title: Fibroblast_S2_c11_sc2

source_name: Primary fibroblast cell line S2, cell 11, sister cell 2


title: Thymus_D3 [8909358001_E]

status: Public on May 01 2016

type: RNA

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

country: USA

institute: Case Western Reserve University

description:
D3
8909358001_E

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

molecule: total RNA

organism: Macaca mulatta

source_name: Subject: Monkey_5348

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: 44 outbred, Indian-origin, adult or juvenile female rhesus monkeys (Macaca mulatta) were genotyped and selected as negative for the protective MHC class I alleles Mamu-A*01, Mamu-B*08, and Mamu-B*17.  Animals were randomly allocated to groups.  All monkeys were housed at Bioqual, Rockville, MD.

extract_protocol: Plasma SIV RNA levels were measured using a gag targeted quantitative real-time RT-PCR assay, and tissue levels of SIV RNA and DNA were measured using gag targeted, nested quantitative hybrid real time/digital RT-PCR and PCR assays, essentially as described (Hansen et al., 2013). SIV-specific cellular immune responses in blood and tissues were assessed by multiparameter ICS assays essentially as previously described (Baden et al., 2015; Barouch et al., 2012; Li et al., 2011).  9-color ICS assays were performed with predetermined titers of mAbs against CD3 (SP34; Alexa700), CD4 (L200; AmCyan), CD8 (SK1; allophycocyanin-cyanine 7 [APC-Cy7]), CD28 (L293; peridinin chlorophyll-A-cyanine 5.5 [PerCP-Cy5.5]), CD95 (DX2; phycoerythrin [PE]), CD69 (TP1.55.3; phycoerythrin-Texas Red [energy coupled dye; ECD]; Beckman Coulter), IFN-γ (B27; phycoerythrin-cyanine 7 [PE-Cy7]), IL-2 (MQ1-17H12; allophycocyanin [APC]) and TNF-α (Mab11; fluorescein isothiocya [FITC]). IFN-γ backgrounds were consistently <0.01% in PBMC and <0.05% in tissues.

treatment_protocol: Animals were infected with 5x104 TCID50 of our SIVmac251 challenge stock (Barouch et al., 2012; Liu et al., 2010; Liu et al., 2009) by the intravaginal route and were necropsied on day 0, 1, 3, 7, or 10 following infection.

tag: tissue

value: Thymus

tag: status

value: SIV


title: 53151 7539308042_R04C02

type: genomic

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol, iScan

data_processing: Methylation data was background subtracted in GenomeStudio and normalized by beta-mixture quantile (BMIQ) normalization to adjust for the type II bias. Normalization was done using the waterRmelon Bioconductor R package (Pidsley R, CC YW, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics. 2013;14:293)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: BE

label_protocol: standard Illumina protocol

extract_protocol: Most DNA extractions were performed via the phenol-chloroform-isoamyl alcohol method [Maniatis T, Fritsch E, Sambrook J. Molecular cloning: A laboratory manual] a small set of 22 tumors/matched normal DNA was extracted AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA).

value: BE


title: Fibroblast_S2_c9_sc2

city: Leuven

first: Eftychia

last: Dimitriadou

address: Herestraat 49, ON1, bus 602

country: Belgium

institute: KU Leuven

description: Genomiphi V2 whole genome amplified material.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA)

data_processing: Raw data were further processed using GenomeStudio.

source_name: Primary fibroblast cell line S2, cell 9, sister cell 2

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 staining by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: Primary fibroblasts were grown in 75-cm2 plastic flasks (BD Falcon, USA) under standard culture conditions in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium complemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA).

extract_protocol: The genome of collected single cells was amplified using either Genomiphi V2 (GE Healthcare, UK) or RepliG-sc (Qiagen, NL) whole genome amplification kit.

treatment_protocol: Single fibroblasts were plated separately and the two cells that derived following a cell division were isolated individually.

tag: gender

value: Female

tag: cell line


title: 40363 7539308042_R03C02

source_name: Normal

value: Normal


title: 1463 7539308044_R06C01


title: Fibroblast_S2_c11_sc1

scan_protocol: According to the manual of Infinium II Assay (Illumina, USA)

source_name: Primary fibroblast cell line S2, cell 11, sister cell 1


title: Brain_lymphocytes_D7 [8909358001_D]

description:
D7
8909358001_D

source_name: Subject: Monkey_5353


title: Fibroblast_S2_c15_sc1

source_name: Primary fibroblast cell line S2, cell 15, sister cell 1


title: Blood_D7 [8909358001_C]

description:
D7
8909358001_C

source_name: Subject: Monkey_5354

tag: name used in manuscript

value: Blood

tag: subset


title: 54045 7539308042_R04C01


title: Tonsil_D7 [8909358001_B]

description:
D7
8909358001_B

value: Tonsil


title: Fibroblast_S2_c9_sc1

source_name: Primary fibroblast cell line S2, cell 9, sister cell 1


title: WB_S3_MC

description: Twin of Sibling 2, DNA extracted from whole blood.

source_name: Whole blood, Sibling 3 (S3), multicell

extract_protocol: The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome/Illumina, USA).

value: whole blood


title: WB_Mother_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Mother, multicell


title: 53118 7539308042_R01C02


title: 55013 7539308042_R01C01

source_name: Control

value: Control


title: 53150 7507875012_R06C02


title: 55009 7539308042_R02C01

source_name: GERD

value: GERD


title: WB_Father_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Father, multicell

value: Male


title: 40334 7539308042_R02C02


title: Splenocytes_D7 [8381688093_J]

description:
D7
8381688093_J

source_name: Subject: Monkey_5325

value: Splenocytes


title: 54009 7539308042_R03C01


title: Duodenum_D7 [8381688093_L]

description:
D7
8381688093_L

value: Duodenum


title: Fibroblast_S1_c56_sc1

description: RepliG-sc whole genome amplified material.

source_name: Primary fibroblast cell line S1, cell 56, sister cell 1


title: Cecum_D7 [8381688093_K]

description:
D7
8381688093_K

value: Cecum


title: Colon_D7 [8381688093_G]

description:
D7
8381688093_G

value: Colon


title: Fibroblast_S1_c55_sc2

source_name: Primary fibroblast cell line S1, cell 55, sister cell 2


title: Rectum_D7 [8381688093_H]

description:
D7
8381688093_H

value: Rectum


title: genital_pelvic_LN_D7 [8381688093_F]

description:
D7
8381688093_F

value: LN


title: Fibroblast_S1_c56_sc2

source_name: Primary fibroblast cell line S1, cell 56, sister cell 2


title: Fibroblast_S1_c 54_sc2

source_name: Primary fibroblast cell line S1, cell 54, sister cell 2


title: Liver_D7 [8909358001_A]

description:
D7
8909358001_A

value: Liver


title: Uterus_D7 [8381688093_E]

description:
D7
8381688093_E

value: Uterus

value: SIV


title: Lung_D7 [8381688093_I]

description:
D7
8381688093_I

value: Lung


title: Fibroblast_S2_c15_sc2

source_name: Primary fibroblast cell line S2, cell 15, sister cell 2

value: Female


title: Bone_Marrow_D7 [8381688093_D]

description:
D7
8381688093_D


title: Brain_Lymphocyte_D7 [8381688093_A]

description:
D7
8381688093_A


title: pararectal_paracolonic_D7 [8381688093_B]

description:
D7
8381688093_B


title: PAH020 7507875012_R06C01

source_name: Tumour

value: Tumour


title: axillary_LN_D7 [8292044049_L]

description:
D7
8292044049_L


title: Fibroblast_S1_c53_sc1

source_name: Primary fibroblast cell line S1, cell 53, sister cell 1


title: Mid_Vagina_D7 [8292044049_K]

description:
D7
8292044049_K

value: FRT


title: Fibroblast_S1_c55_sc1

source_name: Primary fibroblast cell line S1, cell 55, sister cell 1


title: PAH033 7507875012_R02C02

source_name: Normal

value: Normal


title: Cervix_D7 [8292044049_J]

description:
D7
8292044049_J

value: Cervix


title: Fibroblast_S1_c52_sc2

source_name: Primary fibroblast cell line S1, cell 52, sister cell 2


title: 53035 7507875012_R05C02

value: Control


title: Fibroblast_S1_c54_sc1

source_name: Primary fibroblast cell line S1, cell 54, sister cell 1


title: PAH027 7507875012_R03C01


title: Fibroblast_S1_c52_sc1

source_name: Primary fibroblast cell line S1, cell 52, sister cell 1


title: PAH029 7507875012_R04C01


title: ileocecal_LN_D7 [8292044049_H]

description:
D7
8292044049_H


title: WB_S2_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Sibling 2 (S2), multicell

value: whole blood


title: Ileum_D7 [8292044049_G]

description:
D7
8292044049_G

value: Ileum


title: 3257 7471147021_R06C02


title: Fibroblast_S1_c53_sc2

source_name: Primary fibroblast cell line S1, cell 53, sister cell 2


title: Tonsil_D7 [8292044049_F]

description:
D7
8292044049_F

value: Tonsil


title: 3519 7507875012_R01C01


title: 2804 7471147021_R06C01


title: Fibroblast_S1_c51_sc1

source_name: Primary fibroblast cell line S1, cell 51, sister cell 1


title: Fibroblast_S1_c51_sc2

source_name: Primary fibroblast cell line S1, cell 51, sister cell 2


title: Fibroblast_S1_c37_sc2

source_name: Primary fibroblast cell line S1, cell 37, sister cell 2


title: 2804 7471147021_R05C01


title: Thymus_D7 [8292044049_E]

description:
D7
8292044049_E

source_name: Subject: Monkey_5325

value: Thymus


title: 3213 7471147021_R04C02


title: Fibroblast_S1_c38_sc2

source_name: Primary fibroblast cell line S1, cell 38, sister cell 2


title: 3213 7471147021_R05C02


title: Liver_D7 [8292044049_B]

description:
D7
8292044049_B


title: Jejunum_D7 [8292044049_C]

description:
D7
8292044049_C

value: GI

value: Jejunum


title: Fibroblast_S1_c37_sc1

source_name: Primary fibroblast cell line S1, cell 37, sister cell 1


title: Fibroblast_S1_c38_sc1

source_name: Primary fibroblast cell line S1, cell 38, sister cell 1


title: 2681 7471147021_R04C01


title: Blood_D7 [8292044049_D]

description:
D7
8292044049_D

value: Blood


title: Fibroblast_S1_c35_sc2

source_name: Primary fibroblast cell line S1, cell 35, sister cell 2


title: Tumour 9408455026_J

data_processing: The intensities were extracted using the GenomeStudio software (Illumina). Data was background corrected, log2-transformed and quantile normalized as implemented in the Lumi package (Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008;24(13):1547-8.)

source_name: Esophagus

extract_protocol: RNA extractions were performed via the phenol-chloroform-isoamyl alcohol method (Maniatis T, Fritsch E, Sambrook J. Molecular cloning: A laboratory manual. New York: Cold Spring Harbor Laboratory; 1982)

value: EAC


title: Fibroblast_S1_c29_sc2

source_name: Primary fibroblast cell line S1, cell 29, sister cell 2


title: Fibroblast_S1_c31_sc2

source_name: Primary fibroblast cell line S1, cell 31, sister cell 2


title: Fibroblast_S1_c35_sc1

source_name: Primary fibroblast cell line S1, cell 35, sister cell 1


title: 303 7471147021_R03C02

source_name: Tumour


title: 2681 7471147021_R03C01

source_name: Normal


title: mesenteric_LN_D7 [8381688093_C]

description:
D7
8381688093_C

value: LN


title: Inguinal_LN_D7 [8292044049_A]

description:
D7
8292044049_A

value: SIV


title: Fibroblast_S1_c31_sc1

source_name: Primary fibroblast cell line S1, cell 31, sister cell 1


title: 303 7471147021_R02C02


title: Fibroblast_S1_c27_sc2

source_name: Primary fibroblast cell line S1, cell 27, sister cell 2


title: 2646 7471147021_R02C01


title: Tumour 9408455026_C


title: Tumour 9408455012_K


title: Tumour 9408455026_H


title: Fibroblast_S1_c29_sc1

source_name: Primary fibroblast cell line S1, cell 29, sister cell 1


title: 2810 7471147021_R01C02


title: Tumour 9408455012_I


title: Fibroblast_S1_c26_sc1

source_name: Primary fibroblast cell line S1, cell 26 sister cell 1


title: Fibroblast_S1_c25_sc2

source_name: Primary fibroblast cell line S1, cell 25, sister cell 2


title: Normal 9408455026_G

value: Normal adjacent esophagus


title: Fibroblast_S1_c27_sc1

source_name: Primary fibroblast cell line S1, cell 27, sister cell 1

value: Female


title: 2646 7471147021_R01C01


title: Tumour 9408455012_H


title: 824 3999876164_R02C02

value: Tumour


title: Fibroblast_S1_c26_sc2

source_name: Primary fibroblast cell line S1, cell 26, sister cell 2


title: Fibroblast_S1_c20_sc2

source_name: Primary fibroblast cell line S1, cell 20, sister cell 2


title: SOG132 3999876164_R02C01

source_name: BE

value: BE


title: SOG132 3999876164_R03C01

source_name: Stomach

value: Stomach


title: Tumour 9408455012_J


title: Tumour 9408455012_G


title: Normal 9408455012_C


title: Tumour 9408455012_F


title: Normal 9408455012_B


title: Tumour 9408455012_D


title: Fibroblast_S1_c25_sc1

source_name: Primary fibroblast cell line S1, cell 25, sister cell 1


title: Fibroblast_S1_c23_sc2

source_name: Primary fibroblast cell line S1, cell 23, sister cell 2


title: Tumour 9408455012_E

source_name: Esophagus


title: Tumour 9408455026_D


title: Fibroblast_S1_c23_sc1

source_name: Primary fibroblast cell line S1, cell 23, sister cell 1


title: 3257 3999876164_R01C02

value: Normal


title: SOG040 3999876157_R03C01


title: SOG115 3999876157_R06C02


title: Tumour 9408455010_K


title: Tumour 9408455010_I


title: Tumour 9408455010_J


title: Tumour 9408455010_L


title: Tumour 9408455010_H


title: Normal 9408455012_A


title: Fibroblast_S1_c16_sc2

source_name: Primary fibroblast cell line S1, cell 16, sister cell 2


title: SOG129 3999876157_R03C02


title: Fibroblast_S1_c18_sc1

source_name: Primary fibroblast cell line S1, cell 18, sister cell 1


title: SOG093 3999876157_R02C02


title: Fibroblast_S1_c17_sc2

source_name: Primary fibroblast cell line S1, cell 17, sister cell 2


title: Fibroblast_S1_c16_sc1

source_name: Primary fibroblast cell line S1, cell 16, sister cell 1


title: Tumour 9408455010_C


title: Fibroblast_S1_c17_sc1

source_name: Primary fibroblast cell line S1, cell 17, sister cell 1


title: Fibroblast_S1_c18_sc2

source_name: Primary fibroblast cell line S1, cell 18, sister cell 2


title: SOG034 3999876157_R02C01

source_name: Tumour


title: SOG033 3999876157_R01C01


title: SOG023 3999876086_R05C02


title: Tumour 9408455001_K


title: Tumour 9408455010_E


title: Tumour 9408455001_C


title: Fibroblast_S1_c15_sc2

source_name: Primary fibroblast cell line S1, cell 15, sister cell 2


title: Tumour 9408455001_G


title: Fibroblast_S1_c14_sc2

source_name: Fibroblast cell line S1, cell 14, sister cell 2


title: Tumour 9408455001_L


title: Fibroblast_S1_c15_sc1

source_name: Primary fibroblast cell line S1, cell 15, sister cell 1


title: Tumour 9408455010_D


title: Fibroblast_S1_c14_sc1

source_name: Primary fibroblast cell line S1, cell 14, sister cell 1


title: Normal 9407205113_K


title: Normal 9407205113_L


title: Fibroblast_S1_c11_sc1

source_name: Primary fibroblast cell line S1, cell 11, sister cell 1


title: Normal 9407205113_I

source_name: Stomach


title: Fibroblast_S1_ c8_sc2

source_name: Primary fibroblast cell line S1, cell 8, sister cell 2


title: SOG040 3999876086_R04C01


title: Normal 9407205113_J


title: SOG049 3999876086_R04C02


title: Normal 9407205113_G


title: Normal 9407205113_E


title: Fibroblast_S1_c11_sc2

source_name: Primary fibroblast cell line S1, cell 11, sister cell 2


title: SOG049 3999876086_R03C02


title: SOG048 3999876086_R02C02


title: Tumour 9388254086_K


title: Tumour 9407205113_B


title: Fibroblast_S1_c20_sc1

source_name: Primary fibroblast cell line S1, cell 20, sister cell 1


title: Tumour 9407205113_C


title: Fibroblast_S1_c8_sc1

source_name: Primary fibroblast cell line S1, cell 8, sister cell 1


title: Tumour 9407205113_A


title: SOG033 3999876021_R06C02


title: SOG048 3999876086_R01C02

source_name: Normal


title: Normal 9388254065_E

source_name: Esophagus


title: Tumour 9388254086_J


title: Normal 9407205113_H


title: Tumour 9388254086_H


title: Normal 9388254065_D


title: SOG034 3999876086_R01C01


title: SOG047 3999876086_R05C01


title: Normal 9388254065_C


title: Tumour 9388254065_L


title: SOG047 3999876086_R06C01


title: SOG030 3999876021_R03C02


title: SOG032 3999876021_R04C02


title: SOG027 3999876021_R05C01


title: SOG030 3999876021_R02C02


title: SOG028 3999876021_R06C01


title: SOG023 3999876021_R04C01


title: SOG017 3999876021_R03C01


title: Tumour 9377361006_I


title: Normal 9388254065_B


title: Tumour 9377361006_G

value: Barrett's


title: SOG005 3999876021_R02C01


title: Tumour 9377361006_C


title: Tumour 9377361006_A


title: SOG005 3999876021_R01C01


title: Tumour 9377361006_B


title: Tumour 9370786050_L


title: BE 9377361006_H


title: BE 9377361006_F


title: Normal 9388254065_A


title: BE 9377361006_D


title: Tumour 9388254086_I


title: SOG101 3999876020_R04C02


title: Normal 9388254065_F


title: Tumour 9370786050_J


title: SOG003 3999876020_R06C02


title: Tumour 9370786050_K


title: SOG003 3999876020_R05C02


title: SOG093 3999876020_R02C02


title: SOG093 3999876020_R03C02


title: SOG085 3999876020_R04C01


title: BE 9377361006_E


title: Tumour 9370786050_H


title: Tumour 9370786050_G


title: Normal 9370786050_I


title: SOG065 3999875096_R05C01


title: SOG085 3999876020_R03C01


title: Tumour 9370786050_C


title: Tumour 9370786050_F


title: Tumour 9370786050_B


title: SOG052 3999875096_R04C01


title: SOG076 3999875096_R05C02


title: SOG072 3999875096_R03C02


title: SOG052 3999875096_R03C01


title: Tumour 9370786050_A


title: SOG072 3999875096_R04C02


title: Tumour 9370786050_E


title: Tumour 9370786050_D


title: SOG070 3999875096_R02C02


title: Ovcar8, JQ1 biological rep1

city: Bethesda

first: Marianne

middle: Kwang-Hee

last: Kim

state: MD

address: 10 Center Dr. 4B55

department: Women's Malignancies Branch

institute: NIH/NCI

description: Gene expression data from Ovcar8 JQ1

hyb_protocol: Hybridized to Affymetrix H133 Plus 2.0 gene chips,  following manufacturer protocol

scan_protocol: Scanned by Affymetrix GeneChip scanner 3000,  following manufacturer protocol

data_processing: CEL files were imported into GeneSpring software (Agilent), probe levels were normalized by the GC-RMA algorithm.

label: biotin

source_name: Ovcar8 JQ1

label_protocol: RNA (1ug) was reverse transcribed using iScript reverse transcriptase (BioRad)

growth_protocol: RPMI plus 10% fetal bovine serum (Hyclone, Pittsburg, PA) and standard antibiotics.

extract_protocol: Total RNA was isolated using RNeasy mini kit with on-column DNase treatment (Qiagen)

treatment_protocol: siRNA transfected cells (20 nM final concentration) were harvested at 48 hours post-transfection. JQ1 treatment was done for 24 hours at a final concentration of 0.5 uM in Ovcar8 and DMSO treated cells were used for a baseline control

tag: cell type

value: adherent ovarian cancer cells

tag: treatment


title: HuEx_77_NCI-H2198

first: Eric

middle: C

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized with Human Exon 1.0 ST Arrays (Affymetrix) at 45C, 60 rpm for 16 hrs.

scan_protocol: Arrays were washed and stained using Affymetrix Fluidics Station 450 and scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Probe set summarization and normalization with the core annotated probes was performed by robust multi-array averaging (RMA) and summarized at the gene level using AROMA.

label: fluorescence

source_name: human cell line

label_protocol: Sense strand cDNA from 100ng total RNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

extract_protocol: Total RNA, including the miRNA fraction, was extracted from samples using Qiagen miRNeasy Mini Kit (Qiagen, Valencia CA) according to manufacturer's instructions.  Agilent RNA Integrity Number (RIN) >8.5 indicated good quality RNA for all samples.

value: SCLC


title: Ovcar8, JQ1 biological rep3

description: Gene expression data from Ovcar8 JQ1


title: Ovcar8, JQ1 biological rep2

description: Gene expression data from Ovcar8 JQ1


title: Ovcar8 DMSO, biological rep2

description: Gene expression data from Ovcar8 DMSO

source_name: Ovcar8 Control

value: Control (for JQ1)


title: Ovcar8 DMSO, biological rep3

description: Gene expression data from Ovcar8 DMSO


title: HuEx_78_SW 1271


title: HuEx_8_NCI-H82


title: Ovcar8 siBRD4, biological rep3

description: Gene expression data from Ovcar8 siBRD4

source_name: Ovcar8 siBRD4


title: HuEx_74_DMS 53


title: HuEx_9_NCI-H128


title: LNCaP CRISP-3 knockdown clone rep2

city: Mumbai

first: Bhakti

middle: Rajesh

last: Pathak

address: Jehangir Merwanji Street

department: Structural Biology

country: India

institute: National Institute for research in Reproductive Health

description: Global gene expression profile of CRISP_3 knockdown clone of LNCaP at passage 13

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent   SurePrint G3 Human Exon 4x180K Microarray (AMADID -028679). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Agilent Feature Extraction software Version 11.5. Raw data were analyzed using Agilent GeneSpring GX software. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization)

source_name: CRISP-3 knockdown clone of LNCaP

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

growth_protocol: Cells were grown in RPMI containing 10%FCS

extract_protocol: RNA isolations were performed using Trizol method according to the manufacturer’s instructions

treatment_protocol: Stable clones with shRNA against CRISP-3 or with empty vector were selected on puromycin. Clones at two different passages were taken for global gene expression profiling.

value: LNCaP

value: Prostate cancer


title: HuEx_76_NCI-H2029


title: Ovcar8 siBRD4, biological rep2

description: Gene expression data from Ovcar8 siBRD4


title: HuEx_75_DMS 79


title: SOG022 3999875096_R01C01


title: HuEx_72_COR-L32


title: Ovcar8 DMSO, biological rep1

description: Gene expression data from Ovcar8 DMSO


title: SOG022 3999875096_R02C01

source_name: Tumour


title: SOG067 3999875096_R01C02


title: LNCaP CRISP-3 knockdown clone rep1

description: Global gene expression profile of CRISP_3 knockdown clone of LNCaP at passage 2


title: HuEx_73_COR-L47


title: HuEx_71_COLO 668


title: HuEx_70_NCI-H69VCR/R

value: Made resistant


title: MPP

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of biophysics, Chinese Academy of Sciences

description: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction.
Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 2 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

organism: Mus musculus

source_name: WT C57/BL6 mouse bone marrow

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: WT C57/BL6 mice were maintained in SPF conditions.

extract_protocol: Sorted cells were subjected to total RNA extraction with TRIZOL reagent. Total RNAs were digested with Rnase R to remove linear RNAs and enrich circular RNAs.

treatment_protocol: 8 week-old mice were anesthetized and bone marrow cells were flushed out, followed by LT-HSC and MPP sorting through a BD AriaIII sorter.

tag: strain

tag: genotype/variation

value: WT

value: bone marrow

value: MPP


title: LT-HSC

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

value: LT-HSC


title: Ovcar8 siNeg, biological rep3

description: Gene expression data from Ovcar8 siNeg

source_name: Ovcar8 siNeg

value: siNeg


title: LNCaP Empty vector clone rep2

description: Global gene expression profile of empty vector clone of LNCaP at passage 15

source_name: Empty vector clone of LNCaP


title: 1074 100973270018_R04C01


title: control sample2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: total RNA 48h mock infection

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent 8X60K Human Whole Genome Microarray Gene expression (AMADID: 039494) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

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

data_processing: Images Analysis using Agilent Feature Extraction Software Version 11.5 to obtain raw data.

source_name: cell culture system

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

growth_protocol: Cells were grown in complete DMEM medium

extract_protocol: Total RNA was extracted using qiagen column (RNeasy mini kit) as per manufacturer's protocol

treatment_protocol: Test samples were virus infected and total RNA was then extracte.

value: hepatic cell line Huh7.5

tag: infection

value: control


title: Ovcar8 siBRD4, biological rep1

description: Gene expression data from Ovcar8 siBRD4


title: HuEx_7_NCI-H69


title: control sample1

description: total RNA 48h mock infection


title: Ovcar8 siNeg, biological rep2

description: Gene expression data from Ovcar8 siNeg


title: test sample1

description: total RNA 48h post infection

value: HCV (JFH-1)


title: Ovcar8 siNeg, biological rep1

description: Gene expression data from Ovcar8 siNeg


title: test sample2

description: total RNA 48h post infection


title: LNCaP Empty vector clone rep1

description: Global gene expression profile of empty vector clone of LNCaP at passage 2


title: monkey 1030 1

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

hyb_protocol: Hybridization, staining and washing of the arrays were performed in the Affymetrix Fluidics station 4

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Affymetrix Power Tools, using RMA normalization.

organism: Chlorocebus sabaeus

source_name: corpus luteum

label_protocol: Labeled cRNA probes were generated from total RNA using MessageAmp Premier RNA Amplification Kit

extract_protocol: Frozen CL tissue was first minced into small 2 mm pieces in a sterile dish on ice and then placed in TRIzol® Reagent (Life Technologies) followed by a brief homogenization on ice using a tissue homogenizer. Chloroform was added in 1:5 ratio and the samples were centrifuged 12,000x g for 15 minutes at +4ºC to allow the separation of layers as per the manufacturer’s instructions.

treatment_protocol: Two adult female vervet monkeys 16 years of age from the Vervet Research Colony (VRC) at the Wake Forest University Primate Center were used for this study. Each monkey was assigned to one of the two experimental groups: Ad libitum (monkey 1030) or calorie restriction group (monkey 1031).  Each vervet served as its own control to measure the effect of weight change within each animal

tag: age

tag: diet

value: ad lib


title: HuEx_69_NCI-H69/LX10


title: monkey 1030 2


title: monkey 1031 2

value: calory restriction


title: SW 1271_miRNA

description: Total RNA including small RNA

hyb_protocol: Samples were hybridized for 16 hrs to NanoString human miRNA probeset, which contains probe pairs specific for each miRNA with different fluorescent barcode labels. The probe pair consists of a Reporter Probe, which carries the fluorescent signal on its 5' end, and a Capture Probe which carries a biotin on its 3' end.    After hybridization, excess probes are washed away using a two step magnetic bead-based purification on the nCounter™ Prep Station and are immobilized in the cartridge for data collection.

scan_protocol: Data Collection is carried out in the nCounter Digital Analyzer. Digital images are processed and the barcode counts are tabulated in a RCC format.

data_processing: Data were analyzed using custom R scripts

source_name: SCLC

label_protocol: Total RNA (100 ng) was ligated to unique oligonuceotide tag to increase the length of the short miRNA for subsequent detection in a single reaction without amplification using NanoString kit following manufacturer’s suggested protocol.

growth_protocol: The sixty-three small cell lung carcinoma (SCLC) cell lines used in the study were purchased from American Type Culture Collection (ATCC, Manassas, VA) or were obtained from the National Cancer Institute cell line repository (NCI, Frederick, MD). In addition, NCI-H28 mesothelioma, NCI-H2066 mixed SCLC/NSCLC, NCI-H1650 NSCLC, and A549/ATCC NSCLC were purchased from ATCC and included as comparators to the SCLC lines. Cells were maintained in a 5% CO2-humidified incubator at 37 degrees C.


title: NCI-H2198_miRNA

description: Total RNA including small RNA


title: NCI-H2029_miRNA

description: Total RNA including small RNA


title: DMS 53_miRNA

description: Total RNA including small RNA

value: DMS 53


title: COR-L47_miRNA

description: Total RNA including small RNA


title: monkey 1031 1


title: COR-L32_miRNA

description: Total RNA including small RNA


title: HuEx_66_NCI-H2066

value: NSCLC


title: HuEx_65_NCI-H1882

value: SCLC


title: HuEx_64_NCI-H1694


title: COLO 668_miRNA

description: Total RNA including small RNA

value: COLO 668


title: DMS 79_miRNA

description: Total RNA including small RNA

value: DMS 79


title: NCI-H847_miRNA

description: Total RNA including small RNA


title: HuEx_61_NCI-H1341


title: HuEx_60_NCI-H847


title: Human primary keratinocytes, formaldehyde, bio rep 1

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Gene expression data from formaldehyde treated-cultured human epidermal primary keratinocytes for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Cultured human primary epidermal keratinocytes, formaldehyde treated, 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

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

treatment_protocol: At passge 2, when NHKs were confluent in culture, 200 μM of formaldehyde were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell

value: human epidermal keratinocytes

value: formaldehyde for 24 hours


title: HuEx_63_NCI-H1672


title: SBI-756 resistant 14,UACC1120

city: Rockville

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

description:
Sample name: R7_UACC1120
Melanoma cell lines resistant to SBI-756 without treatment

hyb_protocol: Per manufacturer’s protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Operating Software (GCOS)

data_processing: The robust multi-array average (GCRMA) method (Bioconductor;bioconductor.org) was used to background-adjust and normalize expression intensity values.  Probesets with present calls in less than four of the seven most SBI-756-sensitive and –resistant samples, respectively, were filtered.

source_name: SBI-756 resistant UACC melanoma cell line

label_protocol: Per manufacturer’s protocol

extract_protocol: Per manufacturer’s protocol

tag: tumor stage

value: metastasis


title: NCI-H735_miRNA

description: Total RNA including small RNA


title: SBI-756 resistant 12,UACC1118

description:
Sample name: R5_UACC1118
Melanoma cell lines resistant to SBI-756 without treatment

value: SBI-756 resistant UACC melanoma cell line


title: HuEx_68_NCI-H69/CPR

value: Made resistant


title: HuEx_62_NCI-H1650


title: Human primary keratinocytes, formaldehyde, bio rep 2


title: NCI-H69/LX10_miRNA

description: Total RNA including small RNA

source_name: Made resistant


title: HuEx_67_NCI-H2141


title: NCI-H69VCR/R_miRNA

description: Total RNA including small RNA


title: SBI-756 resistant 13,UACC2512

description:
Sample name: R6_UACC2512
Melanoma cell lines resistant to SBI-756 without treatment


title: NCI-H69/CPR_miRNA

description: Total RNA including small RNA


title: SBI-756 resistant 11,UACC2404

description:
Sample name: R4_UACC2404
Melanoma cell lines resistant to SBI-756 without treatment


title: HuEx_59_NCI-H735


title: SBI-756 resistant 10,UACC1940

description:
Sample name: R3_UACC1940
Melanoma cell lines resistant to SBI-756 without treatment


title: HuEx_58_A549/ATCC


title: HuEx_57_NCI-H2330


title: NCI-H2141_miRNA

description: Total RNA including small RNA


title: HuEx_56_NCI-H2081


title: SBI-756 resistant 8,UACC647

description:
Sample name: R1_UACC647
Melanoma cell lines resistant to SBI-756 without treatment


title: NCI-H2066_miRNA

description: Total RNA including small RNA

source_name: NSCLC


title: HuEx_6_NCI-H28

value: Mesothelioma


title: NCI-H1882_miRNA

description: Total RNA including small RNA


title: SBI-756 resistant 9,UACC2496

description:
Sample name: R2_UACC2496
Melanoma cell lines resistant to SBI-756 without treatment


title: SBI-756 sensitive 7,UACC1592

description:
Sample name: S7_UACC1592
Melanoma cell lines sensitive to SBI-756 without treatment

source_name: SBI-756 sensitive UACC melanoma cell line


title: NCI-H1694_miRNA

description: Total RNA including small RNA


title: HuEx_54_NCI-H1836


title: NCI-H1672_miRNA

description: Total RNA including small RNA


title: HuEx_52_NCI-H1436


title: SBI-756 sensitive 6,UACC558

description:
Sample name: S6_UACC558
Melanoma cell lines sensitive to SBI-756 without treatment

value: SBI-756 sensitive UACC melanoma cell line


title: HuEx_53_NCI-H1618


title: HuEx_51_NCI-H1417


title: HuEx_55_NCI-H1876


title: NCI-H1650_miRNA

description: Total RNA including small RNA


title: NCI-H1341_miRNA

description: Total RNA including small RNA


title: NCI-H2330_miRNA

description: Total RNA including small RNA


title: NCI-H711_miRNA

description: Total RNA including small RNA


title: NCI-H1048_miRNA

description: Total RNA including small RNA


title: NCI-H2081_miRNA

description: Total RNA including small RNA


title: HuEx_50_NCI-H1092


title: SBI-756 sensitive 4,UACC3337

description:
Sample name: S4_UACC3337
Melanoma cell lines sensitive to SBI-756 without treatment


title: HuEx_5_WI-38

value: Fibroblast


title: NCI-H1876_miRNA

description: Total RNA including small RNA


title: HuEx_49_NCI-H1048


title: NCI-H1836_miRNA

description: Total RNA including small RNA


title: SBI-756 sensitive 3,UACC2545

description:
Sample name: S3_UACC2545
Melanoma cell lines sensitive to SBI-756 without treatment


title: SBI-756 sensitive 5,UACC2641

description:
Sample name: S5_UACC2641
Melanoma cell lines sensitive to SBI-756 without treatment


title: NCI-H1618_miRNA

description: Total RNA including small RNA


title: SBI-756 sensitive 2,UACC3291

description:
Sample name: S2_UACC3291
Melanoma cell lines sensitive to SBI-756 without treatment


title: SBI-756 sensitive 1,UACC952

description:
Sample name: S1_UACC952
Melanoma cell lines sensitive to SBI-756 without treatment


title: NCI-H1436_miRNA

description: Total RNA including small RNA


title: NCI-H1417_miRNA

description: Total RNA including small RNA


title: HuEx_46_COR L88


title: LXFS 650L_miRNA

description: Total RNA including small RNA

value: LXFS 650L


title: NCI-H1092_miRNA

description: Total RNA including small RNA


title: HuEx_47_LXFS 650L


title: HuEx_45_LXFS 605L


title: HuEx_48_NCI-H711


title: HuEx_44_NCI-H841


title: HuEx_41_NCI-H719


title: COR L88_miRNA

description: Total RNA including small RNA

value: COR L88


title: CTR A 3

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

source_name: Primary astrocytes

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.

value: striatum

value: Primary astrocytes

value: Vehicle


title: NCI-H841_miRNA

description: Total RNA including small RNA


title: HuEx_40_NCI-H1522

source_name: human cell line


title: CTR N 1

source_name: Primary neurons

value: Primary neurons


title: CTR A 4


title: HuEx_42_NCI-H748

value: SCLC


title: NCI-H774_miRNA

description: Total RNA including small RNA


title: ALD N 4

value: Aldosterone


title: HuEx_39_NCI-H220


title: HuEx_4_MRC-9


title: HuEx_38_NCI-H2107


title: HuEx_43_NCI-H774


title: NCI-H748_miRNA

description: Total RNA including small RNA


title: CTR A 2


title: NCI-H719_miRNA

description: Total RNA including small RNA


title: ALD N 2


title: NCI-H2107_miRNA

description: Total RNA including small RNA


title: NCI-H220_miRNA

description: Total RNA including small RNA


title: HuEx_37_NCI-H1105


title: HuEx_35_NCI-H720


title: NCI-H1522_miRNA

description: Total RNA including small RNA


title: ALD N 3


title: ALD N 1


title: ALD A 4


title: HuEx_32_NCI-H345


title: HuEx_34_NCI-H660


title: NCI-H1105_miRNA

description: Total RNA including small RNA


title: HuEx_36_SHP-77


title: ALD A 3


title: SHP-77_miRNA

description: Total RNA including small RNA


title: HuEx_33_NCI-H510


title: ALD A 1


title: HuEx_30_NCI-H249


title: ALD A 2


title: LXFS 605L_miRNA

description: Total RNA including small RNA

value: LXFS 605L


title: NCI-H660_miRNA

description: Total RNA including small RNA


title: HuEx_3_NLRna2

value: Normal lung RNA


title: CTR A 1


title: HuEx_31_NCI-H250


title: NCI-H720_miRNA

description: Total RNA including small RNA


title: PRG N 4

value: Progesterone


title: NCI-H510_miRNA

description: Total RNA including small RNA


title: PRG N 1


title: HuEx_26_DMS 187


title: PRG N 3


title: HuEx_25_DMS 114


title: HuEx_27_DMS 273


title: NCI-H250_miRNA

description: Total RNA including small RNA


title: NCI-H345_miRNA

description: Total RNA including small RNA


title: NCI-H249_miRNA

description: Total RNA including small RNA


title: PRG A 4


title: PRG N 2


title: PRG A 2


title: HuEx_23_NCI-H1930


title: HuEx_29_NCI-H209


title: HuEx_24_NCI-H2171


title: DMS 273_miRNA

description: Total RNA including small RNA

value: DMS 273


title: BxPC3, biological replicate 1

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

description: miRNA expression data from PDAC cell line

hyb_protocol: 400 ng labelled RNA were hybridized for 18 hr at 48C (rotation 60 rpm) on GeneChip® miRNA 3.0 Array. Chips were washed in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console software Build 1.2.1.20 (Affymetrix, Santa Clara, CA, USA) using the Affymetrix default analysis setting for RMA+DAGB workflow

source_name: BxPC3, biological replicate 1

label_protocol: 400 ng of cellular RNA enriched for small RNAs were labeled using the FlashTag Biotin HSR Labeling Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: BxPC3 cells were maintained in RPMI 1640 medium supplemented with 10% FBS (Atlanta Biologicals, Lawrenceville, GA), 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA). BxPC3-R cells were maintained in the full RPMI medium supplemented with 0.6 uM cisplatin.

extract_protocol: Cellular RNA enriched for small RNAs (<200 nts) was isolated using the mirVana miRNA Isolation Kit (ThermoFisher Scientific) according to the manufacturer’s instructions

value: cell line (parental)

value: PDAC


title: PRG A 1


title: BxPC3, biological replicate 2

source_name: BxPC3, biological replicate 2


title: NCI-H209_miRNA

description: Total RNA including small RNA


title: HuEx_21_NCI-H1688


title: ESR N 4

value: Estradiol


title: BxPC3-R, biological replicate 2

description: miRNA expression data from PDAC cell line resistant to cisplatin

source_name: BxPC3-R, biological replicate 2

value: cell line (cisplatin-resistant)


title: HuEx_22_NCI-H1963


title: DMS 114_miRNA

description: Total RNA including small RNA

value: DMS 114


title: DMS 187_miRNA

description: Total RNA including small RNA

value: DMS 187


title: PRG A 3


title: ESR N 3


title: ESR N 2


title: BxPC3-R, biological replicate 1

source_name: BxPC3-R, biological replicate 1


title: HuEx_2_NLRna1


title: ESR N 1


title: WI-38_miRNA

description: Total RNA including small RNA

source_name: Fibroblast

value: Fibroblast


title: HuEx_19_NCI-H865


title: NLRna2_miRNA

description: Total RNA including small RNA

source_name: Normal lung RNA


title: TC-2742-2-Ebf2 (tc-2742-mycEbf)

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

scan_protocol: Standard protocol provided by Affymetrix for GeneChip® Human Gene 2.0 ST Array using GeneChip 3000-7G

data_processing:
Data were processed using GeneChip® Command Console® Software (AGCC)
HuGene-1_1-st-v1.pgf
HuGene-1_1-st-v1.mps

growth_protocol: Cell lines grown in RPMI-1640 with 5%FBS

extract_protocol: RNA isolated using Trizol

treatment_protocol: Experimental cells transfected with Human Ebf2 plasmids

value: Epithelial (TC-2742-2) cells

tag: source of cell line

value: tumor derived, Female

tag: protocol

value: Ebf2 expressed


title: NLRna1_miRNA

description: Total RNA including small RNA


title: ESR A 4

tag: tissue

value: striatum

value: Primary astrocytes


title: HuEx_16_NCI-H524

value: SCLC


title: NCI-H889_miRNA

description: Total RNA including small RNA


title: ESR A 3


title: NCI-H865_miRNA

description: Total RNA including small RNA


title: HuEx_15_NCI-H446


title: HuEx_17_NCI-H526


title: HuEx_14_NCI-H378


title: TC-2742-2-Ebf2 (r-tc-2742-mycEbf)

hyb_protocol: Standard protocol provided by Affymetrix for GeneChip® Human Gene 2.0 ST Array


title: HuEx_13_NCI-H211


title: NCI-H82_miRNA

description: Total RNA including small RNA


title: ESR A 2


title: amiR-snf4 light-grown seedling, biological rep3

city: Cologne

first: Csaba

last: Koncz

address: Carl-von-Linne-Weg 10

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

description: Gene expression data from 5 days old amiR-SNF4 silenced light-grown seedlings

hyb_protocol: After amplification and fragmentation, 12.5 μg of cRNA was hybridized for 16 hr at 45°C on GeneChip ATH1-121501 Genome Array. GeneChips were washed and stained with Fluidics Script FS450_004 in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with Affymetrix GeneChip Operating Software (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: Arabidopsis amiR-SNF4 silenced light-grown seedlings 5 days after germination

label_protocol: Biotinylated cRNA was prepared according to the standard Ambion protocol from 1 μg total RNA (MessageAmp II-Biotin Enhanced Kit, 2008, Ambion).

growth_protocol: Seedlings were grown in solid MSAR medium containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period.

extract_protocol: Total RNA was isolated with RNeasy Mini kit supplied with RNase-Free DNase set (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Whole seedling were collected at 4h after the start of the light period for RNA preparation.

value: young seedlings

tag: cultivar

tag: genotype

value: amiR-SNF4 silenced

value: germinated seedlings 7 days after sewing collected at 4h after the start of the light period using a photoperiod of 8h light and 16h dark with 120 mol/m2s light intensity at 22°C


title: DHT N 4

value: Primary neurons

value: Dihydrotestosterone


title: NCI-H69_miRNA

description: Total RNA including small RNA

tag: cell line


title: HuEx_12_NCI-H196


title: MiaPaCa-Endothelial (r-mia-endo)

source_name: r-mia-endo

label_protocol: Standard protocol provided by Affymetrix for GeneChip® Human Gene 2.0 ST Array

value: Mesenchymal pancreatic adenocarcinoma (MiaPaCa) cells

value: male

value: Ebf2-Endothelial differentiated


title: NCI-H526_miRNA

description: Total RNA including small RNA

source_name: SCLC


title: TC-2742-2-Control (r-tc-2742-null)

value: Control


title: ESR A 1

value: Estradiol


title: DHT N 3


title: HuEx_11_NCI-H187


title: DHT N 2


title: amiR-snf4 light-grown seedling, biological rep1


title: TC-2742-2-Control (tc-2742-null)


title: DHT N 1


title: MiaPaCa-Control (r-mia-null)

source_name: r-mia-null


title: NCI-H446_miRNA

description: Total RNA including small RNA


title: NCI-H524_miRNA

description: Total RNA including small RNA


title: MiaPaCa-Endothelial (mia-endo)

source_name: mia-endo


title: amiR-snf4 light-grown seedling, biological rep2


title: wt light-grown seedling, biological rep3

description: Gene expression data from 5 days old wild type light-grown seedlings

source_name: Arabidopsis light-grown wild type seedlings 5 days after germination

value: wild type control


title: HuEx_10_NCI-H146


title: HuEx_1_NARna

value: Normal adrenal RNA


title: DHT A 3


title: MiaPaCa-Control (mia-null)

source_name: mia-null


title: wt light-grown seedling, biological rep1


title: DHT A 4


title: DHT A 2


title: NCI-H28_miRNA

description: Total RNA including small RNA

source_name: Mesothelioma

value: Mesothelioma


title: wt light-grown seedling, biological rep2


title: MiaPaCa-Control (2-Null)


title: NCI-H2171_miRNA

description: Total RNA including small RNA


title: MiaPaCa-Adipose (6-Adip)

value: Ebf2-Adipose differentiated


title: NCI-H211_miRNA

description: Total RNA including small RNA


title: amiR-snf4 dark-grown seedling, biological rep3

description: Gene expression data from 5 days old amiR-SNF4 silenced dark-grown seedlings

source_name: Arabidopsis amiR-SNF4 silenced dark-grown seedlings 5 days after germination

value: 5 days old dark-grown seedlings


title: NCI-H1963_miRNA

description: Total RNA including small RNA


title: DHT A 1

source_name: Primary astrocytes

value: striatum

value: Primary astrocytes


title: NCI-H378_miRNA

description: Total RNA including small RNA

value: SCLC


title: MiaPaCa-Adipose (5-Adip)


title: HuEx_20_NCI-H889

source_name: human cell line


title: amiR-snf4 dark-grown seedling, biological rep2

value: young seedlings

value: amiR-SNF4 silenced


title: DEX N 3

source_name: Primary neurons

value: Primary neurons

value: Dexamethasone


title: NCI-H1930_miRNA

description: Total RNA including small RNA


title: shAR+shSTAT5-3

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: AR+STAT5 knockdown CWR22Pc cells, sequentially transduced with 1) AR-shRNA, 2) STAT5-shRNA lentiviruses

hyb_protocol: Affymetrix gene chips, Human Gene 2.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (3.4 μg) in 150 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips (Human Gene 2.0 ST array) were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Raw intensity files from the Affymetrix Human Gene 2.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.3.1. Gene-level expression measurements were computed using the iterPLIER algorithm with default parameters.

source_name: CWR22Pc prostate cancer cell line

label_protocol: Amplified cDNA was synthesized from 50 ng of total RNA using NuGen Ovation Pico WTA systems V2 (NuGen Technologies, Inc.). 5 μg cDNA was fragmented and chemically labeled with biotin to generate biotinylated cDNA using Encore biotin module (NuGen Technologies, Inc.).

growth_protocol: CWR22Pc cells were maintained in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin and L-glutamine and 0.8 nM dihydrotestosterone (DHT).

extract_protocol: CWR22Pc cells were harvested and total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). A DNase I digestion step was included to eliminate DNA contamination.

treatment_protocol: CWR22Pc cells were sequentially transduced three days apart (day 0>day 3) as follows: 1) shCtrl>shCtrl (control); 2) shAR>shCtrl (AR knockdown alone); 3) shStat5a/b>shCtrl (Stat5a/b knockdown alone); 4) shAR>shStat5a/b (sequential AR knockdown followed by Stat5a/b knockdown). On day 6, cells were harvested.

tag: shRNA


title: DEX N 4


title: DEX N 2


title: wt dark-grown seedling, biological rep3

description: Gene expression data from 5 days old wild type dark-grown seedlings

source_name: Arabidopsis dark-grown wild type seedlings 5 days after germination


title: wt dark-grown seedling, biological rep2


title: amiR-snf4 dark-grown seedling, biological rep1


title: NCI-H187_miRNA

description: Total RNA including small RNA


title: shSTAT5-3

description: STAT5 knockdown CWR22Pc cells, sequentially transduced with 1) STAT5-shRNA, 2) scramble-shRNA lentiviruses


title: shAR+shSTAT5-2


title: DEX N 1


title: MiaPaCa-Control (1-Null)

value: Mesenchymal pancreatic adenocarcinoma (MiaPaCa) cells


title: NCI-H1688_miRNA

description: Total RNA including small RNA


title: DEX A 4


title: NCI-H196_miRNA

description: Total RNA including small RNA


title: wt dark-grown seedling, biological rep1


title: shSTAT5-2


title: NCI-H146_miRNA

description: Total RNA including small RNA


title: shAR+shSTAT5-1


title: DEX A 2


title: NCI-H128_miRNA

description: Total RNA including small RNA


title: shAR-3

description: AR knockdown CWR22Pc cells, sequentially transduced with 1) AR-shRNA, 2) scramble-shRNA lentiviruses

value: shAR+scramble


title: NARna_miRNA

description: Total RNA including small RNA

source_name: Normal adrenal RNA

value: NARna


title: DEX A 1


title: shSTAT5-1


title: Spleen.Day3LPS.PlasmaCell.1.GX

first: Benjamin

middle: G

last: Barwick

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
PlasmaCell.1.GX
6085341003_F_Grn
LPS Plasma Cell replicate 1

hyb_protocol: Hybridization was performed following the manufacturer's instructions (Illumina)

scan_protocol: BeadArrays were scanned following the manufacturer's instructions (Illumina) using an iScan

data_processing: Data were quantile normalized using GenomeStudio (v2011.1) and exported for analysis

source_name: Spleen Day 3 LPS Mouse

label_protocol: cDNA was labelled following the manufacturer's instructions (Illumina)

extract_protocol: RNA was extracted using the RNeasy mini prep kit (Qiagen) following the manufacturer's instructions

tag: gender

value: female

value: Spleen

value: 10 weeks

value: Plasma cell

tag: agent

value: LPS


title: MRC-9_miRNA

description: Total RNA including small RNA

source_name: Fibroblast

tag: cell type

value: Fibroblast


title: Spleen.Day3LPS.Plasmablast.3.GX

description:
Plasmablast.3.GX
6085341003_E_Grn
LPS Plasmablast replicate 3

tag: strain

value: Plasmablast


title: DEX A 3

value: striatum

tag: treatment


title: Spleen.Day3LPS.Plasmablast.2.GX

description:
Plasmablast.2.GX
6085341003_D_Grn
LPS Plasmablast replicate 2


title: shAR-1


title: Spleen.Day3LPS.Plasmablast.1.GX

description:
Plasmablast.1.GX
6085341003_C_Grn
LPS Plasmablast replicate 1


title: CTR N 4

value: Vehicle


title: CTR N 3


title: Spleen.Day3LPS.PlasmaCell.2.GX

description:
PlasmaCell.2.GX
6085341003_G_Grn
LPS Plasma Cell replicate 2


title: CTR N 2


title: Spleen.NaiveMouse.Bcell.2.GX

description:
Bcell.2.GX
6085341003_B_Grn
Naïve B cell replicate 2

source_name: Spleen Naive Mouse

value: B cell

value: control


title: shAR-2


title: shCtrl-3

description: Control CWR22Pc cells, sequentially transduced with 1) scramble-shRNA, 2) scramble-shRNA lentiviruses

value: scramble+scramble


title: shCtrl-2


title: Spleen.NaiveMouse.Bcell.1.GX

description:
Bcell.1.GX
6085341003_A_Grn
Naïve B cell replicate 1


title: shCtrl-1


title: HCT116-xeno_Sel034-4h_1

status: Public on Mar 01 2016

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

institute: Uniwersytet Warszawski

description: SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol. Hybridization performed in AROS (Denmark) http://arosab.com/services/microarrays/gene-expression/

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized using lumi library in R 3.1.1, separately for xenograft samples (1-21) and cell culture samples (22-24)

source_name: HCT cell line xenograft

label_protocol: Standard Illumina labeling protocol

extract_protocol: Following extraction tumors were preserved in RNAlater (Qiagen) and stored at -80°C. A scoop of a tumor (~25mg) was homogenized with pestle under liquid nitrogen and immediately processed according to RNeasy Mini Kit protocol (Qiagen). RNA concentration was measured with NanoDrop spectrophotometer and stored at -80°C. Prior to microarray analyses the quality of the RNA samples was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

value: inhibitor 4h


title: HCT116-xeno_Sel034-16h_1

description: SAMPLE 19

value: inhibitor 16h


title: HCT116-xeno_control_5

description: SAMPLE 14


title: HCT116-xeno_Sel034-4h_3

description: SAMPLE 18


title: VA5018

status: Public on Feb 29 2016

city: San Francisco

first: Esteban

middle: G.

last: Burchard

state: CA

institute: University of California, San Francisco (UCSF)

description: normal blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Processed matrix includes SWAN normalized and COMBAT corrected average Beta

label: Cy5 and Cy3

source_name: genomic DNA from whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Promega Wizard Kits according to standard instructions

value: Female

tag: sample type

value: DNA

tag: lymphocytes

tag: monocytes

tag: ethnicity

value: Mexican


title: HCT116-xeno_Sel034-16h_3

description: SAMPLE 21


title: HCT116-xeno_Sel034-16h_2

description: SAMPLE 20


title: HCT116-xeno_Sel034-4h_2

description: SAMPLE 17


title: HCT116-xeno_control_4

description: SAMPLE 13


title: HCT116-xeno_control_6

description: SAMPLE 15


title: VA5022

description: normal blood sample


title: VA5016

description: normal blood sample

value: Male

value: Other Latino


title: colo205-xeno_Sel034-4h_1

description: SAMPLE 4

source_name: colo205 cell line xenograft


title: colo205-xeno_Sel034-16h_3

description: SAMPLE 9


title: VA1048

description: normal blood sample


title: VA5002

description: normal blood sample


title: VA5007

description: normal blood sample


title: HCT116-xeno_control_2

description: SAMPLE 11


title: HCT116-xeno_control_3

description: SAMPLE 12


title: colo205-xeno_Sel034-4h_2

description: SAMPLE 5


title: colo205-xeno_control_3

description: SAMPLE 3


title: VA5047

description: normal blood sample


title: VA1025

description: normal blood sample


title: colo205-xeno_control_1

description: SAMPLE 1


title: colo205-xeno_control_2

description: SAMPLE 2


title: VA1018

description: normal blood sample


title: VA1009

description: normal blood sample


title: VA1011

description: normal blood sample

value: Mixed Latino


title: colo205-xeno_Sel034-4h_3

description: SAMPLE 6


title: TX5158

description: normal blood sample


title: TX5155

description: normal blood sample


title: TX5106

description: normal blood sample


title: TX5098

description: normal blood sample


title: TX5090

description: normal blood sample


title: TX5086

description: normal blood sample

value: Puerto Rican


title: TX5058

description: normal blood sample


title: TX5062

description: normal blood sample


title: TX5056

description: normal blood sample


title: TX5043

description: normal blood sample


title: TX5104

description: normal blood sample


title: TX5054

description: normal blood sample


title: TX5042

description: normal blood sample


title: TX5088

description: normal blood sample


title: TX5038

description: normal blood sample


title: TX5028

description: normal blood sample


title: TX5041

description: normal blood sample


title: TX5021

description: normal blood sample


title: TX5036

description: normal blood sample


title: TX5013

description: normal blood sample


title: TX5023

description: normal blood sample


title: TX5022

description: normal blood sample


title: TX5017

description: normal blood sample


title: TX5015

description: normal blood sample


title: TX5020

description: normal blood sample


title: TX1198

description: normal blood sample


title: TX1196

description: normal blood sample


title: TX5009

description: normal blood sample


title: TX1194

description: normal blood sample


title: TX1185

description: normal blood sample


title: TX1179

description: normal blood sample


title: TX1180

description: normal blood sample


title: TX1167

description: normal blood sample


title: TX1125

description: normal blood sample


title: TX1110

description: normal blood sample


title: TX1097

description: normal blood sample


title: TX1182

description: normal blood sample


title: TX1105

description: normal blood sample


title: TX1123

description: normal blood sample


title: TX1084

description: normal blood sample


title: TX1060

description: normal blood sample


title: TX1055

description: normal blood sample


title: TX1037

description: normal blood sample


title: TX1052

description: normal blood sample


title: TX1050

description: normal blood sample


title: SJ5437

description: normal blood sample


title: TX1058

description: normal blood sample


title: SJ5423

description: normal blood sample


title: SJ1456

description: normal blood sample


title: SJ1459

description: normal blood sample


title: SJ5424

description: normal blood sample


title: SJ5429

description: normal blood sample


title: SJ5436

description: normal blood sample


title: colo205-xeno_Sel034-16h_1

description: SAMPLE 7


title: TX5029

description: normal blood sample


title: SJ1298

description: normal blood sample


title: SJ1156

description: normal blood sample


title: SJ1359

description: normal blood sample


title: SJ1033

description: normal blood sample


title: SJ1093

description: normal blood sample


title: SJ1204

description: normal blood sample


title: SJ1241

description: normal blood sample


title: SF5157

description: normal blood sample


title: SF5153

description: normal blood sample


title: SJ1367

description: normal blood sample


title: SF5154

description: normal blood sample


title: SF5139

description: normal blood sample


title: SF5150

description: normal blood sample


title: SF5136

description: normal blood sample


title: SF5126

description: normal blood sample


title: SF5131

description: normal blood sample


title: TX1067

description: normal blood sample


title: SF5164

description: normal blood sample


title: SF5105

description: normal blood sample


title: SF5119

description: normal blood sample


title: SF1120

description: normal blood sample


title: RI1010

description: normal blood sample


title: RI1005

description: normal blood sample


title: OK1008

description: normal blood sample


title: SF5135

description: normal blood sample


title: OK1007

description: normal blood sample


title: NY50283

description: normal blood sample


title: NY50290

description: normal blood sample


title: NY50282

description: normal blood sample


title: NY50292

description: normal blood sample


title: OK1006

description: normal blood sample


title: NY50278

description: normal blood sample


title: NY50291

description: normal blood sample


title: NY50273

description: normal blood sample


title: NY50248

description: normal blood sample


title: NY50271

description: normal blood sample


title: NY50245

description: normal blood sample


title: NY50247

description: normal blood sample


title: NY50244

description: normal blood sample


title: NY50242

description: normal blood sample


title: SF1117

description: normal blood sample


title: NY50237

description: normal blood sample


title: SF1099

description: normal blood sample


title: NY50241

description: normal blood sample


title: NY50231

description: normal blood sample


title: NY50294

description: normal blood sample


title: NY50228

description: normal blood sample


title: NY50229

description: normal blood sample


title: NY50224

description: normal blood sample


title: SF1113

description: normal blood sample


title: NY50222

description: normal blood sample


title: NY50206

description: normal blood sample


title: NY50196

description: normal blood sample


title: NY50217

description: normal blood sample


title: NY50204

description: normal blood sample


title: NY50220

description: normal blood sample


title: NY50192

description: normal blood sample


title: RI1004

description: normal blood sample


title: NY50188

description: normal blood sample


title: NY10328

description: normal blood sample


title: NY10316

description: normal blood sample


title: NY10303

description: normal blood sample


title: NY50235

description: normal blood sample


title: NY10319

description: normal blood sample


title: NY10266

description: normal blood sample


title: NY10288

description: normal blood sample


title: NY10285

description: normal blood sample


title: NY10265

description: normal blood sample


title: NY50226

description: normal blood sample


title: NY10258

description: normal blood sample


title: NY10263

description: normal blood sample


title: NY10257

description: normal blood sample


title: NY10246

description: normal blood sample


title: NY10245

description: normal blood sample


title: NY10244

description: normal blood sample


title: NY50190

description: normal blood sample


title: NW5093

description: normal blood sample


title: NW5074

description: normal blood sample


title: NY10236

description: normal blood sample


title: NY10239

description: normal blood sample


title: NW5086

description: normal blood sample


title: NW5036

description: normal blood sample


title: NY10243

description: normal blood sample


title: NY10299

description: normal blood sample


title: NW5008

description: normal blood sample


title: NW5035

description: normal blood sample


title: NW1096

description: normal blood sample


title: NW5007

description: normal blood sample


title: NW1068

description: normal blood sample


title: NW1065

description: normal blood sample


title: NY10248

description: normal blood sample


title: NW1062

description: normal blood sample


title: NW1052

description: normal blood sample


title: NW1030

description: normal blood sample


title: NY10241

description: normal blood sample


title: NW1029

description: normal blood sample


title: NW1024

description: normal blood sample


title: NW5039

description: normal blood sample


title: LC5105

description: normal blood sample


title: LC5102

description: normal blood sample


title: NW1004

description: normal blood sample


title: NW1010

description: normal blood sample


title: NW1012

description: normal blood sample


title: TX5039

description: normal blood sample


title: NW1005

description: normal blood sample


title: LC5089

description: normal blood sample


title: LC5092

description: normal blood sample


title: NW1060

description: normal blood sample


title: LC5085

description: normal blood sample


title: NW1011

description: normal blood sample


title: NW1013

description: normal blood sample


title: NW5073

description: normal blood sample


title: LC5084

description: normal blood sample


title: LC5083

description: normal blood sample


title: LC5078

description: normal blood sample


title: LC5082

description: normal blood sample


title: LC5077

description: normal blood sample


title: LC5076

description: normal blood sample


title: LC5106

description: normal blood sample


title: LC5101

description: normal blood sample


title: LC1104

description: normal blood sample


title: LC1101

description: normal blood sample


title: NW1067

description: normal blood sample


title: LC1094

description: normal blood sample


title: LC1085

description: normal blood sample


title: LC1077

description: normal blood sample


title: LC1087

description: normal blood sample


title: LC1093

description: normal blood sample


title: LC5087

description: normal blood sample


title: LC1091

description: normal blood sample


title: LC1076

description: normal blood sample


title: HCT116-xeno_control_1

description: SAMPLE 10


title: HR5555

description: normal blood sample


title: NY10240

description: normal blood sample


title: HR5520

description: normal blood sample


title: HR5524

description: normal blood sample


title: HR5510

description: normal blood sample


title: HR5506

description: normal blood sample


title: HR5496

description: normal blood sample


title: HR5492

description: normal blood sample


title: NW1059

description: normal blood sample


title: HR5489

description: normal blood sample


title: HR5459

description: normal blood sample


title: HR5468

description: normal blood sample


title: HR5455

description: normal blood sample


title: HR5451

description: normal blood sample


title: HR5528

description: normal blood sample


title: HR5448

description: normal blood sample


title: HR5447

description: normal blood sample


title: HR5445

description: normal blood sample


title: HR5438

description: normal blood sample


title: HR5444

description: normal blood sample


title: HR5387

description: normal blood sample


title: HR5409

description: normal blood sample


title: HR5482

description: normal blood sample


title: HR5385

description: normal blood sample


title: HR5512

description: normal blood sample


title: HR5362

description: normal blood sample


title: HR5358

description: normal blood sample


title: HR5384

description: normal blood sample


title: HR5374

description: normal blood sample


title: HR5357

description: normal blood sample


title: HR5379

description: normal blood sample


title: HR5325

description: normal blood sample


title: HR5319

description: normal blood sample


title: HR5491

description: normal blood sample


title: HR5481

description: normal blood sample


title: HR5470

description: normal blood sample


title: HR5277

description: normal blood sample


title: HR5276

description: normal blood sample


title: HR5260

description: normal blood sample


title: HR5267

description: normal blood sample


title: HR5261

description: normal blood sample


title: HR5441

description: normal blood sample


title: HR5249

description: normal blood sample


title: HR5255

description: normal blood sample


title: HR5253

description: normal blood sample


title: HR5248

description: normal blood sample


title: HR5245

description: normal blood sample


title: HR5241

description: normal blood sample


title: HR5179

description: normal blood sample


title: HR5172

description: normal blood sample


title: HR5170

description: normal blood sample


title: HR5117

description: normal blood sample


title: HR5359

description: normal blood sample


title: HR5165

description: normal blood sample


title: HR1570

description: normal blood sample


title: HR1561

description: normal blood sample


title: HR1564

description: normal blood sample


title: HR1562

description: normal blood sample


title: HR5278

description: normal blood sample


title: HR1554

description: normal blood sample


title: HR1557

description: normal blood sample


title: HR5111

description: normal blood sample


title: HR1550

description: normal blood sample


title: HR1551

description: normal blood sample


title: HR1552

description: normal blood sample


title: HR1553

description: normal blood sample


title: HR1545

description: normal blood sample


title: HR1540

description: normal blood sample


title: HR1512

description: normal blood sample


title: HR1532

description: normal blood sample


title: HR5246

description: normal blood sample


title: HR1509

description: normal blood sample


title: HR1488

description: normal blood sample


title: HR1501

description: normal blood sample


title: HR1482

description: normal blood sample


title: HR1475

description: normal blood sample


title: HR1481

description: normal blood sample


title: HR1474

description: normal blood sample


title: HR1449

description: normal blood sample


title: HR1428

description: normal blood sample


title: HR1450

description: normal blood sample


title: HR1441

description: normal blood sample


title: HR1462

description: normal blood sample


title: HR1461

description: normal blood sample


title: HR1436

description: normal blood sample


title: HR1412

description: normal blood sample


title: HR1416

description: normal blood sample


title: HR1391

description: normal blood sample


title: HR1411

description: normal blood sample


title: HR1399

description: normal blood sample


title: HR1402

description: normal blood sample


title: HR1383

description: normal blood sample


title: HR1511

description: normal blood sample


title: HR1384

description: normal blood sample


title: HR1395

description: normal blood sample


title: HR1502

description: normal blood sample


title: HR1373

description: normal blood sample


title: HR1377

description: normal blood sample


title: colo205-xeno_Sel034-16h_2

description: SAMPLE 8


title: HR1372

description: normal blood sample


title: HR1352

description: normal blood sample


title: HR1465

description: normal blood sample


title: HR1363

description: normal blood sample


title: HR1349

description: normal blood sample


title: HR1345

description: normal blood sample


title: HR1325

description: normal blood sample


title: HR1327

description: normal blood sample


title: HR1326

description: normal blood sample


title: HR1323

description: normal blood sample


title: HR1318

description: normal blood sample


title: HR1311

description: normal blood sample


title: HR1304

description: normal blood sample


title: HR1319

description: normal blood sample


title: HR1336

description: normal blood sample


title: HR1378

description: normal blood sample


title: HR1300

description: normal blood sample


title: HR1297

description: normal blood sample


title: HR1295

description: normal blood sample


title: HR1296

description: normal blood sample


title: HR1299

description: normal blood sample


title: HR1302

description: normal blood sample


title: HR1294

description: normal blood sample


title: HR1289

description: normal blood sample


title: HR1287

description: normal blood sample


title: HR1277

description: normal blood sample


title: HR1283

description: normal blood sample


title: HR1281

description: normal blood sample


title: HR1354

description: normal blood sample


title: HR1273

description: normal blood sample


title: HR1272

description: normal blood sample


title: HR1276

description: normal blood sample


title: HR1271

description: normal blood sample


title: HR1382

description: normal blood sample


title: HR1264

description: normal blood sample


title: HR1240

description: normal blood sample


title: HR1238

description: normal blood sample


title: HR1244

description: normal blood sample


title: HR1253

description: normal blood sample


title: HR1312

description: normal blood sample


title: HR1234

description: normal blood sample


title: HR1257

description: normal blood sample


title: HR1233

description: normal blood sample


title: HR1230

description: normal blood sample


title: HR1231

description: normal blood sample


title: HR1226

description: normal blood sample


title: HR1262

description: normal blood sample


title: HR1232

description: normal blood sample


title: HR1222

description: normal blood sample


title: HR1218

description: normal blood sample


title: HR1219

description: normal blood sample


title: HR1220

description: normal blood sample


title: HR1214

description: normal blood sample


title: HR1221

description: normal blood sample


title: HR1204

description: normal blood sample


title: HR1216

description: normal blood sample


title: HR1208

description: normal blood sample


title: HR1202

description: normal blood sample


title: HR1199

description: normal blood sample


title: HR1198

description: normal blood sample


title: HR1189

description: normal blood sample


title: HR1191

description: normal blood sample


title: HR1184

description: normal blood sample


title: HR1181

description: normal blood sample


title: HR1179

description: normal blood sample


title: HR1176

description: normal blood sample


title: HR1173

description: normal blood sample


title: HR1174

description: normal blood sample


title: HR1170

description: normal blood sample


title: HR1171

description: normal blood sample


title: HR1161

description: normal blood sample


title: HR1175

description: normal blood sample


title: HR1158

description: normal blood sample


title: HR1100

description: normal blood sample


title: HR1112

description: normal blood sample


title: HR1139

description: normal blood sample


title: HR1149

description: normal blood sample


title: HR1068

description: normal blood sample


title: HR1124

description: normal blood sample


title: HR1076

description: normal blood sample


title: CM5234

description: normal blood sample


title: CM5236

description: normal blood sample


title: CM5220

description: normal blood sample


title: CM5219

description: normal blood sample


title: CM5225

description: normal blood sample


title: CM5218

description: normal blood sample


title: CM5217

description: normal blood sample


title: HR1038

description: normal blood sample


title: CM5214

description: normal blood sample


title: CM5210

description: normal blood sample


title: CM5200

description: normal blood sample


title: CM5201

description: normal blood sample


title: CM5190

description: normal blood sample


title: HR1127

description: normal blood sample


title: CM5189

description: normal blood sample


title: CM5184

description: normal blood sample


title: CM5188

description: normal blood sample


title: CM5178

description: normal blood sample


title: CM5193

description: normal blood sample


title: CM5177

description: normal blood sample


title: CM5194

description: normal blood sample


title: CM5179

description: normal blood sample


title: CM5169

description: normal blood sample


title: CM5170

description: normal blood sample


title: CM5167

description: normal blood sample


title: CM5161

description: normal blood sample


title: CM5165

description: normal blood sample


title: CM5157

description: normal blood sample


title: CM5149

description: normal blood sample


title: CM5159

description: normal blood sample


title: CM5144

description: normal blood sample


title: CM5143

description: normal blood sample


title: CM5147

description: normal blood sample


title: CM5213

description: normal blood sample


title: CM5142

description: normal blood sample


title: CM5141

description: normal blood sample


title: CM5136

description: normal blood sample


title: CM5133

description: normal blood sample


title: CM5124

description: normal blood sample


title: CM5129

description: normal blood sample


title: CM5121

description: normal blood sample


title: CM5120

description: normal blood sample


title: CM5171

description: normal blood sample


title: CM5116

description: normal blood sample


title: CM5114

description: normal blood sample


title: CM5115

description: normal blood sample


title: CM5112

description: normal blood sample


title: CM5111

description: normal blood sample


title: CM5168

description: normal blood sample


title: CM5109

description: normal blood sample


title: CM5174

description: normal blood sample


title: CM5108

description: normal blood sample


title: CM5151

description: normal blood sample


title: CM5105

description: normal blood sample


title: CM5101

description: normal blood sample


title: CM5100

description: normal blood sample


title: CM5104

description: normal blood sample


title: CM5093

description: normal blood sample


title: CM5091

description: normal blood sample


title: CM5090

description: normal blood sample


title: CM5089

description: normal blood sample


title: CM5131

description: normal blood sample


title: CM5078

description: normal blood sample


title: CM5077

description: normal blood sample


title: CM5084

description: normal blood sample


title: CM5085

description: normal blood sample


title: CM5074

description: normal blood sample


title: CM5110

description: normal blood sample


title: CM5073

description: normal blood sample


title: CM5072

description: normal blood sample


title: CM5076

description: normal blood sample


title: CM5071

description: normal blood sample


title: CM5068

description: normal blood sample


title: CM5063

description: normal blood sample


title: CM5065

description: normal blood sample


title: CM5069

description: normal blood sample


title: CM1221

description: normal blood sample


title: CM1222

description: normal blood sample


title: CM1225

description: normal blood sample


title: CM1218

description: normal blood sample


title: CM5094

description: normal blood sample


title: CM1216

description: normal blood sample


title: CM1212

description: normal blood sample


title: CM1206

description: normal blood sample


title: CM1215

description: normal blood sample


title: CM1202

description: normal blood sample


title: CM5092

description: normal blood sample


title: CM1208

description: normal blood sample


title: CM1201

description: normal blood sample


title: CM1198

description: normal blood sample


title: CM1195

description: normal blood sample


title: CM1190

description: normal blood sample


title: CM1189

description: normal blood sample


title: CM1181

description: normal blood sample


title: CM1179

description: normal blood sample


title: CM1187

description: normal blood sample


title: CM1188

description: normal blood sample


title: CM1180

description: normal blood sample


title: CM1220

description: normal blood sample


title: CM1174

description: normal blood sample


title: CM1175

description: normal blood sample


title: CM1170

description: normal blood sample


title: CM1164

description: normal blood sample


title: CM1163

description: normal blood sample


title: CM1173

description: normal blood sample


title: CM1158

description: normal blood sample


title: CM1159

description: normal blood sample


title: CM1160

description: normal blood sample


title: CM1151

description: normal blood sample


title: CM1153

description: normal blood sample


title: CM1142

description: normal blood sample


title: CM1137

description: normal blood sample


title: CM1138

description: normal blood sample


title: CM1150

description: normal blood sample


title: CM1154

description: normal blood sample


title: CM1133

description: normal blood sample


title: CM1130

description: normal blood sample


title: CM1192

description: normal blood sample


title: CM1178

description: normal blood sample


title: CM1129

description: normal blood sample


title: CM1128

description: normal blood sample


title: CM1169

description: normal blood sample


title: CM1122

description: normal blood sample


title: CM1106

description: normal blood sample


title: CM1108

description: normal blood sample


title: CM1100

description: normal blood sample


title: CM1123

description: normal blood sample


title: CM1097

description: normal blood sample


title: CM1121

description: normal blood sample


title: CM1096

description: normal blood sample


title: CM1094

description: normal blood sample


title: CM1093

description: normal blood sample


title: CM1092

description: normal blood sample


title: CM1089

description: normal blood sample


title: CM1095

description: normal blood sample


title: CM1146

description: normal blood sample


title: CM1087

description: normal blood sample


title: CM1088

description: normal blood sample


title: CM1078

description: normal blood sample


title: CM1085

description: normal blood sample


title: CM1077

description: normal blood sample


title: CM1082

description: normal blood sample


title: CM1081

description: normal blood sample


title: CM1080

description: normal blood sample


title: CM1070

description: normal blood sample


title: CM1071

description: normal blood sample


title: CM1068

description: normal blood sample


title: CM1067

description: normal blood sample


title: CM1117

description: normal blood sample


title: CM1066

description: normal blood sample


title: CM1104

description: normal blood sample


title: CM1065

description: normal blood sample


title: CH5043

description: normal blood sample


title: CH5042

description: normal blood sample


title: CH5038

description: normal blood sample


title: CH5031

description: normal blood sample


title: CH5026

description: normal blood sample


title: CH5024

description: normal blood sample


title: CH5020

description: normal blood sample


title: CH5017

description: normal blood sample


title: CH5018

description: normal blood sample


title: CH5016

description: normal blood sample


title: CH5013

description: normal blood sample


title: CH5012

description: normal blood sample


title: CH5009

description: normal blood sample


title: CH1028

description: normal blood sample


title: CH5011

description: normal blood sample


title: CH5004

description: normal blood sample


title: CH1023

description: normal blood sample


title: CH1022

description: normal blood sample


title: CH1013

description: normal blood sample


title: CH1015

description: normal blood sample


title: CH1009

description: normal blood sample


title: CH1005

description: normal blood sample


title: CH5039

description: normal blood sample


title: CH5036

description: normal blood sample


title: CH5040

description: normal blood sample


title: CH1006

description: normal blood sample


title: CH5033

description: normal blood sample


title: CH1003

description: normal blood sample


title: CH1004

description: normal blood sample


title: AV5018

description: normal blood sample


title: AV5009

description: normal blood sample


title: AV5011

description: normal blood sample


title: CH1025

description: normal blood sample


title: AV5007

description: normal blood sample


title: AV5006

description: normal blood sample


title: AV5004

description: normal blood sample


title: CH1010

description: normal blood sample


title: AV5001

description: normal blood sample


title: AV1013

description: normal blood sample


title: AV1012

description: normal blood sample


title: AV1010

description: normal blood sample


title: AV1008

description: normal blood sample


title: AV1006

description: normal blood sample


title: AV1002

description: normal blood sample


title: AV1004

description: normal blood sample


title: AV1009

description: normal blood sample


title: AV1001

description: normal blood sample


title: Universal Methylated Human DNA Standard [Methylated]

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description:
Zymo Research Cat no D5011
Methylated

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes.

source_name: control DNA enzymatically modified in vitro with CpG Methylase

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was obtained from commercial sources except for the two normal breast tissue samples for which genomic DNA was isolated from fresh frozen breast tissues in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group6_1_WT_col_CD64+Ly-6Clo

status: Public on Feb 04 2016

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description:
Group6 chip1: WT colonic lamina propria CD64+Ly-6Chi macrophages from WT Th cell-induced colitis without restimulation
Group6_1_WT_col_CD64+Ly-6Clo

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing:
Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the BioRetis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 2 chips of one group (Experiment group) were compared to the 2 chips of any other group (Baseline group) and chips within one group were compared to each other in both directions. This results in 15 different comparisons of 6 groups. Of relevance for this publication were the comparisons of groups 1 vs. 2, groups 3 vs. 4, and groups 5 vs. 6. The following parameters of absolute and comparative analysis were included in the BioRetis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 4 SLR values of Experiment group vs. Baseline group and 4 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.385E-07) or more than 50% of non-parametrically calculated Change calls (one-sided Wilcoxon’s signed rank test after Tukey-Biweight reduction of outliers, calculated by GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction and not No Changed. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chips comparisons (one direction).
ABS_CALL: A: gene is detected as Absent, M: as Marginal present, or P: as Present
DETECTION P-VALUE: Non-parametrical p-value for generation of detection call

source_name: Group 6: macrophages from WT Th cell-induced colitis

growth_protocol: Colitis was induced by i.v. transfer of 4E05 naïve CD4+CD45RBhiCD25- Th cells from WT C57BL/6 or Tbx21-/- mice into congenic Rag1-/- recipients. When signs of colitis became apparent (day 15-17), mice were sacrificed and the inflamed colons were harvested. The epithelial layer was stripped off by 2 rounds of incubation in HBSS with 5 mM EDTA and 10 mM HEPES at 37 °C for 20 minutes with 100 RPM shaking. Lamina propria leukocytes were isolated by 3 rounds of incubation in HBSS containing Ca and Mg with 0.5 µg/ml DNase I (Sigma), 0.5 µg/ml Collagenase D (Roche) and 0.5 U/ml Dispase (BD Biosciences) for 20 minutes at 37 °C with 100 RPM shaking. For sorting, electronic gates were set to identify viable, single leukocytes (FSC/SSC, DAPI-, FSC-height vs. FSC-area). Th cells (CD3+CD4+), monocytes (CD64+Ly-6Chi) and macrophages (CD64+Ly-6Clow) were sorted. Th cells were stimulated for 3 hours in IMDM with 10% FCS containing PMA (10 ng/ml) and ionomycin (1 µg/ml).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

value: colonic lamina propria leukocytes from colitis

tag: genotype of sorted cells

tag: genotype of th cells for colitis induction

tag: activation

tag: flow cytometric cell sorting