title: tumor_ovarian [JB4577V], Dataset B

description:
JB4577V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4534V], Dataset B

status: Public on Jan 10 2018

type: RNA

city: New York

first: Li-Xuan

last: Qin

state: New York

address: 485 Lexington Ave

department: Epidemiology and Biostatistics

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
JB4534V
microRNA expression of tumor tissue.
Total RNA or miRNA

hyb_protocol: Human miRNA v16.0 microarrays (Agilent Technologies), containing 3,523 markers that represent 1,205 human and 142 human viral miRNAs, were used for miRNA expression profiling according to the manufacturer’s protocol.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner G2505C US83903565 using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Raw data were preprocessed with log2 transformation and median probe-set summarization using R-3.3.0 software.

molecule: total RNA

organism: Homo sapiens

source_name: ovarian tumor sample

label_protocol: For samples meeting the quality control standards, 200 ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent). The manufacturer's instructions were followed.

extract_protocol: Sample preparation used strict quality control on the specimens. Freshly harvested tissue was snap frozen for eventual cryomold embedding and RNA extraction or microarray analysis. Before RNA extraction, a 5-um hematoxylin and eosin histologic section was cut from the top of the cryomold to assess for tumor content and percentage of necrosis. For any specimens with less than 60% tumor cell nuclei, we used macrodissection to obtain enriched areas so as to make the specimen usable for RNA extraction and as uniform as possible. All specimens had less than 20% necrosis. All pathology specimens used for molecular study were diagnosed by dedicated gynecologic pathologists to establish histologic cell type, grade of malignancy, and site of origin. RNA was extracted from 30 to 100 mg of macrodissected cryomold tissue using the Ambion mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Total RNA yield and quality were assessed using a NanoDrop spectrophotometer and an Agilent Bioanalyzer.

tag: disease state

value: advanced serous ovarian cancer

tag: tissue

value: tumor

tag: batch


title: 9989536110_R03C02

type: genomic

first: Elisabeth

middle: B.

last: Binder

state: DEUTSCHLAND

address: Kraepelinstraße 2-10

department: Dept. Translational Research in Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

description: blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: minfi Bioconductor R package version 1.18.2; Functional Normalization

label: Cy5 and Cy126

molecule: genomic DNA

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whole blood using the Gentra Puregene Blood Kit (QIAGEN)

value: blood

tag: gender

value: M

tag: diagnosis

value: PD


title: LLC sh Ctrl (01_LLCwt)

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

description: LLC sh Ctrl Lewis lung carcinoma sh Ctrl mouse lung cancer

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.
RMA-16 normalized expression values by Genespring 12.5 GX (Agilent) software.

label: biotin

organism: Mus musculus

source_name: LLC sh Ctrl

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

tag: cell line

value: LLC

tag: treatment

value: sh Ctrl


title: tumor_ovarian [JB4531V], Dataset B

description:
JB4531V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4453V], Dataset B

description:
JB4453V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536109_R04C02

description: blood sample

label: Cy5 and Cy121

value: F

value: Control


title: tumor_ovarian [JB4388V], Dataset B

description:
JB4388V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4442V], Dataset B

description:
JB4442V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536114_R04C02

description: blood sample

label: Cy5 and Cy134


title: tumor_ovarian [JB4387V], Dataset B

description:
JB4387V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536109_R02C01

description: blood sample

label: Cy5 and Cy120


title: tumor_ovarian [JB4450V], Dataset B

description:
JB4450V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4345V], Dataset B

description:
JB4345V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536110_R02C01

description: blood sample

label: Cy5 and Cy124


title: 9989536100_R03C01

description: blood sample

label: Cy5 and Cy118


title: LLC sh IKKA (04_LLCshIKKA)

description: LLC sh IKKA, Lewis lung carcinoma sh IKKA, mouse lung cancer

source_name: LLC sh IKKA

value: sh IKKA


title: 9989536110_R03C01

description: blood sample

label: Cy5 and Cy125


title: tumor_ovarian [JB4448V], Dataset B

description:
JB4448V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536100_R04C02

description: blood sample

label: Cy5 and Cy119


title: 9989536109_R05C01

description: blood sample

label: Cy5 and Cy122


title: tumor_ovarian [JB4419V], Dataset B

description:
JB4419V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536110_R01C01

description: blood sample

label: Cy5 and Cy123


title: tumor_ovarian [JB4160V], Dataset B

description:
JB4160V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4079V], Dataset B

description:
JB4079V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4304V], Dataset B

description:
JB4304V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4196V], Dataset B

description:
JB4196V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536095_R05C01

description: blood sample

label: Cy5 and Cy114


title: 9989536100_R02C01

description: blood sample

label: Cy5 and Cy117


title: tumor_ovarian [JB4189V], Dataset B

description:
JB4189V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4077V], Dataset B

description:
JB4077V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536096_R02C02

description: blood sample

label: Cy5 and Cy116


title: tumor_ovarian [JB4314V], Dataset B

description:
JB4314V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536091_R05C02

description: blood sample

label: Cy5 and Cy110


title: tumor_ovarian [JB4234V], Dataset B

description:
JB4234V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536096_R01C01

description: blood sample

label: Cy5 and Cy115


title: 9989536095_R01C02

description: blood sample

label: Cy5 and Cy113


title: tumor_ovarian [JB4029V], Dataset B

description:
JB4029V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4060V], Dataset B

description:
JB4060V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3979V], Dataset B

description:
JB3979V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536093_R05C01

description: blood sample

label: Cy5 and Cy112


title: tumor_ovarian [JB3905V], Dataset B

description:
JB3905V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3838V], Dataset B

description:
JB3838V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536093_R03C02

description: blood sample

label: Cy5 and Cy111


title: 9989536078_R03C01

description: blood sample

label: Cy5 and Cy107


title: tumor_ovarian [JB3820V], Dataset B

description:
JB3820V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3669V], Dataset B

description:
JB3669V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3663V], Dataset B

description:
JB3663V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB4548V], Dataset B

description:
JB4548V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536091_R01C02

description: blood sample

label: Cy5 and Cy108


title: CD3+CD8+_rep1

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

country: Japan

institute: Kyoto Prefectural University

hyb_protocol: Slide was hybridized with 1.65 μg Cy3-labeled cDNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 16 h of hybridization at 65 °C, the slide was washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. Slides were scanned  after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The intensity signals was imported to CLC Main workbench 6.0 and normalized by the quartile normalization method and log2 transformed.

organism: Sus scrofa

label_protocol: Complementary DNA amplification was carried out from 25 ng of total RNA using an Ovation PicoSL WTA System V2. After amplification, cDNA samples were labeled with Cy3 using Klenow polymerase.

growth_protocol: PBMC was isolated by density gradient centrifugation on Percoll (d = 1.084) . CD3+CD4+, CD3+CD8+ and CD3+CD4+CD8+ were separately sorted by a cell sorter.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified by RNeasy MinElute Cleanup kit.

value: Whole blood

tag: cell type

value: peripheral blood mononuclear cells (PBMC)

tag: cell subtype

value: sorted lymphocyte

tag: sorted fraction


title: 9989536091_R02C01

description: blood sample

label: Cy5 and Cy109


title: CD3+CD8+_rep2


title: CD3+CD8+_rep3


title: tumor_ovarian [JB3457V], Dataset B

description:
JB3457V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: CD3+CD4+_rep2


title: CD3+CD4+_rep3


title: tumor_ovarian [JB3441V], Dataset B

description:
JB3441V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536077_R05C02

description: blood sample

label: Cy5 and Cy104


title: 9989536075_R03C01

description: blood sample

label: Cy5 and Cy101


title: tumor_ovarian [JB3437V], Dataset B

description:
JB3437V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: CD3+CD4+_rep1


title: 9989536078_R01C01

description: blood sample

label: Cy5 and Cy106


title: tumor_endometrial [JB3436E], Dataset B

description:
JB3436E
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: endometrial tumor sample

value: endometrioid endometrial cancer


title: tumor_ovarian [JB3434V], Dataset B

description:
JB3434V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 9989536077_R06C02

description: blood sample

label: Cy5 and Cy105


title: 9989536075_R05C01

description: blood sample

label: Cy5 and Cy103


title: 9989536066_R05C02

description: blood sample

label: Cy5 and Cy99


title: CD3+CD4+CD8+_rep3


title: 9989536066_R04C01

description: blood sample

label: Cy5 and Cy98


title: 9989536075_R03C02

description: blood sample

label: Cy5 and Cy102


title: 9989536066_R06C01

description: blood sample

label: Cy5 and Cy100


title: tumor_endometrial [JB3426E], Dataset B

description:
JB3426E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: CD3+CD4+CD8+_rep1


title: 9989536066_R01C02

description: blood sample

label: Cy5 and Cy96


title: 9989536044_R04C01

description: blood sample

label: Cy5 and Cy93


title: 9989536066_R01C01

description: blood sample

label: Cy5 and Cy95


title: 9989536066_R03C02

description: blood sample

label: Cy5 and Cy97


title: 9989536044_R04C02

description: blood sample

label: Cy5 and Cy94


title: tumor_endometrial [JB3390E], Dataset B

description:
JB3390E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: CD3+CD4+CD8+_rep2


title: 9989536030_R03C02

description: blood sample

label: Cy5 and Cy90


title: tumor_endometrial [JB3197E], Dataset B

description:
JB3197E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB3189E], Dataset B

description:
JB3189E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB3329E], Dataset B

description:
JB3329E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3309V], Dataset B

description:
JB3309V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: PGEC_MH2

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: PGEC derived MH

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

value: PGEC derived MH


title: 9989536030_R04C01

description: blood sample

label: Cy5 and Cy91


title: LoVo_PEAK1_rep2

city: Nanjing

first: Chenbo

last: Ding

address: No. 87, Dingjiaqiao, Gulou District

country: China

institute: Medical School of Southeast University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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 with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: LoVo RNA, PEAK1 overexpression, replicate 2

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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: LoVo-Control cells were cultured in F-12K medium and then transfected with control expression vector for 48hs as negative control.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: LoVo-PEAK1 overexpression cells were cultured in F-12K medium and then transfected with PEAK1 overexpression vector for 48hs.

value: LoVo

tag: transfected with

value: PEAK1 overexpression

value: human colorectal cancer cells

value: male


title: PGEC_MH1


title: 9989536044_R03C01

description: blood sample

label: Cy5 and Cy92

value: blood


title: 9989536027_R05C02

description: blood sample

label: Cy5 and Cy88


title: tumor_ovarian [JB3172V], Dataset B

description:
JB3172V
microRNA expression of tumor tissue.
Total RNA or miRNA

value: advanced serous ovarian cancer

value: tumor


title: 9989536030_R02C02

description: blood sample

label: Cy5 and Cy89

value: M

value: PD


title: LoVo_control_rep2

source_name: LoVo RNA, control, replicate 2

value: negative control


title: tumor_ovarian [JB3137V], Dataset B

description:
JB3137V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: LoVo_control_rep1

source_name: LoVo RNA, control, replicate 1


title: LoVo_control_rep3

source_name: LoVo RNA, control, replicate 3


title: PGEC_IH1

source_name: PGEC derived IH

value: PGEC derived IH


title: LoVo_PEAK1_rep3

source_name: LoVo RNA, PEAK1 overexpression, replicate 3


title: LoVo_PEAK1_rep1

source_name: LoVo RNA, PEAK1 overexpression, replicate 1


title: tumor_endometrial [JB3110E], Dataset B

description:
JB3110E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: MH_2

source_name: MH

value: MH


title: tumor_endometrial [JB3067E], Dataset B

description:
JB3067E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3063V], Dataset B

description:
JB3063V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: IH_1

source_name: IH

value: IH


title: MH_1


title: 9989536027_R01C01

description: blood sample

label: Cy5 and Cy87

value: F


title: tumor_endometrial [JB3058E], Dataset B

description:
JB3058E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: HE_2

source_name: HE

value: HE


title: PGEC_P3_2

source_name: PGEC

value: PGEC


title: PGEC_P16


title: 9989536013_R06C02

description: blood sample

label: Cy5 and Cy84


title: 9989536013_R04C01

description: blood sample

label: Cy5 and Cy83

value: Control


title: tumor_endometrial [JB3012E], Dataset B

description:
JB3012E
microRNA expression of tumor tissue.
Total RNA or miRNA

value: endometrioid endometrial cancer


title: PGEC_P3_3


title: 3999840166_R03C01

description: blood sample

label: Cy5 and Cy79


title: PGEC_P3_1


title: 9989536025_R04C02

description: blood sample

label: Cy5 and Cy85


title: 9989536013_R03C01

description: blood sample

label: Cy5 and Cy82


title: tumor_endometrial [JB2906E], Dataset B

description:
JB2906E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2962E], Dataset B

description:
JB2962E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB3025V], Dataset B

description:
JB3025V
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: ovarian tumor sample


title: 9989536013_R02C02

description: blood sample

label: Cy5 and Cy81

source_name: Blood


title: 3999840166_R04C01

description: blood sample

label: Cy5 and Cy80


title: tumor_endometrial [JB2907E], Dataset B

description:
JB2907E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840163_R01C02

description: blood sample

label: Cy5 and Cy78


title: HE_1


title: tumor_endometrial [JB3020E], Dataset B

description:
JB3020E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2851E], Dataset B

description:
JB2851E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2750E], Dataset B

description:
JB2750E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840162_R04C02

description: blood sample

label: Cy5 and Cy74


title: PGEC_P1


title: tumor_endometrial [JB2865E], Dataset B

description:
JB2865E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: DE_3

source_name: DE

value: DE


title: PGEC_P2


title: 9989536025_R05C01

description: blood sample

label: Cy5 and Cy86


title: 3999840162_R04C01

description: blood sample

label: Cy5 and Cy73


title: 3999840163_R01C01

description: blood sample

label: Cy5 and Cy77


title: DE_1


title: iPSC_2

source_name: iPSC

value: iPSC


title: iPSC_3


title: 3999840162_R06C01

description: blood sample

label: Cy5 and Cy75


title: tumor_endometrial [JB2665E], Dataset B

description:
JB2665E
microRNA expression of tumor tissue.
Total RNA or miRNA

source_name: endometrial tumor sample


title: iPSC_1


title: DE_2


title: tumor_endometrial [JB2669E], Dataset B

description:
JB2669E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2651E], Dataset B

description:
JB2651E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB2737V], Dataset B

description:
JB2737V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2684E], Dataset B

description:
JB2684E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840159_R04C02

description: blood sample

label: Cy5 and Cy69


title: 3999840162_R06C02

description: blood sample

label: Cy5 and Cy76


title: 3999840162_R02C02

description: blood sample

label: Cy5 and Cy72


title: tumor_endometrial [JB2636E], Dataset B

description:
JB2636E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2471E], Dataset B

description:
JB2471E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2630E], Dataset B

description:
JB2630E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2557E], Dataset B

description:
JB2557E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2361E], Dataset B

description:
JB2361E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2373E], Dataset B

description:
JB2373E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2620E], Dataset B

description:
JB2620E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB2466V], Dataset B

description:
JB2466V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840162_R01C02

description: blood sample

label: Cy5 and Cy71


title: tumor_endometrial [JB2341E], Dataset B

description:
JB2341E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840150_R05C01

description: blood sample

label: Cy5 and Cy66


title: tumor_endometrial [JB2446E], Dataset B

description:
JB2446E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840158_R01C01

description: blood sample

label: Cy5 and Cy67


title: 3999840158_R04C01

description: blood sample

label: Cy5 and Cy68


title: 3999840150_R02C01

description: blood sample

label: Cy5 and Cy64


title: tumor_ovarian [JB2299V], Dataset B

description:
JB2299V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840140_R06C01

description: blood sample

label: Cy5 and Cy59


title: tumor_endometrial [JB2260E], Dataset B

description:
JB2260E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2445E], Dataset B

description:
JB2445E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840140_R03C02

description: blood sample

label: Cy5 and Cy57


title: tumor_endometrial [JB2344E], Dataset B

description:
JB2344E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840128_R04C02

description: blood sample

label: Cy5 and Cy52


title: 3999840148_R06C02

description: blood sample

label: Cy5 and Cy63


title: tumor_endometrial [JB2109E], Dataset B

description:
JB2109E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840132_R02C01

description: blood sample

label: Cy5 and Cy53


title: 3999840150_R04C02

description: blood sample

label: Cy5 and Cy65


title: 3999840148_R05C01

description: blood sample

label: Cy5 and Cy62


title: tumor_ovarian [JB2133V], Dataset B

description:
JB2133V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840103_R04C02

description: blood sample

label: Cy5 and Cy49


title: tumor_endometrial [JB2091E], Dataset B

description:
JB2091E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB2070E], Dataset B

description:
JB2070E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840132_R04C02

description: blood sample

label: Cy5 and Cy55


title: tumor_endometrial [JB2024E], Dataset B

description:
JB2024E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB2025V], Dataset B

description:
JB2025V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840161_R02C01

description: blood sample

label: Cy5 and Cy70


title: 3999840140_R01C02

description: blood sample

label: Cy5 and Cy56


title: 3999840103_R06C01

description: blood sample

label: Cy5 and Cy50


title: 3999840140_R04C01

description: blood sample

label: Cy5 and Cy58


title: tumor_endometrial [JB1995E], Dataset B

description:
JB1995E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB1989V], Dataset B

description:
JB1989V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840148_R02C01

description: blood sample

label: Cy5 and Cy61


title: tumor_endometrial [JB1914E], Dataset B

description:
JB1914E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1905E], Dataset B

description:
JB1905E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840128_R02C02

description: blood sample

label: Cy5 and Cy51


title: tumor_endometrial [JB1883E], Dataset B

description:
JB1883E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840132_R02C02

description: blood sample

label: Cy5 and Cy54


title: 3999840148_R01C02

description: blood sample

label: Cy5 and Cy60


title: 3999840103_R04C01

description: blood sample

label: Cy5 and Cy48


title: tumor_endometrial [JB1866E], Dataset B

description:
JB1866E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840098_R06C02

description: blood sample

label: Cy5 and Cy47


title: 3999840098_R06C01

description: blood sample

label: Cy5 and Cy46


title: tumor_endometrial [JB1677E], Dataset B

description:
JB1677E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840095_R06C01

description: blood sample

label: Cy5 and Cy44


title: tumor_ovarian [JB1654V], Dataset B

description:
JB1654V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1603E], Dataset B

description:
JB1603E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1705E], Dataset B

description:
JB1705E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1722E], Dataset B

description:
JB1722E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840098_R02C02

description: blood sample

label: Cy5 and Cy45


title: 3999840095_R01C02

description: blood sample

label: Cy5 and Cy39


title: tumor_endometrial [JB1596E], Dataset B

description:
JB1596E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840095_R05C01

description: blood sample

label: Cy5 and Cy42


title: 3999840095_R03C02

description: blood sample

label: Cy5 and Cy40


title: 3999840071_R02C02

description: blood sample

label: Cy5 and Cy33


title: 3999840079_R04C01

description: blood sample

label: Cy5 and Cy37


title: 3999840072_R06C01

description: blood sample

label: Cy5 and Cy36


title: 3999840088_R01C01

description: blood sample

label: Cy5 and Cy38


title: 3999840095_R05C02

description: blood sample

label: Cy5 and Cy43


title: tumor_endometrial [JB1533E], Dataset B

description:
JB1533E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_ovarian [JB1535V], Dataset B

description:
JB1535V
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1996E], Dataset B

description:
JB1996E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840070_R06C02

description: blood sample

label: Cy5 and Cy31


title: 3999840071_R06C02

description: blood sample

label: Cy5 and Cy35


title: 3999840071_R04C02

description: blood sample

label: Cy5 and Cy34


title: tumor_endometrial [JB1521E], Dataset B

description:
JB1521E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1437E], Dataset B

description:
JB1437E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840071_R02C01

description: blood sample

label: Cy5 and Cy32


title: 3999840070_R05C01

description: blood sample

label: Cy5 and Cy30


title: 3999840061_R06C01

description: blood sample

label: Cy5 and Cy29


title: tumor_endometrial [JB1245E], Dataset B

description:
JB1245E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: tumor_endometrial [JB1394E], Dataset B

description:
JB1394E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: 3999840095_R04C02

description: blood sample

label: Cy5 and Cy41


title: 3999840061_R01C02

description: blood sample

label: Cy5 and Cy25


title: tumor_endometrial [JB1602E], Dataset B

description:
JB1602E
microRNA expression of tumor tissue.
Total RNA or miRNA


title: BJ-hTERT MOCK 72hr n=2

city: Dublin

first: Maureen

middle: J

last: O'Sullivan

state: Dublin 2

address: College Green

department: School of Medicine

country: Ireland

institute: Trinity College Dubiln

hyb_protocol: Carried out by Eurofins

scan_protocol: Carried out by Eurofins

data_processing:
To study the gene expression changes resulting from induction of the fusion gene, we compared gene expression datasets from mock- and doxycycline treated HEK293 and BJ-hTERT HA-YWHAE-NUTM2 cell lines at 24 and 72 hours. Total RNA was extracted from cell lines, assayed by NanoDrop (Thermo Scientific) and 200 ng was used for gene expression analysis using Affymetrix® Human Gene 2.1 ST 24-Array-Plates (Affymetrix, Santa Clara, CA, USA). The arrays were analysed using Gene-Chip Operating Software (GCOS) and Robust Multichip Average (RMA) normalization was performed on three independent experiments.
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_1-st
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: BJ-hTERT MOCK 72hr

label_protocol: Carried out by Eurofins

growth_protocol: HEK293 and BJ-hTERT cell lines were maintained in DMEM (Dulbecco's Modified Eagle Medium, Sigma Aldrich) supplemented with 10% Fetal Bovine Serum (FBS; Sigma Aldrich), and 1% Penicillin/Streptomycin solution (P/S; Life Technologies). Cells were maintained in T75 flasks (75cm2, corning) monitored daily using an inverted phase contrast microscope and subcultured upon reaching 70-80% confluency. Cell were washed with PBS and 1-2mL trypsin ethylene diamine tetra acetic acid (EDTA) (0.05% (w/v) trypsin, 0.02% (w/v) EDTA) was added to detach cells. The trypsin was inactivated with 1-2mL complete media and the cell suspension was centrifuged for 5 minutes at 205g. The supernatant was aspirated and the cell pellet was re-suspended in 10mL complete media. Cells were counted and seeded. Excess cells were divided among T75 flasks containing 10mL complete media and maintained at 37oC and 5% CO2.

extract_protocol: RNA was isolated from mock- and doxycycline-treated cells using the ISOLATE II RNA mini kit (Bioline) following manufacturer’s instructions.

treatment_protocol: HEK293- (5.0x105 cells/well) and BJ-hTERT (4.0x105 cells/well) HA-YWHAE-NUTM2 cell lines were seeded in 6-well plates (Corning) and incubated for 24 hours at 37oC. Subsequently, cells were washed in 1xPBS and media containing tetracycline (stock 1mg/mL, diluted with Ethanol) or doxycycline (stock 1mg/mL, diluted with ddH2O) was added. Cells remained in tetracycline/doxycycline treated-media for a desired time course according to experimental setup. Suspension cells were cultured and treated simultaneously. Control treatment conditions were achieved by substituting tetracycline with Ethanol or doxycycline with ddH2O.

value: BJ-hTERT HA-YWHAE-NUTM2 cells

tag: sample type

value: In-vitro cell culture

tag: treated with

value: MOCK for 72hr


title: 3999840061_R03C01

description: blood sample

label: Cy5 and Cy27

value: blood


title: 3999840061_R02C02

description: blood sample

label: Cy5 and Cy26


title: IPF-020-HPS

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

description: Gene expression data from PBMC extracted from individual IPF-020

hyb_protocol: Biotin-labeled sample was well mixed with hybridization master mix denatured and then hybridized onto Affymetrix miRNA 3.0 array at  at 48ï¿½C and 60 rpm for  18 hours

scan_protocol: Affymetrix scanner 3000

data_processing: Expression Console 1.2  (RMA+DABG)  software package was used for data summarization normalization and quality control. Cel files are used for further analysis.

label: Biotin

source_name: Individual IPF-020

label_protocol: Five hundred nanogram of total RNA was poly A tailed then biotinated using Affymetrix FlashTag Biotin HSR RNA Labeling kit (P/N 703095 v1)

extract_protocol: Total RNA including small RNA is isolated and purified using Qiagen miRNeasy mini kit (Cat #: 217004)

value: Female

tag: state

value: HPS

tag: age


title: BJ-hTERT MOCK 72hr n=1


title: 3999840057_R02C01

description: blood sample

label: Cy5 and Cy22

value: PD


title: BJ-hTERT DOX 72hr n=1

source_name: BJ-hTERT DOX 72hr

value: Doxycycline for 72hr


title: 3999840057_R04C01

description: blood sample

label: Cy5 and Cy23

value: M


title: IPF-018-HPS

description: Gene expression data from PBMC extracted from individual IPF-018

source_name: Individual IPF-018


title: BJ-hTERT DOX 72hr n=3


title: IPF-021-HPS

description: Gene expression data from PBMC extracted from individual IPF-021

source_name: Individual IPF-021


title: BJ-hTERT MOCK 72hr n=3


title: BJ-hTERT DOX 24hr n=3

source_name: BJ-hTERT DOX 24hr

value: Doxycycline for 24hr


title: BJ-hTERT DOX 72hr n=2


title: 3999840057_R04C02

description: blood sample

label: Cy5 and Cy24

value: F


title: IPF-017-HPS

description: Gene expression data from PBMC extracted from individual IPF-017

source_name: Individual IPF-017


title: 3999840056_R05C01

description: blood sample

label: Cy5 and Cy18


title: BJ-hTERT MOCK 24hr n=3

source_name: BJ-hTERT MOCK 24hr

value: MOCK for 24hr


title: IPF-019-HPS

description: Gene expression data from PBMC extracted from individual IPF-019

source_name: Individual IPF-019

value: Male


title: BJ-hTERT MOCK 24hr n=2


title: BJ-hTERT MOCK 24hr n=1


title: 3999840057_R01C01

description: blood sample

label: Cy5 and Cy21

value: Control


title: BJ-hTERT DOX 24hr n=2


title: 3999840056_R06C02

description: blood sample

label: Cy5 and Cy20


title: IPF-013-FPF

description: Gene expression data from PBMC extracted from individual IPF-013

source_name: Individual IPF-013

value: FPF


title: IPF-014-HPS

description: Gene expression data from PBMC extracted from individual IPF-014

source_name: Individual IPF-014


title: BJ-hTERT DOX 24hr n=1


title: IPF-015-unaffected

description: Gene expression data from PBMC extracted from individual IPF-015

source_name: Individual IPF-015

value: unaffected


title: IPF-016-unaffected

description: Gene expression data from PBMC extracted from individual IPF-016

source_name: Individual IPF-016


title: IPF-012-HPS

description: Gene expression data from PBMC extracted from individual IPF-012

source_name: Individual IPF-012


title: 3999840056_R06C01

description: blood sample

label: Cy5 and Cy19

source_name: Blood


title: IPF-011-FPF

description: Gene expression data from PBMC extracted from individual IPF-011

source_name: Individual IPF-011


title: IPF-009-HPS

description: Gene expression data from PBMC extracted from individual IPF-009

source_name: Individual IPF-009


title: HEK293 DOX 72hr n=2

source_name: HEK293 DOX 72hr

value: HEK293 HA-YWHAE-NUTM2 cells


title: 3999840056_R01C02

description: blood sample

label: Cy5 and Cy17


title: IPF-010-unaffected

description: Gene expression data from PBMC extracted from individual IPF-010

source_name: Individual IPF-010


title: HEK293 MOCK 72hr n=2

source_name: HEK293 MOCK 72hr


title: HEK293 DOX 72hr n=3


title: 3999840061_R03C02

description: blood sample

label: Cy5 and Cy28


title: 3999840047_R06C01

description: blood sample

label: Cy5 and Cy12


title: IPF-008-HPS

description: Gene expression data from PBMC extracted from individual IPF-008

source_name: Individual IPF-008


title: IPF-007-HPS

description: Gene expression data from PBMC extracted from individual IPF-007

source_name: Individual IPF-007


title: 3999840056_R01C01

description: blood sample

label: Cy5 and Cy16


title: HEK293 MOCK 72hr n=3


title: Matador_S-1459_3_2dpi

type: SRA

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

country: Switzerland

institute: University of Zürich

library_source: transcriptomic

data_processing:
MAPPING: The RNA sequencing reads were mapped on the reference genome with STAR (Dobin et al. 2013) allowing one mismatch per 100 bp and no multimapper with the following command: STAR –outFilterMultiMapNmax 1 – outFilterMismatchNoverLmax 0.01 – alignIntronMax 500
COUNT: Read counts were determined from the mapping files with featureCounts 1.4.6.
Genome_build: The Blumeria graminis subsp. f.sp. tritici genome with accession number PRJEB23548 was used.
Supplementary_files_format_and_content: The processed data files are count table obtained from featureCount. The first column is the gene ID and the last column is the read count. Other columns are explained in the header of the files.

organism:
Secale cereale
Blumeria graminis f. sp. secalis

source_name: Rye leaves (cv. Matador) infected with B.g. secalis S-1459, 48h post infection

growth_protocol: Ten days old detached leaf segments were infected with fresh spores and the infected leaf segments were kept on benzimidazole agar plates at 20°C and 70% humidity with a 16 hours light/8 hours dark cycle (Parlange et al., 2011).

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit from Qiagen according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols, Illumina sequencing Hi-Seq 2000

treatment_protocol: Leaf segments of each of the replicates were collected at 2 days after infection and directly frozen in liquid nitrogen

value: leaves

value: Matador


title: HEK293 DOX 72hr n=1

value: In-vitro cell culture


title: 3999840048_R06C02

description: blood sample

label: Cy5 and Cy14

value: blood


title: 3999840047_R01C02

description: blood sample

label: Cy5 and Cy11


title: Matador_S-1459_2_2dpi


title: 3999840037_R05C02

description: blood sample

label: Cy5 and Cy9


title: 3999840048_R05C02

description: blood sample

label: Cy5 and Cy13


title: IPF-006-FPF

description: Gene expression data from PBMC extracted from individual IPF-006

source_name: Individual IPF-006

value: Female


title: HEK293 MOCK 72hr n=1

label: biotin

value: MOCK for 72hr


title: HEK293 MOCK 24hr n=3

source_name: HEK293 MOCK 24hr


title: HEK239 DOX 24hr n=3

source_name: HEK239 DOX 24hr


title: Matador_S-1459_1_2dpi


title: Matador_S-1391_3_2dpi

source_name: Rye leaves (cv. Matador) infected with B.g. secalis S-1391, 48h post infection


title: Matador_S-1391_2_2dpi


title: IPF-004-HPS

description: Gene expression data from PBMC extracted from individual IPF-004

label: Biotin

source_name: Individual IPF-004

value: HPS


title: 3999840037_R03C01

description: blood sample

label: Cy5 and Cy8

value: PD


title: IPF-005-HPS

description: Gene expression data from PBMC extracted from individual IPF-005

source_name: Individual IPF-005


title: 3999840035_R06C02

description: blood sample

label: Cy5 and Cy7


title: 3999840047_R01C01

description: blood sample

label: Cy5 and Cy10


title: IPF-003-FPF

description: Gene expression data from PBMC extracted from individual IPF-003

source_name: Individual IPF-003


title: HEK239 DOX 24hr n=2


title: CS_JIW2_3_2dpi

organism:
Triticum aestivum
Blumeria graminis f. sp. tritici

source_name: Wheat leaves (cv. Chinese spring) infected with B.g. tritici JIW2, 48h post infection

value: Chinese Spring


title: HEK239 DOX 24hr n=1

value: Doxycycline for 24hr


title: HEK293 MOCK 24hr n=2


title: CS_JIW2_1_2dpi


title: CS_JIW2_2_2dpi


title: 3999840035_R04C01

description: blood sample

label: Cy5 and Cy6

source_name: Blood

value: M


title: 3999840055_R05C01

description: blood sample

label: Cy5 and Cy15


title: CS_94202_3_2dpi

source_name: Wheat leaves (cv. Chinese spring) infected with B.g. tritici 94202, 48h post infection


title: CS_94202_2_2dpi


title: IPF-002-FPF

description: Gene expression data from PBMC extracted from individual IPF-002

source_name: Individual IPF-002


title: CS_94202_1_2dpi


title: 3999840035_R01C02

description: blood sample

label: Cy5 and Cy4


title: Timbo_THUN-12_1_2dpi

organism:
x Triticosecale
Blumeria graminis f. sp. triticale

source_name: Triticale leaves (cv. Timbo) infected with B.g. triticale THUN-12, 48h post infection

value: Timbo


title: Timbo_THUN-12_2_2dpi


title: Timbo_THUN-12_3_2dpi


title: 3999840035_R03C02

description: blood sample

label: Cy5 and Cy5


title: Timbo_T3-8_3_2dpi

source_name: Triticale leaves (cv. Timbo) infected with B.g. triticale T3-8, 48h post infection


title: IPF-001-unaffected

description: Gene expression data from PBMC extracted from individual IPF-001

source_name: Individual IPF-001


title: Matador_S-1391_1_2dpi


title: CS_96224_3_2dpi

source_name: Wheat leaves (cv. Chinese spring) infected with B.g. tritici 96224, 48h post infection


title: MC38 sh Ctrl

description: MC38 sh Ctrl Mouse colon carcinoma sh Ctrl

source_name: MC38 sh Ctrl

value: control


title: Timbo_T3-8_2_2dpi


title: CS_96224_2_2dpi


title: MC38 sh Kras

description: MC38 sh Kras Mouse colon carcinoma sh Kras

source_name: MC38 sh Kras

value: sh Kras


title: CS_96224_1_2dpi


title: Timbo_T3-8_1_2dpi


title: DSP356_V-1

status: Public on Jan 09 2018

city: MONTREAL

first: Sylvie

last: Mader

state: QC

address: CP 6128 Succursale centre ville

department: Biochemistry and Molecular Medicine

country: Canada

institute: Université de Montréal

description: messenger RNA

data_processing:
ChIP-seq reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads, and all reads were required to have a length of at least 50 bp using Timmomatic. The trimmed reads were mapped onto the hg19 reference genome using the aligner BWA. Properly paired reads were identified as inward-facing reads that are on the same chromosome and separated by a distance less than 600 bp. The number of fragments overlapping each 50 bp window was counted for each library along each standard chromosome and excluding blacklisted regions 2. The starts of adjacent windows were separated by 50 bp.  To remove composition biases between libraries, reads were counted into 2 kbp bins over the genome for each library. Windows were filtered to retain only those with a 4-fold or greater increase in the average abundance above the scaled background estimate.
Gene expression was computed with Kallisto with default parameters (100 bootstraps) on the reference genome GRCh38 with the annotation of Ensembl v85 (with cdna and rna).
Genome_build: hg19 for chipseq and GRCh38 for rnaseq
Supplementary_files_format_and_content: Tab-delimited text file for the chiseq experiment include counts per 50bp window for each sample and calculated using the csaw bioconductor package  as described above
Supplementary_files_format_and_content: Tab-delimited text file for the rnaseq experiment include abundance estimate for each sample using kallisto as described above

source_name: breast cancer cells

growth_protocol: MCF-7 cells were maintained at 37°C, 5% CO2 in AMEM supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin. Three days before experiments, cells were switched to phenol red-free DMEM containing charcoal-stripped FBS, 2% L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
Cell pellets were lysed with QIAzol and RNA was extracted per manufacturer's instructions.
Libraries were prepared according to Roche's instructions. KAPA Stranded RNA-seq Library Preparation Kit.

treatment_protocol: MCF-7 cells were treated with vehicule for 16 h.

value: MCF-7 cells

tag: chip antibody


title: DSP356_V-3

description: messenger RNA


title: PHDF38 shKAP T3

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description:
primary dermal fibroblasts during reprogramming into iPS cells with KAP1/TRIM28 knockdown on timepoint 3 - 14 days after OSKM-lentiviral vector transduction
15

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Genome Studio V2011.2 (Control Normalization + Backgroud)

label: Cy3, Cy5

source_name: primary human dermal fibroblasts during reprogramming into iPS

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: genotype/variation

value: KAP1/TRIM28 knockdown

tag: time


title: DSP356_V-2

description: messenger RNA


title: DSP356_OHT-3

description: messenger RNA

treatment_protocol: MCF-7 cells were treated with 100 nM OHT for 16 h.


title: DSP356_OHT-2

description: messenger RNA


title: Oct4 transfected rep 2

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

description:
T2_S2
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt

data_processing:
Mapping of the reads to the GRCh38 reference genome with Star (version 2.5.2).
Generation of count tables parsing Star output with R (version 3.2.3).
Differential expression was determined with the edgeR (version 3.12) package in R (version 3.2.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts.txt: Tab-delimited text file includes sequencing reads of corresponding genes.
Supplementary_files_format_and_content: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt: Tab-delimited text file includes counts per million of reads of corresponding genes.

source_name: human dermal fibroblasts

growth_protocol: Fibroblasts cultures were established from skin biopsies from human donors. The cells were routinely passaged 1:3 and grown in standard human fibroblast medium (hFib Med: DMEM supplemented with 2mM glutamine, 1% v/v NEAA and 10% FBS).

extract_protocol:
RNA was extracted using the RNeasy® Micro Kit (Qiagen GmbH, Hilden, Germany), introducing the DNase treatment step and according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol:
Infection of the cultures was carried out at passage numbers 4-8. 2.2x10(4) cells were plated in each well in 6-well dishes in standard fibroblast medium (hFib Med). Cultures were infected three days later.
In order to carry out transduction with LV-Oct4 viral particles, the medium was replaced with a 1:1 mixture of hFib Med and reprogramming medium (RM: DMEM:F12, 20% knockout serum replacement, 2mM glutamine, 1% NEAA, 0.1mM beta-mercaptoethanol, 16ng/ml FGF-2 and 30ng/ml IGF-2), supplemented with 8 microg/ml polybrene. Twenty-four hours later, the medium was replaced with 100% RM; the cultures were maintained in this medium for 8 days, changing it every other day. Following culture in RM of the cells transduced with LV-Oct4, these were trypsinised and replated at a density of 2-4x10(4) cells/cm(2) onto laminin-coated wells; cultures were kept in serum-free medium (SFM; consisting of DMEM:F12, 2mM glutamine, 1xN2 and 2xB27), supplemented with 20ng/ml EGF and 50ng/ml IGF-1, for 15 days followed by another 8-26 days in the same medium, with the addition of 20ng/ml FGF-2. The cultures were then replated onto gelatin-coated wells or coverslips, at densities of 3-10x10(4) cells/cm(2), and kept in SFM containing 20ng/ml EGF and 10mM RA for 3 weeks. Medium was changed every other day throughout the experiment.

value: dermal fibroblasts

tag: transfection


title: Oct4 transfected rep 1

description:
T1_S1
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt


title: Control untreated rep 1

description:
P6_S3
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt

treatment_protocol: Infection of the cultures was carried out at passage numbers 4-8. 2.2x10(4) cells were plated in each well in 6-well dishes in standard fibroblast medium (hFib Med). Cultures were infected three days later.


title: ATOH1/POU4F3/GFI1 transfected rep1

description:
3LV-TS1_S1
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt

treatment_protocol:
Infection of the cultures was carried out at passage numbers 4-8. 2.2x10(4) cells were plated in each well in 6-well dishes in standard fibroblast medium (hFib Med). Cultures were infected three days later.
When transducing with hATOH1, mPou4f3 and hGFI1 lentiviruses (3LV), these were added to cultures after changing their medium to fresh hFib Med with 8microg/ml polybrene. The medium was changed to fresh hFib Med 24 hours later. Following removal of the transduction medium, cultures were grown in SFM containing 20ng/ml EGF and 10mM RA for 3 weeks.


title: ATOH1/POU4F3/GFI1 transfected rep2

description:
3LV-TS2_S2
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt


title: DSP356_ICI-3

description: messenger RNA

treatment_protocol: MCF-7 cells were treated with 100 nM ICI for 16 h.


title: Control untreated rep 2

description:
P8_S4
Primary cells
processed data file: Counts.txt
processed data file: Log2CountsPerMillionOfReadsPerSample_AllSamples.txt


title: DSP356_ICI-2

description: messenger RNA


title: DSP356_ICI-1

description: messenger RNA


title: PHDF38 shKAP T0

description:
primary dermal fibroblasts during reprogramming into iPS cells with KAP1/TRIM28 knockdown on timepoint 0 - before OSKM-lentiviral vector transduction
12


title: DSP356_OHT-1

description: messenger RNA


title: DSP356_E-3

description: messenger RNA

treatment_protocol: MCF-7 cells were treated with 5 nM E2 for 16 h.


title: HEK293 MOCK 24hr n=1

source_name: HEK293 MOCK 24hr

value: HEK293 HA-YWHAE-NUTM2 cells

value: MOCK for 24hr


title: DSP488_input

description: genomic DNA

library_source: genomic

extract_protocol:
Nuclei were lysed and samples were sonicated to fragment chromatin.
Libraries were prepared according to Roche's instructions. KAPA DNA HyperPrep Library Kit.

treatment_protocol: pool of cells with different treatments


title: DSP356_E-2

description: messenger RNA


title: DSP356_E-1

description: messenger RNA


title: iPS X.11

description:
induced pluripotent stem cells derived from primary dermal fibroblasts with a usage of OSKM-lentiviral vector
6

source_name: human induced pluripotent stem cells


title: DSP514_input

description: genomic DNA


title: DSP250_input

description: genomic DNA

treatment_protocol: MCF-7 cells were treated with 100 nM ICI for 30 min


title: DSP460_input

description: genomic DNA


title: PHDF38 shKAP T2

description:
primary dermal fibroblasts during reprogramming into iPS cells with KAP1/TRIM28 knockdown on timepoint 2 - 7 days after OSKM-lentiviral vector transduction
14

label: Cy3, Cy6


title: PHDF38 WT T2

description:
primary dermal fibroblasts during reprogramming into iPS cells on timepoint 2 - 7 days after OSKM-lentiviral vector transduction
10

value: WT


title: DSP514_ICI_3h_SUMO_N2

description: genomic DNA

extract_protocol:
Nuclei were lysed. SUMO2/3-DNA complexes were isolated with the appropriate antibody.
Libraries were prepared according to Roche's instructions. KAPA DNA HyperPrep Library Kit.

treatment_protocol: MCF-7 cells were treated with ICI for 3h

value: SUMO2/3 (Cedarlane M114-3)


title: DSP514_ICI_30_SUMO_N1

description: genomic DNA


title: hES

description:
commercially available embryonic cell line BG01V – ATCC® SCRC-2002
7

source_name: human embryonic stem cells

value: embryonic stem cells (BG01V-ATCC® SCRC-2002)


title: DSP488_E2_3h_ERa_N1

description: genomic DNA

extract_protocol:
Nuclei were lysed. ERα-DNA complexes complexes were isolated with the appropriate antibody.
Libraries were prepared according to Roche's instructions. KAPA DNA HyperPrep Library Kit.

treatment_protocol: MCF-7 cells were treated with E2 for 3h

value: ERα HC-20 (Santa Cruz Biotechnology sc-543)


title: DSP514_V_30_SUMO_N2

description: genomic DNA

treatment_protocol: MCF-7 cells were treated with vehicle for 30 min


title: DSP514_V_30_SUMO_N1

description: genomic DNA


title: iPS 13.10

description:
induced pluripotent stem cells derived from primary dermal fibroblasts with a usage of OSKM-lentiviral vector
3


title: DSP514_ICI_3h_ERa_N2

description: genomic DNA


title: DSP514_ICI_3h_ERa_N1

description: genomic DNA


title: DSP488_E2_3h_ERa_N2

description: genomic DNA


title: iPS 13.9

description:
induced pluripotent stem cells derived from primary dermal fibroblasts with a usage of OSKM-lentiviral vector
2


title: DSP488_ICI_3h_ERa_N1

description: genomic DNA


title: DSP514_V_3h_ERa_N2

description: genomic DNA

treatment_protocol: MCF-7 cells were treated with vehicle for 3h


title: DSP514_V_3h_ERa_N1

description: genomic DNA


title: DSP488_V_3h_ERa_N2

description: genomic DNA


title: DSP488_V_3h_ERa_N1

description: genomic DNA


title: DSP514_ICI_30_SUMO_N2

description: genomic DNA


title: DSP460_E2_30_ERa_N2

description: genomic DNA

treatment_protocol: MCF-7 cells were treated with 5 nM E2 for 30 min


title: PHDF 26

description:
primary cell line derived from skin of a patient number 26
4

source_name: primary human dermal fibroblasts

tag: individual

value: patient number 26


title: DSP488_E2_30_ERa_N1

description: genomic DNA


title: PHDF38 shKAP T1

description:
primary dermal fibroblasts during reprogramming into iPS cells with KAP1/TRIM28 knockdown on timepoint 1 - first day after OSKM-lentiviral vector transduction
13


title: DSP250_E2_ERa

description: genomic DNA


title: PHDF38 WT T3

description:
primary dermal fibroblasts during reprogramming into iPS cells on timepoint 3 - 14 days after OSKM-lentiviral vector transduction
11


title: DSP488_ICI_30_ERa_N2

description: genomic DNA


title: DSP250_EtOH_ERa

description: genomic DNA


title: iPS 26.6

description:
induced pluripotent stem cells derived from primary dermal fibroblasts with a usage of OSKM-lentiviral vector
5


title: DSP250_ICI_ERa

description: genomic DNA


title: DSP514_ICI_3h_SUMO_N1

description: genomic DNA


title: DSP488_V_30_ERa_N1

description: genomic DNA


title: E_Peptide_Rep1

city: Chicago

middle: E

last: Speltz

state: IL

address: 833 S Wood St., room 539

department: Department of Medicinal Chemistry and Pharmacognosy

institute: University of Illinois at Chicago

description: Process.RNASeq.DE.txt

data_processing:
RNA-Seq results were trimmed and aligned to the hg38 assembly using ELAND allowing up to 2 mismatches.
Differential gene expression was determined using edgeR as a component of the HOMER software suite. (Detailed instructions for analysis can be found at http://homer.ucsd.edu/homer/. ) Transcript/RepeatID (cmd=analyzeRepeats.pl rna hg38 -raw -condenseGenes -d Veh_Rep1 Veh_Rep2 E2_Rep1 E2_Rep2 TOT_Rep1 TOT_Rep2 ET_Rep1 ET_Rep2 Peptide_Rep1 Peptide_Rep2 E_Peptide_Rep1 E_Peptide_Rep2) (cmd=getDiffExpression.pl o.txt Veh Veh E2 E2 4OHT 4OHT ET ET PEP PEP E_PEP E_PEP -repeats -AvsA -edgeR)
Genes were considered differentially regulated if fold change >2 and p-value <0.05 compared to vehicle treatments
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file; abundance measurements for each condition/repeat, fold-change (log 2) between specified treatment groups, and p-values for fold change calculations.

source_name: human breast adenocarcinoma cell line

growth_protocol: Human MCF-7 were grown in Roswell Park Memorial Institute (RPMI) media supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids, 2 mM L-glutamine, 1% antibiotics penicillin-streptomycin, and 6 ng/ml human recombinant insulin at 37 ˚C in 5% CO2  (T75 flasks).

extract_protocol:
Total RNA was isolated using Trizol. RNA samples were DNase treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research). All samples were quantified using the NanoDrop 1000 instrument (Thermo Fisher Scientific). RNA quality was analyzed on a TapeStation RNA tape (Agilent).
500ng total RNA from each sample was used as input for library prep, using the QuantSeq 3’ mRNA-Seq Library Prep kit (Lexogen). The protocol was followed as written. In brief, the RNA underwent oligo dT priming, reverse transcription, removal of the RNA template, and second strand synthesis via random priming, resulting in double-stranded libraries. Illumina indexes were then incorporated during 16 cycles of PCR amplification. Library yields were assessed with the Qubit dsDNA HS reagent (Invitrogen), and TapeStation D1000 tape (Invitrogen)

treatment_protocol: MCF-7 cells were seeded at a density of 150K celsl/well in 6 well plates in treatment media (phenol red-free RPMI 1640 media supplemented with 5% charcoal–dextran–stripped fetal bovine serum for at least 48 hrs. The cells were incubated overnight (24hr) with the stapled peptides (15 μM). The following day cells were treated with E2 (10 nM) or 4OHT (1 μM) for 2hr and for the E2 and 4OHT treated cells the cells were pretreated with 4OHT for 2hrs

value: Breast cancer cell

value: estradiol (10 nM) + R4k1 (15 μM)


title: E_Peptide_Rep2

description: Process.RNASeq.DE.txt


title: Peptide_Rep2

description: Process.RNASeq.DE.txt

value: R4K1 stapled peptide (15 μM)


title: DSP514_ICI_30_ERa_N1

description: genomic DNA


title: PHDF 13

description:
primary cell line derived from skin of a patient number 13
1

value: patient number 13


title: ET_Rep1

description: Process.RNASeq.DE.txt

value: estradiol (10 nM) + 4-hydroxytamoxifen (1 μM)


title: ET_Rep2

description: Process.RNASeq.DE.txt


title: TOT_Rep2

description: Process.RNASeq.DE.txt

value: 4-hydroxytamoxifen (1 μM)


title: TOT_Rep1

description: Process.RNASeq.DE.txt


title: E2_Rep2

description: Process.RNASeq.DE.txt

value: estradiol (10 nM)


title: Peptide_Rep1

description: Process.RNASeq.DE.txt


title: Veh_Rep2

description: Process.RNASeq.DE.txt

value: vehicle


title: Veh_Rep1

description: Process.RNASeq.DE.txt


title: E18.5 kidney 3

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics from the kidney samples were combined using cellranger aggr with no normalisation, as were those from the organoid samples. The resulting datasets consist of matrix files (kid_matrix.mtx, org_matrix.mtx) containing the UMI count values, barcode files (kid_barcodes.tsv, org_matrix.tsv) containing the detected cell barcodes and genes files (kid_genes.tsv, org_genes.tsv) containing the ENSEMBL ids of the detected genes. These have been converted to dense matrices in CSV format (kidney_counts.csv, org_counts.csv).
Genome_build: mm10 / hg38
Supplementary_files_format_and_content: CSV files containing raw count matrices.

source_name: Developing mouse kidney

growth_protocol: Kidney organoids were made according to a published protocol (Takasata et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173.

extract_protocol:
Mouse kidneys were dissected into ice cold PBS then digested over 15 minutes at 37C in Accutase, with manual dissociation via pippetting through a P1000 tip every 5 minutes. Following dissociation, cells were passed through a 30 micron filter and stored on ice in 50% PBS, 50% DMEM with 10% FCS. Human kidney organoids were dissociated via a similar protocol using Trypsin instead of Accutase and stored on ice in APEL media.
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: Developing mouse kidney

tag: strain


title: E2_Rep1

description: Process.RNASeq.DE.txt


title: E18.5 kidney 2


title: E18.5 kidney 1


title: Residual MHCC97H-POSTN-100ng/ml-rep1

city: Shanghai

first: Rui

last: Zhang

address: Fenglin road of Xuhui district

institute: Zhongshan hospital of Fudan University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

data_processing:
Raw data were normalized by MAS 5.0 algorithm, Affy packages in R. T-test analysis with P < 0.05 was used to screen differential expressed genes.
The original data of the chip are standardized and converted to log2 values to assess the overall distribution of the two sets of data.

source_name: Residual MHCC97H, POSTN-100ng/m treated, 24h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: 10% DMEM

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: MHCC97H was heated at 47℃ to simulate the sublethal temperature, and was administrated with or without exogenous recombinant POSTN for 24 hours.

value: HCC cells


title: Residual MHCC97H-POSTN-0ng/ml-rep3

source_name: Residual MHCC97H, POSTN-0ng/m treated, 24h


title: Donor 5 HIV

city: Gainesville

first: Mark

middle: A

last: Wallet

state: Florida

address: 1275 Center Drive

department: Pathology

institute: University of Florida

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Florida Microarray Core Facility.

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

data_processing: RMA expression value derived from Expression Console software; core-exon analysis

source_name: healthy human peripheral blood monocyte-derived macrophage

label_protocol: Single-stranded cDNA was generated  with the WT Expression Kit (Invitrogen) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Monocytes from healthy human donors were cultured in MDM Medium (DMEM with 4.5 g/L glucose, 10% heat-inactivated human serum, 2 mM L-glutamine, 100 IU penicillin/streptomycin) supplemented with 1 ng/ml M-CSF for 7-10 days. After differentiation into macrophages the medium was replensihed without M-CSF.

extract_protocol: Total RNA was collected and isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Differentiated monocyte-derived macrophages were treated with 500 TCID50 HIV-1-AD8 laboratory strain or treated with an equal volume of MDM medium for 24 hours. After 24 hours the inoculum was removed and the medium was replenished. The infection was allowed to spread for an additional 6 days. Total RNA was collected on day 7 post-infection.

value: infected with HIV-1-AD for 7 days


title: Residual MHCC97HPOSTN-100ng/ml-rep2


title: Donor 3 HIV


title: Donor 4 HIV


title: Donor 5 Untreated

value: untreated


title: Donor 2 HIV


title: Residual MHCC97H-POSTN-0ng/ml-rep1


title: Residual MHCC97H-POSTN-0ng/ml-rep2


title: Donor 1 HIV


title: Donor 2 Untreated


title: Residual MHCC97HPOSTN-100ng/ml-rep3


title: Donor 4 Untreated


title: Donor 1 Untreated


title: Donor 3 Untreated


title: Sorted CD8+ T cells Flu A 12y [Sample125]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
Sample125
Expression data from CD8+ T cells Flu A 12y.

hyb_protocol: Hybridized to Affymetrix Human Gene 1.1 ST microarrays at the University of Pennsylvania Microarray Facility.

scan_protocol: Arrays were scanned following manufacturer's instructions, by the University of Pennsylvania Microarray Facility.

data_processing: Microarray CEL files were imported and normalized using rma function from bioconductor package oligo.

source_name: PBMC

label_protocol: RNA was processed, amplified using NuGen WT-Ovation Pico + Exon Module & labeled

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

value: CD8+ T cells

tag: disease status

value: Flu


title: Sorted CD8+ T cells Flu A 17y [Sample143]

description:
Sample143
Expression data from CD8+ T cells Flu A 17y.


title: Sorted CD8+ T cells Flu A 6y [Sample185]

description:
Sample185
Expression data from CD8+ T cells Flu A 6y.


title: Sorted CD8+ T cells Flu A 6y [Sample167]

description:
Sample167
Expression data from CD8+ T cells Flu A 6y.


title: Sorted CD8+ T cells Flu A 6y [Sample159]

description:
Sample159
Expression data from CD8+ T cells Flu A 6y.


title: Sorted CD8+ T cells Flu A 17y [Sample193]

description:
Sample193
Expression data from CD8+ T cells Flu A 17y.


title: Sorted CD8+ T cells Flu A 13y [Sample160]

description:
Sample160
Expression data from CD8+ T cells Flu A 13y.


title: Sorted CD8+ T cells Flu A 12y [Sample166]

description:
Sample166
Expression data from CD8+ T cells Flu A 12y.


title: Sorted CD8+ T cells Flu A 17y [Sample155]

description:
Sample155
Expression data from CD8+ T cells Flu A 17y.


title: Sorted CD8+ T cells Flu A 5y [Sample176]

description:
Sample176
Expression data from CD8+ T cells Flu A 5y.


title: Sorted CD8+ T cells Flu A 5y [Sample158]

description:
Sample158
Expression data from CD8+ T cells Flu A 5y.


title: Sorted CD8+ T cells Flu A 4y [Sample163]

description:
Sample163
Expression data from CD8+ T cells Flu A 4y.


title: Sorted CD8+ T cells Flu A 3y [Sample152]

description:
Sample152
Expression data from CD8+ T cells Flu A 3y.


title: Sorted CD8+ T cells Flu A 10y [Sample154]

description:
Sample154
Expression data from CD8+ T cells Flu A 10y.


title: Sorted CD8+ T cells Rhino 1y [Sample147]

description:
Sample147
Expression data from CD8+ T cells Rhino 1y.

value: Rhino


title: Sorted CD8+ T cells RSV 1y [Sample192]

description:
Sample192
Expression data from CD8+ T cells RSV 1y.

value: RSV


title: Sorted CD8+ T cells Flu A 3w [Sample174]

description:
Sample174
Expression data from CD8+ T cells Flu A 3w.


title: Sorted CD8+ T cells Flu A 2m [Sample162]

description:
Sample162
Expression data from CD8+ T cells Flu A 2m.


title: Sorted CD8+ T cells Flu A 1y [Sample165]

description:
Sample165
Expression data from CD8+ T cells Flu A 1y.


title: Sorted CD8+ T cells Rhino 2y [Sample178]

description:
Sample178
Expression data from CD8+ T cells Rhino 2y.


title: Sorted CD8+ T cells Flu A 4m [Sample164]

description:
Sample164
Expression data from CD8+ T cells Flu A 4m.


title: Sorted CD8+ T cells Rhino 11m1w [Sample208]

description:
Sample208
Expression data from CD8+ T cells Rhino 11m1w.


title: Sorted CD8+ T cells Flu A 7m2w [Sample169]

description:
Sample169
Expression data from CD8+ T cells Flu A 7m2w.

value: 7m 2w


title: Sorted CD8+ T cells Rhino 2y [Sample179]

description:
Sample179
Expression data from CD8+ T cells Rhino 2y.


title: Sorted CD8+ T cells Flu A 6m [Sample157]

description:
Sample157
Expression data from CD8+ T cells Flu A 6m.


title: Sorted CD8+ T cells Flu A 1y [Sample175]

description:
Sample175
Expression data from CD8+ T cells Flu A 1y.


title: Sorted CD8+ T cells RSV 1y [Sample188]

description:
Sample188
Expression data from CD8+ T cells RSV 1y.


title: Sorted CD8+ T cells RSV 1y [Sample183]

description:
Sample183
Expression data from CD8+ T cells RSV 1y.


title: DSP514_V_30_ERa_N1

description: genomic DNA

value: MCF-7 cells

value: ERα HC-20 (Santa Cruz Biotechnology sc-543)


title: Sorted CD8+ T cells Healthy control 16y6m [Sample12]

description:
Sample12
Expression data from CD8+ T cells Healthy control 16y6m.

value: Healthy


title: Sorted CD8+ T cells RSV 10d [Sample191]

description:
Sample191
Expression data from CD8+ T cells RSV 10d.


title: Sorted CD8+ T cells Healthy control 17y9m [Sample7]

description:
Sample7
Expression data from CD8+ T cells Healthy control 17y9m.


title: Sorted CD8+ T cells Healthy control 10y6m [Sample16]

description:
Sample16
Expression data from CD8+ T cells Healthy control 10y6m.


title: Sorted CD8+ T cells Healthy control 12y4m [Sample13]

description:
Sample13
Expression data from CD8+ T cells Healthy control 12y4m.


title: Sorted CD8+ T cells Healthy control 10y1m [Sample14]

description:
Sample14
Expression data from CD8+ T cells Healthy control 10y1m.


title: Sorted CD8+ T cells Healthy control 12y6m [Sample10]

description:
Sample10
Expression data from CD8+ T cells Healthy control 12y6m.


title: genomic DNA from gastric normal 60

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: minfi's functional normalization function

label: Cy5 and Cy3

source_name: gastric endoscopic biopsy 190

extract_protocol: Standard Illumina Protocol

tag: tissue

value: normal biopsy from gastric cardia


title: genomic DNA from gastric normal 61

source_name: gastric endoscopic biopsy 191


title: Sorted CD8+ T cells Healthy control 10y1m [Sample8]

description:
Sample8
Expression data from CD8+ T cells Healthy control 10y1m.


title: Sorted CD8+ T cells Healthy control 4y7m [Sample18]

description:
Sample18
Expression data from CD8+ T cells Healthy control 4y7m.

value: 4y 7m


title: genomic DNA from gastric normal 59

source_name: gastric endoscopic biopsy 189


title: CON208.3A_u8

city: Seattle

first: Samuel

last: Miller

state: Washington

address: 1959 Pacific Ave Box 357710

institute: University of Washington

data_processing:
Basecalling performed by MiSeq (RTA)
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters)
Filter for map quality >= 20 using Samtools 0.1.18
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz)
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3)
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product

organism: Escherichia coli

source_name: E. coli strain isolated from healthy child stool

growth_protocol: Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed.

extract_protocol:
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction.
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards.

value: healthy child

tag: disease state

value: control

tag: carbon source

value: Glucose

tag: replicate


title: genomic DNA from gastric normal 55

source_name: gastric endoscopic biopsy 185


title: genomic DNA from gastric normal 57

source_name: gastric endoscopic biopsy 187


title: genomic DNA from gastric normal 56

source_name: gastric endoscopic biopsy 186


title: Sorted CD8+ T cells Healthy control 3y11m [Sample1]

description:
Sample1
Expression data from CD8+ T cells Healthy control 3y11m.

tag: cell type


title: genomic DNA from gastric normal 58

source_name: gastric endoscopic biopsy 188


title: genomic DNA from gastric normal 52

source_name: gastric endoscopic biopsy 182


title: genomic DNA from gastric normal 51

source_name: gastric endoscopic biopsy 181


title: genomic DNA from gastric normal 49

source_name: gastric endoscopic biopsy 179

value: normal biopsy from gastric body


title: Sorted CD8+ T cells Healthy control 3y1m [Sample6]

description:
Sample6
Expression data from CD8+ T cells Healthy control 3y1m.

value: 3y 1m


title: genomic DNA from gastric normal 41

source_name: gastric endoscopic biopsy 171


title: genomic DNA from gastric normal 54

source_name: gastric endoscopic biopsy 184


title: genomic DNA from gastric normal 45

source_name: gastric endoscopic biopsy 175


title: genomic DNA from gastric normal 46

source_name: gastric endoscopic biopsy 176


title: CON206.3A_u1


title: genomic DNA from gastric normal 48

source_name: gastric endoscopic biopsy 178


title: CON208.3A_u1


title: genomic DNA from gastric normal 47

source_name: gastric endoscopic biopsy 177


title: genomic DNA from gastric normal 42

source_name: gastric endoscopic biopsy 172


title: Sorted CD8+ T cells Healthy control 2y3m [Sample2]

description:
Sample2
Expression data from CD8+ T cells Healthy control 2y3m.

source_name: PBMC

value: 2y 3m


title: Sorted CD8+ T cells Healthy control 2y [Sample11]

description:
Sample11
Expression data from CD8+ T cells Healthy control 2y.


title: genomic DNA from gastric normal 44

source_name: gastric endoscopic biopsy 174


title: genomic DNA from gastric normal 43

source_name: gastric endoscopic biopsy 173


title: genomic DNA from gastric normal 38

source_name: gastric endoscopic biopsy 168

value: normal biopsy from gastric antrum


title: Sorted CD8+ T cells Healthy control 4y6m [Sample17]

description:
Sample17
Expression data from CD8+ T cells Healthy control 4y6m.

value: CD8+ T cells

value: 4y 6m


title: genomic DNA from gastric normal 39

source_name: gastric endoscopic biopsy 169


title: genomic DNA from gastric normal 53

source_name: gastric endoscopic biopsy 183


title: CF108.4B_u1

source_name: E. coli strain isolated from CF patient stool

value: CF patient

value: cystic fibrosis


title: CF108.4B_u2


title: genomic DNA from gastric normal 50

source_name: gastric endoscopic biopsy 180


title: CF104.3.3_u7


title: CF104.3.3_u1


title: CON208.3A_y6

source_name: E. coli strain isolated from healthy child stool

value: Glycerol


title: CON208.3A_y2


title: CON206.3A_u2


title: genomic DNA from gastric normal 40

source_name: gastric endoscopic biopsy 170


title: genomic DNA from gastric normal 35

source_name: gastric endoscopic biopsy 165


title: genomic DNA from gastric normal 37

source_name: gastric endoscopic biopsy 167


title: CON206.3A_y2


title: genomic DNA from gastric normal 34

source_name: gastric endoscopic biopsy 164


title: genomic DNA from gastric normal 36

source_name: gastric endoscopic biopsy 166


title: Sorted CD8+ T cells Healthy control 1y [Sample15]

description:
Sample15
Expression data from CD8+ T cells Healthy control 1y.


title: Sorted CD8+ T cells Healthy control 10m [Sample9]

description:
Sample9
Expression data from CD8+ T cells Healthy control 10m.


title: Sorted CD8+ T cells Healthy control 1y7m [Sample4]

description:
Sample4
Expression data from CD8+ T cells Healthy control 1y7m.

value: 1y 7m


title: CON206.3A_y1


title: CF108.4B_y8


title: Sorted CD8+ T cells Healthy control 9m [Sample3]

description:
Sample3
Expression data from CD8+ T cells Healthy control 9m.


title: Sorted CD8+ T cells Healthy control 1y6m [Sample5]

description:
Sample5
Expression data from CD8+ T cells Healthy control 1y6m.

value: 1y 6m


title: genomic DNA from gastric normal 29

source_name: gastric endoscopic biopsy 159


title: genomic DNA from gastric normal 33

source_name: gastric endoscopic biopsy 163


title: genomic DNA from gastric normal 30

source_name: gastric endoscopic biopsy 160


title: CF108.4B_y3


title: genomic DNA from gastric normal 32

source_name: gastric endoscopic biopsy 162


title: CF104.3.3_y2


title: CF104.3.3_y9


title: genomic DNA from gastric normal 31

source_name: gastric endoscopic biopsy 161


title: genomic DNA from gastric normal 19

source_name: gastric endoscopic biopsy 149


title: Normal cervical stroma B3

city: Madison

first: Johan

last: den Boon

state: WI

address: 330 North Orchard Street

department: Virology

institute: Morgridge Institute for Research

description: gene expression data

hyb_protocol: At UW-Madison Biotech Center core facilties, biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays according to Affymetrix instructions using Affymetrix Array hybridization stations.

scan_protocol: Gene Array Scanner at UW-Madison Biotech Center core facilties.

data_processing: GC-RMA.

source_name: frozen reproductive tract

label_protocol: Total RNA was converted to cDNA usingT7 promoter-linked oligo-d(T), transcribed into cRNA using T7 RNA polymerase, converted again to cDNA for a second round of T7-cRNA transcription in the presence of biotinylated ribonucleotides.

growth_protocol: Mice were housed and treated in the American Association of Laboratory Animal Care - approved Wisconsin Institute for Medical Research Vivarium of the University of Wisconsin School of Medicine and Public Health (Madison, WI), according to a University of Wisconsin Institutional Animal Care and Use Committee approved protocol.

extract_protocol: Reproductive tracts were harvested and frozen; cervical epithelium and underlying stroma were laser-captured from cryosections; total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: At 4-6 weeks of age, a subset of non-transgenic FVB and K14E6/E7 female mice were anesthetized with 5% isoflurane for subcutaneous insertion of a continuous-release estrogen tablet (17β-estradiol; 0.05 mg/60 days; Innovative Research of America, Sarasota, FL) into the shoulder fat pads. New tablets were inserted every 2 months.

value: FVB

tag: treatment

value: estrogen

tag: cervix location

value: endocervix

tag: tissue type

value: stroma

tag: dissection

value: laser capture


title: genomic DNA from gastric normal 26

source_name: gastric endoscopic biopsy 156


title: Normal cervical stroma B2

description: gene expression data


title: genomic DNA from gastric normal 17

source_name: gastric endoscopic biopsy 147


title: genomic DNA from gastric normal 15

source_name: gastric endoscopic biopsy 145


title: genomic DNA from gastric normal 20

source_name: gastric endoscopic biopsy 150


title: genomic DNA from gastric normal 27

source_name: gastric endoscopic biopsy 157


title: genomic DNA from gastric normal 22

source_name: gastric endoscopic biopsy 152


title: genomic DNA from gastric normal 21

source_name: gastric endoscopic biopsy 151


title: genomic DNA from gastric normal 16

source_name: gastric endoscopic biopsy 146


title: genomic DNA from gastric normal 10

source_name: gastric endoscopic biopsy 140


title: genomic DNA from gastric normal 9

source_name: gastric endoscopic biopsy 139


title: genomic DNA from gastric normal 11

source_name: gastric endoscopic biopsy 141


title: genomic DNA from gastric normal 24

source_name: gastric endoscopic biopsy 154


title: genomic DNA from gastric normal 18

source_name: gastric endoscopic biopsy 148


title: genomic DNA from gastric normal 25

source_name: gastric endoscopic biopsy 155


title: Normal cervical stroma B1

description: gene expression data


title: genomic DNA from gastric normal 5

source_name: gastric endoscopic biopsy 135


title: Cancer cervical stroma D5

description: gene expression data

value: K14-E6/E7 on FVB


title: genomic DNA from gastric normal 23

source_name: gastric endoscopic biopsy 153


title: genomic DNA from gastric normal 28

source_name: gastric endoscopic biopsy 158


title: genomic DNA from gastric normal 12

source_name: gastric endoscopic biopsy 142


title: genomic DNA from gastric normal 13

source_name: gastric endoscopic biopsy 143


title: genomic DNA from gastric normal 8

source_name: gastric endoscopic biopsy 138


title: genomic DNA from gastric normal 6

source_name: gastric endoscopic biopsy 136


title: genomic DNA from gastric normal 4

source_name: gastric endoscopic biopsy 134


title: Cancer cervical stroma D4

description: gene expression data

source_name: frozen reproductive tract


title: genomic DNA from gastric normal 14

source_name: gastric endoscopic biopsy 144


title: Cancer cervical stroma D1

description: gene expression data


title: genomic DNA from gastric normal 1

source_name: gastric endoscopic biopsy 131


title: Cancer cervical stroma D2

description: gene expression data


title: Cancer cervical stroma D3

description: gene expression data


title: genomic DNA from gastric normal 3

source_name: gastric endoscopic biopsy 133


title: CIN1/2 cervical stroma C7

description: gene expression data

value: no estrogen


title: genomic DNA from gastric mild intestinal metaplasia 22

source_name: gastric endoscopic biopsy 130

value: mild intestinal metaplasia biopsy from gastric antrum


title: CIN1/2 cervical stroma C6

description: gene expression data

value: outer cervix


title: genomic DNA from gastric normal 2

source_name: gastric endoscopic biopsy 132

value: normal biopsy from gastric antrum


title: CIN1/2 cervical stroma C5

description: gene expression data


title: CIN1/2 cervical stroma C2

description: gene expression data


title: Normal cervical stroma C3

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 16

source_name: gastric endoscopic biopsy 124


title: genomic DNA from gastric mild intestinal metaplasia 21

source_name: gastric endoscopic biopsy 129


title: genomic DNA from gastric mild intestinal metaplasia 17

source_name: gastric endoscopic biopsy 125


title: genomic DNA from gastric mild intestinal metaplasia 18

source_name: gastric endoscopic biopsy 126


title: CIN1/2 cervical stroma C1

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 9

source_name: gastric endoscopic biopsy 117


title: genomic DNA from gastric mild intestinal metaplasia 19

source_name: gastric endoscopic biopsy 127


title: CIN1/2 cervical stroma C4

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 20

source_name: gastric endoscopic biopsy 128


title: Normal cervical stroma A5

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 8

source_name: gastric endoscopic biopsy 116


title: genomic DNA from gastric normal 7

source_name: gastric endoscopic biopsy 137


title: genomic DNA from gastric mild intestinal metaplasia 12

source_name: gastric endoscopic biopsy 120


title: Normal cervical stroma A4

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 4

source_name: gastric endoscopic biopsy 112


title: genomic DNA from gastric mild intestinal metaplasia 15

source_name: gastric endoscopic biopsy 123


title: genomic DNA from gastric mild intestinal metaplasia 1

source_name: gastric endoscopic biopsy 109


title: genomic DNA from gastric mild intestinal metaplasia 3

source_name: gastric endoscopic biopsy 111


title: genomic DNA from gastric mild intestinal metaplasia 14

source_name: gastric endoscopic biopsy 122


title: Normal cervical stroma A3

description: gene expression data

source_name: frozen reproductive tract


title: genomic DNA from gastric mild intestinal metaplasia 13

source_name: gastric endoscopic biopsy 121


title: genomic DNA from gastric mild intestinal metaplasia 11

source_name: gastric endoscopic biopsy 119


title: genomic DNA from gastric intestinal metaplasia 108

source_name: gastric endoscopic biopsy 108

value: intestinal metaplasia biopsy from gastric body


title: genomic DNA from gastric mild intestinal metaplasia 6

source_name: gastric endoscopic biopsy 114


title: genomic DNA from gastric mild intestinal metaplasia 5

source_name: gastric endoscopic biopsy 113


title: Normal cervical stroma A1

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 107

source_name: gastric endoscopic biopsy 107

value: intestinal metaplasia biopsy from gastric antrum


title: genomic DNA from gastric mild intestinal metaplasia 10

source_name: gastric endoscopic biopsy 118


title: Normal cervical stroma A2

description: gene expression data


title: CIN1/2 cervical epithelium C6

description: gene expression data

value: epithelium


title: genomic DNA from gastric mild intestinal metaplasia 2

source_name: gastric endoscopic biopsy 110


title: CIN1/2 cervical epithelium C7

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 105

source_name: gastric endoscopic biopsy 105


title: genomic DNA from gastric intestinal metaplasia 103

source_name: gastric endoscopic biopsy 103


title: CIN1/2 cervical epithelium C5

description: gene expression data


title: genomic DNA from gastric mild intestinal metaplasia 7

source_name: gastric endoscopic biopsy 115


title: genomic DNA from gastric intestinal metaplasia 100

source_name: gastric endoscopic biopsy 100


title: genomic DNA from gastric intestinal metaplasia 97

source_name: gastric endoscopic biopsy 97


title: genomic DNA from gastric intestinal metaplasia 104

source_name: gastric endoscopic biopsy 104


title: genomic DNA from gastric intestinal metaplasia 99

source_name: gastric endoscopic biopsy 99


title: genomic DNA from gastric intestinal metaplasia 106

source_name: gastric endoscopic biopsy 106


title: CIN1/2 cervical epithelium C4

description: gene expression data

source_name: frozen reproductive tract


title: genomic DNA from gastric intestinal metaplasia 96

source_name: gastric endoscopic biopsy 96


title: genomic DNA from gastric intestinal metaplasia 101

source_name: gastric endoscopic biopsy 101


title: genomic DNA from gastric intestinal metaplasia 102

source_name: gastric endoscopic biopsy 102


title: genomic DNA from gastric intestinal metaplasia 92

source_name: gastric endoscopic biopsy 92


title: genomic DNA from gastric intestinal metaplasia 98

source_name: gastric endoscopic biopsy 98


title: CIN1/2 cervical epithelium C1

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 94

source_name: gastric endoscopic biopsy 94


title: CIN1/2 cervical epithelium C2

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 93

source_name: gastric endoscopic biopsy 93


title: Normal cervical epithelium A4

description: gene expression data


title: Normal cervical epithelium C3

description: gene expression data


title: Normal cervical epithelium A3

description: gene expression data


title: Normal cervical epithelium A5

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 90

source_name: gastric endoscopic biopsy 90


title: genomic DNA from gastric intestinal metaplasia 84

source_name: gastric endoscopic biopsy 84


title: Normal cervical epithelium A2

description: gene expression data


title: genomic DNA from gastric intestinal metaplasia 91

source_name: gastric endoscopic biopsy 91


title: Subject 23, purified CD4+ T cells, unstimulated

city: Rochester

first: Gregory

middle: A.

last: Poland

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description:
cDNA libraries were created from total RNA according to manufacturer's instructions and combined with Illumina adaptor sequences using standard procedures. Twelve samples were multiplexed in each lane. Lanes were balanced by cell type, immune response status and sex. Single-end read sequencing was performed using the Illumina HiSeq 2000.
processed data file: CD4_Cell_miRNA_for_SAS.csv
160719_SN414_0501_BC8YFTACXX.s_97985_CD4_Unstim.FCC8YFTACXX_L2_R1_IGCCAAT

data_processing:
The FASTQ files were processed using a comprehensive pre-processing and analytical pipeline (CAP-miRNA) that assesses read quality (FastQC), trims adapter sequences (Cutadapt), and aligns reads for IGV viewing and detection of mature, precursor, and novel miRNAs (miRDeep2).
Data filtered using a median cuttoff of 4 within each sample type
Normalized using TMM from edgeR (offsets and dispersion provided in processed files )
Genome_build: HG38
Supplementary_files_format_and_content: Comma separated text file contains raw count data and the offset and dispersion generated by the edgeR Rpackage; One row per sample and miRNA for end analysis is SAS GENMOD

source_name: purified CD4+ T cells (from PBMCs isolated from blood)

growth_protocol: Cryopreserved PBMCs/cells were thawed and cultured using standard procedures. B cells and monocytes were purified using a human CD19 MicroBeads positive selection kit (Miltenyi Biotec; San Diego, CA) and a human CD14 MicroBeads positive selection kit (Miltenyi Biotec), respectively. CD4+ T cells were isolated using the CD4+T Cell Isolation Kit (Miltenyi Biotec).

extract_protocol:
Total RNA (including miRNA) from B and T cells was extracted using miRNeasy Mini Kits (Qiagen; Valencia, CA) according to manufacturer’s instructions.
cDNA libraries were created according to the Illumina TruSeq miRNA procedure for small RNAs and combined with Illumina adaptor sequences. miRNA products were PCR-enriched and purified.
Illumina TruSeq miRNA library construction.

treatment_protocol: B cells and monocytes cells were left uninfected, or were infected overnight with the Edmonston strain of MV at a multiplicity of infection 0.2. CD4+ T cells were co-cultured overnight with or without MV-infected monocytes, after which the CD4+ T cell isolation was repeated (on the mixed cultures) to ensure that the T cell samples were not contaminated with monocytes. The purity of the cells was ascertained using flow cytometry.

tag: subject id

value: Subject 23

tag: high/low antibody response to measles vaccination

value: Low

tag: in vitro cell stimulation (or not) with measles virus

value: Unstimulated

value: T cell


title: Subject 23, purified CD4+ T cells, stimulated by mesles virus-infected APCs/macrophages

description:
cDNA libraries were created from total RNA according to manufacturer's instructions and combined with Illumina adaptor sequences using standard procedures. Twelve samples were multiplexed in each lane. Lanes were balanced by cell type, immune response status and sex. Single-end read sequencing was performed using the Illumina HiSeq 2000.
processed data file: CD4_Cell_miRNA_for_SAS.csv
160719_SN414_0501_BC8YFTACXX.s_97985_CD4_Stim.FCC8YFTACXX_L2_R1_IACAGTG

value: Stimulated


title: Normal cervical epithelium A1

description: gene expression data

value: FVB


title: genomic DNA from gastric intestinal metaplasia 87

source_name: gastric endoscopic biopsy 87


title: genomic DNA from gastric intestinal metaplasia 89

source_name: gastric endoscopic biopsy 89


title: genomic DNA from gastric intestinal metaplasia 86

source_name: gastric endoscopic biopsy 86


title: genomic DNA from gastric intestinal metaplasia 88

source_name: gastric endoscopic biopsy 88


title: Subject 23, purified B cells, unstimulated

description:
cDNA libraries were created from total RNA according to manufacturer's instructions and combined with Illumina adaptor sequences using standard procedures. Twelve samples were multiplexed in each lane. Lanes were balanced by cell type, immune response status and sex. Single-end read sequencing was performed using the Illumina HiSeq 2000.
processed data file: B_Cell_miRNA_for_SAS.csv
160719_SN414_0501_BC8YFTACXX.s_97985_B_Unstim.FCC8YFTACXX_L2_R1_ITGACCA

source_name: purified B cells (from PBMCs isolated from blood)

value: B cell


title: genomic DNA from gastric intestinal metaplasia 95

source_name: gastric endoscopic biopsy 95


title: genomic DNA from gastric intestinal metaplasia 82

source_name: gastric endoscopic biopsy 82


title: genomic DNA from gastric intestinal metaplasia 77

source_name: gastric endoscopic biopsy 77


title: genomic DNA from gastric intestinal metaplasia 85

source_name: gastric endoscopic biopsy 85


title: genomic DNA from gastric intestinal metaplasia 83

source_name: gastric endoscopic biopsy 83


title: Subject 23, purified B cells, measles virus-stimulated (in vitro)

description:
cDNA libraries were created from total RNA according to manufacturer's instructions and combined with Illumina adaptor sequences using standard procedures. Twelve samples were multiplexed in each lane. Lanes were balanced by cell type, immune response status and sex. Single-end read sequencing was performed using the Illumina HiSeq 2000.
processed data file: B_Cell_miRNA_for_SAS.csv
160719_SN414_0501_BC8YFTACXX.s_97985_B_Stim.FCC8YFTACXX_L2_R1_ICGATGT


title: genomic DNA from gastric intestinal metaplasia 81

source_name: gastric endoscopic biopsy 81

value: intestinal metaplasia biopsy from gastric cardia


title: genomic DNA from gastric intestinal metaplasia 80

source_name: gastric endoscopic biopsy 80


title: genomic DNA from gastric intestinal metaplasia 72

source_name: gastric endoscopic biopsy 72


title: Subject 22, purified B cells, unstimulated

description:
cDNA libraries were created from total RNA according to manufacturer's instructions and combined with Illumina adaptor sequences using standard procedures. Twelve samples were multiplexed in each lane. Lanes were balanced by cell type, immune response status and sex. Single-end read sequencing was performed using the Illumina HiSeq 2000.
processed data file: B_Cell_miRNA_for_SAS.csv
160719_SN414_0501_BC8YFTACXX.s_7348_B_Unstim.FCC8YFTACXX_L5_R1_IGTGGCC

value: Subject 22


title: genomic DNA from gastric intestinal metaplasia 79

source_name: gastric endoscopic biopsy 79