title: Non-small cell lung cancer patient [21272T]

status: Public on Aug 04 2017

city: Rockville

first: Khadijah

middle: A

last: Mitchell

address: 37 Convent Drive, Building 37, Room 3060

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description:
21272T
MicroRNA expression data from fresh frozen lung tissues.

hyb_protocol: One hundred ng of total RNA was used for hybridization to each chip and incubated for 12 hours. Hybridization assays were left at 65°C until ready for processing and did not exceed 30 hours (nCounter miRNA Expression Assay User Manual).

scan_protocol: After sample processing and hybridization were completed, samples were inserted into the Prep Station for purification and immobilization onto the internal surface of each sample cartridge (~2-3 hours). The Digital Analyzer, a multi-channel epifluorescence scanner configured specifically for use with NanoString’s sample cartridges, was used for all scanning (~4.5 hours) (nCounter Dx Analysis System User Manual).

data_processing: The Digital Analyzer for data imaging and processing (nCounter Dx Analysis System User Manual) and nSolver2 for data analysis (nCounter Expression Data Analysis Guide).

label: Fluorescent dye

source_name: Fresh frozen lung tissue from non-small cell lung cancer patient

label_protocol: One hundred ng of each total RNA sample was labeled with a Reporter CodeSet (nucleic acids with fluorescently labeled tags) according to NanoString protocols (nCounter miRNA Expression Assay User Manual).

extract_protocol: One microgram of total RNA was extracted for each sample using TRIzol following the manufacturer’s protocol (Thermo Fisher Scientific, Waltham, MA). Isolated total RNA was quantified using a NanoDrop 1000 (NanoDrop Products, Wilmington, DE). RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: patient

value: Non-small cell lung cancer

value: I

value: Lung tumor tissue

tag: race

value: AA

value: Male

tag: smoking pack year

tag: survival (months)

value: Unknown


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D15.2]

status: Public on Aug 29 2017

type: RNA

city: Barcelona

first: Montse

last: BARRAGAN

state: Select One

address: Baldiri Reixac, 15

country: Spain

institute: Clinica EUGIN

description: CELs transformed using GCCN-SST with gain_lock=0.75, then processed using RMA-Sketch. These analysis capabilities are available in Affymetrix Power Tools 1.18.0

hyb_protocol: Affymetrix's standard protocol

scan_protocol: AGCC Standard Protocol / GCS 3000

data_processing: Samples were processed using Affymetrix Power Tools (APT) utilizing GCCN-SST RMA with gain lock percent set to 0.75

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Mature MII oocytes

label_protocol: 8 µg cDNA (3.2 µg from the first round and 4.8 µg from the second) were subsequently fragmented by DNAseI and biotinylated by terminal transferase (GeneChip Mapping 250K Nsp assy kit; Affymetrix, CA, USA).

extract_protocol: The zona pellucida was removed by Pronase (Roche Diagnostics, Spain) and oocytes were immediately and individually placed in 45 µl of a Proteinase K-based lysis buffer (20 mM DTT, 0.5% SDS, 1 μg/μl proteinase K, 10 mM Tris.HCl, pH 7.4), incubated at 65ºC for 15 minutes, and stored at -80ºC until use (González-Roca, 2010).   Total RNA extraction and amplification were based on the Pico-Profiling protocol and successive improvements for single oocyte use (Gonzalez-Roca et al, 2010; Vassena et al, 2011). Pico-profiling faithfully amplifies the total RNA from as little as 10 somatic cells, or 1 MII oocyte, with a level of false positive signal in downstream analysis that is equivalent to that obtained without an amplification step. Briefly, RNA was purified individual oocytes using RNA Clean XP bead suspension (Agencourt Bioscience, La Jolla, CA, USA) and eluted in 20 µl water. The RNA preparation was used for library preparation and amplification by Whole Transcriptome Amplification (WTA2, Sigma-Aldrich, Spain). SYBRGreen (Sigma-Aldrich, Spain) was added to the amplification reaction, which was performed in a CFX Real-time instrument (Bio-Rad, CA, USA) to monitor amplification yield. The first amplification reaction was stopped when the SYBRGreen signal reached a plateau, and cDNA was purified and quantified on a Nanodrop ND-1000 spectrophotometer (Thermo-Fischer, MA, USA). A second round of amplification was performed from 10 ng of cDNA.

treatment_protocol: Mature MII oocytes were vitrified on the day of retrieval using an open method and were warmed for the study according to standard procedure (Cryotop®, Kitazato®, BioPharma Co., Ltd; Japan) in five randomized groups, on different days during a period of 14 days, to minimize bias due to the handling process. After warming, oocytes were left for 2 hours at 37ºC and 6% CO2, to allow for reassembly of the metaphase plate (Bromfield et al, 2009).

tag: age

value: Age 20-22 at donation

tag: ovarian reserve

value: low ovarian reserve


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D17.1]

value: high ovarian reserve


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D16.1]


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D15.1]


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D14.1]


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D30.2]

value: Age 33-35 at donation


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D28.1]


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D11.1]


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D20.1]


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D26.1]


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D14.2]


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D21.1]


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D22.1]


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D13.1]


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D9.1]


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D3.1]


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D4.1]


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D23.1]


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D18.1]


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D7.1]


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D8.1]


title: Non-small cell lung cancer patient [21272N]

state: MD

country: USA

description:
21272N
MicroRNA expression data from fresh frozen lung tissues.

tag: disease status

tag: Stage

tag: tissue

value: Normal lung tissue

tag: gender


title: Non-small cell lung cancer patient [20603N]

description:
20603N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20504T]

description:
20504T
MicroRNA expression data from fresh frozen lung tissues.

value: III

value: Female


title: Non-small cell lung cancer patient [19931N]

description:
19931N
MicroRNA expression data from fresh frozen lung tissues.


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D2.1]


title: Non-small cell lung cancer patient [20504N]

description:
20504N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20413T]

description:
20413T
MicroRNA expression data from fresh frozen lung tissues.


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D5.1]


title: Non-small cell lung cancer patient [18544T]

description:
18544T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20336N]

description:
20336N
MicroRNA expression data from fresh frozen lung tissues.

value: EA


title: Non-small cell lung cancer patient [20063N]

description:
20063N
MicroRNA expression data from fresh frozen lung tissues.

value: Not determined

value: Yes


title: Non-small cell lung cancer patient [19931T]

description:
19931T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20336T]

description:
20336T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18082N]

description:
18082N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [19309N]

description:
19309N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [19309T]

description:
19309T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18023N]

description:
18023N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18408T]

description:
18408T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18023T]

description:
18023T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20413N]

description:
20413N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18408N]

description:
18408N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [18544N]

description:
18544N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [17763T]

description:
17763T
MicroRNA expression data from fresh frozen lung tissues.

value: II


title: Non-small cell lung cancer patient [18082T]

description:
18082T
MicroRNA expression data from fresh frozen lung tissues.

value: Non-small cell lung cancer


title: mRNA_OvarianCancer_rep21

status: Public on Aug 31 2017

type: SRA

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

library_source: transcriptomic

data_processing:
Fastq files were generated by CASAVA-1.8.2 from Illumina Hiseq output.
Fastq files were mapped to hg19 reference genome by bowtie2 to generate bam files.
Expression level is quantified by RSEM-1.3.0.
Genome_build: hg19
Supplementary_files_format_and_content: Rsem.genes.results file has columns named TPM and FPKM. Each columns represent Transcripts Per Million mapped reads and Fragments Per Kilobase of transcript and Million mapped reads for each gene.

molecule: polyA RNA

source_name: mRNA from fresh frozen ovarian cancer

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
cDNA library was prepared with Ilumina TruSeq Stranded mRNA Library Preparation Kit

value: primary tumor from ovarian cancer patient

value: female


title: Non-small cell lung cancer patient [17763N]

description:
17763N
MicroRNA expression data from fresh frozen lung tissues.

value: AA


title: Non-small cell lung cancer patient [20063T]

description:
20063T
MicroRNA expression data from fresh frozen lung tissues.

value: I

value: Lung tumor tissue


title: mRNA_OvarianCancer_rep13


title: Non-small cell lung cancer patient [17238T]

description:
17238T
MicroRNA expression data from fresh frozen lung tissues.

value: Male

value: Unknown


title: Non-small cell lung cancer patient [17225T]

description:
17225T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [17238N]

description:
17238N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16437T]

description:
16437T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16848N]

description:
16848N
MicroRNA expression data from fresh frozen lung tissues.


title: KYSE850_KHSRP_KD_3

status: Public on Feb 22 2018

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Oligo Microarrays (G4851B) 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).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.6 (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: KYSE850 esophageal squamous cell carcinoma, treated with KHSRP siRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: cell type

value: Esophageal squamous cell carcinoma cell line

tag: genotype/variation

value: KHSRP knockdown


title: Non-small cell lung cancer patient [16437N]

description:
16437N
MicroRNA expression data from fresh frozen lung tissues.

value: Normal lung tissue


title: Non-small cell lung cancer patient [17225N]

description:
17225N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16848T]

description:
16848T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16191T]

description:
16191T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16191N]

description:
16191N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16076T]

description:
16076T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16052T]

description:
16052T
MicroRNA expression data from fresh frozen lung tissues.

value: III


title: Non-small cell lung cancer patient [15784T]

description:
15784T
MicroRNA expression data from fresh frozen lung tissues.

value: Female


title: Non-small cell lung cancer patient [16052N]

description:
16052N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [16076N]

description:
16076N
MicroRNA expression data from fresh frozen lung tissues.

value: EA


title: Non-small cell lung cancer patient [15805N]

description:
15805N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [17759N]

description:
17759N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15756T]

description:
15756T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15784N]

description:
15784N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15595T]

description:
15595T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15756N]

description:
15756N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15618T]

description:
15618T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15595N]

description:
15595N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15618N]

description:
15618N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15805T]

description:
15805T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15439T]

description:
15439T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15538T]

description:
15538T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [20603T]

description:
20603T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15275T]

description:
15275T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15275N]

description:
15275N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15226N]

description:
15226N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15112T]

description:
15112T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15222T]

description:
15222T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [17759T]

description:
17759T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14960T]

description:
14960T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15112N]

description:
15112N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14990T]

description:
14990T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15053T]

description:
15053T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14990N]

description:
14990N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14960N]

description:
14960N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14811N]

description:
14811N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14811T]

description:
14811T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15439N]

description:
15439N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14516N]

description:
14516N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14516T]

description:
14516T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14442T]

description:
14442T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15222N]

description:
15222N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15226T]

description:
15226T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14468T]

description:
14468T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [15053N]

description:
15053N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13965T]

description:
13965T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13911T]

description:
13911T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13965N]

description:
13965N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14468N]

description:
14468N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13932T]

description:
13932T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13717T]

description:
13717T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13911N]

description:
13911N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13932N]

description:
13932N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [14442N]

description:
14442N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13581T]

description:
13581T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13581N]

description:
13581N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13539T]

description:
13539T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13717N]

description:
13717N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13539N]

description:
13539N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13372N]

description:
13372N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13371T]

description:
13371T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13320T]

description:
13320T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13490T]

description:
13490T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13372T]

description:
13372T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13063N]

description:
13063N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13063T]

description:
13063T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13320N]

description:
13320N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13371N]

description:
13371N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13061T]

description:
13061T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13046T]

description:
13046T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12899T]

description:
12899T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12927T]

description:
12927T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12927N]

description:
12927N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13046N]

description:
13046N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12913T]

description:
12913T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12913N]

description:
12913N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12860T]

description:
12860T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12881T]

description:
12881T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12822N]

description:
12822N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13490N]

description:
13490N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [13061N]

description:
13061N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12821N]

description:
12821N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12819T]

description:
12819T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12819N]

description:
12819N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12899N]

description:
12899N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12688T]

description:
12688T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12784N]

description:
12784N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12690N]

description:
12690N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12752T]

description:
12752T
MicroRNA expression data from fresh frozen lung tissues.

value: unknown


title: Non-small cell lung cancer patient [12703T]

description:
12703T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12703N]

description:
12703N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12752N]

description:
12752N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12784T]

description:
12784T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12664T]

description:
12664T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12822T]

description:
12822T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12670T]

description:
12670T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12688N]

description:
12688N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12821T]

description:
12821T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12690T]

description:
12690T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12606T]

description:
12606T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12664N]

description:
12664N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12670N]

description:
12670N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12374T]

description:
12374T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12411N]

description:
12411N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12606N]

description:
12606N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12374N]

description:
12374N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12411T]

description:
12411T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12084T]

description:
12084T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12084N]

description:
12084N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12251T]

description:
12251T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11908N]

description:
11908N
MicroRNA expression data from fresh frozen lung tissues.

value: Yes


title: Non-small cell lung cancer patient [11812N]

description:
11812N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11812T]

description:
11812T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11787T]

description:
11787T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11787N]

description:
11787N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11697N]

description:
11697N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11671N]

description:
11671N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [12251N]

description:
12251N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11568N]

description:
11568N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11671T]

description:
11671T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11697T]

description:
11697T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11547N]

description:
11547N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11547T]

description:
11547T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11908T]

description:
11908T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11344N]

description:
11344N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11344T]

description:
11344T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11006T]

description:
11006T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11039T]

description:
11039T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11039N]

description:
11039N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10465N]

description:
10465N
MicroRNA expression data from fresh frozen lung tissues.

value: II


title: Non-small cell lung cancer patient [10465T]

description:
10465T
MicroRNA expression data from fresh frozen lung tissues.

value: Non-small cell lung cancer


title: Non-small cell lung cancer patient [10484N]

description:
10484N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10484T]

description:
10484T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11006N]

description:
11006N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10419N]

description:
10419N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10444N]

description:
10444N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10419T]

description:
10419T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [11568T]

description:
11568T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10379T]

description:
10379T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10379N]

description:
10379N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10444T]

description:
10444T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10146T]

description:
10146T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10174T]

description:
10174T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10174N]

description:
10174N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10097T]

description:
10097T
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10146N]

description:
10146N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10111N]

description:
10111N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10097N]

description:
10097N
MicroRNA expression data from fresh frozen lung tissues.


title: Non-small cell lung cancer patient [10111T]

description:
10111T
MicroRNA expression data from fresh frozen lung tissues.


title: Moto-miN rep2

city: Saint Louis

first: Matthew

middle: James

last: McCoy

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

description:
IL3 B
Gene expression after 35 days of miR-9/9*-124, ISL1, and LHX3 exposure.
Replicate 2

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul). The hybridization solutions were applied to Agilent Human v1 4x44K microarrays (G2519F-014850). Hybridization was carried out at 65C for 20 hours. Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). Quantile normalization and log2 transformation were performed using Partek Genomics Suite.

source_name: 22 yr female fibroblast, Moto-miN day35

label_protocol:
RNA transcripts were first amplified by WTA2 kit (Sigma Aldrich). 30ng of total RNA (14ul) was amplified according to manufacturer's protocol. http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/wta2bul.pdf
cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul). The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes. Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer's protocol. cDNAs were quantitated on a Nanodrop spectrophotometer.

growth_protocol: 22-year-old female adult fibroblasts (GM02171) were obtained from NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research and maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 15% fetal bovine serum (Life Technologies), 0.01% β-mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution, and 1% penicillin/streptomycin solution (all from Invitrogen). Cells were never passaged more than 15 times.

extract_protocol: RNA was prepared using TRIZOL extraction (Thermo Fisher, Waltham, MA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To initiate direct conversion, 1.8x10^6 cells were seeded onto Costar 6 well cell culture vessels (Corning; 300,000 cells/well). The following day, each plate was transduced with the following reprogramming cocktail: 750 uL of concentrated lentivirus containing the reverse tetracycline-controlled transactivator (rtTA; Addgene, 66810) and 500 μL of virus containing pT-BCL-9/9*-124 or pT-BCL-9/9*-124 plus 500 μl of each individual TF driven by the EF1α promoter in the presence of polybrene (8 μg/mL; Sigma-Aldrich) all diluted up to 18 mL (3 mL per well) then spinfected at 37°C for 30 minutes at 1,000xG using a swinging bucket rotor. The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with doxycycline (Dox; Sigma Aldrich, 1 μg/mL). After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (Puromycin, 3 μg/ml; Blasticidin 5 μg/ml; Geneticin, 400 ug/mL; all from Invitrogen). Five days post-transduction cells were replated on to poly-ornithine/laminin/fibronectin (PLF) coated glass coverslips. Before PLF coating, glass coverslips were acid treated according to (Richner et al., 2015). To transfer cells, for each well of a 6 well plate, cells were first washed 2x with 1 mL sterile PBS. Then 320 μL of 0.25% Trypsin (Gibco) was added to each well then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes) 1 ml of MEF media supplemented with 1 μg/mL Dox was added to each well. One by one, each well was gently triturated three times to remove remaining attached cells then transferred to a sterile 1.5 mL Eppendorf tube. Cells were then spun at 200xG for 5 minutes at 37°C. The supernatant was aspirated and cells were gently resuspended in 300 μL MEF media supplemented with Dox. Cells were then drop-plated onto 18 mm (150 μL per/c.s.; placed in 12 well plate)  coverslips. Cells were left to settle for 15 minutes in an incubator then each well was flooded with MEF media supplemented with 1 μg/mL Dox. The following day media was then changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, NT-3, CNTF, GDNF (all 10 ng/ml, Peprotech), and Retinoic Acid (1 uM; Sigma-Aldrich) and antibiotics for each vector. Dox was replenished every two days and half the media was changed every 4 days. Drug selection was halted 14 days into conversion. 35 days post-transduction RNA was isolated using TRIZOL.

value: adult fibroblasts

tag: treatment

tag: timepoint


title: Starting FB rep2

description:
Fibro B
Gene expression in starting fibroblasts before neuronal conversion.
Replicate 2

source_name: 22 yr female fibroblast, day0

value: female

value: No treatment


title: miN rep1

description:
9124 A
Gene expression after 35 days of miR-9/9*-124 exposure.
Replicate 1

source_name: 22 yr female fibroblast, miN day35


title: Moto-miN rep1

description:
IL3 A
Gene expression after 35 days of miR-9/9*-124, ISL1, and LHX3 exposure.
Replicate 1


title: HFF Infected 6 hours, rep 1

status: Public on Jul 05 2017

city: Subiaco

first: Genevieve

last: Syn

state: Western Australia

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description:
HFF I 6h 1
T. gondii-infected HFF cells.

hyb_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node).

data_processing: All data analysis was done in R Version 3.1.3 using R package Lumi to read in raw expression values, perform QC background correction and normalisation of data. Differential expression analysis was carried out using the R package Limma.

label: Biotin

source_name: Human foreskin fibroblast, T. gondii, 6h

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 100U/ml Penicillin/100ug ug/ml Streptomycin (Gibco), 2mM Glutamax supplement (Gibco) and 10% heat-inactivated fetal calf serum.

extract_protocol: Cells were harvested using Tri-reagent (Sigma Aldrich) and total RNA was extracted using Direct-Zol RNA Miniprep kit (Zymo research) following manufacturer's instructions.

treatment_protocol: 1 X 10^6 HFF cells were infected with Toxoplasma gondii RH (Type I) strain at a multiplicity of infection of 10 for 2 hours, 6 hours and 24 hours. 1 X 10^6 mock-infected cells were treated exactly the same as infected cells but with the absence of Toxoplasma.

value: HFF

value: Foreskin fibroblast

value: Infection with Toxoplasma gondii

tag: time of infection

value: 6 hours


title: HFF Infected 24 hours, rep 2

description:
HFF I 24h 2
T. gondii-infected HFF cells.

scan_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node).

source_name: Human foreskin fibroblast, T. gondii, 24h

value: 24 hours


title: Chronic_Dnmt3a cKO CD8 T cells replicate #3

status: Public on Jun 30 2017

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Affymetrix Titan Scanner.

data_processing: Partek Genomics Suite 6.6 by the RMA method.

organism: Mus musculus

source_name: Chronic Dnmt3a cKO CD8 T cells

label_protocol: Affymetrix GeneChip WT Pico protocol.

extract_protocol: Total RNA was extracted from sorted CD8 T cells according to the manufacturer's protocol.

tag: strain/background

value: Dnmt3a cKO

tag: infection

value: Chronic LCMV

tag: time point (post-infection)

value: Day 35

value: Antigen-specific CD8 T cells


title: HFF mock-infected 6 hours, rep 1

description:
HFF m 6h 1
Mock-infected HFF cells.

source_name: Human foreskin fibroblast, mock, 6h

label_protocol: Outsourced to Australian Genome Research Facility (Melbourne Node).

value: Mock-infection


title: HFF Infected 24 hours, rep 1

description:
HFF I 24h 1
T. gondii-infected HFF cells.


title: Starting FB rep1

description:
Fibro A
Gene expression in starting fibroblasts before neuronal conversion.
Replicate 1


title: HFF Infected 2 hours, rep 2

description:
HFF I 2h 2
T. gondii-infected HFF cells.

source_name: Human foreskin fibroblast, T. gondii, 2h

value: 2 hours


title: miN rep2

description:
9124 B
Gene expression after 35 days of miR-9/9*-124 exposure.
Replicate 2


title: HFF mock-infected 2 hours, rep 1

description:
HFF m 2h 1
Mock-infected HFF cells.

source_name: Human foreskin fibroblast, mock, 2h


title: HFF mock-infected 6 hours, rep 2

description:
HFF m 6h 2
Mock-infected HFF cells.


title: HFF mock-infected 24 hours, rep 1

description:
HFF m 24h 1
Mock-infected HFF cells.

source_name: Human foreskin fibroblast, mock, 24h


title: HFF Infected 2 hours, rep 1

description:
HFF I 2h 1
T. gondii-infected HFF cells.


title: HFF mock-infected 2 hours, rep 2

description:
HFF m 2h 2
Mock-infected HFF cells.


title: HFF Infected 6 hours, rep 2

description:
HFF I 6h 2
T. gondii-infected HFF cells.


title: Chronic_Dnmt3a cKO CD8 T cells replicate #1


title: Chronic_Dnmt3a cKO CD8 T cells replicate #2


title: Naïve WT CD8 T cells replicate #1

source_name: Naïve WT CD8 T cells

value: WT

value: Naive CD8 T cells


title: HFF mock-infected 24 hours, rep 2

description:
HFF m 24h 2
Mock-infected HFF cells.


title: Naïve Dnmt3a cKO CD8 T cells replicate #2

source_name: Naïve Dnmt3a cKO CD8 T cells


title: Chronic_WT CD8 T cells replicate #1

source_name: Chronic WT CD8 T cells


title: Chronic_WT CD8 T cells replicate #3


title: Chronic_WT CD8 T cells replicate #2


title: Naïve WT CD8 T cells replicate #2


title: Naïve Dnmt3a cKO CD8 T cells replicate #1


title: bladder_cancer_turbt_sample_299

status: Public on May 25 2017

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

description:
GNDX.NAC299
bca_subtype=bladder cancer subtype

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor).

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications.

growth_protocol: Not Applicable.

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded tumor blocks by 1mm punch under RNase-free conditions. Total RNA was extracted and purified using RNeasy FFPE kit (Qiagen, Valencia, CA).

treatment_protocol: Not Applicable.

tag: disease state

value: muscle-invasive bladder cancer (MIBC)

value: pre-NAC

value: transurethral resection of bladder tumor (TURBT)

tag: cstage

tag: cnode

value: Infiltrated Luminal


title: bladder_cancer_turbt_sample_298

description:
GNDX.NAC298
bca_subtype=bladder cancer subtype

tag: age


title: bladder_cancer_turbt_sample_303

description:
GNDX.NAC303
bca_subtype=bladder cancer subtype

value: Luminal


title: bladder_cancer_turbt_sample_301

description:
GNDX.NAC301
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_305

description:
GNDX.NAC305
bca_subtype=bladder cancer subtype

value: Basal


title: bladder_cancer_turbt_sample_304

description:
GNDX.NAC304
bca_subtype=bladder cancer subtype

value: Claudin Low


title: bladder_cancer_turbt_sample_297

description:
GNDX.NAC297
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_295

description:
GNDX.NAC295
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_296

description:
GNDX.NAC296
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_302

description:
GNDX.NAC302
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_294

description:
GNDX.NAC294
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_287

description:
GNDX.NAC287
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_286

description:
GNDX.NAC286
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_293

description:
GNDX.NAC293
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_290

description:
GNDX.NAC290
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_292

description:
GNDX.NAC292
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_291

description:
GNDX.NAC291
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_279

description:
GNDX.NAC279
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_284

description:
GNDX.NAC284
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_282

description:
GNDX.NAC282
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_277

description:
GNDX.NAC277
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_285

description:
GNDX.NAC285
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_271

description:
GNDX.NAC271
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_274

description:
GNDX.NAC274
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_275

description:
GNDX.NAC275
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_280

description:
GNDX.NAC280
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_278

description:
GNDX.NAC278
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_266

description:
GNDX.NAC266
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_288

description:
GNDX.NAC288
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_263

description:
GNDX.NAC263
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_289

description:
GNDX.NAC289
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_281

description:
GNDX.NAC281
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_276

description:
GNDX.NAC276
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_270

description:
GNDX.NAC270
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_283

description:
GNDX.NAC283
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_260

description:
GNDX.NAC260
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_273

description:
GNDX.NAC273
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_269

description:
GNDX.NAC269
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_262

description:
GNDX.NAC262
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_265

description:
GNDX.NAC265
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_257

description:
GNDX.NAC257
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_267

description:
GNDX.NAC267
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_261

description:
GNDX.NAC261
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_272

description:
GNDX.NAC272
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_268

description:
GNDX.NAC268
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_258

description:
GNDX.NAC258
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_259

description:
GNDX.NAC259
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_247

description:
GNDX.NAC247
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_242

description:
GNDX.NAC242
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_252

description:
GNDX.NAC252
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_240

description:
GNDX.NAC240
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_264

description:
GNDX.NAC264
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_256

description:
GNDX.NAC256
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_241

description:
GNDX.NAC241
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_251

description:
GNDX.NAC251
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_243

description:
GNDX.NAC243
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_245

description:
GNDX.NAC245
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_253

description:
GNDX.NAC253
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_249

description:
GNDX.NAC249
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_255

description:
GNDX.NAC255
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_250

description:
GNDX.NAC250
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_246

description:
GNDX.NAC246
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_248

description:
GNDX.NAC248
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_254

description:
GNDX.NAC254
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_244

description:
GNDX.NAC244
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_230

description:
GNDX.NAC230
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_226

description:
GNDX.NAC226
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_300

description:
GNDX.NAC300
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_238

description:
GNDX.NAC238
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_235

description:
GNDX.NAC235
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_239

description:
GNDX.NAC239
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_237

description:
GNDX.NAC237
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_234

description:
GNDX.NAC234
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_229

description:
GNDX.NAC229
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_232

description:
GNDX.NAC232
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_236

description:
GNDX.NAC236
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_233

description:
GNDX.NAC233
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_220

description:
GNDX.NAC220
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_228

description:
GNDX.NAC228
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_219

description:
GNDX.NAC219
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_223

description:
GNDX.NAC223
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_224

description:
GNDX.NAC224
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_225

description:
GNDX.NAC225
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_222

description:
GNDX.NAC222
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_217

description:
GNDX.NAC217
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_221

description:
GNDX.NAC221
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_231

description:
GNDX.NAC231
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_215

description:
GNDX.NAC215
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_211

description:
GNDX.NAC211
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_216

description:
GNDX.NAC216
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_214

description:
GNDX.NAC214
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_212

description:
GNDX.NAC212
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_203

description:
GNDX.NAC203
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_209

description:
GNDX.NAC209
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_204

description:
GNDX.NAC204
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_207

description:
GNDX.NAC207
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_206

description:
GNDX.NAC206
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_201

description:
GNDX.NAC201
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_213

description:
GNDX.NAC213
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_205

description:
GNDX.NAC205
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_208

description:
GNDX.NAC208
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_198

description:
GNDX.NAC198
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_200

description:
GNDX.NAC200
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_202

description:
GNDX.NAC202
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_218

description:
GNDX.NAC218
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_196

description:
GNDX.NAC196
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_195

description:
GNDX.NAC195
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_192

description:
GNDX.NAC192
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_210

description:
GNDX.NAC210
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_199

description:
GNDX.NAC199
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_191

description:
GNDX.NAC191
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_189

description:
GNDX.NAC189
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_194

description:
GNDX.NAC194
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_193

description:
GNDX.NAC193
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_197

description:
GNDX.NAC197
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_190

description:
GNDX.NAC190
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_187

description:
GNDX.NAC187
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_188

description:
GNDX.NAC188
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_186

description:
GNDX.NAC186
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_179

description:
GNDX.NAC179
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_185

description:
GNDX.NAC185
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_172

description:
GNDX.NAC172
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_176

description:
GNDX.NAC176
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_183

description:
GNDX.NAC183
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_180

description:
GNDX.NAC180
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_182

description:
GNDX.NAC182
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_174

description:
GNDX.NAC174
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_171

description:
GNDX.NAC171
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_178

description:
GNDX.NAC178
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_175

description:
GNDX.NAC175
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_181

description:
GNDX.NAC181
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_170

description:
GNDX.NAC170
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_173

description:
GNDX.NAC173
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_166

description:
GNDX.NAC166
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_177

description:
GNDX.NAC177
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_168

description:
GNDX.NAC168
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_163

description:
GNDX.NAC163
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_160

description:
GNDX.NAC160
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_169

description:
GNDX.NAC169
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_161

description:
GNDX.NAC161
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_162

description:
GNDX.NAC162
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_159

description:
GNDX.NAC159
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_157

description:
GNDX.NAC157
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_164

description:
GNDX.NAC164
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_165

description:
GNDX.NAC165
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_158

description:
GNDX.NAC158
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_227

description:
GNDX.NAC227
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_184

description:
GNDX.NAC184
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_152

description:
GNDX.NAC152
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_153

description:
GNDX.NAC153
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_151

description:
GNDX.NAC151
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_155

description:
GNDX.NAC155
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_148

description:
GNDX.NAC148
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_150

description:
GNDX.NAC150
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_147

description:
GNDX.NAC147
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_145

description:
GNDX.NAC145
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_156

description:
GNDX.NAC156
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_149

description:
GNDX.NAC149
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_146

description:
GNDX.NAC146
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_154

description:
GNDX.NAC154
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_144

description:
GNDX.NAC144
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_143

description:
GNDX.NAC143
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_142

description:
GNDX.NAC142
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_134

description:
GNDX.NAC134
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_137

description:
GNDX.NAC137
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_167

description:
GNDX.NAC167
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_139

description:
GNDX.NAC139
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_138

description:
GNDX.NAC138
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_136

description:
GNDX.NAC136
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_141

description:
GNDX.NAC141
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_132

description:
GNDX.NAC132
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_135

description:
GNDX.NAC135
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_133

description:
GNDX.NAC133
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_140

description:
GNDX.NAC140
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_131

description:
GNDX.NAC131
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_129

description:
GNDX.NAC129
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_128

description:
GNDX.NAC128
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_122

description:
GNDX.NAC122
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_130

description:
GNDX.NAC130
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_125

description:
GNDX.NAC125
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_124

description:
GNDX.NAC124
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_126

description:
GNDX.NAC126
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_116

description:
GNDX.NAC116
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_117

description:
GNDX.NAC117
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_123

description:
GNDX.NAC123
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_118

description:
GNDX.NAC118
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_111

description:
GNDX.NAC111
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_121

description:
GNDX.NAC121
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_114

description:
GNDX.NAC114
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_115

description:
GNDX.NAC115
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_112

description:
GNDX.NAC112
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_109

description:
GNDX.NAC109
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_110

description:
GNDX.NAC110
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_105

description:
GNDX.NAC105
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_106

description:
GNDX.NAC106
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_113

description:
GNDX.NAC113
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_127

description:
GNDX.NAC127
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_107

description:
GNDX.NAC107
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_108

description:
GNDX.NAC108
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_120

description:
GNDX.NAC120
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_104

description:
GNDX.NAC104
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_102

description:
GNDX.NAC102
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_119

description:
GNDX.NAC119
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_103

description:
GNDX.NAC103
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_100

description:
GNDX.NAC100
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_101

description:
GNDX.NAC101
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_99

description:
GNDX.NAC99
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_97

description:
GNDX.NAC97
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_94

description:
GNDX.NAC94
bca_subtype=bladder cancer subtype

value: #N/A


title: bladder_cancer_turbt_sample_93

description:
GNDX.NAC93
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_96

description:
GNDX.NAC96
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_95

description:
GNDX.NAC95
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_98

description:
GNDX.NAC98
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_91

description:
GNDX.NAC91
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_83

description:
GNDX.NAC83
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_90

description:
GNDX.NAC90
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_89

description:
GNDX.NAC89
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_80

description:
GNDX.NAC80
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_82

description:
GNDX.NAC82
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_88

description:
GNDX.NAC88
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_85

description:
GNDX.NAC85
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_87

description:
GNDX.NAC87
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_86

description:
GNDX.NAC86
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_81

description:
GNDX.NAC81
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_84

description:
GNDX.NAC84
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_92

description:
GNDX.NAC92
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_79

description:
GNDX.NAC79
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_77

description:
GNDX.NAC77
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_76

description:
GNDX.NAC76
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_74

description:
GNDX.NAC74
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_75

description:
GNDX.NAC75
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_73

description:
GNDX.NAC73
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_71

description:
GNDX.NAC71
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_68

description:
GNDX.NAC68
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_72

description:
GNDX.NAC72
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_69

description:
GNDX.NAC69
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_70

description:
GNDX.NAC70
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_67

description:
GNDX.NAC67
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_78

description:
GNDX.NAC78
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_66

description:
GNDX.NAC66
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_64

description:
GNDX.NAC64
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_63

description:
GNDX.NAC63
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_65

description:
GNDX.NAC65
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_62

description:
GNDX.NAC62
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_59

description:
GNDX.NAC59
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_56

description:
GNDX.NAC56
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_52

description:
GNDX.NAC52
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_51

description:
GNDX.NAC51
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_61

description:
GNDX.NAC61
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_58

description:
GNDX.NAC58
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_54

description:
GNDX.NAC54
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_47

description:
GNDX.NAC47
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_55

description:
GNDX.NAC55
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_57

description:
GNDX.NAC57
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_46

description:
GNDX.NAC46
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_43

description:
GNDX.NAC43
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_53

description:
GNDX.NAC53
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_49

description:
GNDX.NAC49
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_45

description:
GNDX.NAC45
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_48

description:
GNDX.NAC48
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_38

description:
GNDX.NAC38
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_36

description:
GNDX.NAC36
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_37

description:
GNDX.NAC37
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_50

description:
GNDX.NAC50
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_42

description:
GNDX.NAC42
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_41

description:
GNDX.NAC41
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_60

description:
GNDX.NAC60
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_44

description:
GNDX.NAC44
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_35

description:
GNDX.NAC35
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_40

description:
GNDX.NAC40
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_32

description:
GNDX.NAC32
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_34

description:
GNDX.NAC34
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_30

description:
GNDX.NAC30
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_39

description:
GNDX.NAC39
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_31

description:
GNDX.NAC31
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_26

description:
GNDX.NAC26
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_27

description:
GNDX.NAC27
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_33

description:
GNDX.NAC33
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_28

description:
GNDX.NAC28
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_25

description:
GNDX.NAC25
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_23

description:
GNDX.NAC23
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_22

description:
GNDX.NAC22
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_29

description:
GNDX.NAC29
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_24

description:
GNDX.NAC24
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_21

description:
GNDX.NAC21
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_16

description:
GNDX.NAC16
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_17

description:
GNDX.NAC17
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_9

description:
GNDX.NAC9
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_11

description:
GNDX.NAC11
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_8

description:
GNDX.NAC8
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_19

description:
GNDX.NAC19
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_13

description:
GNDX.NAC13
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_18

description:
GNDX.NAC18
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_14

description:
GNDX.NAC14
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_10

description:
GNDX.NAC10
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_15

description:
GNDX.NAC15
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_20

description:
GNDX.NAC20
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_12

description:
GNDX.NAC12
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_7

description:
GNDX.NAC7
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_6

description:
GNDX.NAC6
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_3

description:
GNDX.NAC3
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_5

description:
GNDX.NAC5
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_4

description:
GNDX.NAC4
bca_subtype=bladder cancer subtype


title: bladder_cancer_turbt_sample_2

description:
GNDX.NAC2
bca_subtype=bladder cancer subtype


title: Neuro_Krainc_P02_D01_B25_RPT

status: Public on May 20 2017

city: Tel Aviv

first: David

last: Amar

address: Haim Levanon

department: Computer Science

country: Israel

institute: Tel Aviv University

description:
Neuro_Krainc_P02_D01_B25_RPT.CEL
Whole blood gene expression from GENETIC_UNAFFECTED patient.

hyb_protocol: Samples were processed according to manufacturer’s protocols.

data_processing: Data were preprocessed using RMA. Then the data were log2 transformed and quantile normalized. RMA was selected as it produced better patient correlations than MAS5 and GC-RMA.

source_name: Whole blood

extract_protocol: We collected samples of venous blood using a standardized blood withdrawal protocol. PaxGene (Qiagen) and EDTA tubes were obtained. As participants were recruited at different time points, samples were frozen at -80° C first and RNA was extracted after patient recruitment at all centers was completed.

value: whole blood

tag: disease label

tag: batch

tag: learning set

value: TEST

tag: Sex

value: Male

tag: genetic (mutated pd genes)

value: PARKIN

tag: updrs i

tag: updrs ii

tag: updrs iii score on

tag: updrs iii score off

tag: updrs iv

tag: hoehn & yahr (on)

tag: hoehn & yahr (off)

tag: moca score


title: bladder_cancer_turbt_sample_1

description:
GNDX.NAC1
bca_subtype=bladder cancer subtype

tag: disease state

tag: treatment


title: Mouse 14.5 Mutant Alk5 P_Maxilla_Rep3

status: Public on Jan 13 2017

city: Los Angeles

first: Michael

last: Kesling

address: 2250 Alcazar Street

institute: University of Southern California

description: Gene expression

hyb_protocol: Following fragmentation, 12 µg of cRNA was hybridized for 16hr on Affymetrix Mouse 430_2 (gene version) as recommended by the manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The probe level data was summarized to gene level and was analyzed with PGS 6.6 . RMA (Robust Multi array average) normalization was used

source_name: mouse embyo stage E14.5

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Qiagen Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

extract_protocol: RNA was extracted from tissues using  RNeasy kit (Qiagen Valenica, CA)

tag: background strain

tag: tissue

value: Maxilla

tag: tissue compartment

value: Proximal bone

tag: genotype

value: Alk5 mutant

tag: Stage


title: GFP1_4H_LPS

status: Public on May 03 2017

city: Boston

first: Kate

middle: L

last: Jeffrey

state: Massachusetts

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

description: replicate 1

hyb_protocol: RNA was hybridized to Illumina MouseRef-8 v2.0 expression BeadChip kits.

scan_protocol: The chips were scanned using Illumina BeadArray Reader followed by analysis using the R/Bioconductor BioC 2.5 suite of tools (www.bioconductor.org/).

data_processing: Data analysis and graphical representation was performed using GeneSpring (Agilent Technologies).  Normalization: average.

label: BIOTIN

source_name: Bone marrow derived macrophages

label_protocol: 500 ng of total RNA from 3 biological replicates per group were used to prepare biotin-labelled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow extracted from the femur and tibia of 6-8 week female C57BL/6 mice using 5 ng/mL each of recombinant M-CSF and IL-3 (Peprotech) for 7 days.

extract_protocol: Total RNA was extracted using the Qiagen RNAeasy isolation kit according to the manufacturer's protocol.

treatment_protocol: Mouse bone marrow was transduced with lentivirus containing short-hairpin (sh)RNA against Sp140 or a control shRNA against green fluorescent protein (GFP, The Broad Institute RNAi consortium) on day 1. Bone marrow was then differentiated to macrophages with 5 ng/mL IL-3 and M-CSF for 7 days. On day 5 of maturation, lentivirus transduced cells were selected with puromycin (4 mg/mL). Cells were subsequently treated with LPS (100ng/mL) for 4h or 0h.

tag: strain

tag: age

value: 6-8 weeks

tag: genotype/variation

value: control

tag: agent

value: LPS

tag: cell type

value: BMDM


title: SP140-1_0h

description: replicate 1

value: SP140 knockdown


title: GFP3_0H

description: replicate 3


title: GFP1_0H

description: replicate 1


title: GFP2_4H_LPS

description: replicate 2


title: Mouse 14.5 Mutant Alk5 D_Maxilla_Rep2

description: Gene expression

value: Distal bone


title: Mouse 14.5 Control Alk5 P_Maxilla_Rep2

description: Gene expression


title: SP140-2_4h_LPS

description: replicate 2


title: Mouse 14.5 Control Alk5 P_Maxilla_Rep1

description: Gene expression


title: SP140-2_0h

description: replicate 2


title: SP140-3_0h

description: replicate 3


title: Mouse 14.5 Mutant Alk5 D_Maxilla_Rep3

description: Gene expression


title: Mouse 14.5 Control Alk5 D_Maxilla_Rep3

description: Gene expression


title: GFP3_4H_LPS

description: replicate 3


title: GFP2_0H

description: replicate 2


title: Mouse 14.5 Mutant Alk5 P_Maxilla_Rep2

description: Gene expression


title: Mouse 14.5 Mutant Alk5 D_Mandible _Rep3

description: Gene expression

value: Mandible


title: Mouse 14.5 Mutantl Alk5 P_Mandible _Rep2

description: Gene expression


title: Mouse 14.5 Mutant Alk5 P_Mandible _Rep1

description: Gene expression


title: Mouse 14.5 Mutant Alk5 D_Maxilla_Rep1

description: Gene expression


title: Mouse 14.5 Mutant Alk5 P_Mandible _Rep3

description: Gene expression


title: Mouse 14.5 Mutant Alk5 D_Mandible _Rep2

description: Gene expression


title: Mouse 14.5 Mutant Alk5 D_Mandible _Rep1

description: Gene expression


title: Mouse 14.5 Control Alk5 D_Maxilla_Rep2

description: Gene expression


title: SP140-1_4h_LPS

description: replicate 1


title: SP140-3_4h_LPS

description: replicate 3


title: Mouse 14.5 Control Alk5 D_Maxilla_Rep1

description: Gene expression


title: Mouse 14.5 Mutant Alk5 P_Maxilla_Rep1

description: Gene expression


title: Mouse 14.5 Control Alk5 P_Maxilla_Rep3

description: Gene expression


title: Mouse 14.5 Control Alk5 P_Mandible _Rep3

description: Gene expression


title: Mouse 14.5 Control Alk5 P_Mandible _Rep2

description: Gene expression


title: Mouse 14.5 Control Alk5 P_Mandible_Rep1

description: Gene expression


title: Mouse 14.5 Control Alk5 D_Mandible _Rep1

description: Gene expression


title: Mouse 14.5 Control Alk5 D_Mandible _Rep2

description: Gene expression


title: Mouse 14.5 Control Alk5 D_Mandible _Rep3

description: Gene expression


title: Mouse-14.5 Mutant_Tgfbr2 P_Mandible_Rep1

description: AM460-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 1P).CEL

data_processing:
The probe level data was summarized to gene level and was analyzed with Partek  genomics suite 6.6
RMA (Robust Multi array average) normalization was used

growth_protocol: mouse Samples

tag: developemental stage

value: embyo stage E14.5

value: Tgfbr2 mutant


title: Mouse-14.5 Control_Tgfbr2 P_Mandible_Rep3

description: AM472-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 3P).CEL

source_name: control_E14.5_Mandible_Proximal bone


title: Mouse-14.5 Control_Tgfbr2 P_Mandible_Rep2

description: AM464-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 2P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Maxilla_Rep1

description: AM459-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 1D).CEL

source_name: Tgfbr2 mutant_E14.5_Maxilla_Distal bone


title: Mouse-14.5 Mutant_Tgfbr2 P_Mandible_Rep2

description: AM468-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 2P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Mandible_Rep2

description: AM469-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 2D).CEL


title: Mouse-14.5 Mutant_Tgfbr2 P_Maxilla_Rep1

description: AM458-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 1P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Maxilla_Rep3

description: AM475-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 3D).CEL


title: Mouse-14.5 Control_Tgfbr2 P_Maxilla_Rep3

description: AM470-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 3P).CEL

source_name: control_E14.5_Maxilla_Proximal bone


title: Mouse-14.5 Control_Tgfbr2 D_Mandible_Rep1

description: AM457-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 1D).CEL

source_name: control_E14.5_Mandible_Distal bone


title: Mouse-14.5 Control_Tgfbr2 P_Maxilla_Rep1

description: AM454-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 1P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Mandible_Rep3

description: AM477-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 3D).CEL


title: Mouse-14.5 Control_Tgfbr2 P_Maxilla_Rep2

description: AM462-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 2P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 P_Maxilla_Rep3

description: AM474-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 3P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Mandible_Rep1

description: AM461-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 1D).CEL


title: Mouse-14.5 Control_Tgfbr2 D_Mandible_Rep3

description: AM473-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 3D).CEL


title: Mouse-14.5 Mutant_Tgfbr2 P_Mandible_Rep3

description: AM476-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mnd 3P).CEL


title: Mouse-14.5 Mutant_Tgfbr2 D_Maxilla_Rep2

description: AM467-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 2D).CEL


title: Mouse-14.5 Mutant_Tgfbr2 P_Maxilla_Rep2

description: AM466-Mouse430_2-01-1 (mutant Tgfbr2 14.5 Mx 2P).CEL


title: Mouse-14.5 Control_Tgfbr2 P_Mandible_Rep1

description: AM456-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 1P).CEL


title: Mouse-14.5 Control_Tgfbr2 D_Maxilla_Rep1

description: AM455-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 1D).CEL

source_name: control_E14.5_Maxilla_Distal bone


title: Mouse-14.5 Control_Tgfbr2 D_Maxilla_Rep3

description: AM471-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 3D).CEL


title: Mouse-14.5 Control_Tgfbr2 D_Maxilla_Rep2

description: AM463-Mouse430_2-01-1 (control Tgfbr2 14.5 Mx 2D).CEL


title: Mouse-14.5Control_Tgfbr2  D_Mandible_Rep2

description: AM465-Mouse430_2-01-1 (control Tgfbr2 14.5 Mnd 2D).CEL


title: Low HG - H9 cells cultured in 80% mebil gel for 7days with mTeSR1 medium, rep 3

status: Public on Oct 24 2016

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

hyb_protocol: 0.6 µg of synthesized cRNA samples were hybridized to SurePrint G3 Human GE 8×60K Ver.2.0 microarrays (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: Agilent DNA microarray scanner (G2565CA) was used to obtain DNA microarray images.

data_processing: Data were pre-processed using limma R/Bioconductor package including RMA background correction, quantile normalisation and log2 transformation. Control probes were removed after normalisation. Detection threshold (log2) for Stemformatics graphing uses 95th percentile of negative control probe expression as per limma recommendation. Median expression is median (log2) of above-threshold expression of all non-control probes.

source_name: H9 cells cultured in 80% mebil gel for 7days with mTeSR1 medium.

label_protocol: A total of 100 ng of ribonucleic acid (RNA) from each sample was amplified and labeled with cyanine 3 (Cy3) fluorescent dye to synthesize complementary viral RNA (cRNA) using a One-Color, Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: H9 human embryonic stem cells (hESCs) were cultured in mTeSR-1 medium (Stem Cell Technology) supplemented with 10 µM Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 (Wako Pure Chemical Industries, Osaka, Japan) on day 1, and the medium was changed daily.

extract_protocol: RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer recommended protocol. After culturing hPSCs in the microfluidic device, the system was placed on ice and the cells were transferred into a 1.5-mL tube. The cells were then allowed to settle to the bottom of the tube with gravity. After centrifuging for 5 min at 300 xg, the supernatants were aspirated to remove the culture medium and trypsin. The cell pellet was then treated with cell lysis buffer from the RNeasy Mini Kit. After homogenizing the lysates, 70% ethanol was added, and the mixture was applied to a spin column in a tube, and centrifuged at 8,000 xg for 15 sec. The spin column was rinsed with a washing buffer. Finally, RNase-free water was used to elute total RNA from the spin column. The total concentration of retrieved RNA was quantified using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific), and its quality was evaluated with the BioAnalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The dissociated hPSCs were resuspended in mTeSR-1 medium mixed with different concentrations of PNIPAAm-β-PEG hydrogel (HG) (Mebiol Inc., Hiratsuka, Japan) supplemented with 10 µM Y-27632. HG concentrations of  61 and 76 mg ml-1 were utilized to obtain cellular matrices with stiffness properties identified as “Low HG” and  “HG”,  respectively.

value: embryonic stem cell

value: in vitro


title: Low HG - H9 cells cultured in 80% mebil gel for 7days with mTeSR1 medium, rep 1


title: fibroblast, rep 1

description: fibroblast, rep 1

source_name: fibroblast

value: Fibroblast

value: fetal lung


title: HG - H9 cells cultured in 100% mebil gel for 7days with mTeSR1 medium, rep 3

source_name: H9 cells cultured in 100% mebil gel for 7days with mTeSR1 medium.


title: SP - H9 cells cultured in suspension for 5days with mTeSR1 medium, rep 2

source_name: H9 cells cultured in suspension for 5days with mTeSR1 medium.


title: SP - H9 cells cultured in suspension for 5days with mTeSR1 medium, rep 1


title: fibroblast, rep 2

description: fibroblast, rep 2


title: SP - H9 cells cultured in suspension for 5days with mTeSR1 medium, rep 3


title: Low HG - H9 cells cultured in 80% mebil gel for 7days with mTeSR1 medium, rep 2


title: HG - H9 cells cultured in 100% mebil gel for 7days with mTeSR1 medium, rep 2


title: MG - H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium, rep 2

source_name: H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium.


title: HG - H9 cells cultured in 100% mebil gel for 7days with mTeSR1 medium, rep 1


title: fibroblast, rep 3

description: fibroblast, rep 3


title: MG - H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium, rep 3


title: WT-24

status: Public on Sep 20 2016

city: cleveland

first: Yuxin

last: Wang

state: OH

address: 9500 Euclid avenue

department: Cancer Biology

institute: cleveland clinic foundation

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

source_name: fibrosarcoma cell line

label_protocol: Standard Illumina protocol

growth_protocol: U6A cells were growed in DMEM medium with 5%FBS

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: U6A cells were treated with 100 IU/ml IFN-beta as indicated.

tag: cell line

value: fibrosarcoma cell line

value: cells expressing wild-type STAT2


title: WT-4


title: MG - H9 cells cultured on a matrigel coated dish for 3days with mTeSR1 medium, rep 1


title: LT-MSCs 5-4

status: Public on Jul 04 2016

data_processing: The data were background corrected, log2 tranformed and quantile normalised using lumi (version 1.1.0)

source_name: Parenchymal lung tissue

growth_protocol: Passage 2-4, DMEM+10 FCS, Pen/strep, Standard plastic cell culture dishes (cells never reach > 80% confluence)

extract_protocol: Adherent cells were washed 2x in sterile PBS, lysed with RLT buffer (Rneasy extraction kit) + β-mercaptoethanol, RNA either stored @ -20 for <2months or extract immediately. Extraction performed using Rneasy extraction kit (Qiagen). RNA stores at -80 for 1-3 months

tag: sample type

value: Healthy control


title: LT-MSCs 5-3


title: A-MSCs 3

source_name: Bronchoalveolar lavage fluid

value: Lung transplant patient


title: LT-MSCs 3-3


title: LT-MSCS 1-3


title: LT-MSCs 2-4


title: A-MSCs 4


title: LT-MSCs 1-4


title: WT-0


title: LT-MSCs 4-3


title: LT-MSCs 3-4


title: WT-8


title: LT-MSCs 2-1


title: A-MSCs 5


title: LT-MSCs 2-2


title: A-MSCs 6


title: LT-MSCs 4-4


title: LT-MSCs 1-2


title: A-MSCs 7


title: LT-MSCs 6-4


title: LT-MSCs 4-1


title: A-MSCs 2


title: A-MSCs 8


title: A-MSCs 9


title: LT-MSCs 6-1


title: A-MSCs 1


title: A-MSCs 11


title: LT-MSCs 5-2


title: LT-MSCs 6-2


title: LT-MSCs 2-3


title: A-MSCs 12


title: A-MSCs 10


title: LT-MSCs 3-1


title: LT-MSCs 3-2


title: LT-MSCs 4-2


title: LT-MSCs 6-3


title: LT-MSCs 5-1


title: LT-MSCs 1-1


title: Clec4e-/-_IR_rep3

status: Public on Mar 24 2016

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were background corrected, log2 tranformed and quantile normalised using the Affymetrix Power Tools (version 1.14.4.1).

source_name: Brain hemisphere

label_protocol: Samples were amplified with the GeneChip WT Pico Kit (902623, Affymetrix) and processed with the Mouse 2.0ST Gene Array WT pico assay (902463, Affymetrix).

extract_protocol: RNA was isolated with RNeasy Micro Kit (74004, Qiagen), and yield and quality measured with the RNA 6000 Pico Kit (Agilent Technologies, 5067-1513) for Agilent Bioanaliser.

treatment_protocol: After a midline neck incision, the left external carotid and pterygopalatine arteries were isolated and ligated with 5-0 silk thread. The internal carotid artery was occluded with a clip at the peripheral site of the bifurcation to the pterygopalatine artery and the common carotid artery was then ligated with 5-0 silk thread. The external carotid artery was cut and a 6-0 nylon suture with a blunted tip (0.20 mm) was inserted. The clip at the internal carotid artery was then removed for advancement of the nylon suture into the middle cerebral artery to slightly more than 6 mm from the internal carotid-pterygopalatine artery bifurcation. After 1 h occlusion, the nylon suture and the ligatures were removed to initiate reperfusion for 24 h up to 72 h. In the sham group, these arteries were visualized but were not disturbed.

tag: surgery

value: I/R

tag: collection date

tag: mouse colony

value: UQ (University of Queensland)

tag: mouse date of birth

tag: number of mice per sample

tag: number of hemispheres per sample

tag: number of cells per sample

tag: rna yield (pg/ul)

tag: rna rin


title: Clec4e-/-_IR_rep5

tag: strain

tag: genotype


title: Clec4e-/-_IR_rep4


title: Clec4e-/-_IR_rep2


title: WT_IR_rep5

value: Wild type


title: WT_sham_rep2

value: sham

value: NUS (National University of Singapore)


title: Clec4e-/-_sham_rep3


title: WT_IR_rep2


title: WT_IR_rep3


title: Clec4e-/-_IR_rep1


title: WT_IR_rep1


title: Clec4e-/-_sham_rep2


title: WT_sham_rep1


title: Clec4e-/-_sham_rep1


title: WT_sham_rep3


title: WT_IR_rep4


title: Diabetic 3, untreated

status: Public on Nov 10 2015

hyb_protocol: Following fragmentation, 5ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner GC3000 7G with Affymetrix GeneChip Comand Console software.

data_processing: The data were background corrected, log2 tranformed and quantile normalised using the Affymetrix Power Tools (version 1.14.4).

source_name: Diabetic monocyte, untreated

label_protocol: Biotinylated cRNA were prepared from 5ng total RNA using the NuGen Pico WTA V2 and Nugen Encore Biotin labelling kits accoring to the manufacturer's guidelines.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% L-glutamine and 1% penicillin-streptomycin

extract_protocol: Extraction of total RNA was performed using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MSC-treated samples were co-cultured with human bone marrow-derived MSCs using an in vitro transwell system for 48 hours. Untreated samples were cultured for 48 hours without MSCs.

tag: tissue

value: blood

value: peripheral blood monocyte

tag: gender

value: male

tag: age

tag: diagnosis

value: diabetes


title: Control 1, non-diabetic, untreated

source_name: Control monocyte, non-diabetic, untreated

tag: cell type

value: female

value: healthy


title: Diabetic 5, untreated


title: Control 2, non-diabetic, MSC-treated

source_name: Control monocyte, non-diabetic, MSC-treated


title: Control 4, non-diabetic, MSC-treated


title: Control 1, non-diabetic, MSC-treated


title: Diabetic 4, MSC-treated

source_name: Diabetic monocyte, MSC-treated


title: Diabetic 1, MSC-treated


title: Control 2, non-diabetic, untreated


title: Control 3, non-diabetic, MSC-treated


title: Control 4, non-diabetic, untreated


title: Diabetic 3, MSC-treated


title: Control 3, non-diabetic, untreated


title: Diabetic 5, MSC-treated


title: Diabetic 4, untreated


title: Diabetic 2, untreated


title: Diabetic 2, MSC-treated


title: Diabetic 1, untreated


title: Pre-transplant sample of DBD patient 07

status: Public on Nov 12 2009

city: Seoul

first: Chang-Hyun

last: Kang

address: Yeongun-dong, Chongro-gu

country: South Korea

institute: Seoul National University Hospital

description:
Gene expression data from DBD donor lungs just after preservation
sample name: No_41

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U-133 plus2. GeneChips were washed and stained in the Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3700 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: DBD pre-transplant sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

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

value: lung

tag: donation source

value: DBD

tag: sampling time

value: pre-transplant


title: Post-transplant sample of DBD patient 12

description:
Gene expression data from DBD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_46
sample name: No_56

source_name: DBD post-transplant sample

value: post-transplant


title: Post-transplant sample of DBD patient 07

description:
Gene expression data from DBD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_41
sample name: No_51


title: Pre-transplant sample of DBD patient 11

description:
Gene expression data from DBD donor lungs just after preservation
sample name: No_45


title: Pre-transplant sample of DBD patient 10

description:
Gene expression data from DBD donor lungs just after preservation
sample name: No_44


title: Post-transplant sample of DBD patient 08

description:
Gene expression data from DBD donor lungs 2 hours after reperfusion, this is post-transplant data of sample No_42
sample name: No_52