kazuya

last: Kusama

address: 1-1-1 Yayoi, Bunkyo-ku

institute: The University of Tokyo

description: Gene expression data from BeWo cells treated with N6-phenyl-cAMP for 48h.

hyb_protocol: Following fragmentation, ss-cDNA were hybridized for 16 hr at 45 C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

source_name: Human choriocarcinoma cell line

label_protocol: Biotinylated single-stranded cDNA was obtained with standard protocols by the GeneChip WT Plus Reagent Kit.

growth_protocol: BeWo cells were grown at 37 C in Ham’s F 12/Dulbecco’s modified Eagle’s medium (1:1) medium supplemented with 10% (v/v) FBS, 40 units/ml of penicillin, and 40 µg/ml of streptomycin at 37 °C under 5% CO2 in humidified air.

extract_protocol: Isogen extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Human placenta choriocarcinoma cell line BeWo cells were treated without or with Epac- or PKA-selective cAMP analogs for 48 h, of which RNAs were extracted and subjected to Affymetrix microarrays.

value: BeWo

value: choriocarcinoma cell line


title: cont1

description: Gene expression data from BeWo cells.


title: NHA-H9_CIC-KO_rep1

description:
H9 1
Adult brain

source_name: Normal human astrocytes, CRISPR CIC-KO, isogenic

value: CRISPR CIC-KO


title: pka3


title: pka2


title: cont3

description: Gene expression data from BeWo cells.


title: cont2

description: Gene expression data from BeWo cells.


title: NHA-B82_ATXN1L-KO_rep1

description:
B82 1
Adult brain


title: NHA-A2_CIC-KO_rep3

description:
A2 3
Adult brain


title: NHA-B82_ATXN1L-KO_rep3

description:
B82 3
Adult brain


title: epac3

description: Gene expression data from BeWo cells treated with 8-(4-chlorophenyltio)-2’-O-methyl cAMP for 48h.

value: 8-(4-chlorophenyltio)-2'-O-methyl cAMP


title: NHA-H9_CIC-KO_rep3

description:
H9 3
Adult brain


title: epac1


title: epac2


title: NHA-H9_CIC-KO_rep2

description:
H9 2
Adult brain


title: NHA-A2_CIC-KO_rep2

description:
A2 2
Adult brain


title: NHA-A2_CIC-KO_rep1

description:
A2 1
Adult brain


title: NHA-parental_WT_rep3

description:
NHA 3
Adult brain

source_name: Normal human astrocytes, parental

value: parental


title: HEK-B21_ATXN1L-KO_rep1

description: B21 1

source_name: HEK cell line, CRISPR ATXN1L-KO, isogenic

value: HEK

value: embryonic kidney


title: HEK-B21_ATXN1L-KO_rep3

description: B21 3


title: HEK-A30_ATXN1L-KO_rep3

description: A30 3


title: NHA-parental_WT_rep1

description:
NHA 1
Adult brain


title: HEK-B21_ATXN1L-KO_rep2

description: B21 2


title: HEK-A10_ATXN1L-KO_rep2

description: A10 2


title: HEK-A30_ATXN1L-KO_rep2

description: A30 2


title: HEK-A10_ATXN1L-KO_rep3

description: A10 3


title: HEK-A30_ATXN1L-KO_rep1

description: A30 1


title: HEK-A10_ATXN1L-KO_rep1

description: A10 1


title: NHA-parental_WT_rep2

description:
NHA 2
Adult brain


title: 3mo_9cGNAV_F_L345_D

type: SRA

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

library_source: transcriptomic

data_processing:
Genome build: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Supplementary file format and content: Text file with raw gene and cpm counts, and rpkm values

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L345 DRG sample D

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9Âµl) was reverse transcribed and amplified using the SMARTerÂ® Ultraâ„¢ Low Input RNA for IlluminaÂ® Sequencing - HV (Clontech, cat# 634828) according to the manufacturerâ€™s instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeqâ„¢ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98Â°C for 30s; 12 cycles of 98Â°C for 10s, 64Â°C for 30s, 72Â°C for 30s; 72Â°C for 5 minutes and then hold at 4Â°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 18 pooled DRGs dissected from 3 RetFloxedEGFP:NaV1.8Cre mice at spinal segment  levels L3, L4 & L5. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

tag: genotype

value: RetFloxedEGFP/

tag: component sampled

value: peripheral nervous system,dorsal root ganglion

tag: age

value: (P90) Adult

value: female

tag: pooled sample

value: yes

tag: pool size

value: Pooled sample of 18 DRGs from 3 mice


title: 3mo_9CGNAV_F_L6S1_C

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_C

treatment_protocol: Total RNA was extracted from 12 pooled DRGs dissected from 3 RetFloxedEGFP:NaV1.8Cre mice at spinal segment  levels L6 and S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: dorsal root ganglion,peripheral nervous system

tag: Sex

value: Pooled sample of 12 DRGs from 3 mice


title: E12.5_RET-EGFP_FACS-DRG_C

source_name: E12.5 Ret-EGFP mouse FACSd T11-S1 DRG sample C

treatment_protocol: Total RNA was pooled from 300 DRGs dissected from 15 Ret-EGFP embryos  from different mothers at spinal segment  levels T11-S1. Following DRG dissection, cells were FACS sorted (E12.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ/

value: male and female

value: Pooled sample of 300 FACSd DRGs from  15 embryos


title: E18.5_RetFloxedEGFP-NAV1.8Cre_M_DRG_C

source_name: E18.5 Ret-FloxedEGFP:NaV1.8Cre FACSd male mouse DRG sample_C

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from 1 RetFloxedEGFP:NaV1.8Cre embryo at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: male

value: Pooled sample of 20 DRGs from 1 mouse


title: 3mo_9cGNAV_M_L6S1_C

source_name: 3 month male Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_C


title: E12.5_RET-EGFP_FACS-DRG_B

source_name: E12.5 Ret-EGFP mouse FACSd T11-S1 DRG sample B

treatment_protocol: Total RNA was pooled from 340 DRGs dissected from 17 Ret-EGFP embryos (10M, 7F) from different mothers at spinal segment  levels T11-S1. Following DRG dissection, cells were FACS sorted (E12.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 340 FACSd DRGs from  17 embryos


title: E12.5_RET-EGFP_FACS-DRG_D

source_name: E12.5 Ret-EGFP mouse FACSd T11-S1 DRG sample D

treatment_protocol: Total RNA was pooled from 60 DRGs dissected from 3 Ret-EGFP embryos  from different mothers at spinal segment  levels T11-S1. Following DRG dissection, cells were FACS sorted (E12.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 60 FACSd DRGs from  3 embryos


title: 3mo_9CGNAV_F_L6S1_B

source_name: 3 month female Ret-FloxedEGFP:NaV1.8Cre FACSd mouse L6S1 DRG sample_B

treatment_protocol: Total RNA was extracted from 16 pooled DRGs dissected from 4 RetFloxedEGFP:NaV1.8Cre mice at spinal segment  levels L6 and S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 16 DRGs from 4 mice


title: E18.5_RET-EGFP_F_FACS-DRG_C

source_name: E18.5 female Ret-EGFP mouse FACSd T11-S1 DRG sample C

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from 1 Ret-EGFP embryo at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Pooled sample of 20 FACSd DRGs from 1 female embryo


title: HEK-N4_WT_rep3

description: N4 3

source_name: HEK cell line, CRISPR control, isogenic

value: HEK

value: embryonic kidney

tag: genotype/variation

value: CRISPR control


title: 3mo_Ret-EGFP_M_L6S1_E

data_processing:
Genome build: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. see website jainlab protocol
Supplementary file format and content: Text file with summary gene counts
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Supplementary file format and content: Text file with raw gene counts

source_name: 3 month male Ret-EGFP mouse L6S1 DRG sample E

treatment_protocol: Total RNA was extracted from 12 pooled DRGs dissected from 3 Ret-EGFP mice at spinal segment levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: (P90) Adult


title: HEK-N8_WT_rep2

description: N8 2


title: HEK-N8_WT_rep1

description: N8 1


title: HEK-N4_WT_rep2

description: N4 2


title: HEK-parental_WT_rep1

description: 293 1

source_name: HEK cell line, parental

value: parental


title: E18.5_RET-EGFP_F_FACS-DRG_B

source_name: E18.5 female Ret-EGFP mouse FACSd T11-S1 DRG sample B

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from 1 Ret-EGFP embryo at spinal segment  levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: female

value: yes


title: HEK-N4_WT_rep1

description: N4 1


title: HEK-parental_WT_rep3

description: 293 3


title: HEK-parental_WT_rep2

description: 293 2


title: PLC PLKO.1 siCTCF

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

description: Gene expression after transduction of lentivirues experssing shRNA against CTCF

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 014850_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PLC5 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Agilent One-Color Quick Amp labeling kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA extraction was performed using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and the extraction was done according to the manufacturer’s instructions. The quantity and quality of each RNA sample was determined using NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) RNA Pico Kit.

treatment_protocol: PLC5 cells were grow in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.   Cells were transduced with lentiviuses expressing non-targeting or shRNA against CTCF. After 24 hours, cells were cultered in puromycin containing medium (5 ug) for another 24 hours. Cells were returned to normal medium for another 48 hours before total mRNAs were corrected for whole genome gene expression array analysis.


title: mC36-F_aGBM_Imatinib

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

country: Switzerland

institute: Hoffmann La Roche LTD

description:
mc36
Gene expression data from kidney exposed to F_aGBM_Imatinib

hyb_protocol: Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400

scan_protocol: Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using Bioconductor Affy Package

label_protocol: Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)

tag: strain background

value: 3-6 month

tag: tissue

value: kidney

tag: treatment


title: mC38-F_aGBM_Imatinib

description:
mc38
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mC34-F_aGBM_Imatinib

description:
mc34
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mC35-F_aGBM_Imatinib

description:
mc35
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mB32-E_aGBM_DDRi-HD

description:
mb32
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mB3-E_aGBM_DDRi-HD

description:
mb3
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mB26-E_aGBM_DDRi-HD

description:
mb26
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mB31-E_aGBM_DDRi-HD

description:
mb31
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mC40-F_aGBM_Imatinib

description:
mc40
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mC39-F_aGBM_Imatinib

description:
mc39
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: PLC PLKO.1 shCont

description: Gene expression after transduction of lentivirues experssing non-targeting shRNA


title: mA7-D_aGBM_DDRi-LD

description:
ma7
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mA22-D_aGBM_DDRi-LD

description:
ma22
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mouse_WT_LN2

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref-8 v2.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA)

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array probes transformed by logarithm and normalized by quantile method

source_name: Wild_mouse_lymph node

label_protocol: Total RNA was amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (EPICENTRE, Madison, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted and purified from the spleen of WT and RAG2 KO pigs using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s  protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA).

value: wild type

value: lymph node


title: mouse_Rag2_KO_LN3

source_name: RAG2 KO_mouse_lymph node

value: RAG2 KO


title: mB27-E_aGBM_DDRi-HD

description:
mb27
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mA23-D_aGBM_DDRi-LD

description:
ma23
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mB30-E_aGBM_DDRi-HD

description:
mb30
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mouse_Rag2_KO_LN1


title: mouse_WT_LN3


title: mA24-D_aGBM_DDRi-LD

description:
ma24
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mouse_Rag2_KO_TH3

value: thymus


title: mC37-F_aGBM_Imatinib

description:
mc37
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mouse_Rag2_KO_LN2


title: mA21-D_aGBM_DDRi-LD

description:
ma21
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mouse_Rag2_KO_TH2


title: mB5-E_aGBM_DDRi-HD

description:
mb5
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mouse_WT_LN1


title: HEK-N8_WT_rep3

description: N8 3

tag: cell type


title: mouse_WT_TH


title: mA18-D_aGBM_DDRi-LD

description:
ma18
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mouse_Rag2_KO_TH1


title: mA20-D_aGBM_DDRi-LD

description:
ma20
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mV13-C_aGBM_Vehicle

description:
mv13
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mouse_WT_TH5


title: mouse_Rag2_KO_SP1

source_name: RAG2 KO_mouse_spleen

value: spleen


title: mV9-C_aGBM_Vehicle

description:
mv9
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mV15-C_aGBM_Vehicle

description:
mv15
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mA19-D_aGBM_DDRi-LD

description:
ma19
Gene expression data from kidney exposed to D_aGBM_DDRi-LD


title: mouse_WT_SP2


title: mouse_WT_SP4


title: mA25-A_PBS

description:
ma25
Gene expression data from kidney exposed to A_PBS


title: mA28-A_PBS

description:
ma28
Gene expression data from kidney exposed to A_PBS


title: mA2-A_PBS

description:
ma2
Gene expression data from kidney exposed to A_PBS


title: mV16-C_aGBM_Vehicle

description:
mv16
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mV8-C_aGBM_Vehicle

description:
mv8
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mA4-A_PBS

description:
ma4
Gene expression data from kidney exposed to A_PBS


title: mouse_WT_SP3


title: mouse_Rag2_KO_SP2


title: mouse_WT_TH4


title: mV11-C_aGBM_Vehicle

description:
mv11
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mV14-C_aGBM_Vehicle

description:
mv14
Gene expression data from kidney exposed to C_aGBM_Vehicle


title: mouse_Rag2_KO_SP3


title: mA17-A_PBS

description:
ma17
Gene expression data from kidney exposed to A_PBS


title: mA1-A_PBS

description:
ma1
Gene expression data from kidney exposed to A_PBS


title: mB29-E_aGBM_DDRi-HD

description:
mb29
Gene expression data from kidney exposed to E_aGBM_DDRi-HD


title: mC33-F_aGBM_Imatinib

description:
mc33
Gene expression data from kidney exposed to F_aGBM_Imatinib


title: mA6-A_PBS

description:
ma6
Gene expression data from kidney exposed to A_PBS


title: mA12-A_PBS

description:
ma12
Gene expression data from kidney exposed to A_PBS


title: Cordblood_lowpregnancyanxiety_PELS_36

status: Public on Sep 29 2017

city: Leuven

first: Stephan

last: Claes

address: Herestraat 49

department: Department of Neurosciences

country: Belgium

institute: KU Leuven

hyb_protocol: Standard HM450 BeadChip protocol on bisulfite treated DNA

data_processing:
Raw data quality control and normalization were implemented using the wateRmelon package in R (Bioconductor). Probes with a detection p-value of more than 0.01 or a bead count of less than 3 in more than 5% of samples were removed. Additionally, cross-hybridizing probes, SNP probes and probes on the X or Y chromosomes were removed.
The singal_intensities.txt contains unmethylated and methylated signal intensities.

source_name: Cordblood_low pregnancy anxiety

extract_protocol: Cord blood DNA isolation

tag: gender

value: Male

tag: pregnancy anxiety

value: low pregnancy anxiety

value: cord blood


title: Cordblood_lowpregnancyanxiety_PELS_29

scan_protocol: Standard HM450 BeadChip protocol on bisulfite treated DNA


title: Cordblood_lowpregnancyanxiety_PELS_27

label_protocol: Standard HM450 BeadChip protocol on bisulfite treated DNA

value: Female


title: Cordblood_lowpregnancyanxiety_PELS_35


title: Cordblood_lowpregnancyanxiety_PELS_44


title: Cordblood_highpregnancyanxiety_PELS_32

source_name: Cordblood_high pregnancy anxiety

value: high pregnancy anxiety


title: Cordblood_highpregnancyanxiety_PELS_40


title: Cordblood_lowpregnancyanxiety_PELS_26


title: Cordblood_highpregnancyanxiety_PELS_37


title: Cordblood_highpregnancyanxiety_PELS_42


title: Cordblood_highpregnancyanxiety_PELS_28


title: Cordblood_lowpregnancyanxiety_PELS_41


title: Cordblood_highpregnancyanxiety_PELS_25


title: Cordblood_highpregnancyanxiety_PELS_34


title: Cordblood_lowpregnancyanxiety_PELS_38


title: Cordblood_lowpregnancyanxiety_PELS_33


title: Cordblood_lowpregnancyanxiety_PELS_30


title: Cordblood_highpregnancyanxiety_PELS_23


title: Cordblood_highpregnancyanxiety_PELS_19


title: Cordblood_lowpregnancyanxiety_PELS_21


title: Cordblood_lowpregnancyanxiety_PELS_17


title: Cordblood_highpregnancyanxiety_PELS_45


title: Cordblood_highpregnancyanxiety_PELS_08rep3

description: Please note that four technical replicates were carried out for  PELS_08 sample and only the 'replicate 3' was included in further analyses.


title: Cordblood_highpregnancyanxiety_PELS_43


title: Cordblood_highpregnancyanxiety_PELS_24


title: Cordblood_highpregnancyanxiety_PELS_31


title: Cordblood_lowpregnancyanxiety_PELS_39


title: Cordblood_highpregnancyanxiety_PELS_22


title: Cordblood_highpregnancyanxiety_PELS_20


title: Cordblood_highpregnancyanxiety_PELS_16


title: Cordblood_lowpregnancyanxiety_PELS_18


title: Cordblood_lowpregnancyanxiety_PELS_14


title: A3-3, case15

city: Hangzhou

first: Xinyuan

last: Hao

state: Zhejiang

address: No.9 Meiling South Road, Xihu District

country: China

institute: TRICAAS

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Camellia sinensis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The 8-year-old potted tea cultivar “Longjing 43” was used as the plant material, and regular pest management and fertilization were applied.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: The treatment was divided into the following four stages: pretreatment stage (control), which included one week of suitable growth conditions simulating the outside conditions to which the plants were exposed prior to moving; gradual cooling stage (CA), which included five weeks of CA simulating the conditions that occur during the fall; resuming stage under warmth (de-cold acclimation), which included one week of de-cold acclimation simulating the conditions that usually appear during the early spring and even occasionally the winter; and freezing stage (cold stress), which included one day of frost simulating the conditions that often occur during late spring during tea plant sprouting.

value: mature leaf

tag: developmental stage

value: fully unfolded new leaves

tag: cultivar

value: Longjing 43

value: cold acclimation and rapid cold stress


title: Cordblood_highpregnancyanxiety_PELS_13


title: C2-3, case18


title: A1-2, case12


title: W1-1, control6

value: control


title: A2-3, case14


title: W1-3, control5


title: C2-2, case17


title: C1-1, case8


title: C1-2, case9


title: A4-2, case16


title: A4-1, case6


title: W1-2, control4


title: C1-3, case10


title: A4-3, case7


title: A1-3, case13


title: Cordblood_lowpregnancyanxiety_PELS_05


title: C2-1, case11


title: A3-1, case4


title: N1-1, control1


title: Cordblood_highpregnancyanxiety_PELS_06


title: Cordblood_lowpregnancyanxiety_PELS_15


title: A3-2, case5


title: Cordblood_lowpregnancyanxiety_PELS_04


title: A2-2, case3


title: A1-1, case1


title: Cordblood_highpregnancyanxiety_PELS_03


title: N1-3, control3


title: N1-2, control2


title: Cordblood_highpregnancyanxiety_PELS_09


title: 6_Human LAM_shGFP_rapamycin [gene expression]

status: Public on Sep 28 2017

city: New York

first: John

last: Blenis

state: NY

address: 413 East 69th Street

department: Meyer Cancer Center and Department of Pharmacology

institute: Weill Cornell Medicine

description:
6_1998L
Gene expression analysis; RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 5.5 μg of cDNA were hybridized for 16 hr at 45 celsius on Human Transcriptome 2.0 Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2 at the Partners Healthcare Microarray Core Facility, Harvard Medical School.

data_processing:
Raw data were processed by Affymetrix Expression Console Software 1.4.1. using Analysis algorithm RMA to generate CHP files for gene expression and splice isoform analyses.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: human LAM_shGFP_rapamycin

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit GeneChip WT Plus, Lot # 4215353, followed by labeling 5.5 μg cDNA using Affymetrix GeneChip WT Terminal Labeling (part of WT Plus kit).

growth_protocol: Lymphangioleiomyomatosis (LAM 621-101) cells were cultured on petri-dish.

extract_protocol: Total RNA was isolated from cells cultured on 60 mm petri-dish using RNeasy Mini Kit (Qiagen) and treated with DNase I (Qiagen) according to the manufacturer’s instructions. All samples passed RIN scores and 260/280 ratios from QC.

treatment_protocol: Cells stably expressing shRNA targeting GFP (pLKO-puro-shGFP) or SRPK2 (pLKO-puro-shSRPK2) were treated with DMSO (vehicle control) or 100 nM rapamycin (dissolved in DMSO, Sigma) for 24 hr.

value: female

tag: cell line

value: Lymphangioleiomyomatosis cell line

tag: treated with

value: 100 nM rapamycin for 24 hr


title: Cordblood_highpregnancyanxiety_PELS_02


title: WT.4

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: The raw data were normalized using 6 housekeeping genes (Actb, Gapdh, Hprt, Ldha, Ms4a1 and Tbp).  nSolver Analysis Software was used for normalization and we followed their internal protocol with geometric mean as normalization factor.

source_name: Spleen

extract_protocol: Buffer RLT

value: 6 Weeks Old

tag: strain

tag: genotype

value: WT

value: CD4+ T cells


title: 2_Human LAM_shGFP_DMSO [gene expression]

description:
2_1998H
Gene expression analysis; RMA expression value derived from Expression Console software

source_name: human LAM_shGFP_DMSO

value: stably expressing shRNA targeting GFP (pLKO-puro-shGFP)

value: DMSO (vehicle control) for 24hrs


title: 4_Human LAM_shGFP_rapamycin [gene expression]

description:
4_1998J
Gene expression analysis; RMA expression value derived from Expression Console software


title: WT.2

scan_protocol: Refer to the NanoString nCounter Assay System Manual.

tag: age

value: spleen


title: 5_Human LAM_shGFP_rapamycin [gene expression]

description:
5_1998K
Gene expression analysis; RMA expression value derived from Expression Console software


title: Cordblood_lowpregnancyanxiety_PELS_07

value: low pregnancy anxiety

value: cord blood


title: EV.2

label_protocol: Refer to the NanoString nCounter Assay System Manual.

value: Female


title: EV.4

description: Refer to the NanoString nCounter Assay System Manual


title: EV.3

label: Refer to the NanoString nCounter Assay System Manual


title: 9_Human LAM_shSRPK2_DMSO [gene expression]

description:
9_1998O
Gene expression analysis; RMA expression value derived from Expression Console software

source_name: human LAM_shSRPK2_DMSO

value: stably expressing shRNA targeting SRPK2 (pLKO-puro-shSRPK2)


title: WT.1


title: 1_Human LAM_shGFP_DMSO [gene expression]

description:
1_1998A
Gene expression analysis; RMA expression value derived from Expression Console software


title: 7_Human LAM_shSRPK2_DMSO [gene expression]

description:
7_1998M
Gene expression analysis; RMA expression value derived from Expression Console software


title: M426.2


title: Cordblood_lowpregnancyanxiety_PELS_01


title: Cordblood_highpregnancyanxiety_PELS_11

value: high pregnancy anxiety


title: Cordblood_lowpregnancyanxiety_PELS_12

value: Male


title: EV.1


title: M425.2


title: M425.1


title: M424.2


title: M424.1


title: M426.1


title: M418.1


title: WT.3


title: Cordblood_lowpregnancyanxiety_PELS_10


title: M418.2


title: A2-1, case2

value: mature leaf

value: fully unfolded new leaves

value: Longjing 43

value: cold acclimation and rapid cold stress


title: M421.2


title: M415.2


title: M415.1


title: M410.1


title: M412.2


title: M412.1


title: 8_Human LAM_shSRPK2_DMSO [gene expression]

description:
8_1998N
Gene expression analysis; RMA expression value derived from Expression Console software

value: female

value: Lymphangioleiomyomatosis cell line


title: M421.1

value: 6 Weeks Old

value: WT


title: M410.2

value: CD4+ T cells


title: M409.2


title: M402.2


title: M406.1


title: M406.2


title: M409.1


title: M402.1


title: M400.2


title: M397.2


title: M396.2


title: M400.1


title: M396.1


title: M394.1


title: M397.1


title: M393.2


title: M388.2


title: M392.1


title: M393.1


title: M392.2


title: M388.1


title: M390.1


title: 3_Human LAM_shGFP_DMSO [gene expression]

description:
3_1998I
Gene expression analysis; RMA expression value derived from Expression Console software

value: stably expressing shRNA targeting GFP (pLKO-puro-shGFP)

value: DMSO (vehicle control) for 24hrs


title: M390.2

value: spleen


title: M386.2


title: M394.2


title: M378.2


title: M374.1


title: M378.1


title: M371.1


title: M373.1


title: M373.2


title: M377.1


title: M377.2


title: M374.2


title: M369.2


title: M369.1


title: M366.1


title: M367.1


title: M366.2


title: M364.2


title: M365.2


title: M365.1


title: M386.1


title: M371.2


title: M367.2


title: M359.1


title: M360.2


title: M360.1


title: M354.1


title: M354.2


title: M356.2


title: M364.1


title: M352.1


title: M352.2


title: M356.1


title: M351.1


title: M351.2


title: M350.2


title: M347.1


title: M339.2


title: M347.2


title: M350.1


title: M342.2


title: M341.2


title: M359.2


title: M342.1


title: M344.1


title: M344.2


title: M338.1


title: M338.2


title: M339.1


title: M331.2


title: M331.1


title: M325.2


title: M341.1


title: M319.1


title: M325.1


title: M306.1


title: M278.2


title: M306.2


title: M247.1


title: M271.2


title: M247.2


title: M271.1


title: M241.2


title: M241.1


title: M235.1


title: M215.1


title: M235.2


title: M215.2


title: M222.2


title: M319.2


title: M176.2


title: M203.1


title: M176.1


title: M203.2


title: M151.2


title: M131.1


title: M131.2


title: M278.1


title: M111.2


title: M151.1


title: M111.1


title: M222.1


title: Td.WT_1

description: WT Tcons retrovirally transduced with WT

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: Spleen

tag: phenotype markers

tag: amplification technique

value: Ambion WT Expression Kit

tag: separation method

value: Dissection / Trimming


title: M95.2

tag: Sex

value: Female


title: M71.2


title: M95.1


title: Td.M176_1

description: WT Tcons retrovirally transduced with M176 mutant

value: Male


title: M71.1


title: Td.WT_2


title: Td.M354_2

description: WT Tcons retrovirally transduced with M354 mutant


title: Td.M176_2


title: Td.M354_1


title: Tr.WT_2

description: Foxp3(WT/WT) Tregs


title: M59.2


title: M46.2


title: M59.1


title: Tr.M354_1

description: Foxp3(M354/M354) Tregs


title: Tr.M354_2

description: Foxp3(M354/M354) Tregs


title: M34.1


title: Tr.M176_1

description: Foxp3(M176/M176) Tregs


title: Tr.WT_1

description: Foxp3(WT/WT) Tregs


title: M34.2


title: M46.1


title: M21.1


title: G8-R39

city: Toledo

first: Gerardo

last: Avila Martín

address: Finca La Peraleda s/n

department: Research Unit

country: Spain

institute: National Paraplejic Hospital

description: Moderate contusion + water 1 days

hyb_protocol: Standard affymetrix hybridization protocol for FS450

scan_protocol: Standard affymetrix scan protocol for GS 3000

data_processing: Affymetrix Expression Console used to calculate RMA.

organism: Rattus norvegicus

source_name: Moderate contusion + water 1 days

label_protocol: Standard affymetrix protrocol to apmplify and generate biotinilated complementary RNA

extract_protocol: Trizol

treatment_protocol: injection of HOA associated with albumine (commercial name 'minerval').

value: spinal cord

value: Wistar

tag: group

value: Moderate contusion + water 1 days


title: G8-R38

description: Moderate contusion + water 1 days

tag: tissue


title: Tr.M176_2

description: Foxp3(M176/M176) Tregs


title: G8-R37

description: Moderate contusion + water 1 days


title: G9-R41

description: Moderate contusion + A-HOA 1 days

source_name: Moderate contusion + A-HOA 1 days

value: Moderate contusion + A-HOA 1 days


title: G9-R44

description: Moderate contusion + A-HOA 1 days


title: G9-R3

description: Moderate contusion + A-HOA 1 days


title: G9-R45

description: Moderate contusion + A-HOA 1 days


title: M21.2


title: G8-R6

description: Moderate contusion + water 1 days


title: M7.1


title: G5-R23

description: Moderate contusion + A-HOA 7 days

source_name: Moderate contusion + A-HOA 7 days

value: Moderate contusion + A-HOA 7 days


title: G4-R20

description: Moderate contusion

source_name: Moderate contusion

value: Moderate contusion


title: M7.2

value: 6 Weeks Old


title: M14.1

value: WT


title: M14.2

value: CD4+ T cells