title: NSCLC_sample_147 A


title: NSCLC_sample_13A

status: Public on Aug 31 2016

type: genomic

city: Uppsala

first: Patrick

last: Micke

address: Rudbeck laboratory

country: Sweden

institute: Uppsala University

description:
Hybridized to 250K_Nsp
GSM707480
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

hyb_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ). The arrays were then washed using Affymetrix fluidics stations.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Copy number values for individual SNPs were extracted and converted from CEL files using R package aroma.affymetrix v2.11.1.
The copy number values were calculated as 2*(sample chip effect/median reference chip effect). On X chromosome the information on the sex was used to assess plausible copy number estimates (men:  sample chip effect/median male reference chip effect, women: 2*sample chip effect/median female reference chip effect). No segmentation perfermormed yet.
As reference data set 90 publicly available HapMap samples were used ((CEU), The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003)).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: NSCLC tissue fresh frozen

growth_protocol: human cancer tissue

extract_protocol: DNA were extracted from 2 to 10 frozen tissue sections (10  mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany).

tag: tissue

value: non-small cell lung cancer

tag: dead

tag: survival

tag: age

tag: who performance status

tag: stadium

tag: smoking

tag: Sex

value: male

tag: histology

value: Squamous cell carcinoma

tag: cell line

value: crude cancer tissue


title: hip_330_ko_18m

status: Public on Mar 31 2016

type: RNA

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with IlluminaGUI in R. Batch effect was corrected using the ComBat algorithm (PMID: 16632515). Nine outlier samples were excluded.

label: biotin

molecule: total RNA

organism: Mus musculus

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

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

tag: mouse id

tag: strain background

tag: gender

value: F

tag: genotype/variation

value: KO; Grn-/-

tag: region

value: hippocampus (hip)

tag: timepoint/age

value: 18 months


title: NSCLC_sample_135A

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

label_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ).


title: NSCLC_sample_131A

description:
Hybridized to 250K_Nsp
GSM707478
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

value: female


title: NSCLC_sample_133A

description:
Hybridized to 250K_Nsp
GSM707433
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

value: Adenocarcinoma


title: NSCLC_sample_138 A


title: ctx_330_ko_18m

description: replicate 3

value: cortex (ctx)


title: NSCLC_sample_247A

description:
Hybridized to 250K_Nsp
GSM707504
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: crb_242_wt_18m

description: replicate 3

value: M

value: WT; Grn+/+

value: cerebellum (crb)


title: hip_248_wt_18m

description: replicate 3


title: hip_242_wt_18m

description: replicate 3


title: crb_330_ko_18m

description: replicate 3


title: NSCLC_sample_123A


title: crb_250_het_18m

description: replicate 3

value: het; Grn+/-


title: NSCLC_sample_111A


title: ctx_246_ko_18m

description: replicate 3


title: NSCLC_sample_112B

description:
Hybridized to 250K_Nsp
GSM707474
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: crb_244_wt_18m

description: replicate 3


title: ctx_245_het_18m

description: replicate 3


title: NSCLC_sample_107A


title: ctx_219_ko_18m

description: replicate 3


title: NSCLC_sample_128A


title: crb_219_ko_18m

description: replicate 3


title: NSCLC_sample_116A


title: ctx_242_wt_18m

description: replicate 3


title: NSCLC_sample_11C

description:
Hybridized to 250K_Nsp
GSM707475
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: crb_246_ko_18m

description: replicate 3


title: hip_246_ko_18m

description: replicate 3


title: NSCLC_sample_12B

description:
Hybridized to 250K_Nsp
GSM707477
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: hip_79_wt_16m

description: replicate 3

value: 16 months


title: hip_245_het_18m

description: replicate 3


title: NSCLC_sample_105A


title: NSCLC_sample_10B


title: hip_244_wt_18m

description: replicate 3


title: ctx_247_het_18m

description: replicate 3


title: hip_260_het_18m

description: replicate 3


title: ctx_244_wt_18m

description: replicate 3


title: crb_79_wt_16m

description: replicate 3


title: NSCLC_sample_101 A


title: hip_82_ko_16m

description: replicate 3


title: ctx_79_wt_16m

description: replicate 3


title: ctx_35_het_12m

description: replicate 3

value: 12 months


title: hip_34_het_12m

description: replicate 3


title: ctx_82_ko_16m

description: replicate 3


title: crb_248_wt_18m

description: replicate 3


title: hip_44_ko_12m

description: replicate 3


title: ctx_250_het_18m

description: replicate 3


title: crb_58_ko_12m

description: replicate 3


title: ctx_248_wt_18m

description: replicate 3


title: hip_219_ko_18m

description: replicate 3


title: ctx_42_wt_12m

description: replicate 3


title: crb_44_ko_12m

description: replicate 3


title: NSCLC_sample_110A

value: non-small cell lung cancer


title: crb_41_wt_12m

description: replicate 3


title: hip_41_wt_12m

description: replicate 3


title: hip_32_wt_12m

description: replicate 3


title: crb_42_wt_12m

description: replicate 3


title: hip_58_ko_12m

description: replicate 3


title: ctx_34_het_12m

description: replicate 3


title: crb_36_het_12m

description: replicate 3


title: hip_247_het_18m

description: replicate 3


title: ctx_58_ko_12m

description: replicate 3


title: ctx_32_wt_12m

description: replicate 3


title: hip_36_het_12m

description: replicate 3


title: ctx_625_wt_6m

description: replicate 3

value: 6 months


title: ctx_39_ko_12m

description: replicate 3


title: ctx_36_het_12m

description: replicate 3


title: hip_39_ko_12m

description: replicate 3


title: ctx_41_wt_12m

description: replicate 3


title: crb_34_het_12m

description: replicate 3


title: hip_35_het_12m

description: replicate 3


title: crb_39_ko_12m

description: replicate 3


title: crb_457_ko_9m

description: replicate 3

value: 9 months


title: ctx_665_wt_6m

description: replicate 3


title: ctx_44_ko_12m

description: replicate 3


title: crb_35_het_12m

description: replicate 3


title: hip_457_ko_9m

description: replicate 3


title: hip_668_het_6m

description: replicate 3


title: hip_680_ko_6m

description: replicate 3


title: ctx_648_ko_6m

description: replicate 3


title: ctx_391_ko_9m

description: replicate 3


title: hip_648_ko_6m

description: replicate 3


title: crb_391_ko_9m

description: replicate 3


title: ctx_668_het_6m

description: replicate 3


title: crb_400_het_9m

description: replicate 3


title: hip_391_ko_9m

description: replicate 3


title: NSCLC_sample_114A

value: crude cancer tissue


title: crb_680_ko_6m

description: replicate 3

value: F


title: crb_404_wt_9m

description: replicate 3


title: hip_665_wt_6m

description: replicate 3


title: crb_669_het_6m

description: replicate 3


title: crb_245_het_18m

description: replicate 3


title: crb_648_ko_6m

description: replicate 3

value: KO; Grn-/-


title: crb_659_wt_6m

description: replicate 3


title: ctx_401_het_9m

description: replicate 3


title: crb_393_het_9m

description: replicate 3


title: crb_649_ko_6m

description: replicate 3


title: crb_434_ko_9m

description: replicate 3


title: hip_669_het_6m

description: replicate 3

value: hippocampus (hip)


title: crb_668_het_6m

description: replicate 3


title: ctx_434_ko_9m

description: replicate 3


title: crb_399_wt_9m

description: replicate 3


title: hip_393_het_9m

description: replicate 3


title: ctx_457_ko_9m

description: replicate 3


title: ctx_677_het_6m

description: replicate 3


title: hip_383_wt_9m

description: replicate 3


title: crb_677_het_6m

description: replicate 3


title: ctx_399_wt_9m

description: replicate 3


title: crb_383_wt_9m

description: replicate 3


title: hip_649_ko_6m

description: replicate 3


title: ctx_659_wt_6m

description: replicate 3


title: ctx_404_wt_9m

description: replicate 3


title: hip_434_ko_9m

description: replicate 3


title: ctx_400_het_9m

description: replicate 3


title: crb_401_het_9m

description: replicate 3


title: ctx_649_ko_6m

description: replicate 3


title: ctx_383_wt_9m

description: replicate 3


title: ctx_393_het_9m

description: replicate 3


title: ctx_680_ko_6m

description: replicate 3


title: hip_677_het_6m

description: replicate 3


title: crb_625_wt_6m

description: replicate 3


title: hip_401_het_9m

description: replicate 3


title: ctx_669_het_6m

description: replicate 3


title: hip_404_wt_9m

description: replicate 3


title: crb_263_ko_2m

description: replicate 3

value: 2 months


title: hip_659_wt_6m

description: replicate 3


title: hip_400_het_9m

description: replicate 3


title: ctx_261_ko_2m

description: replicate 3


title: ctx_314_wt_2m

description: replicate 3


title: hip_315_wt_2m

description: replicate 3


title: hip_399_wt_9m

description: replicate 3


title: crb_665_wt_6m

description: replicate 3


title: hip_252_ko_2m

description: replicate 3


title: hip_304_het_2m

description: replicate 3


title: hip_301_het_2m

description: replicate 3


title: ctx_249_ko_2m

description: replicate 3


title: ctx_301_het_2m

description: replicate 3


title: hip_308_wt_2m

description: replicate 3


title: crb_252_ko_2m

description: replicate 3


title: ctx_252_ko_2m

description: replicate 3


title: ctx_263_ko_2m

description: replicate 3


title: ctx_306_ko_2m

description: replicate 3


title: hip_306_ko_2m

description: replicate 3


title: hip_311_wt_2m

description: replicate 3


title: ctx_311_wt_2m

description: replicate 3


title: hip_249_ko_2m

description: replicate 3


title: crb_317_wt_2m

description: replicate 3


title: hip_309_het_2m

description: replicate 3


title: ctx_315_wt_2m

description: replicate 3


title: crb_261_ko_2m

description: replicate 3


title: hip_307_het_2m

description: replicate 3


title: crb_301_het_2m

description: replicate 3


title: crb_293_wt_2m

description: replicate 3


title: hip_314_wt_2m

description: replicate 3


title: crb_309_het_2m

description: replicate 3


title: crb_307_het_2m

description: replicate 3


title: ctx_303_het_2m

description: replicate 3


title: crb_256_ko_2m

description: replicate 1


title: crb_306_ko_2m

description: replicate 2


title: hip_317_wt_2m

description: replicate 2


title: hip_305_het_2m

description: replicate 1


title: ctx_317_wt_2m

description: replicate 3


title: ctx_304_het_2m

description: replicate 3


title: hip_256_ko_2m

description: replicate 3


title: ctx_308_wt_2m

description: replicate 2


title: ctx_256_ko_2m

description: replicate 2


title: crb_311_wt_2m

description: replicate 2


title: hip_261_ko_2m

description: replicate 1


title: ctx_307_het_2m

description: replicate 2


title: crb_305_het_2m

description: replicate 3


title: ctx_293_wt_2m

description: replicate 1


title: crb_314_wt_2m

description: replicate 1


title: WT littermate, rep1

status: Public on Feb 29 2016

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description:
WT-1
WT 1
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

source_name: Total skin, WT

label_protocol: Standard Illumina labeling protocol.

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

treatment_protocol: Pups were washed with PBS and total skin was collected at P0. No treatment performed before RNA isolation.

value: WT

value: skin

tag: developmental stage

value: postnatal day (P) 0


title: Psen1-, Psen2- and RBPjk-null, rep1

description:
PSR-1
PSR mut 1
Replicate 1

source_name: Total skin, PSRmut

value: Psen1-, Psen2- and RBPjk-null

tag: tissue


title: RBPjk-null, rep3

description:
RBPj-3
RBP mut 3
Replicate 3

source_name: Total skin, RBPjmut

value: RBPjk-null


title: WT littermate, rep3

description:
WT-3
WT 3
Replicate 3


title: Psen1-, Psen2- and RBPjk-null, rep3

description:
PSR-3
PSR mut 3
Replicate 3


title: WT littermate, rep2

description:
WT-2
WT 2
Replicate 2


title: WT littermate, rep4

description:
WT-4
WT 4
Replicate 4


title: Psen1-, Psen2- and RBPjk-null, rep2

description:
PSR-2
PSR mut 2
Replicate 2


title: RBPjk-null, rep2

description:
RBPj-2
RBP mut 2
Replicate 2


title: Psen1-, Psen2- and RBPjk-null, rep4

description:
PSR-4
PSR mut 4
Replicate 4


title: RBPjk-null, rep4

description:
RBPj-4
RBP mut 4
Replicate 4


title: ctx_309_het_2m

description: replicate 1

value: M

value: cortex (ctx)


title: Psen1- and Psen2-null, rep4

description:
PS-4
PS mut 4
Replicate 4

source_name: Total skin, PSmut

value: Psen1- and Psen2-null


title: Psen1- and Psen2-null, rep2

description:
PS-2
PS mut 2
Replicate 2


title: Psen1- and Psen2-null, rep3

description:
PS-3
PS mut 3
Replicate 3


title: Psen1- and Psen2-null, rep1

description:
PS-1
PS mut 1
Replicate 1


title: RBPjk-null, rep1

description:
RBPj-1
RBP mut 1
Replicate 1


title: WT littermate from PS line_3

description: Replicate 3

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

source_name: Epidermis

label_protocol: not provided

treatment_protocol: Epidermis is collected after total skin was treated with 5mg/ml Dispase (Roche) at 4C for 3 hours.

tag: genotype

value: wildtype

value: Epidermis

value: Embryonic day (E) 18.5


title: RBPjk null_2

description: Replicate 2

value: RBPjk null


title: Psen1 and Psen2 null_2

description: Replicate 2

value: Psen1 and Psen2 null


title: WT littermate from PS line_2

description: Replicate 2


title: RBPjk null_3

description: Replicate 3


title: Psen1 and Psen2 null_1

description: Replicate 1


title: WT littermater from RBPjk line_2

description: Replicate 2


title: Psen1 and Psen2 null_3

description: Replicate 3


title: RBPjk null_1

description: Replicate 1


title: WT littermate from PS line_1

description: Replicate 1


title: WT littermater from RBPjk line_3

description: Replicate 3


title: WT littermater from RBPjk line_1

description: Replicate 1


title: H3K4me3_aggregate

status: Public on Jan 20 2015

type: SRA

city: Bethesda

first: Ian

last: Fingerman

state: MD

address: 45 Center Dr.

department: NCBI Epigenomics

institute: National Institutes of Health

description:
H3K4me3, average track made using previously generated average tracks (average of 20 tracks from various cells and tissues)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000

library_source: genomic

data_processing:
For each tissue type, input tracks were selected based on the following criteria. Experiments from the Roadmap Epigenomics datasets were pooled, based on body site, tissue or cell type.  Donor age was weighed and sample data from adults was segregated from those of fetal or neonatal.  Donor sex was not taken into account, so some cases the track average is generated from pooled male and female tissues. Each input track was normalized by scaling all values to achieve a constant genome-wide summed signal. In the final track, the value in each 20 bp window is the arithmetic mean of the scaled input values.
Genome_build: GRCh37
Supplementary_files_format_and_content: WIG files generated by track averaging

source_name: derived from many tissues/cell types

extract_protocol:
Refer to extraction protocols described in the individual sample inputs for each average track
Refer to library contruction protocols described in the individual sample inputs for each average track

tag: tissue type

value: many tissues represented

tag: cell type

value: many cell types represented


title: B.IFNar1KO.Sp#2

status: Public on Nov 20 2015

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

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

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 6 Weeks Old

tag: genetic background

value: Male

tag: cell family

value: B Cell

tag: phenotype markers

value: CD19+ IgM+

tag: exclusion markers

tag: source prep description

value: Sacrifice at 2hr after sc treatment with 10000u IFNa

tag: separation method

value: FACSAria

tag: amplification technique

value: Ambion WT Expression Kit


title: B.IFNar1KO.IFNa.2hr.Sp#2

tag: Sex


title: B.IFNar1KO.Sp#1


title: MF.IFNar1KO.PC#2

source_name: Peritoneal Cavity

value: Macrophage


title: MF.IFNar1KO.IFNa.2hr.PC#1


title: B.IFNar1KO.IFNa.2hr.Sp#1


title: MF.IFNar1KO.PC#1


title: leaf

status: Public on Mar 05 2008

city: Davis

first: Abhaya

middle: M

last: Dandekar

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

description: no additional information

hyb_protocol: Combimatrix protocols were followed, using fluorolink Cy5-labeled streptavidin

scan_protocol: GenePix scanner used

data_processing: Combimatrix software was used to identify spots and intensities. Avadis Prophetic 3.3 by Strand Genomics (Bangalore, India) was used for microarray statistical analysis. Intensities were converted to log base 2. To confirm correct orientation for each contig, intensities for ‘sense’ and ‘antisense’ versions were compared, with the assumption that ‘sense’ orientation probes would have an aggregate higher intensity across libraries. In the few instances where intensities were very close or conflicted with listed orientations, component ESTs were manually inspected.  Next, the mean of all negative control spots was subtracted from the value of all other spots on the array, with a minimum resulting value of 1. A spike-in-based spot normalization was employed. For each array, the mean of all spike-ins was calculated, ignoring two spike-in concentrations that had fallen to 1 after negative control subtraction. Each mean was then multiplied by a coefficient to make it equal to the highest mean spike-in value. The coefficient used for a given array was then applied to each spot on that array. Following normalization, probes were aggregated by median polishing scripts designed by Strand Genomics.

organism: Citrus sinensis

source_name: Washington navel orange leaf

label_protocol: RNA was amplified and labeled with MessageAmp II aRNA kits (Ambion, Austin, TX), following instructions for single-round amplification and biotinylation with 11-CTP and 16-UTP biotin. 3 micrograms total RNA was used for each sample, calculated by UV spectrometry.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen; Carlsbad, CA), followed by RNA purification using an RNA/DNA cleanup kit (Qiagen; Valencia, CA). RNA concentration and purity were assessed by UV spectrophotometry. The RNA was stored at -80˚C in water.

tag: synonym

value: Citrus sinensis (L.) Osbeck

tag: Tissues dissected from five fruit and pooled; frozen, ground in liquid nitrogen.


title: MF.IFNar1KO.IFNa.2hr.PC#2


title: UKA Rat 4x44K No. 2 Processed

status: Public on Apr 01 2008

city: Aachen

first: Ralf

last: Weiskirchen

state: NRW

address: Pauwelsstr. 30

department: Institute of Clinical Chemistry and Pathobiochemistry

country: Germany

institute: RWTH University Hospital Aachen

description: Agilent Feature Extraction Software (FES) and further analyzed using the Rosetta Resolver gene expression data analysis system

hyb_protocol: Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent)

scan_protocol: Agilent's DNA microarray scanner

organism: Rattus norvegicus

source_name: Hepatic stellate cells, one animal, transfected with siRNA targeting endoglin

label_protocol: RNA was labeled using the Agilent Low RNA Input Linear Amp Kit

extract_protocol: Qiagen RNeasy

tag: RNA was taken from hepatic stellate cells that were transfected with a siRNA targeting endoglin

source_name: Hepatic stellate cells, one animal, transfected with siRNA control

tag: RNA was taken from hepatic stellate cells that were transfected with a control siRNA


title: UKA Rat 4x44K No. 1 Processed

data_processing: Agilent Feature Extraction Software (FES)

source_name: Hepatic stellate cells, one animal, untreated

label_protocol: RNA was labeled using the the Agilent Low RNA Input Linear Amp Kit

tag: RNA was taken from normal untreated hepatic stellate cells

tag: RNA was taken from control siRNA transfected hepatic stellate cells


title: UKA Rat 4x44K No. 3 Processed

source_name: Pooled hepatic stellate, three animals, untreated

tag: RNA was taken from a pool (3 animals) of normal untreated hepatic stellate cells

source_name: Pooled hepatic stellate, three animals, transfected with siRNA control

tag: RNA was taken from a pool (3 animals) of hepatic stellate cells that were transfected with a siRNA control


title: UKA Rat 4x44K No. 4 Processed

source_name: Pooled hepatic stellate cells, three animals, transfected with siRNA targeting endoglin

tag: RNA was taken from a pool (3 animals) of hepatic stellate cells that were transfected with a siRNA targeting endoglin

source_name: Pooled hepatic stellate cells, three animals, transfected with siRNA control


title: MEF

status: Public on Jul 03 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Mouse fibroblasts

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

source_name: MEFs

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: 24 h after transduction, the medium was replaced with D-MEM (high glucose) with L-Glutamate and Phenol Red (Wako, 044-29765) /Medium199 with Earle’s Salts, L-Glutamate and 22g/L Sodium Bicarbonate (Gibco, 11150-059)/10% Hyclone Characterized FBS (Thermo Scientific, SV30014.03) medium and changed every 2-3 days.

extract_protocol: RNA samples were extracted from cells using ReliaPrep™ RNA Cell Miniprep System (Promega).

treatment_protocol: pMx retrovirus were used for transduction with Polybrene (Miilopore). Synthetic mimics of mature miRNA-133a (Thermo Scientific) were transfected simultaneously into cells with Lipofectamine 2000 (Invitrogen)

tag: cell type

value: MEFs

tag: treatment

value: without any treatment

tag: time

value: control