title: A1533_ep_L49

description: gene expression


title: C29m: TU-A89-TU088_TU087R

status: Public on Mar 19 2019

type: genomic

city: Otsu

first: Hiroyuki

last: Sugihara

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

country: Japan

institute: Shiga University of Medical Science

description:
Grid: 021924_D_F_20090227
protocol: CGH_1105_Oct12
Feature Extraction software: 11.5.1.1

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 8x60K  (Agilent, GPL10152) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 11.5.1.1. Linear normalization method with default parameters (protocol CGH_1105_Oct12 and Grid: 021924_D_F_20090227)  was used in signal intensity extraction procedure.

molecule: genomic DNA

organism: Homo sapiens

source_name: intramucosal part of invasive colorectal cancer

label_protocol: 250ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent – 5190-3400).

growth_protocol: Colorectal archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected in this study. Formalin-fixed paraffin embedded tissues (FFPE) of colorectal carcinomas from 48 patients from 2012 to 2017.

extract_protocol: The samples were obtained from 5-micrometer-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each  sample was dissected from at least > 6mm2 area, in which neoplastic cells accounted for 90% of total cell count. These cells were then digested in 200 mg/ml proteinase K solution for 70±2 hours at 37ºC. Genome DNA was extracted with phenol-chloroform-isoamyl alcohol extraction method and further treated using the Maxtract high density extraction column(QIAGEN).Eluted DNA was assessed for purity using the Nanodrop-1000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. GenomeDNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit (SIGMA). For each WGA 100 ng (Nanodrop) or 10 ng (Qubit) of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit (SIGMA).

tag: tissue

tag: excision year

tag: analysis year

tag: gender

value: M

tag: age

tag: pathologic stage

source_name: corresponding non-neoplastic sample

value: corresponding non-neoplastic sample


title: C29a: TU-A88-TU087_TU087R

source_name: adenoma part of invasive colorectal cancer


title: A1562_ep_L31

type: RNA

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

country: USA

institute: Fox Chase Cancer Center

description: gene expression

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis (701021 Rev.5) protocol from Affymetrix, following the instructions for 49 formta (standard)/64 format array.

scan_protocol: The scanner used was Affymetrix® GeneChip® Scanner 3000 and the software used was Affymetrix GeneChip Command Console, v.3.2.

data_processing: The data were (1) RMA normalized; (2) For each subject a linear regression model was fitted across all genes. The gene expression values in the whole tissue were modeled as a linear function of the gene expression in epithelial and stromal tissues.

label: biotin

molecule: total RNA

source_name: Human breast biopsy

label_protocol: RNA amplification and labelling was performed using MessageAmpTM Premier RNA Amplification Kit (Life Technologies)

extract_protocol: The RNA extraction from the collected cells was performed using the Arcturus® PicoPure®RNA Isolation Kit (Life Technologies).

treatment_protocol: Core needle biopsies specimens was collected from the breast of premenopausal women free of any breast abnormality.  Laser capture microdissection was performed to select and capture all the epithelial tissue present in each section.  The tissue left on the slide was then scraped into a different tube and classified as stroma. RNA was also extracted from a second core biopsy, in which no LCM was performed

tag: subject id

tag: organ

value: breast

value: epithelium

tag: tissue abbrevation

value: ep

tag: batch


title: A1497_ep_L30

description: gene expression


title: A1497_st_L29

description: gene expression

value: stroma

value: st


title: C28m: TU-A87-TU086_TU085R

value: intramucosal part of invasive colorectal cancer


title: C28a: TU-A86-TU085_TU085R

value: adenoma part of invasive colorectal cancer


title: A1489_wt_L19

description: gene expression

value: whole

value: wt


title: A1479_wt_L43

description: gene expression


title: C27i: TU-A84-TU084_TU082R

source_name: invasive part of invasive colorectal cancer


title: C27m: TU-A83-TU083_TU082R


title: A1501_wt_L42

description: gene expression


title: C27a: TU-A82-TU082_TU082R


title: C26m: TU-A80-TU080_TU079R


title: C29i: TU-A90-TU089_TU087R

value: invasive part of invasive colorectal cancer


title: C26i: TU-A81-TU081_TU079R


title: C25a: TU-A77-TU077_TU077R

value: Tis


title: C25m: TU-A78-TU078_TU077R


title: A1562_wt_L18

description: gene expression


title: A1485_st_L17

description: gene expression


title: A1485_ep_L24

description: gene expression


title: A1489_ep_L20

description: gene expression


title: C24m: TU-A76-TU076_TU075R

value: F


title: A1501_ep_L05

description: gene expression


title: 51NC

city: Beijing

first: yongmei

last: song

country: China

institute: State Key Laboratory of Molecular Oncology

description: CAL-51 trasfected with microRNA negtive control for 48h

hyb_protocol: 15µg fragmented cRNA, with contol oligo B2 and eukaryotic hybridization controls (bioB, bioC, bioD, cre) was hybridized to each GeneChip array at 45℃ for 16 hours (Affymetrix GeneChipHybridization Oven 640) according to manufacturer’s instructions

scan_protocol: fter hybridization, the GeneChip arrays were washed, and then stained with streptavidin phycoerythrinonan (SAPE) with Affymetrix Fluidics Station 450 followed by scanning with the Affymetrix GeneChip Scanner 3000 7G

data_processing:
The hybridization data were analyzed using Affymetrix GeneChip Command Console Software (AGCC), which uses statistical criteria to generate a ‘present’or ‘absent’ call for genes represented by each probe set on the array. Afterwards, genes with ‘absent’ scores were filtered out and the remaining genes were analyzed. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method
To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a FDR significance level of <5%.

label_protocol: 100ng of total RNA was used for cDNA synthesis, and produce biotin-tagged cRNA with GeneChip IVT Labeling kit (Affymetrix).

growth_protocol: CAL-51 were cultured in DMEM medium supplemented with 10 % fetal bovine serum (FBS) and antibiotics.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: CAL-51 cells transfected with microRNA negative control or miR-4306 mimic for 48h

tag: cell typ

value: Human breast cancer cell line


title: A1479_st_L02

description: gene expression


title: A1501_st_L16

description: gene expression


title: 231NC

description: MDA-MB-231 trasfected with microRNA negtive control for 48h

source_name: MDA-MB-231 transfected with microRNA negative control for 48h

growth_protocol: MDA-MB-231 were cultured in DMEM medium supplemented with 10 % fetal bovine serum (FBS) and antibiotics.

treatment_protocol: MDA-MB-231 cells transfected with microRNA negative control or miR-4306 mimic for 48h


title: parous_B50

description: gene expression

scan_protocol: The scanner used was Affymetrix® GeneChip® Scanner 3000 and the software used was Command Console.

data_processing: The data were (1) RMA normalized; (2) filtered to exclude probesets present (P) in fewer than 25% of both parous & nulliparous samples; (3) batch normalized with ComBat (default parameters); (4) filtered to remove probesets with variance in the lowest quartile

label_protocol: GeneChip Expression 3’-Amplification Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) was used for sample preparation following manufacturer's protocol.

extract_protocol: Total RNA from core needle biopsies specimens was isolated using the Qiagen Allprep RNA/DNA Mini Kit according to manufacturer's instructions (Qiagen, Alameda, CA, USA)

treatment_protocol: Core needle biopsies specimens was collected from the breast of premenopausal women free of any breast abnormality.  Samples were kept in RNA later.

tag: parity

value: parous

tag: years since last pregnancy


title: C23i: TU-A74-TU074_TU073R


title: C26a: TU-A79-TU079_TU079R


title: 231-4306

description: MDA-MB-231 trasfected with miR-4306 mimic for 48h

source_name: MDA-MB-231 transfected with miR-4306 mimic for 48h


title: C22m: TU-A72-TU072_TU071R


title: C23a: TU-A73-TU073_TU073R


title: C22a: TU-A71-TU071_TU071R


title: C21a: TU-A69-TU069_TU069R


title: Patient with HRSV, sample number 45

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: PBMC gene expression from inftant with HRSV bronchiolitis

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 and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The expression values were extracted by Agilent Feature Extraction software version 9.5.3. Spots with two or more flags (low intensity, saturation, controls, etc.) were considered as NA, that is, without valid expression value. The R software version 2.11.1 and an in-house script were used for: i) excluding transcripts spots presenting one or more NAs per group; iii) converting gene expression values to log base 2. Then, the gene expression matrix with only expressed transcripts were obtained. Subsequently, data normalization was performed using R software and the Lowess method.

source_name: Infant with HRSV bronchiolitis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: PBMC were lysed with 300 µl of RLT buffer and the total RNA was extracted using RNeasy Mini Kit (Qiagen, cat. no. 74106). RNA purity analysis and quantification were performed using the NanoVue spectrophotometer (GE Heathcare Life Sciences, Marlborough, MA). RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA). All samples presenting RIN ≥ 7.0 were stored at -80°C until used in hybridization experiments.

treatment_protocol: Whole blood was collected in EDTA-containing tube within a maximum of 24 hours after hospital admission. Immediately, the peripheral blood mononuclear cells (PBMC) were separated by gradient centrifugation using Ficoll-Paque Plus (GE Heathcare, cat. no. 17144002). After cell separation, PBMC were collected and preserved in RNAlater (Qiagen, cat. no. 76106) and stored at -20oC until RNA extraction.

value: PBMC

value: Male

tag: age (days)


title: Patient with HRSV, sample number 24


title: Patient with HRSV, sample number 32


title: Patient with HRSV, sample number 2

value: Female


title: Patient with HRV, sample number 81

description: PBMC gene expression from inftant with HRV bronchiolitis

source_name: Infant with HRV bronchiolitis


title: Patient with HRSV, sample number 6


title: A1562_st_L13

description: gene expression

value: breast


title: C18m: TU-A67-TU067_TU066R

value: M

value: corresponding non-neoplastic sample


title: C21m: TU-A70-TU070_TU069R


title: Patient with HRV, sample number 46


title: C18a: TU-A66-TU066_TU066R


title: Patient with HRV, sample number 117


title: C17i: TU-A65-TU065_TU063R


title: C17a: TU-A63-TU063_TU063R


title: C17m: TU-A64-TU064_TU063R


title: C16i: TU-A62-TU062_TU060R


title: C16m: TU-A61-TU061_TU060R


title: C16a: TU-A60-TU060_TU060R


title: C15a: TU-A58-TU058_TU058R


title: C14m: TU-A57-TU057_TU056R


title: C15m: TU-A59-TU059_TU058R


title: C18i: TU-A68-TU068_TU066R


title: Patient with HRV, sample number 109


title: C14a: TU-A56-TU056_TU056R


title: Patient with HRSV, sample number 48


title: C13a: TU-A53-TU053_TU053R


title: 514306

description: CAL-51 trasfected with miR-4306 mimic for 48h


title: C13m: TU-A54-TU054_TU053R


title: C12ln: TU-A52-TU052_TU050R

source_name: lymph node metastasis from colorectal cancer


title: C10i: TU-A47-TU047_TU046-47R


title: C11m: TU-A49-TU049_TU048-49R


title: C11a: TU-A48-TU048_TU048-49R


title: Patient with HRV, sample number 116


title: C12m: TU-A50-TU050_TU050R


title: C12i: TU-A51-TU051_TU050R


title: C10m: TU-A46-TU046_TU046-47R


title: C9ln: TU-A45-TU045_TU043-45R

value: lymph node metastasis from colorectal cancer


title: C9i: TU-A44-TU044_TU043-45R


title: C8i: TU-A42-TU042_TU041-42R


title: C9m: TU-A43-TU043_TU043-45R


title: C8a: TU-A41-TU041_TU041-42R


title: C6m: TU-A36-TU036_TU036R


title: C4i: TU-A32-TU032_TU032R


title: C4a: TU-A30-TU030_TU030R


title: LGG_22033_X86

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: raw data file and column: DASL.4; X102380.05

hyb_protocol: RNA was hybridized to each array according to the manufacturer's standard hybridization protocol.

scan_protocol: The arrays were scanned using standard Illumina scanning protocol

data_processing: The data was quantile normalized using 'preprocessCore' (an R package) and corrected for batch effects using the 'ber' package in R.

label: Biotin

source_name: low grade glioma

label_protocol: As per manufacturer (Illumina)

extract_protocol: Total RNA was extracted from resection material of patients treated within the EORTC22033 clinical trial. RNA was isolated using theHigh Pure RNA Paraffin Kit (Roche Applied Science, Mannheim, Germany)

tag: treatment therapy

value: TMZ

tag: igs

value: Total removal

tag: histology

value: AOD GrII

tag: performance

value: mutated

tag: progression free survival (pfs) event

value: Yes

tag: pfs (days)


title: LGG_22033_X97

description: raw data file and column: DASL.2; 102217-60

tag: gender

value: Partial removal

value: AOA GrII


title: LGG_22033_X92

description: raw data file and column: DASL.2; 102217-04

tag: age


title: LGG_22033_X81

description: raw data file and column: DASL.5; X102413.06

value: undetermined


title: LGG_22033_X84

description: raw data file and column: DASL.1; X102012.070

value: RT


title: LGG_22033_X70

description: raw data file and column: DASL.2; 102217-31

value: Biopsy

value: AA GrII

value: normal


title: C7i: TU-A40-TU040_TU040R

tag: tissue

value: invasive part of invasive colorectal cancer

tag: excision year

tag: analysis year

tag: pathologic stage


title: C7m: TU-A39-TU039_TU039R

value: intramucosal part of invasive colorectal cancer


title: C5ln: TU-A35-TU035_TU035R

value: F


title: C7a: TU-A38-TU038_TU038R

value: adenoma part of invasive colorectal cancer

value: M

value: corresponding non-neoplastic sample


title: LGG_22033_X685

description: raw data file and column: DASL.2; 102217-01

value: Female

value: No


title: LGG_22033_X698

description: raw data file and column: DASL.1; X102012.147

value: TMZ

value: AOD GrII

value: mutated


title: C5m: TU-A33-TU033_TU033R


title: LGG_22033_X71

description: raw data file and column: DASL.2; 102217-79

value: Partial removal

value: AOA GrII


title: LGG_22033_X85

description: raw data file and column: DASL.1; X102012.072

value: Male

value: Yes


title: C5i: TU-A34-TU034_TU034R

description:
Grid: 021924_D_F_20090227
protocol: CGH_1105_Oct12
Feature Extraction software: 11.5.1.1


title: LGG_22033_X75

description: raw data file and column: DASL.1; X102012.071

value: Total removal


title: LGG_22033_X682

description: raw data file and column: DASL.1; X102012.135

value: RT


title: LGG_22033_X68

description: raw data file and column: DASL.1; X102012.074

value: normal


title: LGG_22033_X684

description: raw data file and column: DASL.1; X102012.150


title: LGG_22033_X669

description: raw data file and column: DASL.5; X102413.32


title: LGG_22033_X667

description: raw data file and column: DASL.1; X102012.144


title: LGG_22033_X668

description: raw data file and column: DASL.4; X102380.23


title: LGG_22033_X666

description: raw data file and column: DASL.1; X102012.157

value: AA GrII


title: C4m: TU-A31-TU031_TU031R

value: intramucosal part of invasive colorectal cancer

value: F


title: C6i: TU-A37-TU037_TU037R

value: invasive part of invasive colorectal cancer

value: M


title: C3m: TU-A28-TU028_TU028R

value: corresponding non-neoplastic sample


title: C3a: TU-A27-TU027_TU027R

value: adenoma part of invasive colorectal cancer


title: C3i: TU-A29-TU029_TU029R


title: C2m: TU-A25-TU025_TU025R


title: C2i: TU-A26-TU026_TU026R


title: LGG_22033_X664

description: raw data file and column: DASL.2; 102217-77

value: Female


title: C1m2: TU-A23-TU023_TU023R


title: C1m1: TU-A22-TU022_TU022R


title: C1a: TU-A21-TU021_TU021R


title: LGG_22033_X663

description: raw data file and column: DASL.2; 102217-90

value: TMZ


title: LGG_22033_X662

description: raw data file and column: DASL.1; X102012.148

value: AOD GrII

value: mutated


title: LGG_22033_X645

description: raw data file and column: DASL.5; X102413.30

value: Biopsy

value: AOA GrII

value: No


title: C1i: TU-A24-TU024_TU024R


title: LGG_22033_X647

description: raw data file and column: DASL.3; X1022329.025

value: Male

value: Partial removal

value: Yes


title: LGG_22033_X654

description: raw data file and column: DASL.5; X102413.31

value: RT


title: LGG_22033_X64

description: raw data file and column: DASL.4; X102380.04

value: normal


title: LGG_22033_X631

description: raw data file and column: DASL.4; X102380.22


title: LGG_22033_X628

description: raw data file and column: DASL.2; 102217-58


title: LGG_22033_X615

description: raw data file and column: DASL.4; X102380.21

value: Total removal


title: LGG_22033_X642

description: raw data file and column: DASL.5; X102413.29

value: AA GrII


title: LGG_22033_X623

description: raw data file and column: DASL.1; X102012.133


title: LGG_22033_X612

description: raw data file and column: DASL.3; X1022329.007

value: undetermined


title: SHR/Izm untreated mesenteric artery-biological rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Whole mesenteric artery derived from SHR/Izm untreated rat strain.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction, LOWESS normalization, and dye-normalization.

organism: Rattus norvegicus

source_name: whole mesenteric artery, SHR/Izm, untreated

label_protocol: 100 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole mesenteric artery stored in RNAlater (Ambion), derived from WKY, SHR and SHRSP rats using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks.

tag: strain/background

value: SHR/Izm

value: 6 weeks

value: mesenteric arteries

tag: treatment

value: untreated


title: LGG_22033_X604

description: raw data file and column: DASL.1; X102012.143

value: AOD GrII


title: SHRSP/Izm untreated mesenteric artery-biological rep1

description: Whole mesenteric artery derived from SHRSP/Izm untreated rat strain.

source_name: whole mesenteric artery, SHRSP/Izm, untreated

value: SHRSP/Izm


title: LGG_22033_X613

description: raw data file and column: DASL.4; X102380.20

value: mutated


title: SHRSP/Izm untreated mesenteric artery-biological rep2


title: SHRSP/Izm untreated mesenteric artery-biological rep4


title: SHRSP/Izm untreated mesenteric artery-biological rep3


title: LGG_22033_X6

description: raw data file and column: DASL.1; X102012.087


title: SHR/Izm untreated mesenteric artery-biological rep2


title: SHR/Izm untreated mesenteric artery-biological rep4


title: LGG_22033_X594

description: raw data file and column: DASL.2; 102217-19

value: Female

value: TMZ


title: LGG_22033_X603

description: raw data file and column: DASL.4; X102380.19

value: AOA GrII

value: No


title: WKY/Izm untreated mesenteric artery-biological rep3

description: Whole mesenteric artery derived from WKY/Izm untreated rat strain.

source_name: whole mesenteric artery, WKY/Izm, untreated

value: WKY/Izm


title: LGG_22033_X60

description: raw data file and column: DASL.5; X102413.04

value: RT

value: Biopsy


title: SHR/Izm untreated mesenteric artery-biological rep1


title: WKY/Izm untreated mesenteric artery-biological rep4


title: WKY/Izm untreated mesenteric artery-biological rep2


title: WKY/Izm 1K1C (1kidney 1clip) mesenteric artery-biological rep4

description: Whole mesenteric artery derived from WKY/Izm 1-kidney 1-clip rat strain.

source_name: whole mesenteric artery, WKY/Izm, 1K1C

value: 1-kidney 1-clip (1K1C)


title: WKY/Izm untreated mesenteric artery-biological rep1


title: C24a: TU-A75-TU075_TU075R

description:
Grid: 021924_D_F_20090227
protocol: CGH_1105_Oct12
Feature Extraction software: 11.5.1.1

value: adenoma part of invasive colorectal cancer

value: F

value: Tis

value: corresponding non-neoplastic sample


title: C13i: TU-A55-TU055_TU053R

value: invasive part of invasive colorectal cancer


title: WKY/Izm 1K1C (1kidney 1clip) mesenteric artery-biological rep3

value: 6 weeks

value: mesenteric arteries


title: LGG_22033_X59

description: raw data file and column: DASL.5; X102413.03

value: Total removal

value: AOD GrII

value: normal

value: Yes


title: WKY/Izm 2K1C (2kidney 1clip) mesenteric artery-biological rep4

description: Whole mesenteric artery derived from WKY/Izm 2-kidney 1-clip rat strain.

source_name: whole mesenteric artery, WKY/Izm, 2K1C

value: 2-kidney 1-clip (2K1C)


title: 253118111239 2-4

description: microRNA expression in triple negative breast cancer cell line CAL-51

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: breast cancer line CAL-51

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

growth_protocol: MCF-7, MDA-MB-231 and CAL-51 were cultured in DMEM medium supplemented with 10 % fetal bovine serum (FBS) and antibiotics. ZR-75-1 was cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum (FBS) and antibiotics.

treatment_protocol: Primary cultured breast cancer cells completely adhered to the wall at 24 hours, entered the logarithmic phase，at 37 ºC in a humidified incubator with 5% CO2. RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.

tag: cell line

value: triple negative breast cancer cell line


title: LGG_22033_X572

description: raw data file and column: DASL.5; X102413.27

value: Female

value: AA GrII

value: mutated


title: LGG_22033_X580

description: raw data file and column: DASL.1; X102012.122

value: Male

value: RT

value: Biopsy


title: LGG_22033_X591

description: raw data file and column: DASL.1; X102012.139

value: Partial removal

value: AOA GrII

value: No


title: LGG_22033_X600

description: raw data file and column: DASL.4; X102380.18

value: TMZ


title: LGG_22033_X570

description: raw data file and column: DASL.2; 102217-14


title: LGG_22033_X58

description: raw data file and column: DASL.3; 1022329.016


title: LGG_22033_X593

description: raw data file and column: DASL.1; X102012.130


title: LGG_22033_X574

description: raw data file and column: DASL.5; X102413.28


title: WKY/Izm 2K1C (2kidney 1clip) mesenteric artery-biological rep1

value: WKY/Izm

value: 6 weeks

value: mesenteric arteries


title: 253118111239 1-4

description: microRNA expression in triple negative breast cancer cell line MDA-MB-231

source_name: breast cancer line MDA-MB-231


title: WKY/Izm 1K1C (1kidney 1clip) mesenteric artery-biological rep2

value: 1-kidney 1-clip (1K1C)


title: 253118111240 2-3

description: microRNA expression in luminal type breast cancer cell line MCF-7

source_name: breast cancer line MCF-7

value: luminal type breast cancer cell line


title: WKY/Izm 2K1C (2kidney 1clip) mesenteric artery-biological rep2

value: 2-kidney 1-clip (2K1C)


title: LGG_22033_X568

description: raw data file and column: DASL.1; X102012.099

value: Yes


title: WKY/Izm 1K1C (1kidney 1clip) mesenteric artery-biological rep1


title: WKY/Izm 2K1C (2kidney 1clip) mesenteric artery-biological rep3


title: 253118111240 1-4

description: microRNA expression in luminal type breast cancer cell line ZR-75-1

source_name: breast cancer line ZR-75-1


title: LGG_22033_X635

description: raw data file and column: DASL.2; 102217-95

value: Female

value: AOD GrII


title: Patient with HRV, sample number 66

description: PBMC gene expression from inftant with HRV bronchiolitis

value: PBMC


title: LGG_22033_X56

description: raw data file and column: DASL.4; X102380.03

value: Male

value: Total removal

value: normal


title: LGG_22033_X558

description: raw data file and column: DASL.4; X102380.17

value: Partial removal

value: mutated


title: LGG_22033_X57

description: raw data file and column: DASL.3; X1022329.017

value: RT

value: Biopsy

value: undetermined


title: LGG_22033_X566

description: raw data file and column: DASL.2; 102217-75

value: TMZ


title: LGG_22033_X555

description: raw data file and column: DASL.1; X102012.128

value: AOA GrII

value: No


title: LGG_22033_X550

description: raw data file and column: DASL.3; X1022329.022


title: LGG_22033_X562

description: raw data file and column: DASL.5; X102413.25


title: LGG_22033_X532

description: raw data file and column: DASL.2; 102217-98


title: ChIP Suz12 + RNAseH1

type: SRA

city: Berlin

first: Elena

last: Torlai Triglia

state: Deutschland

address: Robert Rössle Str 10

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 2.0.5 with default parameters. The reference for Bowtie was produced from the Mouse Genome version mm9.
ChIP-seq data were filtered using a 95% quantile threshold for read duplication.
Bam files were converted to Bed and then to Bedgraph using bedtools v2.17.0 (bamToBed and genomeCoverageBed, respectively)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig from UCSC, format described in http://genome.ucsc.edu/goldenpath/help/bigWig.html

organism: Mus musculus

source_name: ES cells

growth_protocol: 46C mouseESCs were plated on gelatin-coated (0.1% (v/v)) Nunc 10 cm dishes in serum-free ESGRO Complete Clonal Grade Medium (Millipore, # SF001-B) to which was added 1000U/ml LIF (Millipore, # ESG1107). Cells were grown for 48h, with a medium change at 24h.

extract_protocol:
After reversing the cross-links and Proteinase K treatment, the chromatin was purified using the MinElute PCR Purification kit (Cat. 28004, Qiagen) and DNA concentration for library preparation was determined using Qubit fluorometric quantitation (ThermoFisher Scientific).
Libraries were prepared from 8ng of DNA using the NEBNext Ultra II DNA library kit for Illumina (Cat. E7645S, NEB), following the manufacturers’ instructions. Size selection was performed prior to PCR amplification using RNA clean XP beads (Cat. A63987, Beckman Coulter). Adaptors, PCR amplification and Index Primers were used to multiplex libraries (Multiplex oligos for Illlumina, Cat. E7335S and E7500S, NEB). Libraries were purified using RNA clean XP beads (Cat. A63987, Beckman Coulter) and library size was assessed before high-throughput sequencing by Bioanalyzer (Agilent) using the High Sensitivity DNA analysis kit (Cat. 5067-4626, Agilent). ChIP-seq libraries were sequenced paired-end on an Illumina HiSeq2500 sequencer at the Wellcome Trust Sanger Institute (Cambridge, UK).

treatment_protocol: In Samples Section

tag: cells

value: 46c ES cells

tag: antibody

value: Cells were transfected with RNaseH1-GFP construct for 48 hrs

tag: source

value: Fixed chromatin


title: LGG_22033_X544

description: raw data file and column: DASL.5; X102413.24

value: Female

tag: treatment therapy

tag: igs


title: LGG_22033_X520

description: raw data file and column: DASL.2; 102217-46

tag: histology

tag: performance


title: LGG_22033_X509

description: raw data file and column: DASL.4; X102380.16

value: AOD GrII

tag: progression free survival (pfs) event

tag: pfs (days)


title: ChIP Suz12 - RNAseH1

value: Cells were mock transfected for 48 hrs


title: LGG_22033_X506

description: raw data file and column: DASL.2; 102217-08

tag: gender

value: Male

tag: age

value: AA GrII

value: Yes


title: LGG_22033_X543

description: raw data file and column: DASL.2; 102217-40


title: LGG_22033_X488

description: raw data file and column: DASL.1; X102012.118


title: LGG_22033_X478

description: raw data file and column: DASL.2; 102217-09

value: Total removal


title: LGG_22033_X564

description: raw data file and column: DASL.5; X102413.26

value: Partial removal

value: mutated


title: LGG_22033_X483

description: raw data file and column: DASL.1; X102012.119

value: RT


title: LGG_22033_X474

description: raw data file and column: DASL.1; X102012.112


title: LGG_22033_X503

description: raw data file and column: DASL.1; X102012.127


title: LGG_22033_X5

description: raw data file and column: DASL.2; 102217-27

value: normal


title: LGG_22033_X514

description: raw data file and column: DASL.1; X102012.120


title: LGG_22033_X494

description: raw data file and column: DASL.1; X102012.117

value: TMZ


title: LGG_22033_X557

description: raw data file and column: DASL.1; X102012.096


title: ChIP Ezh2 + RNAseH1


title: LGG_22033_X518

description: raw data file and column: DASL.1; X102012.098


title: LGG_22033_X496

description: raw data file and column: DASL.1; X102012.121


title: ChIP Ezh2 - RNAseH1


title: 67 Muscle.Basal_20

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Muscle

extract_protocol:
Tissues were harvested, snap frozen in liquid nitrogen and kept at -80C. Total RNA was isolated from quadriceps muscle and liver fragments.
Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen).

tag: time

tag: dose

value: Basal


title: 72 Muscle.High_3h

value: High


title: 71 Muscle.Low_3h

value: Low


title: 66 Liver.High_3h

source_name: Liver


title: 70 Muscle.Basal_3h


title: LGG_22033_X466

description: raw data file and column: DASL.2; 102217-21

value: No


title: LGG_22033_X487

description: raw data file and column: DASL.1; X102012.154


title: 69 Muscle.High_20


title: LGG_22033_X477

description: raw data file and column: DASL.2; 102217-70


title: LGG_22033_X476

description: raw data file and column: DASL.1; X102012.115


title: LGG_22033_X463

description: raw data file and column: DASL.1; X102012.126

value: AOA GrII


title: 65 Liver.Low_3h


title: LGG_22033_X457

description: raw data file and column: DASL.3; X1022329.023

value: Biopsy

value: undetermined


title: 64 Liver.Basal_3h


title: LGG_22033_X464

description: raw data file and column: DASL.1; X102012.153

value: Female


title: 68 Muscle.Low_20


title: LGG_22033_X458

description: raw data file and column: DASL.4; X102380.15

value: Male


title: LGG_22033_X46

description: raw data file and column: DASL.2; 102217-05

value: AOD GrII


title: LGG_22033_X440

description: raw data file and column: DASL.5; X102413.23

value: Yes


title: 62 Liver.Low_20


title: 61 Liver.Basal_20


title: 63 Liver.High_20


title: LGG_22033_X441

description: raw data file and column: DASL.4; X102380.14

value: AA GrII


title: 60 Muscle.High_3h


title: 58 Muscle.Basal_3h


title: 59 Muscle.Low_3h


title: LGG_22033_X450

description: raw data file and column: DASL.1; X102012.125


title: 57 Liver.High_3h


title: 55 Liver.Basal_3h


title: 56 Liver.Low_3h


title: LGG_22033_X435

description: raw data file and column: DASL.1; X102012.116

value: Partial removal


title: LGG_22033_X437

description: raw data file and column: DASL.2; 102217-69

value: mutated


title: LGG_22033_X431

description: raw data file and column: DASL.2; 102217-07


title: LGG_22033_X429

description: raw data file and column: DASL.4; X102380.13

value: Total removal


title: LGG_22033_X423

description: raw data file and column: DASL.2; 102217-12

value: RT


title: LGG_22033_X414

description: raw data file and column: DASL.1; X102012.158


title: LGG_22033_X421

description: raw data file and column: DASL.4; X102380.12


title: 53 Muscle.High_20


title: 52 Muscle.Basal_20


title: LGG_22033_X438

description: raw data file and column: DASL.3; X1022329.008

value: TMZ


title: LGG_22033_X410

description: raw data file and column: DASL.1; X102012.109


title: 51 Liver.High_20


title: LGG_22033_X41

description: raw data file and column: DASL.1; X102012.086


title: 50 Liver.Low_20


title: LGG_22033_X45

description: raw data file and column: DASL.5; X102413.02


title: 54 Muscle.Low_20


title: LGG_22033_X406

description: raw data file and column: DASL.5; X102413.21


title: LGG_22033_X407

description: raw data file and column: DASL.2; 102217-67


title: LGG_22033_X43

description: raw data file and column: DASL.1; X102012.079


title: LGG_22033_X417

description: raw data file and column: DASL.3; X1022329.009


title: 49 Liver.Basal_20

value: Basal


title: 48 Muscle.High_3h

value: High


title: 47 Muscle.Low_3h

value: Low


title: 46 Muscle.Basal_3h


title: LGG_22033_X396

description: raw data file and column: DASL.5; X102413.18

value: No


title: LGG_22033_X403

description: raw data file and column: DASL.5; X102413.20

value: AOA GrII


title: 45 Muscle.High_20


title: 44 Muscle.Low_20


title: LGG_22033_X395

description: raw data file and column: DASL.1; X102012.104


title: LGG_22033_X408

description: raw data file and column: DASL.1; X102012.114


title: 43 Muscle.Basal_20


title: 42 Liver.High_3h


title: 41 Liver.Low_3h


title: LGG_22033_X500

description: raw data file and column: DASL.2; 102217-43


title: 40 Liver.Basal_3h


title: 39 Liver.High_20


title: 38 Liver.Low_20


title: LGG_22033_X380

description: raw data file and column: DASL.1; X102012.105


title: 37 Liver.Basal_20


title: 36 Muscle.High_3h


title: LGG_22033_X405

description: raw data file and column: DASL.2; 102217-41


title: LGG_22033_X386

description: raw data file and column: DASL.5; X102413.17


title: LGG_22033_X374

description: raw data file and column: DASL.1; X102012.101


title: LGG_22033_X369

description: raw data file and column: DASL.3; X1022329.005


title: LGG_22033_X382

description: raw data file and column: DASL.1; X102012.093


title: LGG_22033_X352

description: raw data file and column: DASL.1; X102012.106


title: LGG_22033_X357

description: raw data file and column: DASL.1; X102012.102


title: LGG_22033_X362

description: raw data file and column: DASL.4; X102380.11


title: 35 Muscle.Low_3h


title: LGG_22033_X364

description: raw data file and column: DASL.1; X102012.103


title: 33 Muscle.High_20


title: 34 Muscle.Basal_3h


title: LGG_22033_X351

description: raw data file and column: DASL.2; 102217-52

value: Biopsy


title: LGG_22033_X348

description: raw data file and column: DASL.1; X102012.107


title: LGG_22033_X522

description: raw data file and column: DASL.2; 102217-81


title: LGG_22033_X350

description: raw data file and column: DASL.3; X1022329.013


title: LGG_22033_X35

description: raw data file and column: DASL.1; X102012.084


title: 32 Muscle.Low_20


title: LGG_22033_X338

description: raw data file and column: DASL.2; 102217-65


title: 30 Liver.High_3h


title: 31 Muscle.Basal_20


title: 29 Liver.Low_3h


title: 28 Liver.Basal_3h


title: 27 Liver.High_20


title: LGG_22033_X329

description: raw data file and column: DASL.2; 102217-91


title: LGG_22033_X499

description: raw data file and column: DASL.2; 102217-47


title: 26 Liver.Low_20


title: 24 Muscle.High_3h


title: 23 Muscle.Low_3h


title: 25 Liver.Basal_20


title: LGG_22033_X346

description: raw data file and column: DASL.2; 102217-66

value: undetermined


title: LGG_22033_X322

description: raw data file and column: DASL.3; X1022329.012

value: normal


title: LGG_22033_X510

description: raw data file and column: DASL.1; X102012.155

value: Male


title: LGG_22033_X516

description: raw data file and column: DASL.2; 102217-22

value: Female


title: LGG_22033_X33

description: raw data file and column: DASL.2; 102217-83

value: AOD GrII

value: Yes


title: LGG_22033_X292

description: raw data file and column: DASL.1; X102012.051

value: AA GrII


title: 19 Liver.Basal_3h


title: 18 Muscle.High_20


title: LGG_22033_X289

description: raw data file and column: DASL.2; 102217-64


title: LGG_22033_X323

description: raw data file and column: DASL.0; 1394

value: Partial removal

value: mutated


title: LGG_22033_X283

description: raw data file and column: DASL.3; X1022329.003

value: RT


title: 16 Muscle.Basal_20


title: LGG_22033_X31

description: raw data file and column: DASL.2; 102217-82


title: 15 Liver.High_20


title: 21 Liver.High_3h


title: 14 Liver.Low_20


title: LGG_22033_X286

description: raw data file and column: DASL.2; 102217-55


title: 12 Muscle.High_3h


title: 13 Liver.Basal_20


title: 11 Muscle.Low_3h


title: LGG_22033_X281

description: raw data file and column: DASL.5; X102413.16


title: LGG_22033_X296

description: raw data file and column: DASL.1; X102012.050


title: LGG_22033_X277

description: raw data file and column: DASL.2; 102217-51


title: LGG_22033_X275

description: raw data file and column: DASL.1; X102012.091

value: TMZ


title: LGG_22033_X284

description: raw data file and column: DASL.2; 102217-39


title: LGG_22033_X279

description: raw data file and column: DASL.1; X102012.092


title: LGG_22033_X300

description: raw data file and column: DASL.1; X102012.089


title: LGG_22033_X270

description: raw data file and column: DASL.2; 102217-97

value: Total removal


title: LGG_22033_X271

description: raw data file and column: DASL.2; 102217-63


title: 8 Muscle.Low_20


title: 9 Muscle.High_20

value: High


title: LGG_22033_X276

description: raw data file and column: DASL.1; X102012.090


title: 7 Muscle.Basal_20

value: Basal


title: LGG_22033_X262

description: raw data file and column: DASL.4; X102380.10

value: No


title: 6 Liver.High_3h


title: LGG_22033_X269

description: raw data file and column: DASL.3; X1022329.026


title: LGG_22033_X268

description: raw data file and column: DASL.1; X102012.083

value: AOA GrII


title: LGG_22033_X26

description: raw data file and column: DASL.3; X1022329.014


title: 5 Liver.Low_3h

value: Low


title: 10 Muscle.Basal_3h


title: 2 Liver.Low_20


title: 1 Liver.Basal_20


title: LGG_22033_X267

description: raw data file and column: DASL.2; 102217-53


title: LGG_22033_X257

description: raw data file and column: DASL.1; X102012.053


title: RNAseq_EdU_plus_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: RNAseq experiment

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ChIPseq peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIPseq and RNAseq profiles)
Supplementary_files_format_and_content: Files .bed (BED, signal enriched regions)

growth_protocol: E14TG2a from mouse embryo (male blastocyst, strain 129/Ola) (SIGMA) were cultured on tissue culture plates coated with 0.1% gelatin (Millipore) in naïve. Briefly, ESCs were growth in serum-free medium N2B27 media (DMEM/F12:Neurobasal 1:1, 0.5x N-2 supplement, 1x B-27 serum-free supplement, 50 µM 2-mercaptoethanol; Bovine Albumin Fraction V 0.033%; 1X Glutamax; 1X MEM non-essential aminoacids; 1X Penicillin-Streptomycin; all from Gibco) supplemented with 1 µM PD0325901 (Tocris), 3 uM CHIR99021 (Tocris) and Leukemia Inhibitory Factor (LIF).

extract_protocol:
RNA extraction was performed using the RNeasy mini kit (Qiagen) following manufacturer’s instruction. RNA samples were quantified and quality was evaluated using Bioanalyzer (RIN > 9.9). A total of 0.5 ug of RNA was used as starting material for library preparation with rRNA depletion using TruSeq Stranded Total RNA Library Prep kit (Ilumina) following the manufacturer´s instruction.
Libraries were prepared according to Illumina instructions.

treatment_protocol: Chromatin material for ChIP-seq was prepared using the ChIP-IT High Sensitivity kit from Active Motif, following the manufacture’s instruction. ChIP-seq libraries were prepared with 2-10 ng of ChIP DNA material using the NEBNext Ultra DNA library Prep kit for Illumina (New England Biolabs) following manufacturer’s instruction. ChIP-seq libraries were amplified for 10-15 PCR cycles.

tag: cell type

value: mouse Embryonic Stem Cells (mESCs)

tag: genotype

value: WT


title: RNAseq_EdU_plus_R1

description: RNAseq experiment

tag: treatment


title: LGG_22033_X254

description: raw data file and column: DASL.1; X102012.054

value: Male


title: LGG_22033_X25

description: raw data file and column: DASL.1; X102012.085


title: LGG_22033_X245

description: raw data file and column: DASL.3; X1022329.019

value: Female

value: Biopsy


title: LGG_22033_X246

description: raw data file and column: DASL.2; 102217-10

value: AOD GrII


title: RNAseq_sh6_R2_shAhcy

description: RNAseq experiment

tag: cell line

value: Ahcy mutant


title: LGG_22033_X253

description: raw data file and column: DASL.1; X102012.059


title: RNAseq_EdU_minus_R2

description: RNAseq experiment


title: RNAseq_EdU_minus_R1

description: RNAseq experiment


title: LGG_22033_X243

description: raw data file and column: DASL.5; X102413.15

value: AA GrII

value: Yes


title: 3 Liver.High_20


title: RNAseq_sh5_R1_shAhcy

description: RNAseq experiment


title: LGG_22033_X235

description: raw data file and column: DASL.4; X102380.08

value: RT

value: mutated


title: LGG_22033_X232

description: raw data file and column: DASL.1; X102012.062

value: Partial removal


title: LGG_22033_X227

description: raw data file and column: DASL.2; 102217-54

value: TMZ

value: Total removal


title: RNAseq_sh4_R1_shAhcy

description: RNAseq experiment


title: RNAseq_shC_R2_shControl

description: RNAseq experiment

value: shC


title: LGG_22033_X244

description: raw data file and column: DASL.4; X102380.09

value: AOA GrII

value: No


title: LGG_22033_X221

description: raw data file and column: DASL.5; X102413.13


title: RNAseq_sh6_R1_shAhcy

description: RNAseq experiment

value: mouse Embryonic Stem Cells (mESCs)


title: LGG_22033_X207

description: raw data file and column: DASL.5; X102413.12

value: normal


title: LGG_22033_X208

description: raw data file and column: DASL.1; X102012.082


title: RNAseq_sh4_R2_shAhcy

description: RNAseq experiment


title: ChIPseq_IgG

description: ChIPseq experiment

tag: chip antibody

value: IgG (Abcam ab172730 (rabbit))

value: WT


title: RNAseq_shC_R1_shControl

description: RNAseq experiment


title: ChIPseq_Ahcy_Replicate1

description: ChIPseq experiment

value: AHCY (MBL RN126PW (rabbit))


title: LGG_22033_X241

description: raw data file and column: DASL.5; X102413.14

value: Male

value: Biopsy


title: 17 Muscle.Low_20

value: Low


title: ChIPseq_Ahcy_Replicate2

description: ChIPseq experiment


title: LGG_22033_X196

description: raw data file and column: DASL.5; X102413.11

value: Female

value: AA GrII

value: Yes


title: germ_F1-rep3

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
B6_DBA_H3K4me3_spermatocyte_peak_associations_wF1s.txt.gz
170316_walker_B6_DBA_H3K4me3_spermatocyte_peakome_wF1s_reads.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the mm10 or DBA/2J REL-1509 genome assembly using bwa v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: processed files are text files representing the position of an identified H3K4me3 peak in both mm10 and DBA/2J coordinates as identified by sequence homology. Large matrix of all H3K4me3 peaks and read counts for each of the four cell types. One file is the read counts and positions of DSBs in male germ cells represented by DMC1-associated ssDNA fragments

source_name: male germ cells

growth_protocol: Crude isolation of germ cells was conducted from male mice at 14 days post-partum (dpp). Hepatocyte and cardiomyocyte isolation from female animals. Mouse embryonic stem cells were derived following protocol from Czechanski et al. 2014. Nature Protocols. For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection for all germ cell data or the KAPA hyper kit (Kapa Biosystems) for mESC, cardiomyocytes, and hepatocytes.

value: 14 days post-partum

tag: strain

tag: ChIP

tag: antibody


title: LGG_22033_X203

description: raw data file and column: DASL.1; X102012.060

tag: treatment therapy

value: RT

tag: igs

value: Partial removal

value: AOD GrII

value: mutated


title: germ_F1-rep4


title: LGG_22033_X200

description: raw data file and column: DASL.3; X1022329.027

value: TMZ

tag: histology

tag: performance


title: LGG_22033_X194

description: raw data file and column: DASL.5; X102413.10

value: AOA GrII

tag: progression free survival (pfs) event

tag: pfs (days)


title: LGG_22033_X181

description: raw data file and column: DASL.1; X102012.063

tag: gender

tag: age


title: LGG_22033_X188

description: raw data file and column: DASL.4; X102380.07

value: Total removal

value: No


title: germ_F1-rep1


title: germ_D2-rep3


title: LGG_22033_X193

description: raw data file and column: DASL.2; 102217-73


title: WGBS_RPE Exp1

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
Quality control of sequencing reads was performed using FastQC.
Adapter removal was performed using Trim Galore! version 0.4.5.
The cleaned reads were then aligned to the Mus musculus reference genome (Genome Reference Consortium 37, mm10) using bismark v0.16.1.
The cytosine2coverage and bismark_methylation_extractor modules of bismark were used to infer the methylation state of all cytosines in a CpG, CHH or CHG context (for every single mappable read) and to compute the percentage methylation for each CpG site.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using bismark_methylation_extractor module of bismark.

source_name: RPE

extract_protocol:
Genomic DNA was purified from RPE samples using the DNeasy Blood & Tissue Kit (QIAGEN #69504). DNA concentration of the samples was measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-487 Standard Sensitivity genomic DNA Analysis Kit (Advanced Analytical).  Genomic DNA was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001). 1μl of this sample was used to assess the size of the DNA fragments obtained by High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). DNA concentration of the sample was measured after shearing using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific).
WGBS libraries were prepared using the Whole Genome Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030034) following the kit manual. 1μg of sheared genomic DNA was used to start library preparation for each sample. Following library preparation, samples were bisulfite converted and amplified by PCR using 9 amplification cycles. Final PCR clean-up was performed twice using a 1.1x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). DNA concentration of the libraries was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The library profiles were checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). WGBS libraries were sequenced on a HiSeq3000 (Illumina) using 150 bp Paired-end sequencing (PE150).

tag: tissue

value: retinal pigment epithelium (RPE)

tag: developmental stage

value: adult


title: LGG_22033_X18

description: raw data file and column: DASL.4; X102380.01

value: Male


title: germ_F1-rep2


title: 14869X24: 12 week Braf;Ppargc1a/+ tumors 5

city: Los Angeles

first: John

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

description: processed data file: Galaxy753-DESeq2_DEgenes_brafvbrafpgcko.tab

data_processing:
FASTQC
Salmon Transcript Quantification from RNA-seq data (Galaxy Version 0.8.2)
DESeq2 Determines differentially expressed features from count tables (Galaxy Version 2.11.40.1)
DESeq2 normalized counts output
Genome_build: GRCm38
Supplementary_files_format_and_content: Galaxy173-DESeq2_DEgenes_brafvbrafpi3k.tab: tab delimited file with differentially expressed genes
Supplementary_files_format_and_content: Galaxy175-Normalized_counts_file_brafvbrafpi3k.tab: tab delimited file with normalized expression
Supplementary_files_format_and_content: Galaxy753-DESeq2_DEgenes_brafvbrafpgcko.tab: tab delimited file with differentially expressed genes
Supplementary_files_format_and_content: Galaxy831-Normalized_counts_file_brafvbrafpgcko.tab: tab delimited file with normalized expression

source_name: Lung

extract_protocol:
Qiagen Rneasy micro
Nugen Ovation Ultralow v2

value: Lung

tag: weeks post induction

value: 12 Week

tag: genotype

value: CAT/+; PGC1a mutant/+

tag: Sex


title: 14869X23: 12 week Braf;Ppargc1a/+ tumors 4

value: Female


title: 14869X22: 12 week Braf;Ppargc1a/+ tumors 3


title: LGG_22033_X178

description: raw data file and column: DASL.4; X102380.06

value: Yes


title: 14869X19: 12 week Braf;Ppargc1a Null tumors 3

value: CAT/+; PGC1a mutant/mutant


title: germ_D2-rep2

value: 14 days post-partum


title: WGBS_RPE Exp2


title: germ_D2-rep1


title: 14869X16: 12 week Braf;Ppargc1a Null tumors 2


title: germ_D2-input

value: Input DNA


title: 14869X15: 12 week Braf;Ppargc1a Null tumors 1


title: 14869X20: 12 week Braf;Ppargc1a Null tumors 4


title: LGG_22033_X167

description: raw data file and column: DASL.1; X102012.067

value: Partial removal

value: AOD GrII


title: LGG_22033_X173

description: raw data file and column: DASL.1; X102012.068

value: TMZ

value: AA GrII

value: mutated


title: germ_BXD99-3


title: LGG_22033_X156

description: raw data file and column: DASL.1; X102012.152

value: Biopsy

value: normal

value: No


title: LGG_22033_X161

description: raw data file and column: DASL.2; 102217-15

value: Total removal


title: 14869X13: 12 week Braf;Ppargc1a/+ tumors 1

value: Lung


title: 11997X17: 12 week Braf;PIK3CA tumors2

description: processed data file: Galaxy173-DESeq2_DEgenes_brafvbrafpi3k.tab

value: 12 Week

value: CAT/+; HR/+


title: LGG_22033_X152

description: raw data file and column: DASL.2; 102217-56

value: Male

value: RT


title: germ_BXD99-2


title: 11997X16: 12 week Braf tumors 2

value: CAT/+

value: Female


title: 11997X15: 12 week Braf tumors 1


title: germ_BXD99-1

value: 14 days post-partum


title: 11997X14: 12 week Braf;PIK3CA tumors1


title: LGG_22033_X151

description: raw data file and column: DASL.5; X102413.09

value: Partial removal


title: 22 Muscle.Basal_3h

tag: time

tag: dose

value: Basal


title: 20 Liver.Low_3h

value: Low


title: 11997X10: 6 week Braf;PIK3CA tumors 1

value: 6 Week


title: 11997X13: 6 week Braf;PIK3CA tumors 4


title: 11997X12: 6 week Braf;PIK3CA tumors 3


title: 4 Liver.Basal_3h


title: germ_BXD8

description:
B6_DBA_H3K4me3_spermatocyte_peak_associations_wF1s.txt.gz
170316_walker_B6_DBA_H3K4me3_spermatocyte_peakome_wF1s_reads.txt.gz

tag: strain

tag: ChIP


title: 14869X14: 12 week Braf;Ppargc1a/+ tumors 2

value: CAT/+; PGC1a mutant/+


title: germ_BXD89

tag: antibody


title: 11997X8: 6 week Braf tumors 3


title: germ_BXD87


title: 11997X11: 6 week Braf;PIK3CA tumors 2


title: 11997X7: 6 week Braf tumors 2


title: LGG_22033_X149

description: raw data file and column: DASL.1; X102012.123

tag: treatment therapy

value: TMZ

tag: igs

value: AA GrII

value: mutated

value: Yes


title: LGG_22033_X150

description: raw data file and column: DASL.2; 102217-71

value: Biopsy

tag: histology

value: AOD GrII

tag: performance

value: No


title: 11997X6: 6 week Braf tumors 1

value: Lung


title: germ_BXD86


title: germ_BXD85


title: 11997X1: 2 week Braf tumors 1

value: 2 Week


title: LGG_22033_X14

description: raw data file and column: DASL.5; X102413.01

value: RT

tag: progression free survival (pfs) event

tag: pfs (days)


title: LGG_22033_X147

description: raw data file and column: DASL.1; X102012.066

tag: gender

value: Male

tag: age

value: AOA GrII

value: normal


title: LGG_22033_X138

description: raw data file and column: DASL.3; X1022329.002


title: CD8+ T Cells Pool2 Fat

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
cd8_fat2
cd8_fat2_D_S8

data_processing:
Initial processing and basecalling was done using Casava v1.9
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
Alignment to the mm9 genome was performed using Tophat2
Reads were counted at mm9 genes using HTseq-count
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file contains read counts per gene for each replicate

molecule: polyA RNA

source_name: CD8+ T Cells pool Fat

extract_protocol:
Virus-specific TCR-transgenic T cells were given to 10-20 mice followed by infection to generate memory cells. At day 50 post-infection, memory cells in the spleen or adipose tissue were identified by surface stained and FACS-sorted to ~98% purity by a FACSAria-II machine at the UNC FACS core. RNA was extracted from ~10^5 sorted cells (pooled from 5-10 mice each in 2 independent replicates; Table S1), and purified on oligo(dT) dynabeads
cDNA libraries were constructed using TruSeq Adapters

tag: genotype/variation

value: wild-type

tag: infected with

value: Lymphocytic choriomeningitis virus (LCMV)

tag: time-point

value: 50 days post infection

tag: tissue

value: fat; adipose tissue

tag: cell type

value: CD8+ T Cells


title: germ_BXD84-2

value: 14 days post-partum


title: CD8+ T Cells Pool1 Fat

description:
cd8_fat1
cd8_fat1_C_S7


title: LGG_22033_X137

description: raw data file and column: DASL.1; X102012.075

source_name: low grade glioma

value: Female

value: Partial removal

value: mutated


title: LGG_22033_X136

description: raw data file and column: DASL.1; X102012.069


title: germ_BXD84-1


title: CD8+ T Cells Pool1 Spleen

description:
cd8_spleen1
cd8_spleen1_A_S5

source_name: CD8+ T Cells pool Spleen

value: spleen


title: CD4+ T Cells Pool2 Spleen

description:
cd4_spleen2
cd4_spleen2_2_S2

source_name: CD4+ T Cells pool Spleen

value: CD4+ T Cells


title: CD4+ T Cells Pool1 Fat

description:
cd4_fat1
cd4_fat1_3_S3

source_name: CD4+ T Cells pool Fat


title: germ_BXD83


title: germ_BXD81


title: CD4+ T Cells Pool1 Spleen

description:
cd4_spleen1
cd4_spleen1_1_S1


title: 11997X5: 2 week Braf;PIK3CA tumors 2

value: Lung

tag: weeks post induction

tag: genotype

value: CAT/+; HR/+

tag: Sex


title: germ_BXD77

tag: strain

tag: ChIP

tag: antibody


title: LGG_22033_X132

description: raw data file and column: DASL.5; X102413.08

tag: treatment therapy

value: RT

tag: igs

tag: histology

value: No


title: 11997X4: 2 week Braf;PIK3CA tumors 1

value: 2 Week

value: Male


title: LGG_22033_X114

description: raw data file and column: DASL.1; X102012.146

value: AOA GrII

tag: performance

value: normal

tag: progression free survival (pfs) event

tag: pfs (days)


title: germ_BXD74

tag: age


title: LGG_22033_X125

description: raw data file and column: DASL.2; 102217-24

tag: gender

value: TMZ

value: Total removal


title: germ_BXD73


title: germ_BXD71-2


title: germ_BXD71-1


title: CD8+ T Cells Pool2 Spleen

description:
cd8_spleen2
cd8_spleen2_B_S6

tag: genotype/variation

value: wild-type

tag: infected with

value: Lymphocytic choriomeningitis virus (LCMV)

tag: time-point

value: 50 days post infection

value: CD8+ T Cells


title: LGG_22033_X127

description: raw data file and column: DASL.2; 102217-78

value: Female

value: Biopsy

value: AA GrII

value: mutated

value: Yes


title: LGG_22033_X107

description: raw data file and column: DASL.1; X102012.151

value: RT


title: LGG_22033_X102

description: raw data file and column: DASL.1; X102012.073

value: Partial removal

value: AOD GrII


title: LGG_22033_X113

description: raw data file and column: DASL.2; 102217-33

value: Male


title: A3H: total RNA from myofibroblasts ATM3 derived from patient-matched adjacent tissue cultured under hypoxia

city: Liverpool

first: Hanna

last: Najgebauer

address: Crown Street

department: Cellular and Molecular Physiology

country: United Kingdom

institute: University of Liverpool

description: adjacent tissue

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The data were processed using the Bioconductor package lumi (version 2.18.0)

label_protocol: not provided

growth_protocol: Primary myofibroblast cultures were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% penicillin-streptomycin, 1% antibiotic-antimycotic and 1% non-essential amino acid solution. Cells were cultured under normoxic (21% O2) or hypoxic (1% O2) conditions for 48h. Thereafter cells were washed three times in 1x PBS and incubated in serum-free DMEM supplemented with 1% penicillin-streptomycin, 1% antibiotic-antimycotic and 1% non-essential amino acid solution for 24 hours under normoxic or hypoxic conditions. Cells were lysed at 80-90% confluence for RNA extraction.

extract_protocol: Total RNA was purified using miRNeasy Mini Kit (Qiagen, cat. no. 217004) according to manufacturer’s instructions

tag: patient

value: ATM

tag: tissue

value: myofibroblasts derived from patient-matched adjacent tissue cultured under hypoxia


title: N3H: total RNA from gastric myofibroblasts NTM3 derived from organ donors cultured under hypoxia

description: normal tissue

value: NTM

value: gastric myofibroblasts derived from organ donors cultured under hypoxia


title: N1H: total RNA from gastric myofibroblasts NTM1 derived from organ donors cultured under hypoxia

description: normal tissue


title: C2H: total RNA from myofibroblasts CAM2 derived from gastric tumour cultured under hypoxia

description: tumour

value: CAM

value: myofibroblasts derived from gastric tumour cultured under hypoxia


title: N3N: total RNA from gastric myofibroblasts NTM3 derived from organ donors

description: normal tissue

value: gastric myofibroblasts derived from organ donors


title: N2H: total RNA from gastric myofibroblasts NTM2 derived from organ donors cultured under hypoxia

description: normal tissue


title: A2H: total RNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue cultured under hypoxia

description: adjacent tissue


title: LGG_22033_X116

description: raw data file and column: DASL.5; X102413.07

value: Total removal

value: AOA GrII


title: LGG_22033_X105

description: raw data file and column: DASL.2; 102217-96

value: TMZ


title: C3H: total RNA from myofibroblasts CAM3 derived from gastric tumour cultured under hypoxia

description: tumour


title: A3N: total RNA from myofibroblasts ATM3 derived from patient-matched adjacent tissue

description: adjacent tissue

value: myofibroblasts derived from patient-matched adjacent tissue


title: germ_BXD6

description:
B6_DBA_H3K4me3_spermatocyte_peak_associations_wF1s.txt.gz
170316_walker_B6_DBA_H3K4me3_spermatocyte_peakome_wF1s_reads.txt.gz

value: 14 days post-partum


title: A1H: total RNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue cultured under hypoxia

description: adjacent tissue

value: Female


title: germ_BXD70


title: germ_BXD69


title: CP-171

city: Murcia

first: Angel

last: Esteban-Gil

state: Murcia

address: Campus de Ciencias de la Salud Carretera Buenavista s/n

department: Biomedical Informatics and Bioinformatics Platform

institute: Institute for Biomedical Research of Murcia (IMIB)

hyb_protocol: A 100ng RNA total product was hybridized to the Human miRNA Microarray Version 3 (Agilent p/n G4470C-021827)

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol.

data_processing: Data extracted using Agilent Feature Extraction Software 10.7.1 following the Agilent protocol miRNA_107_Sep09_patch and the QC Metric Set miRNA_QCMT_Sep09.  Agilent raw data were pre-processed using Agilent background correction, and quantile normalization was applied to obtain homogeneous scales in all samples.

source_name: Colorectal tissue

label_protocol: Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay. Using NanoDrop measurements, an approximately 50 ng/l dilution was prepared from each total RNA sample. This dilution was quantified again by spectrometry and 100 ng of sample were used to produce Cyanine 3-pCp 3’-end labeled RNA using the miRNA Complete Labeling and Hybridization Kit (Agilent p/n 5190-0456) according to the manufacturer’s instructions

growth_protocol: The clinico-pathological features of the patients have been previously reported. Updated follow-up information was obtained from cancer registry files and approval for the study was granted by the Local Ethical Board. SACs were diagnosed on the basis of criteria proposed by Mäkinen et al., and hMSI-Hs according to prior established criteria (mucinous, signet-ring cell, and medullary carcinoma, tumor infiltrating and peritumoral lymphocytes, “Crohn-like” inflammatory response, poor differentiation, tumor heterogeneity, and “pushing” tumor border).

extract_protocol: A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.

tag: Sex

value: female

tag: status

value: polyp


title: germ_BXD75

tag: strain

tag: ChIP


title: germ_BXD68-2

tag: antibody


title: CP-303


title: germ_BXD68-1


title: DEGRON_STH1 biological replicate 1

city: London

first: Sofía

last: Muñoz

address: 1 Midland Rd

institute: The Francis Crick Institute

description: nucleosomal DNA

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”.
BWA (version 0.5.9-r16) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the yeast sacCer3 genome downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Genome-wide wig files were generated by treating each pair of reads as a single fragment, and normalising to 10 million reads.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in complete synthetic medium lacking methionine, arrested 1.5 hour with alpha-factor, and shifted to medium containing methionine and indole-3-acetic acid (IAA) for 2 hours before release from alpha-factor block into synchronous cell cycle progression until reaching a nocodazole-imposed mitotic arrest.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina HiSeq 2500 or 4000 platform. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehide. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (ThermoFisher) at 37°C for 20 minutes. The samples were then treated with Proteinase K and RNase A to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel.
Sequencing libraries were prepared using the Kapa Hyper Prep kit according to the manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

tag: genotype

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2, STH1-PK3::TRP1


title: N1N: total RNA from gastric myofibroblasts NTM1 derived from organ donors

description: normal tissue

value: Male


title: DEGRON_STH1_K501R biological replicate 1

description: nucleosomal DNA

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2, STH1K501R-PK3::TRP1


title: DEGRON biological replicate 1

description: nucleosomal DNA

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2


title: A2N: total RNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue

description: adjacent tissue

value: ATM


title: CP-304


title: CP-48

value: tumoral


title: CP-305

value: male


title: CP-47


title: germ_BXD67


title: C2N: total RNA from myofibroblasts CAM2 derived from gastric tumour

description: tumour

value: CAM

value: myofibroblasts derived from gastric tumour


title: WT biological replicate 1

description: nucleosomal DNA


title: A1N: total RNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue

description: adjacent tissue


title: germ_BXD66


title: germ_BXD65


title: CP-40


title: germ_BXD64


title: C3N: total RNA from myofibroblasts CAM3 derived from gastric tumour

description: tumour


title: CP-43


title: CP-42

value: normal


title: germ_BXD63


title: CP-39


title: germ_BXD62


title: germ_BXD61


title: Arabidopsis ATH1_lateral root cap tissue marker_4 hour Dex treated (T2) genetic background_second biological replicate

city: la jolla

first: Wolfgang

last: Busch

state: CALIFORNIA

address: Salk institute, 10010 n torrey pines rd

institute: Salk Institute for Biological Studies

description: Gene expression data from J2632-UAS::ARR1ΔDDK-GR sorted cells under standard conditions for 5 days after 4 hour of dexamethasone treatment

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

organism: Arabidopsis thaliana

source_name: J2632 sorted cells

label_protocol: Affy two-cycle labeling (raw 22-27)

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol: Affimetrix Kit

treatment_protocol: Seedling roots, 5 days after germination, either protoplasted cells or tissue

tag: ecotype

tag: cell type

value: Lateral Root Cap cells

tag: treatment

value: dexamethasone

tag: time

value: 4 hour


title: CP-163

tag: age


title: germ_BXD5

value: 14 days post-partum


title: CP-161


title: germ_BXD56-2


title: Arabidopsis ATH1_lateral root cap tissue marker_4 hour Dex treated (T2) genetic background_first biological replicate

scan_protocol: Standard Operating Procedure performed at the Duke Microarray Facility


title: germ_BXD56-1


title: germ_BXD55


title: CD4+ T Cells Pool2 Fat

description:
cd4_fat2
cd4_fat2_4_S4

value: wild-type

value: Lymphocytic choriomeningitis virus (LCMV)

value: 50 days post infection

value: fat; adipose tissue

value: CD4+ T Cells


title: germ_BXD51


title: germ_BXD50


title: germ_BXD49


title: CP-32

value: female


title: CP-23


title: CP-170


title: CP-27


title: Arabidopsis ATH1_lateral root cap tissue marker_1 hour Dex treated (T1) genetic background_second biological replicate

description: Gene expression data from J2632-UAS::ARR1ΔDDK-GR sorted cells under standard conditions for 5 days after 1 hour of dexamethasone treatment

value: 1 hour


title: Arabidopsis ATH1_lateral root cap tissue marker_1 hour Dex treated (T1) genetic background_first biological replicate


title: Arabidopsis ATH1_lateral root cap tissue marker_untreated (T0) genetic background_second biological replicate

description: Gene expression data from J2632-UAS::ARR1ΔDDK-GR sorted cells under standard conditions for 5 days

value: control


title: CP-18

value: tumoral


title: Arabidopsis ATH1_lateral root cap tissue marker_untreated (T0) genetic background_first biological replicate


title: CP-3

value: male


title: CP-6


title: CP-15


title: CP-7


title: germ_BXD48-1


title: CP-12


title: N2N: total RNA from gastric myofibroblasts NTM2 derived from organ donors

description: normal tissue

tag: gender

value: Female

value: NTM

value: gastric myofibroblasts derived from organ donors


title: CP-172

value: normal


title: germ_BXD44


title: left ventricle S EXP3

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

description:
Expression data from Sus scrofa ventricle aged 13 months
Sus scrofa ventricle age-matched to complete AV-block  pigs

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45℃ on GeneChip Procine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Expression Console Software 1.4 using Affymetrix default analysis settings and RMA as normalization method.

organism: Sus scrofa

source_name: ventricle, EXP

label_protocol: biotin

growth_protocol: Pigs in the CTL and complete AV-block(EXP) groups received usual diet and were raised in the cages under the temperature of 20-24 ℃ and humidity of 50-70%.

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

treatment_protocol: Pacemaker with VDD setting was implanted after AV block (EXP) was created by using a thermocontrol ablation catheter in pacing group. Ventricular lead was fixed over RV septum and atrial lead was fixed over RA appendage in all pigs. all animals were sacrificed and then pared ventricular tissues were obtained after 6-month observation period.

value: 13 months

value: EXP

value: LV

tag: tissue region

value: LV septal tissue


title: germ_BXD42

value: 14 days post-partum


title: CP-29


title: germ_BXD43


title: germ_BXD39-2


title: left ventricle S CTL3

source_name: ventricle, CTL

value: CTL


title: left ventricle S EXP1


title: germ_BXD39-1


title: germ_BXD40


title: CP-24


title: germ_BXD45


title: left ventricle S EXP2


title: germ_BXD48-2


title: germ_BXD38


title: left ventricle S CTL2


title: left ventricle FW EXP3

value: LV free wall


title: left ventricle FW EXP2


title: RPE 1 hTert: 300nM PTX 24h rep 1

first: Ivana

last: Gasic

address: 200 Longwood Avenue

institute: Harvard Medical School

data_processing:
Sequenced reads were de-multiplexed, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNA-seq reads were mapped using STAR (version 2.1.0j) and processed using HTSeq-count (version 0.6.1)
GRCh38 reference genome and transcript annotations were used for gene mapping
Entrez Gene identifiers and org.Hs.eg.db database were used for genome wide annotation
Differential gene expression and statistical analysis were performed using edgeR package
Genome_build: GRCh 38
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements (CPM values) for each Sample

source_name: RPE 1 hTert

growth_protocol: RPE 1 hTert cells were grown to full confluency, and maintained as such for 5 days to induce quiescence

extract_protocol:
Total RNA was collected and purified using the PureLink RNA Mini Kit (Invitrogen, Thermo Fisher Scientific, USA). RNA concentration and quality were determined using NanoDrop and Bioanalyzer respectively
500 ng of purified RNA was used as input for the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, USA). Barcoded libraries were pooled and sequenced by The Bauer Core Facility at Harvard University, where the pooled library was quantitated using KAPA and single-end sequenced on an Illumina NextSeq (Illumina, USA).

treatment_protocol: Quiescent cells were treated with microtubule poisons combretastatin A4 and paclitaxel for 6 or 24 hours

value: RPE 1 hTert


title: germ_BXD34


title: RPE 1 hTert: 300nM PTX 24h rep 3


title: RPE 1 hTert: 300nM PTX 24h rep 2


title: RPE 1 hTert: 3nM PTX 24h rep 3


title: left ventricle S CTL1


title: CP-159

value: female


title: left ventricle FW EXP1


title: PKHD1-KO CCs vs PKHD1-Hetero CCs

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: PKHD1-Hetero CCs

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

growth_protocol: A human iPS cell line, TkDA3-4 clone (established from dermal fibroblasts of a normal healthy human) was cultured using the Cellartis® DEF-CS™ 500 culture system (Takara Bio, Shiga, Japan).  The TkDA3-4 cell line was differentiated into the hepatic lineage using the Cellartis Definitive Endoderm Differentiation Kit and Cellartis Hepatocyte Differentiation Kit (Takara Bio). At day 12, the CD13-high/CD133+ fraction in the harvested cells was sorted onto mouse embryonic fibroblasts feeder layers using fluorescence-activated cell sorting, and was then cultured as iPS-derived hepatic progenitor-like cells (HPCs). HPCs were cultured in HPC medium, a 1:1 mixture of DMEM and H-CFU-C medium (DMEM/F-12 supplemented with 10% FBS, insulin-transferrin-selenium X, 10 mM nicotinamide, 10-7 M dexamethasone, 2.5 mM HEPES buffer solution, penicillin/streptomycin/glutamine, and nonessential amino acids). For expansion, the cells were cultured in standard medium supplemented with 0.25 mM A-83-01, 10 mM Y-27632, 40 ng/ml rhHGF, and 20 ng/ml rhEGF. The medium was replaced every 3 days. After 10–12 days of culture, colonies formed by individual HPC were trypsinized using 0.05% trypsin-EDTA, and replated onto freshly plated mouse embryonic fibroblasts.

extract_protocol: Total RNA samples were extracted from the cultured cells using a RNeasy Mini Kit  according to the manufacturer’s protocols.

treatment_protocol: HPCs were differentiated into cholangiocytic cysts (CCs) using a protocol previously described with some modifications. Briefly, HPCs were passaged and trypsinized using 0.05% trypsin-EDTA, washed in DMEM containing 10% FBS, and counted. The cells were suspended in an extracellular matrix gel consisting of a mixture of 50% biliary culture medium, 10% type I collagen and 40% EHS gel, then placed onto each cell culture insert (8×10e4 cells/ml extracellular matrix, 2×10e4 cells/insert). After incubation at 37°C for 1 h, biliary culture medium was added above and below the insert, followed by incubation for 10 days. The medium was changed every 2 days.

value: induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells

source_name: PKHD1-KO CCs


title: germ_BXD33


title: germ_BXD32


title: RPE 1 hTert: 3nM PTX 24h rep 1


title: left ventricle FW CTL2


title: germ_BXD31


title: left ventricle FW CTL3


title: germ_BXD2


title: RPE 1 hTert: 100nM CA4 24h rep 1


title: germ_BXD29


title: RPE 1 hTert: 100nM CA4 24h rep 2


title: RPE 1 hTert: 100nM CA4 24h rep 3


title: RPE 1 hTert: 1nM CA4 24h rep 3


title: RPE 1 hTert: 3nM PTX 24h rep 2


title: germ_BXD28


title: RPE 1 hTert: 1nM CA4 24h rep 2


title: germ_BXD27


title: left ventricle FW CTL1


title: germ_BXD22


title: RPE 1 hTert: DMSO 24h rep 3


title: germ_BXD21


title: RPE 1 hTert: 1nM CA4 24h rep 1


title: RPE rep3

description: RNA samples were extracted from RPE isolated from adult mice using the Absolutely RNA Nanoprep kit

hyb_protocol: Biotinylated complementary RNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarray slides enclosed in custom hybridization chambers (for more information on the MEEBO oligonucleotide set please refer to http://alizadehlab.stanford.edu/). The slides were hybridized for 16-18 hours in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. The spot intensities were then normalized. After removing data for low quality spots, the mouse probes’ intensities were filtered to identify all probes with an intensity above a normalized threshold. For statistical analysis, microarray data were examined for differences by One-way ANOVA or Student's t-test. Values of P < 0.05 were designated as statistically significant.

label_protocol: Biotin-labeled complementary RNA was made from the total RNA according to Van Gelder’s protocol (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.)

extract_protocol: RNA samples were extracted from RPE of adult (3-month-old) mice using the Absolutely RNA Nanoprep kit (Agilent Technologies, Santa Clara, CA).

value: 2.5-3 month-old

value: retinal pigment epithelium (RPE)


title: ISK

city: shanghai

first: yiran

last: li

address: Gaoke West Road 2699

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China

description: SAMPLE 4

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 (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: endometrial cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ishikawa and SPEC-2 cells were purchased from the American Type Culture Collection and maintained according to the provider’s instruction in DMEM/F12 media supplemented with 10% FBS (Gibco, Carlsbad, CA)

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Transfection of Ishikawa and SPEC-2 cells with the AMFR down-expressing plasmid, cells were grown until confluent and were incubated in serum-free medium for 24 h before analysis

tag: cell line

value: Ishikawa (ISK)

value: endometrial cancer cells


title: spec-2

description: SAMPLE 2


title: RPE 1 hTert: DMSO 24h rep 2


title: spec-2/shAMFR

description: SAMPLE 1

source_name: endometrial cancer_shAMFR

tag: transfected with

value: AMFR down-expressing plasmid


title: ZH11-D3-Input

city: Wuhan

first: Yu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description:
processed data file: Peaks_ZH11_D_VS_SNAC1OE_N.txt
processed data file: Peaks_ZH11_N_VS_ZH11_D.txt

data_processing:
Sequencing reads were mapped to rice reference genome using Hisat2 (for RNA-seq) and Bowtie2 (for ChIP-seq).
RNA-seq transcripts were assembled and counted by StringTie and the differential expression was determined by DESeq2.
ChIP-seq peaks were called by MACS2 and peak annotation and differential binding identification were done by ChIPseeker and DiffBind, respectively.
Genome_build: Rice Genome Annotation Project (RGAP) Release 7
Supplementary_files_format_and_content: All_gene_FPKM.txt: Tab-delimited text file includes FPKM values for each RNA-seq sample.
Supplementary_files_format_and_content: Peaks_*.txt: Tab-delimited text files include normalized peak counts and fold changes for ChIP-seq samples.

organism: Oryza sativa Japonica Group

source_name: 4-leaf-stage seedling

growth_protocol: The transgenic and ZH11-WT seeds were sprouted on half-strength MS medium in the dark for 2-3 days at 28°C, and then 4-5 days in the greenhouse. The seedlings were then moved to pots with sand/paddy (1:3) soil under natural conditions at Wuhan, China.

extract_protocol:
The total RNAs were extracted from the leaves of SNAC1-OE lines and ZH11-WT plants using TRIzol reagent (InvitrogenTM) according to the manufacturer’s instructions. The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3g shoot tissues from 4-leaf-stage seedlings were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by custom-made anti-SNAC1 polyclonal antibody generated using full-length SNAC1 protein. The combined DNAs were eluted, purified, and dissolved in ddH2O.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After germination, the 1-week-old seedlings that were of uniform growth status were moved to pots filled with sandy soil. The transgenic and WT plants were grown in a half-and-half manner (10 plants each) in the pots. At the 4-leaf stage, the seedlings were subjected to drought stress treatment by stopping water for 10-15 days until the leaves were curled and turned yellow.

value: 4-leaf-stage seedling

tag: genotype/variation

value: Drought

tag: chip antibody

tag: sample type

value: ChIP-seq Input


title: RPE 1 hTert: DMSO 24h rep 1


title: RPE rep1

source_name: RPE

tag: tissue


title: H_72h_3: Lung_hypoxia_72hr_rep3

city: Tianjin

first: Wei

last: Cai

address: No. 92 Weijin Road, Nankai District

institute: School of disaster medical research，Tianjin University

description: Gene expression data from lung tissue under hypoxic exposure

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 4.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

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

source_name: Rattus norvegicus lung, hypoxic exposure, 72hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA ( Expression Analysis Technical Manual, 2012, Affymetrix).

growth_protocol: Right lung tissue was taken after 24,48, and 72 hours of normoxic and hypoxic exposure.

treatment_protocol: Right lower lobe was placed in a -80°C low temperature freezer for RNA extraction.

tag: strain

value: Sprague-Dawley

value: male

value: right lung

value: 8 weeks old


title: ZH11-D1-Input


title: germ_BXD20

source_name: male germ cells

value: 14 days post-partum

tag: ChIP


title: RPE rep2


title: H_72h_1: Lung_hypoxia_72hr_rep1


title: germ_BXD1

tag: antibody


title: H_72h_2: Lung_hypoxia_72hr_rep2


title: H_48h_3: Lung_hypoxia_48hr_rep3

source_name: Rattus norvegicus lung, hypoxic exposure, 48hr


title: ZH11-D3-IP

value: ChIP-seq IP


title: RPE 1 hTert: 300nM PTX 6h rep 3

value: RPE 1 hTert


title: ISK/shAMFR

description: SAMPLE 3


title: H_48h_2: Lung_hypoxia_48hr_rep2


title: ZH11-D2-IP


title: ZH11-D2-Input


title: germ_BXD19


title: germ_BXD18


title: RPE 1 hTert: 300nM PTX 6h rep 2


title: H_48h_1: Lung_hypoxia_48hr_rep1


title: RPE 1 hTert: 300nM PTX 6h rep 1


title: ZH11-D1-IP


title: germ_BXD15


title: RPE 1 hTert: 3nM PTX 6h rep 2


title: germ_BXD16


title: ZH11-N1-Input

description:
processed data file: Peaks_ZH11_N_VS_SNAC1OE_N.txt
processed data file: Peaks_ZH11_N_VS_ZH11_D.txt

value: Normal


title: ZH11-N2-Input


title: H_24h_2: Lung_hypoxia_24hr_rep2

source_name: Rattus norvegicus lung, hypoxic exposure, 24hr


title: C1N: total RNA from myofibroblasts CAM1 derived from gastric tumour

description: tumour

value: Female

tag: patient

value: CAM

value: myofibroblasts derived from gastric tumour


title: H_24h_1: Lung_hypoxia_24hr_rep1


title: ZH11-N3-IP


title: RPE 1 hTert: 100nM CA4 6h rep 3


title: germ_BXD14


title: RPE 1 hTert: 3nM PTX 6h rep 1


title: ZH11-N2-IP


title: H_24h_3: Lung_hypoxia_24hr_rep3


title: C_3: Lung_hypoxia_0hr_rep3

description: Gene expression data from lung tissue under normoxic exposure

source_name: Rattus norvegicus lung, hypoxic exposure, 0hr


title: C_2: Lung_hypoxia_0hr_rep2


title: ZH11-N1-IP


title: RPE 1 hTert: 100nM CA4 6h rep 2


title: 7h-vehicle (3438-MS-31)

city: Frederick

first: Kalyan

middle: C

last: Vinnakota

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
Software tool Kallisto was used to generate Rnor_6.0 transcriptome index from ENSEMBL genome assembly release 92
Software tool Kallisto was used to obtain transcript abundances (units of Transcripts Per Million) in each sample with the Rnor6 transcriptome index generated in the previous step
Software tool Sleuth was used to assess differential expression of genes from the transcript abundances obtained using Kallisto
Genome_build: Rnor_6.0 ENSEMBL genome assembly release 92
Supplementary_files_format_and_content: The output of Kallisto for each sample, provided here as a .tar.gz archive, consists of a folder with the following contents: abundance.tsv (a text file that contains a total summary of transcript abundances), 100 bs_abundance_<i>.tsv files (i ranges from 0 to 99, each file is one bootstrap of transcript abundances), and run_info.json (a text file that contains information on the Kallisto run)

extract_protocol:
Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche).

value: 7h fasting

value: liver


title: germ_BXD11


title: RPE 1 hTert: 3nM PTX 6h rep 3


title: 7h-vehicle (3438-MS-19)


title: C_1: Lung_hypoxia_0hr_rep1


title: SNAC1-N3-Input

description:
processed data file: Peaks_ZH11_D_VS_SNAC1OE_N.txt
processed data file: Peaks_ZH11_N_VS_SNAC1OE_N.txt


title: germ_BXD102


title: germ_BXD13


title: 7h-vehicle (3438-MS-17)


title: SNAC1-N2-Input


title: RPE 1 hTert: 1nM CA4 6h rep 3


title: germ_BXD12


title: 7h-vehicle (3438-MS-16)


title: SNAC1-N1-Input


title: germ_B6-rep3


title: RPE 1 hTert: 1nM CA4 6h rep 2


title: RPE 1 hTert: 100nM CA4 6h rep 1


title: 7h-vehicle (3438-MS-15)


title: RPE 1 hTert: 1nM CA4 6h rep 1


title: germ_B6-rep2


title: 7h-vehicle (3438-MS-6)


title: RPE 1 hTert: DMSO 6h rep 3


title: germ_B6-input

value: Input DNA


title: SNAC1-N1-IP

value: 4-leaf-stage seedling


title: 7h-vehicle (3438-MS-2)


title: SNAC1-N2-IP


title: 7h-vehicle (3438-MS-5)


title: RPE 1 hTert: DMSO 6h rep 2


title: ZH11-N3-RNAseq

description: processed data file: All_gene_FPKM.txt

value: RNA-seq


title: germ_BXD100


title: RPE 1 hTert: DMSO 6h rep 1


title: 13h-vehicle (3438-MS-69)

value: 13h fasting


title: SNAC1-N3-IP


title: ZH11-N1-RNAseq

description: processed data file: All_gene_FPKM.txt


title: 13h-vehicle (3438-MS-66)

value: Sprague-Dawley


title: 13h-vehicle (3438-MS-67)


title: C1H: total RNA from myofibroblasts CAM1 derived from gastric tumour cultured under hypoxia

description: tumour

value: myofibroblasts derived from gastric tumour cultured under hypoxia


title: 13h-vehicle (3438-MS-25)


title: RPE 1 hTert: DMSO 6h rep 4


title: ZH11-D2-RNAseq

description: processed data file: All_gene_FPKM.txt

value: Drought


title: ZH11-D1-RNAseq

description: processed data file: All_gene_FPKM.txt


title: SNAC1-N3-RNAseq

description: processed data file: All_gene_FPKM.txt


title: ZH11-N3-Input

value: ChIP-seq Input


title: 13h-vehicle (3438-MS-11)


title: germ_B6-rep1

value: 14 days post-partum


title: 13h-vehicle (3438-MS-9)


title: ZH11-N2-RNAseq

description: processed data file: All_gene_FPKM.txt


title: ZH11-D3-RNAseq

description: processed data file: All_gene_FPKM.txt


title: Telmisartan_1

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

description: Gene expression data from mice after 6-week repeat oral administration

hyb_protocol: Approximately 5.5 μg of labeled cDNA was hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45°C for 16 h.

scan_protocol: The hybridized arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: All data analyses were performed with the GeneChip Command Console Software (Affymetrix). All data were normalized using the robust multi-array average (RMA).

source_name: STAM NASH-HCC mice

label_protocol: The cDNA was fragmented and biotin-labeled using GeneChip WT terminal labeling kit (Applied Biosystems).

growth_protocol: At 2 days after birth, the mice received a single subcutaneous injection of 200 μg streptozotocin (STZ; Sigma, St. Louis, MO, USA). Then, after 4 weeks of age, they received 60 kcal% fat HFD32 chow (CLEA Japan Inc., Tokyo, Japan) ad libitum and were assigned to receive either vehicle or telmisartan.

extract_protocol: Total RNA was extracted from the frozen liver tissues with a RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Telmisartan (Sigma) was dissolved in 0.5% (v/v) carboxymethyl cellulose (Sigma) and orally administered (5 mg/kg/day) to the mice from 6 to 12 weeks of age (n = 7 per group).

value: Liver

tag: agent

value: Telmisartan


title: 13h-vehicle (3438-MS-10)


title: SNAC1-N2-RNAseq

description: processed data file: All_gene_FPKM.txt

value: Normal


title: Telmisartan_3


title: SNAC1-N1-RNAseq

description: processed data file: All_gene_FPKM.txt


title: Telmisartan_2


title: SNAC1-D3-RNAseq

description: processed data file: All_gene_FPKM.txt


title: Vehicle control_3

value: Vehicle