title: Neo-liver_4_rep1

city: Chiba

first: Rie

last: Utoh

state: Chiba

address: 1-33 Yayoi-cho, Inage-ku

department: Department of Applied Chemistry and Biotechnology

institute: Chiba University

description: Gene expression at 250-300 days after hepatocyte transplantation

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >13.0 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 Sureprint G3 Mouse Gene Expression Microarrays 8x60k (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using  parameters (protocol GE1_1010_Sep10, QC and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Neo-liver under kidney capsule, liver injury, replicate 1

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

extract_protocol: Total RNA was prepared using TRIzol (Life Technology, Carlsbad, CA) and RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's instructions. Genomic DNA was eliminated by Qiagen RNase-Free DNase.  RNA was quantified using a NanoDrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All RNA samples have high integrity with RIN (RNA integrity number) values greater than 7.

value: neo-liver

value: FVB/N


title: CT06_036

status: Public on Dec 25 2017

type: RNA

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

description:
FFPE
pre-treatment

hyb_protocol: Affymetrix standardized protocol for U133p2 array

data_processing: R, affypackage, justRMA

label: Biotin-PE

molecule: total RNA

organism: Homo sapiens

source_name: non-small cell lung cancer

label_protocol: Affymetrix SensationPlus™ FFPE Amplification and 3’ IVT Labeling

extract_protocol: RecoverAll total RNA extraction

tag: tissue

value: non-small cell lung cancer


title: CT06_041

description:
FFPE
pre-treatment

scan_protocol: Affymetrix standardized protocol for U133p2 array


title: Neo-liver_3_rep1

country: Japan

organism: Mus musculus

tag: gender

value: female

tag: strain

tag: age


title: M3_infected_day7_splenocyte_rep1

city: Kunming

first: Xiaolong

last: Zhang

address: 935 jiaoling Road

country: China

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
M3-day7-1
Gene expression of M3 infected mice splenocytes at day 7 post-infection.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (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.
Raw data were normalized by Quantile algorithm, limma packages in R.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

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

treatment_protocol: The HSV-1 mutant strain M3 or wild type strain Mckrae infected BALB/c mice and uninfected control mice were sacrificed at indicated time points post-infection (day 7/ day 30/ day 60). The splenocyte of the mice were homogenated into single cells.

tag: strain/background

value: BALB/c

value: 4 weeks

tag: cell type

value: splenocytes

tag: infection

value: HSV-1 mutant strain M3

tag: time point

value: day 7


title: CT06_035

description:
FFPE
pre-treatment


title: Neo-liver_2_rep1


title: CT06_038

description:
FFPE
pre-treatment


title: CT06_034

description:
FFPE
pre-treatment


title: Host liver_1_rep1

source_name: Host liver, liver injury, replicate 1

value: liver


title: Host liver_4_rep1


title: CT06_032

description:
FFPE
pre-treatment


title: Host kidney_4_rep1

source_name: Host kidney, liver injury, replicate 1

value: kidney


title: Neo-liver_1_rep1


title: CT06_031

description:
FFPE
pre-treatment


title: Control liver_3_rep1

source_name: Control liver, normal mouse, replicate 1


title: M3_infected_day60_splenocyte_rep3

description:
M3-day60-3
Gene expression of M3 infected mice splenocytes at day 60 post-infection.

value: day 60


title: Host liver_3_rep1


title: CT06_030

description:
FFPE
pre-treatment


title: Host liver_2_rep1


title: CT06_027

description:
FFPE
pre-treatment


title: CT06_033

description:
FFPE
pre-treatment


title: CT06_026

description:
FFPE
pre-treatment


title: Control liver_1_rep1


title: Control liver_2_rep1


title: CT06_025

description:
FFPE
pre-treatment


title: CT06_028

description:
FFPE
pre-treatment


title: Host kidney_3_rep1


title: CT06_023

description:
FFPE
pre-treatment


title: Host kidney_2_rep1


title: Host kidney_1_rep1


title: CT06_022

description:
FFPE
pre-treatment


title: CT06_029

description:
FFPE
pre-treatment


title: CT06_024

description:
FFPE
pre-treatment


title: CT06_017

description:
FFPE
pre-treatment


title: CT06_021

description:
FFPE
pre-treatment


title: CT06_019

description:
FFPE
pre-treatment


title: CT06_014

description:
FFPE
pre-treatment


title: CT06_016

description:
FFPE
pre-treatment


title: CT06_015

description:
FFPE
pre-treatment


title: neurons differentiated from NPC, rep 1

city: São Paulo

first: Carolini

last: Kaid Dávila

state: SP

address: Rua Corinto, 512

department: Department of Genetics

country: Brazil

institute: Instituto de Biociências - USP

description:
Neuron 1
Gene expression data

hyb_protocol: Independent microarray hybridizations were carried out for each sample using Affymetrix GeneChip® Human Gene 2.0 ST whole-transcript arrays, measuring both protein coding and long intergenic non-coding RNA transcripts (lincRNA).

scan_protocol: Microarray chips were scanned by GeneChip® Scanner 3000 7G System and a quality control was processed by Affymetrix® Expression Console Software (Affymetrix).

data_processing: Differentially expressed genes were identified with a p-value cutoff of 0.05 adjusted for false discovery rate [Benjamini & Hochberg, 1995], using Transcriptome Analysis Console (Affymetrix).

label: biotin

source_name: Cell culture

label_protocol: Affymetrix Protocol

treatment_protocol: Each cell type was maintained under standard culture conditions.

tag: cell line

value: Neuron

value: neurons differentiated from NPC


title: CT06_010

description:
FFPE
pre-treatment


title: CT06_004

description:
FFPE
pre-treatment


title: neural progenitor cell differentiated from hiPS, rep 1

description:
NPC 1
Gene expression data

value: NPC


title: Medulloblastoma cell line USP13-MED, rep 1

description:
USP13-MED 1
Gene expression data

value: Medulloblastoma cell line


title: CT06_005

description:
FFPE
pre-treatment


title: CT06_011

description:
FFPE
pre-treatment


title: human induced pluripotency cell, rep 1

description:
hiPS 1
Gene expression data

value: hiPS

value: human induced pluripotency cells


title: Cerebellum RNA, rep 2

description:
Cerebellum 2
Gene expression data

source_name: Brain tissue

value: normal cerebellum


title: ATRT cell line, rep 1

description:
USP7-ATRT 1
Gene expression data

value: Atypical teratoid rhabdoid tumor cell line


title: CT06_006

description:
FFPE
pre-treatment

value: non-small cell lung cancer


title: CT06_009

description:
FFPE
pre-treatment


title: Medulloblastoma cell line Daoy, rep 1

description:
Daoy 1
Gene expression data

value: Daoy


title: CT06_002

description:
FFPE
pre-treatment


title: Medulloblastoma cell line USP13-MED, rep 2

description:
USP13-MED 2
Gene expression data


title: CT06_053

description:
FFPE
pre-treatment


title: CT06_007

description:
FFPE
pre-treatment


title: EED ChIP-seq of WT mESC replicate 2

status: Public on Dec 24 2017

type: SRA

city: Beijing

first: Yuanyuan

last: Li

address: Tsinghua University, Qinghua Yuan, Haidian District

institute: Tsinghua Universary

library_source: genomic

data_processing:
ChIP-seq reads were aligned to mm9 with Bowtie2 (version 2.2.2) with parameters -t -q -N 1 -L 25. All unmapped reads, multiplely mapped reads and PCR duplicates were removed. To generate the ChIP-Seq signals for each histone modification shown in the UCSC genome browser, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM). To minimize the batch and cell type variation, the RPKM values were further normalized through Z-score transformation, by subtracting the mean of RPKM across the genome and divided by the standard deviation of RPKM across the genome.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited BEDGRAPH files including number of reads in 100bp bin in the genome for each ChIP-seq sample

molecule: genomic DNA

source_name: mESCs

growth_protocol: mESCs were passaged every 48-72h in DMEM(Gibco) supplemented with 15% FBS (HyClone), 1% non-essential amino acids(Gibco), 0.5% 2-mercaptoethanol(Gibco), 1% penicillin/streptomycin(Millipore), 0.01% leukemia inhibiting factor(LIF)(Millipore) and 1% glutamine(Gibco) on gelatinized plates.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37°C;Chromatin was fragmented by sonication to obtain fragments 100–700bp in length. For each ChIP assay,5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

tag: chip-antibody

value: EED (Active Motif, Cat.61203 )

tag: genotype

value: WT

value: mESCs


title: EED ChIP-seq of Dnmt3a/3b DKO mESC replicate 1

value: Dnmt 3a-/- Dnmt 3b-/-


title: CT06_001

description:
FFPE
pre-treatment


title: EED ChIP-seq of Dnmt3a/3b DKO mESC replicate 2


title: Crohns_disease8

type: genomic

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: Crohn's disease sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: Raw data were processed using the GenomeStudio application by Macrogen (Macrogen Inc.). The methylumi and lumi packages implemented in R were used to correct background signal and dye bias, respectively. The corrected signals were further normalized using the beta-mixture quantile normalization method (BMIQ). Briefly, CpG sites with high confidence (P < 0.05) were only used in this study.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from eight Crohn's disease (CD) and three normal biopsy tissues using Qiagen DNeasy Kit according to standard instructions

value: Male

tag: disease state

value: Crohn's disease


title: WEDEV10-1G

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

description: whole embryo (AEL:16h20m - 19h20m), biological replicate 1

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/5-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA)

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization

organism: Drosophila melanogaster

source_name: whole embryo, stage: 16h20m - 19h20m AEL

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng of total RNA was used.

growth_protocol: incubated at 25C

extract_protocol: Total RNA extracted using RNeasy (QIAGEN) manufacturer's instructions

treatment_protocol: Whole bodies of fly embryos at a specified developmental time  were homogenized for RNA extraction.

value: whole embryos

tag: developmental stage

value: EGFP-vasa

source_name: pooled whole embryos of 0-24h AEL

value: 0 - 24h AEL


title: WEDEV9-1G

description: whole embryo (AEL:13h20m - 16h20m), biological replicate 1

source_name: whole embryo, stage: 13h20m - 16h20m AEL


title: WEDEV7-1G

description: whole embryo (AEL:9h20m - 11h20m), biological replicate 1

source_name: whole embryo, stage: 9h20m - 11h20m AEL


title: WEDEV5-1G

description: whole embryo (AEL:5h20m - 7h20m), biological replicate 1

source_name: whole embryo, stage: 5h20m - 7h20m AEL

value: 5h20m - 7h20m AEL


title: WEDEV4-1G

description: whole embryo (AEL:4h20m - 5h20m), biological replicate 1

source_name: whole embryo, stage: 4h20m - 5h20m AEL

value: 4h20m - 5h20m AEL


title: WEDEV11-1G

description: whole embryo (AEL:19h20m - 24h00m), biological replicate 1

source_name: whole embryo, stage: 19h20m - 24h00m AEL


title: WEDEV6-1G

description: whole embryo (AEL:7h20m - 9h20m), biological replicate 1

source_name: whole embryo, stage: 7h20m - 9h20m AEL

value: 7h20m - 9h20m AEL


title: WEDEV8-1G

description: whole embryo (AEL:11h20m - 13h20m), biological replicate 1

source_name: whole embryo, stage: 11h20m - 13h20m AEL


title: Crohns_disease2

description: Crohn's disease sample

value: Female


title: Cerebellum RNA, rep 1

description:
Cerebellum 1
Gene expression data

value: normal cerebellum


title: CT06_013

description:
FFPE
pre-treatment


title: Crohns_disease1

description: Crohn's disease sample


title: WEDEV3-1G

description: whole embryo (AEL:3h20m - 4h20m), biological replicate 1

source_name: whole embryo, stage: 3h20m - 4h20m AEL

value: 3h20m - 4h20m AEL


title: A549 cells with scrambled knockdown, biological rep3

first: HONG

last: WANG

address: No.8 East Avenue, Fengtai District,

department: Department of Lung Cancer

institute: The Affiliated Hospital of Military Medical Sciences, The 307th Hospital of Chinese People’s Liberation Army

hyb_protocol: GeneChip Hybridization Oven 645

scan_protocol: GeneChip Scanner 3000

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

source_name: A549 cells

label_protocol: GeneChip 3’IVT PLUS Kit

growth_protocol: A549 cells cells were cultured in RPMI1640 medium containing 10% FBS and 1% antibiotics. These cell lines were cultured at 37°C in a 5% CO2 incubator.

extract_protocol: total RNA was extracted using Trizol reagents. RNA quantity and quality were determined using NanoDrop 2000 and Agilent Bioanalyzer 2100.

treatment_protocol: lentivirus expressing either GMDS- or Scr-shRNA was added to the A549 cells (MOI=5 and 5 ul lentivirus was used per well for 6-well plate) and culturing for another 2-5 days,

value: A549 human lung adenocarcinoma

tag: shRNA

value: Scr-shRNA


title: A549 cells with scrambled knockdown, biological rep2


title: LTAD

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: Gene expression data from LTAD cells cultured in horomone-free medium

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS. Cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for24h. LTAD cells, derived from LNCaP cells after long term androgen deprivation, are culture in Phenol red-free RPMI 1640 containing 10% charcoal/dextran treated FBS.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: LTAD cells were transfected with siControl or siPSF.

value: LTAD

value: prostate cancer


title: LNCaP

source_name: Gene expression data from LNCaP cells incubated in hormone-free medium for 24 h

value: LNCaP


title: CT06_012

description:
FFPE
pre-treatment

source_name: non-small cell lung cancer

value: non-small cell lung cancer


title: Crohns_disease7

description: Crohn's disease sample

value: Male


title: Normal2

description: Normal sample

value: Normal


title: A549 cells with GMDS knockdown, biological rep3

value: GMDS-shRNA


title: WEDEV2-1G

description: whole embryo (AEL:2h20m - 3h20m), biological replicate 1

source_name: whole embryo, stage: 2h20m - 3h20m AEL

value: whole embryos

value: 2h20m - 3h20m AEL

value: EGFP-vasa


title: A549 cells with scrambled knockdown, biological rep1


title: Crohns_disease4

description: Crohn's disease sample

value: Crohn's disease


title: Normal3

description: Normal sample


title: Crohns_disease5

description: Crohn's disease sample


title: Crohns_disease6

description: Crohn's disease sample


title: WEDEV1-1G

description: whole embryo (AEL:1h20m - 2h20m) , biological replicate #1

source_name: whole embryo, stage: 1h20m - 2h20m AEL

value: 1h20m - 2h20m AEL

value: 0 - 24h AEL


title: Crohns_disease3

description: Crohn's disease sample

value: Female


title: WEDEV0-1G

description: whole embryo (AEL:0h0m - 1h20m) , biological replicate #1

source_name: whole embryo, stage: 0h0m - 1h20m AEL

value: 0h0m - 1h20m AEL


title: Wibi_0-11_DIV16_rep2

status: Public on Dec 23 2017

city: Pisa

first: Marco

last: Terrigno

address: Via Giuseppe Moruzzi, 1

country: Italy

institute: Scuola Normale Superiore

description: Gene expression of ESC-derived neurons at 16 days of differentation in vitro treated with WNT and BMP inhibitors from day 0 to day 11

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 (G2564C) using one color scan default setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were background-corrected and normalized between arrays by means of Bioconductor package limma (Smyth, 2005).

source_name: cell culture, WiBi 0-11, DIV16

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent Technologies) 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: The protocol of ES neuralization consisted of three steps. In Step-I, dissociated ES cells were washed with DMEM/F12, seeded on gelatin-coated culture dishes (65000 cells per cm2) and cultured in CDMM plus 2.5μM Wnt inhibitor (53AH, Cellagen Technology) and 0.25μM BMP inhibitor (LDN193189, Sigma) for 3 days. In Step-II, ES cell were dissociated and seeded (65000 cells per cm2) on Poly-ornithine (Sigma; 20 μg/ml in sterile water, 24 hours coating at 37°C) and natural mouse Laminin (Invitrogen; 2.5 μg/ml in PBS, 24 hours coating at 37°C). Cells were cultured for 4 additional days in CDMM Plus Wnt/BMP inhibitors, changing the medium daily. Serum employed for Trypsin inactivation was carefully removed by several washes in DMEM/F12. In Step-III, cells were dissociated and seeded (125000 cells per cm2) on Poly-ornithine and Laminin coated wells. Subsequently, isocortical culture were kept in CDMM Plus Wnt/BMP inhibitors for four (WiBi 11) additional days, whereas hippocampal culture (CHIR8) were grown in CDMM supplemented with CHIR 3μM (Santa Cruz Biotechnology). On the eleventh day of differentiation in vitro DMEM/F12 was replaced with Neurobasal and NEAA were removed from the CDMM to avoid glutamate-induced excitotoxicity.

extract_protocol: Total RNA was extracted with NucleoSpin RNA II columns (Macherey–Nagel). RNA from three different sets of experiments was pooled. RNA quality was assessed with Agilent Bioanalyzer RNA 6000 Nano kit.

tag: strain background

value: male

value: ESC-derived neurons

tag: treated with

value: WNT and BMP inhibitors


title: Mouse_Midbrain_E15

description: Gene expression of E15 mouse midbrain

source_name: embryonic midbrain, E15

value: mixed (male/female)

value: midbrain


title: A549 cells with GMDS knockdown, biological rep2

value: A549 human lung adenocarcinoma


title: sort_b13

city: Berkeley

first: Michael

middle: B

last: Cole

state: CA

address: 378 Stanley Hall

country: USA

institute: UC Berkeley

library_source: transcriptomic

data_processing:
[RNA-Seq Expression Quantification] RNA-seq reads were aligned to the RefSeq hg38 transcriptome (GRCh38.2) using Bowtie2 (Langmead et al., 2012). The resulting transcriptome alignments were processed by RSEM to estimate the abundance (expected counts and TPM) of RefSeq transcripts (Li et al., 2011), aggregating by gene symbol.
[Filtering] For each library we computed transcriptome alignment metrics using FastQC, Picard tools, and in-house scripts. Computed metrics included: (1) number of reads, (2) number of aligned reads, (3) percentage of aligned reads, (4) number of duplicate reads, (5) primer sequence contamination, (6) average insert size (7) variance of insert size, (8) sequence complexity, (9) percentage of unique reads (10) ribosomal read fraction, (11) coding read fraction, (12) UTR read fraction, (13) intronic read fraction, (14) intergenic read fraction, (15) mRNA read fraction, (16) coefficient of variation of coverage, (17) mean 5’ coverage bias, (18) mean 3’ coverage bias, and (19) mean 5’ to 3’ coverage bias.
We excluded from further analysis libraries with poor values for number of aligned reads (< 2,290,866), the percentage of aligned reads (< 15%), or the percentage of detected transcripts (< 69% of protein-coding genes expressed at least 100 TPM in at least 10% of cells). 19 samples passed.
Following cell filtering, protein-coding genes were retained for downstream analysis if they were expressed at least 10 TPM in at least one sample.
[Data Normalization] In order to normalize TPM data for residual compositional bias, we applied the DESeq normalization method, followed by gene-level regression on the first PC of QC metrics, retaining the residual for downstream analysis.

source_name: HI dendritic cell

extract_protocol:
Total RNA was isolated using a RNeasy plus Micro RNA kit (Qiagen, Hilden, Germany)
[Trombetta et al CPMB 2014]
[Whole Transcriptome Amplification]: Two μL of extracted RNA were added to 8 μL of water and cleaned with 2.2x volume beads. 1 μL of this cleaned RNA was used in a WTA reaction. Whole transcriptome amplification was performed on these samples analogous to the amplification of the single cell samples.
[Preparation of cDNA Libraries  for RNAseq]: WTA products were diluted to a concentration of 0.1 to 0.4 ng/μL and tagmented and amplified using Nextera XT DNA Sample preparation reagents (Illumina). Tagmentation was performed according to manufacturer’s instructions, modified to use ¼ the recommended volume of reagents, extended tagmentation time to 10 minutes and extended PCR time to 60s. PCR primers were ordered form Integrated DNA Technologies. Nextera products were then cleaned twice with at 0.9x volume of SPRI beads and eluted in water. The library was quantified using Qubit and analyzed using a high sensitivity DNA chip. The library was diluted to 2.2 pM and sequenced on a NextSeq 500 (Illumina)

treatment_protocol: For the functional studies on DC subsets, BVD-negative CD14- CD11c+ HLADR+ DCs were sorted into three subpopulations expressing high, intermediate, and low levels of CD64 and PD-L-1, exposed to HIV or Media conditions for 24H or 48H.

tag: exposure

value: HIV

tag: donor

tag: platerun


title: sort_b14

source_name: LO dendritic cell

value: MED


title: Chir_11-16_DIV16_rep2

description: Gene expression of ESC-derived neurons at 16 days of differentation in vitro treated with WNT and BMP inhibitors from day 0 to day 11 and with WNT agonist from day 11 to day 16

source_name: cell culture, CHIR 11, DIV16

tag: gender

tag: tissue

value: WNT and BMP inhibitors and WNT agonist


title: Chir_8-16_DIV16_rep1

description: Gene expression of ESC-derived neurons at 16 days of differentation in vitro treated with WNT and BMP inhibitors from day 0 to day 8 and with WNT agonist from day 8 to day 16

source_name: cell culture, CHIR 8-16, DIV16


title: sort_b19


title: sort_b18


title: Wibi_0-16_DIV16_rep2

description: Gene expression of ESC-derived neurons at 16 days of differentation in vitro treated with WNT and BMP inhibitors from day 0 to day 16

source_name: cell culture, WiBi 16, DIV16


title: A549 cells with GMDS knockdown, biological rep1

value: GMDS-shRNA


title: Chir_11-16_DIV16_rep1


title: Chir_8-16_DIV16_rep2


title: sort_b16

source_name: INT dendritic cell


title: Wibi_0-11_DIV16_rep1


title: LTAD_siControl

source_name: Gene expression data from LTAD cells treated with siControl

value: LTAD

value: prostate cancer


title: Mouse_Ventral-Telencephalon_E15

description: Gene expression of E15 mouse ventral telencephalon

source_name: embryonic ventral telencephalon E15

tag: strain

value: ventral telencephalon


title: sort_b11


title: sort_b17


title: LTAD_siPSF

source_name: Gene expression data from LTAD cells treated with siPSF

tag: cell type


title: Wibi_0-16_DIV16_rep1


title: siRacGAP1 rep3

city: Shanghai

first: Xiao-Mei

last: Yang

address: Room 419, Wenxuan Building of Medicine,  800 Dongchuan Road,  Shanghai

institute: Shanghai Cancer Institute

description:
gene expression in  RacGAP1 siRNA treated for 72 hours
15

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS5 algorithm, Affy packages in R.

source_name: SMMC7721, RacGAP1 siRNA treated

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

growth_protocol: SMMC7721 cells were incubated with DMEM/10% FBS

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit (Cat#740903, MN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: SMMC7721 cells were transfected with scrambled siRNA or RacGAP1 siRNA for 72 hours

tag: transfected with

value: RacGAP1 siRNA


title: Mouse_Hippocampus_E15

description: Gene expression of E15 mouse hippocampus

source_name: embryonic hippocampus, E15

value: hippocampus


title: Mouse_Cortex_E15

description: Gene expression of E15 mouse cortex

source_name: embryonic cortex, E15

value: cortex


title: Normal1

description: Normal sample

value: Male

value: Normal


title: sort_b12

tag: time point


title: sort_b15


title: sort_b10


title: sort_b9


title: sort_b8


title: sort_b6


title: sort_b7


title: sort_b4


title: sort_b2


title: sort_b1


title: siRacGAP1 rep1

description:
gene expression in  RacGAP1 siRNA treated for 72 hours
13

tag: cell line


title: siRacGAP1 rep2

description:
gene expression in  RacGAP1 siRNA treated for 72 hours
14


title: AB3832

status: Public on Dec 22 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: PA-GFP tumor

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

value: C57BL/6 PA-GFP

value: B16.F10 melanoma tumor

tag: selection marker

value: PA-GFP+

tag: infection

tag: treatment

value: Photoactivation of straight fibroblast area

tag: replicate id

tag: mouse age

value: 8-9 weeks


title: control rep3

description:
gene expression in scrambled siRNA treated for 72 hours
9

source_name: SMMC7721, scrambled siRNA treated

value: scrambled siRNA


title: AB3836

value: Photoactivation of curly fibroblast area


title: AB3834


title: AB3835


title: AB3830


title: control rep2

description:
gene expression in scrambled siRNA treated for 72 hours
8


title: NALM6-sh-Luc-rep2

first: Mei

last: Mei

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: Control probes were  pre-labeled with Cy3 on arrays by the manufacturer. Cy3 signal was not used in data processing.

hyb_protocol: HOA v5.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: HOA v5.1 The arrays were scanned by GenePix 4000B scanner (635nm power 100 PMT 520 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: NALM6 cells with luciferase knockdown (control)

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

tag: clone number

value: clone G5

tag: shRNA

value: Luc


title: AB3833


title: AB3829


title: NALM6-sh-PRMT5-rep2

source_name: NALM6 cells with PRMT5 knockdown


title: AB3831


title: AB3828


title: NALM6-sh-PRMT5-rep3


title: NALM6-sh-Luc-rep3


title: AB3825


title: sort_b5

tag: exposure

value: MED


title: AB3826


title: NALM6-sh-PRMT5-rep1


title: sort_b3

value: HIV

tag: donor


title: AB3827


title: control rep1

description:
gene expression in scrambled siRNA treated for 72 hours
7


title: NALM6-sh-Luc-rep1


title: Expression profile of M. longissimus [FCE_13]

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description:
FCE_13
Gene expression data derived from muscle tissue.

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays (Freeman et al. in BMC Biol 2012, 10:90). Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 was performed according to Affymetrix protocols.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: M. longissimus, low RFI

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using QIAzol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment, the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: rfi

value: low

tag: Sex

value: female

value: M. longissimus


title: Expression profile of M. longissimus [FCE_12]

description:
FCE_12
Gene expression data derived from muscle tissue.

tag: tissue


title: Expression profile of M. longissimus [FCE_06]

description:
FCE_06
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_01]

description:
FCE_01
Gene expression data derived from muscle tissue.

source_name: M. longissimus, high RFI

value: high


title: Expression profile of M. longissimus [FCE_07]

description:
FCE_07
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_02]

description:
FCE_02
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_08]

description:
FCE_08
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_20]

description:
FCE_20
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_15]

description:
FCE_15
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_14]

description:
FCE_14
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_10]

description:
FCE_10
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_18]

description:
FCE_18
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_05]

description:
FCE_05
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_19]

description:
FCE_19
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_04]

description:
FCE_04
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_17]

description:
FCE_17
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_03]

description:
FCE_03
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_11]

description:
FCE_11
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_09]

description:
FCE_09
Gene expression data derived from muscle tissue.


title: Expression profile of M. longissimus [FCE_16]

description:
FCE_16
Gene expression data derived from muscle tissue.


title: Satellite cells at day8, biological rep3

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip MouseGene2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: The data were normalized with RMA.

source_name: Satellite cells at day8

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 750 pg total RNA.

growth_protocol: Tibialis Anterior mouse muscle was injured with cardiotoxin and muscles were recovered before (day0) and days 2, 4, 8 post-injury. Muscles were minced, enzymatically digested.

extract_protocol: RNeasy Mini Kit (Qiagen).

treatment_protocol: Endothelial cells (ECs)  and Satellite cells (SCs) were isolated by FACS as CD45-Sca1+CD34+CD31+ and as CD45-Sca1-CD34+/loCD31-alpha7integrin+, respectively.

value: Tibialis anterior muscle

value: Day 8 post-injury

value: Satellite cells


title: Endothelial cells at day8, biological rep2

source_name: Endothelial cells at day8


title: Endothelial cells at day4, biological rep2

source_name: Endothelial cells at day4

value: Day 2 post-injury


title: Endothelial cells at day8, biological rep3


title: Satellite cells at day8, biological rep2

value: Day 4 post-injury


title: Satellite cells at day8, biological rep1


title: Endothelial cells at day8, biological rep1


title: Satellite cells at day4, biological rep3

source_name: Satellite cells at day4


title: Endothelial cells at day4, biological rep3


title: Satellite cells at day4, biological rep2

value: resting


title: Satellite cells at day4, biological rep1


title: Endothelial cells at day2, biological rep3

source_name: Endothelial cells at day2

value: Endothelial cells


title: Endothelial cells at day4, biological rep1


title: Satellite cells at day2, biological rep3

source_name: Satellite cells at day2


title: Satellite cells at day2, biological rep2


title: Endothelial cells at day2, biological rep2


title: Endothelial cells at day2, biological rep1


title: Satellite cells at day2, biological rep1


title: Endothelial cells at day0, biological rep3

source_name: Endothelial cells at day0


title: Tonsil squamous cell carcinoma patient 08, blood, before/no treatment

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

institute: Aalborg University Hospital

hyb_protocol: As described in the user guide, appendix A, of the The Encore™Biotin Module  (NuGEN)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing:
RMA normalized using R (v3.4.1), the affy-package (v1.54.0) from Bioconductor, and probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_22.0.0].
Probe set data extracted from custom CDF [Brainarray, huex10sthsensgcdf_22.0.0]

label: Biotin

source_name: Tonsil squamous cell carcinoma patient,Blood

label_protocol: The samples were prepared for hybridization to Affymetrix GeneChip Human Exon 1.0 ST Arrays using Affymetrix GeneChip WT Terminal Labeling and Controls Kit (P/N 901524)

growth_protocol: not applicable

extract_protocol: The frozen samples of the oral mucosa/mononuclear cells were homogenized using TRIzolR Reagent (InvitrogenTM) and total RNA was isolated using the mirVanaTM miRNA Isolation Kit (AmbionR/InvitrogenTM) (Life Technologies Corporation). RNA amplification was performed using the “AmbionR WT Expression Kit” (Applied BiosystemsR) starting with 100 ng total RNA and a TP Basic Thermocycler real time PCR instrument (BiometraR). Amplificatio System (NuGEN Technologies, Inc., San Carlos, CA)

treatment_protocol: Consecutive homo sapiens buccal mucosa  and peripheral blood secured from 8 patients with tonsil squamous cell carcinoma one biopsy and blood test before radiotherapy (RT), one biopsy and blood test after 5 days of RT (2 Gy each day) and three weeks after the last exposure to RT. Mononuclear cells were isolated from the blood.

tag: disease state

value: Tonsil squamous cell carcinoma

tag: mucositis grade

tag: person id

value: blood mononuclear cells

tag: patient received cisplatin treatment

value: yes

value: control

tag: time


title: Tonsil squamous cell carcinoma patient 09, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 09, mucosa, after 7 days of radio therapy

source_name: Tonsil squamous cell carcinoma patient,mucosa

value: oral buccal mucosa

value: no

value: radiotherapy (RT)

value: Day 5 after treatment


title: Satellite cells at day0, biological rep2

source_name: Satellite cells at day0

tag: time point

tag: cell type


title: Endothelial cells at day0, biological rep2


title: Satellite cells at day0, biological rep3


title: Tonsil squamous cell carcinoma patient 09, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 09, mucosa, Day 20 after last treatment

tag: treatment

value: Day 21 after treatment


title: Tonsil squamous cell carcinoma patient 09, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 08, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 08, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 09, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 09, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 09, blood, before/no treatment


title: Tonsil squamous cell carcinoma patient 08, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 08, mucosa, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 09, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 09, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 07, blood, before/no treatment


title: Endothelial cells at day0, biological rep1


title: Satellite cells at day0, biological rep1


title: Tonsil squamous cell carcinoma patient 08, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 08, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 07, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 07, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 08, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 08, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 08, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 07, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 07, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 07, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 07, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 07, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 07, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 07, mucosa, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 06, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 06, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 04, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 04, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 06, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 06, mucosa, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 06, blood, before/no treatment


title: Tonsil squamous cell carcinoma patient 04, blood, before/no treatment


title: Tonsil squamous cell carcinoma patient 06, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 06, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 05, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 05, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 05, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 06, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 06, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 05, blood, before/no treatment


title: Tonsil squamous cell carcinoma patient 03, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 03, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 04, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 05, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 05, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 01, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 01, mucosa, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 03, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 03, blood, after 7 days of radio therapy


title: Healthy control 11, blood, before/no treatment

source_name: Healthy control,Blood

value: Healthy control


title: Tonsil squamous cell carcinoma patient 06, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 03, blood, before/no treatment


title: Healthy control 11, mucosa, before/no treatment

source_name: Healthy control,mucosa


title: Tonsil squamous cell carcinoma patient 04, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 04, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 05, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 05, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 01, mucosa, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 01, mucosa, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 01, blood, Day 5 after treatment

description: Tonsil squamous cell carcinoma patient 01, blood, after 7 days of radio therapy


title: Tonsil squamous cell carcinoma patient 05, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 05, mucosa, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 01, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 01, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 01, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 03, mucosa, before/no treatment


title: Tonsil squamous cell carcinoma patient 03, blood, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 03, blood, Day 20 after last treatment


title: Tonsil squamous cell carcinoma patient 03, mucosa, Day 21 after treatment

description: Tonsil squamous cell carcinoma patient 03, mucosa, Day 20 after last treatment


title: Healthy control 10, mucosa, before/no treatment


title: Healthy control 10, blood, before/no treatment


title: Healthy control 08, mucosa, before/no treatment


title: Healthy control 06, mucosa, before/no treatment


title: Healthy control 06, blood, before/no treatment


title: Healthy control 01, blood, before/no treatment


title: Healthy control 05, mucosa, before/no treatment


title: Peripheral Blood_CD4_Control_miRNA_Sample 4

status: Public on Dec 21 2017

city: Bursa

first: Ferah

last: Budak

address: Gorukle

department: Medical Faculty

country: Turkey

institute: Uludag University

description: microRNA expression in control_sample 4

hyb_protocol: Spike Kit (Agilent, UK) and Agilent microRNA Hybridization Kit (Agilent, UK) were used to hybridize into Human miRNA Microarray, Release 19.0, 8x60K(v19) microarray slides (Agilent, UK)

scan_protocol: Human miRNA Microarray, Release 19.0, 8x60K(v19) microarray slides (Agilent, UK) scanned using Nimblegen MS200 array scanner.

data_processing:
The TIFF image files obtained were processed using Agilent Feature Extraction software to extract raw data and obtain QC reports.
The data of the samples that pass QC parameters were subject to quantile normalization and analyzed using GeneSpring GX (Agilent, UK) 13.0 software after which microRNA’s with P values of >0,05 and Fold change values of >2 and <-2 were determined to be statistically significant. A data matrix with all normalized singals including control probes is available on the series record. The data matrix does not contain signal for control probes.

source_name: Peripheral Blood

label_protocol: MicroRNAs from RNA samples were marked with Cy3 fluorescent dye while transforming them into cDNA using 100ng RNA Agilent miRNA labeling Kit (Agilent, UK)

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from the 20 ml blood samples obtained from the patients in acute, chronic and healthy control groups via intensity gradient centrifuge method with Ficoll (Biochrom, Germany). PBMC fraction of patient whole blood was stained using CD4-FITC, CD8 PE, CD3 PerCP (Beckton Dickinson (BD), Biosciences, USA) antibodies to distinguish the CD4+ T cells for FACS. Antibodies were supplied by BD Biosciences, Inc. (USA) and used at the minimal saturating concentration, determined by titration prior to the experiment. PBMCs were stained with the antibody combination for 20 minutes at room temperature, washed twice and resuspended in PBS supplemented with 1% FCS. CD4+ T cells were sorted on FACSAria (BD Biosciences cell-sorter, USA) and kept at 4°C throughout sorting. Live PBMCs were gated based on forward versus side scatter profiles, followed by CD3+ based gating for T lymphocyte identification. The CD3+ positive population was subdivided by CD8/CD4 expression and used for the identification of CD4+ (CD4+, CD8-) T cells. Purity was determined for CD4+ T cells isolated by FACS for CD4+ T cells (99.8% purity). Sorted cells were immediately centrifuged and pellets were resuspended in TriPure Isolation Reagent (Roche, Germany) at -80°C until use. miRNeasy Kit (Qiagen, Germany) was used in accordance with the manufacturer protocol for the total RNA isolation from the isolated CD4+ T cells. The measurements of concentrations and purities were carried out using Nanodrop (Thermo Scientific, USA). RNA qualities were determined in Agilent Bioanalyzer (Agilent, UK) device using Agilent RNA 6000 Nano Kit.

value: whole blood

value: CD4 T cell

tag: diagnosis

value: healthy control

tag: gender

value: female

tag: age


title: Peripheral Blood_CD4_Control_miRNA_Sample 3

description: microRNA expression in control_sample 3

value: male


title: Peripheral Blood_CD4_Control_miRNA_Sample 5

description: microRNA expression in control_sample 5


title: Healthy control 05, blood, before/no treatment


title: Healthy control 08, blood, before/no treatment


title: Healthy control 04, blood, before/no treatment


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 6

description: microRNA expression in chronic brucella infection_sample 6

value: chronic brucellosis


title: Healthy control 07, mucosa, before/no treatment


title: PVTT/hPCL3s

first: yuezhen

last: deng

address: 320 Yueyang Road, Shanghai, China

institute: The Chinese Academy of Science

description: gene expression data from PVTT overexpressing hPCL3s cell

hyb_protocol: Following fragmentation, RNA were hybridized, washed and stained according to the manufacture's instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: PVTT overexpressing hPCL3s cells (transcripts)

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

growth_protocol: Control palsmids and hPCL3s expression vectors was forced to express in PVTT cells, and obtained the PVTT/con and PVTT/hPCL3s cells.

extract_protocol: TRIZOL extraction of total RNA was performed according to the manufacture's instructions.

treatment_protocol: Cells grew to about 70% confluence and was harvested with TRIZOL.

value: PVTT cells stably expressing the hPCL3s vector


title: Peripheral Blood_CD4_Control_miRNA_Sample 6

description: microRNA expression in control_sample 6


title: Peripheral Blood_CD4_Control_miRNA_Sample 7

description: microRNA expression in control_sample 7


title: Healthy control 03, blood, before/no treatment


title: Peripheral Blood_CD4_Control_miRNA_Sample 8

description: microRNA expression in control_sample 8


title: Peripheral Blood_CD4_Control_miRNA_Sample 1

description: microRNA expression in control_sample 1


title: Healthy control 04, mucosa, before/no treatment


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 8

description: microRNA expression in chronic brucella infection_sample 8


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 7

description: microRNA expression in chronic brucella infection_sample 7


title: Healthy control 01, mucosa, before/no treatment


title: Healthy control 07, blood, before/no treatment


title: Healthy control 03, mucosa, before/no treatment


title: PVTT/con

description: gene expression data from PVTT control cell

source_name: PVTT control cells (transcripts)

value: PVTT cells stably expressing the control vector


title: Peripheral Blood_CD4_Control_miRNA_Sample 2

description: microRNA expression in control_sample 2


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 4

description: microRNA expression in chronic brucella infection_sample 4


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 5

description: microRNA expression in chronic brucella infection_sample 5


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 3

description: microRNA expression in chronic brucella infection_sample 3


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 2

description: microRNA expression in chronic brucella infection_sample 2


title: 9 dpi fsr1 mutant 6

city: College Station

first: Man

middle: S

last: Kim

state: TX

address: 202N  LF Peterson, Texas A&M Univ., Plant Pathology & Microbiology

department: Plant Pathology & Microbiology

institute: Texas A&M University

data_processing:
Illumina’s HCS 1.5.15.1 and RTA 1.13.48.0 were used for basic processing such as quality prefiltering, base calling, and uncertainty assessment
RNA sequencing reads were aligned to 'Fusarium verticillioides strain 7600' using Bowtie2
Reads were counted with Samtools
Genome_build: http://fungi.ensembl.org/Fusarium_verticillioides/Info/Index
Supplementary_files_format_and_content: text file with read counts

organism:
Zea mays
Fusarium verticillioides

source_name: 9 dpi fsr1 mutant

growth_protocol: Maize inbred B73 stalks were inoculated with F. verticillioides  wild type and fsr1 mutant and incubated for 3, 6, d days

extract_protocol:
For each sample, sectioning was performed on at least three independent stalk samples from each stage of infection, and isolated tissues were pooled for RNA extraction with Trizol reagent (Invitrogen).
Standard QA/QC procedure for RNA samples was implemented and library construction was performed at the Texas A&M AgriLife Research Genomics and Bioinformatics Service (College Station, TX).

treatment_protocol: Fungal spores were inculated directed into maize stalks through sterile needle wonds

tag: host

value: maize

tag: maize strain

value: maize (B73)

value: Fungal mycelia and maize stalk mixture

tag: fungal genotype

value: fsr1 mutant

tag: time (dpi)


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 4

description: microRNA expression in acute brucella infection_sample 4

value: acute brucellosis


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 5

description: microRNA expression in acute brucella infection_sample 5


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 3

description: microRNA expression in acute brucella infection_sample 3


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 7

description: microRNA expression in acute brucella infection_sample 7


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 2

description: microRNA expression in acute brucella infection_sample 2


title: 9 dpi fsr1 mutant 5


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 6

description: microRNA expression in acute brucella infection_sample 6


title: 9 dpi fsr1 mutant 4


title: 9 dpi fsr1 mutant 3


title: Naïve_CAR-T2

city: Bethesda

first: Stefano

last: Marenco

state: MD

address: Building 10, Room 4N306

institute: National Institute of Mental Health

description:
Gene expression data from day 5 CAR T cell derived from the Naïve mouse
Naïve_mouse_2_CAR-T

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

data_processing: The array data were analyzed with Microarray Suite using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Day 5 CAR T cell derived from Naïve mouse's spleen

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

extract_protocol: TRNA were extracted with Rneasy MimiKit (Qiagen) following manufactory's protocol.

treatment_protocol: A single cell suspension was made from freshly harvested mouse spleen and T cells were enriched using mouse CD3+ T-cell enrichment column (R&D, Minneapolis, MN) following the manufactures’ protocol. T cells were activated for 24 hours with Mouse T-Activator CD3/CD28 Dynabeads (Life Technologies, Grand Island, NY) in the presence of IL-15 (10U/ml) and IL-7 (10ng/ml) in complete mouse media (CMM). Activated T cells were then transduced with the mCD19 retroviral supernatant harvested from the stable producer line. Dynabeads were removed 24 hours following the 2nd spinoculation. The transduced T cells were harvested after 5 days. RNA was extracted from these T cells and used for microarray hybridization and global gene expression on Affymetrix chips (mouse Gene ST 1.0). The array results were further analyzed for differential gene expression between samples

tag: strain

value: Naïve

value: CAR T cell


title: Peripheral Blood_CD4_Chronic Brucellosis_miRNA_Sample 1

description: microRNA expression in chronic brucella infection_sample 1

tag: tissue


title: Tumor_CAR-T2

description:
Gene expression data from day 5 CAR T cell derived from the Tumor Bearing mouse
ALL_mouse_2_CAR-T

source_name: Day 5 CAR T cell derived from Tumor Bearing mouse's spleen

tag: disease state

value: Tumor Bearing


title: Peripheral Blood_CD4_Acute Brucellosis_miRNA_Sample 1

description: microRNA expression in acute brucella infection_sample 1


title: brain_CA-ROSC_120min_rep1

city: GUANGZHOU

first: rong

last: liu

address: YANJIANGXILU NO.151

institute: GUANGZHOU MEDICAL UNIVERSITY

description: gene expression post-cardiac arrest 120min in brain

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat lncRNA(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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: Animals were housed in a pathogen-free laboratory at 20-22°C with a 10 h light and 14 h dark cycle

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: After fasting overnight (with access to water), 5 healthy male Wistar rats were anesthetized by intraperitoneal pentobarbital injection (30 mg/kg; Sigma, Natick, MA, USA). Ventricular fibrillation (VF) was induced as described previously(14, 15). VF was successfully induced by alternating current (50 Hz, 6 V) for 10 s with external transthoracic needles. After successful induction of VF, the ventilator was disconnected. Eight minutes after VF, manual chest compressions were performed on the rats along with mechanical ventilation. Rats were maintained for 2 h after successful ROSC (CA, n = 5). Four sham-operated rats served as the blank control (BC, n = 4)

value: Wistar

value: Male

value: CA

value: cerebral cortices


title: 6 dpi fsr1 mutant 6

source_name: 6 dpi fsr1 mutant


title: brain_CA-ROSC_120min_rep2


title: Tumor_CAR-T1

description:
Gene expression data from day 5 CAR T cell derived from the Tumor Bearing mouse
ALL_mouse_1_CAR-T


title: brain_blank control_rep2

description: gene expression in blank control brain

source_name: brain,blank control,replicate 2

value: control


title: brain_blank control_rep3

description: gene expression in blank control brain

source_name: brain,blank control,replicate 3


title: brain_CA-ROSC_120min_rep3


title: Naïve_CAR-T1

description:
Gene expression data from day 5 CAR T cell derived from the Naïve mouse
Naïve_mouse_1_CAR-T


title: Naïve_CAR-T3

description:
Gene expression data from day 5 CAR T cell derived from the Naïve mouse
Naïve_mouse_3_CAR-T


title: brain_CA-ROSC_120min_rep5


title: brain_blank control_rep1

description: gene expression in blank control brain

source_name: brain,blank control,replicate 1


title: 9 dpi fsr1 mutant 2


title: Tonsil squamous cell carcinoma patient 01, blood, before/no treatment

value: Tonsil squamous cell carcinoma

tag: mucositis grade

value: blood mononuclear cells

value: no


title: brain_blank control_rep4

description: gene expression in blank control brain

source_name: brain,blank control,replicate 4


title: 6 dpi fsr1 mutant 1


title: 3 dpi fsr1 mutant 3

source_name: 3 dpi fsr1 mutant


title: 6 dpi fsr1 mutant 5


title: 9 dpi fsr1 mutant 1


title: 6 dpi fsr1 mutant 4


title: 3 dpi fsr1 mutant 2


title: brain_CA-ROSC_120min_rep4


title: 3 dpi fsr1 mutant 6


title: 6 dpi fsr1 mutant 3


title: 3 dpi fsr1 mutant 4


title: 6 dpi fsr1 mutant 2


title: 3 dpi fsr1 mutant 1


title: 9 dpi wild type 4

source_name: 9 dpi wild type

value: wildtype


title: 9 dpi wild type 3

value: maize


title: 9 dpi wild type 6

value: maize (B73)


title: 6 dpi wild type 6

source_name: 6 dpi wild type

value: Fungal mycelia and maize stalk mixture


title: 6 dpi wild type 4


title: 3 dpi fsr1 mutant 5

value: fsr1 mutant


title: ATAC-seq_Ikzf2_KO_2

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq: Alignment by STAR version 2.3.0
RNA-seq: Gene quantification by htseq-count and RefSeq gene annotation
ATAC-seq: Alignment by bowtie2 version 2.2.5
ATAC-seq: Duplicate removal by picard MarkDuplicates version 1.140
ATAC-seq: Peak calling by macs2 version 20160309 with the parameters -p 1e-2 --nomodel --shift -100 --extsize 200 --keep-dup all
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Gene quantification txt file
Supplementary_files_format_and_content: ATAC-seq: Signal track bigWig file

source_name: Leukemic stem cells from Ikzf2Δ/Δ mice

extract_protocol:
RNA extraction using TRIzol and RNeasy RNA extraction kit. Samples were prepared with a standard Illumina kit using the TruSeq RNA SamplePrep Guide (Illumina). For ATAC-seq samples nuclei were subjected to transposase reaction (Illumina Nextera DNA Sample Preparation Kit) following manufacturer’s instructions and DNA was purified using the Agencourt AMPure XP beads (Beckman Coulter).
RNA libraries were prepared for sequencing using standard Illumina protocols. For ATAC-seq samples, DNA was barcoded and library was generated (using NEBNext Q5 Hot Start HiFi PCR mix and Nextera primers) for sequencing.

treatment_protocol: Frozen leukemic bone marrow cells were thawed in 2% FBS/ RPMI media for sorting

value: MLL-AF9 transformed leukemic bone marrow cells

tag: isolation of cell population

value: c-KIT High sorted

tag: genotype

value: Ikzf2 KO


title: 9 dpi wild type 5


title: 9 dpi wild type 1


title: 6 dpi wild type 3


title: 6 dpi wild type 2


title: 3 dpi wild type 5

source_name: 3 dpi wild type


title: 3 dpi wild type 4


title: 9 dpi wild type 2


title: ATAC-seq_Ikzf2_WT_2

source_name: Leukemic stem cells from Ikzf2f/f mice

value: Ikzf2 WT


title: 3 dpi wild type 6


title: ATAC-seq_Ikzf2_WT_1


title: 6 dpi wild type 5


title: 6 dpi wild type 1


title: RNA-seq_Ikzf2_KO_2


title: ATAC-seq_Ikzf2_KO_1


title: 3 dpi wild type 2


title: 3 dpi wild type 1


title: RNA-seq_Ikzf2_WT_2


title: RNA-seq_Ikzf2_KO_1


title: 3 dpi wild type 3


title: RNA-seq_Ikzf2_WT_1


title: Male_LFD_Replicate3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression data from colon epithelium

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing:
Data was obtained using the GeneChip® Command Console software.
RMA

source_name: colon epithelium from mice on the LFD

label_protocol: Two hundred and fifty nanograms (250 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: Male and female C57Bl6 mice were purchased from JAX.

extract_protocol: Total RNA was extracted by Qiagen Rneasy mini kit according to the manufacturer's instructions.

treatment_protocol: One week acclimation after shipment, mice were put on the HFD and LFD for 20 weeks. Colon epithelium was collected.

value: male

value: colon epithelium


title: female_HFD_Replicate3

source_name: colon epithelium from mice on the HFD

value: female


title: female_LFD_Replicate3


title: female_LFD_Replicate1


title: Male_LFD_Replicate1


title: female_LFD_Replicate2


title: Male_LFD_Replicate2


title: female_HFD_Replicate1


title: female_HFD_Replicate2


title: Male_HFD_Replicate3


title: HaCaT cells_30 μM apratyramide_3 h_rep1

city: Gainesville

first: Hendrik

last: Luesch

address: 1345 center drive

institute: University of Florida

hyb_protocol: The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix Human Transcriptome 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned using a GeneChip 7G Scanner.

data_processing: Expression data was generated using the limma package in R/Bioconductor, with RMA normalization.

source_name: Human keratinocyte cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip WT PLUS Reagent Kit).

growth_protocol: Human keratinocyte HaCaT cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37 ºC humidified air and 5% CO2.

extract_protocol: RNA was isolated at each time point using the Qiagen RNeasy kit

treatment_protocol: A total of 2 x 105 HaCaT cells were seeded in 6-well plates and incubated further for 24 h in growth medium prior to treatment.

value: 30 μM apratyramide for 3 h

tag: cells

value: Human keratinocyte cells


title: Male_HFD_Replicate2


title: HaCaT cells_DMSO_12 h_rep2

value: 0.3% DMSO for 12 h


title: HaCaT cells_30 μM apratyramide_3 h_rep2


title: HaCaT cells_30 μM apratyramide_12 h_rep2

value: 30 μM apratyramide for 12 h


title: Male_HFD_Replicate1


title: J3_WT_3

status: Public on Dec 20 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

description: 15_J3_3g VR_(MoGene-2_0-st).CEL

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Mouse Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V17 was used for annotation.

label_protocol: 100 ng of total RNA is reverse transcribed  following the Ovation picoSL V2 protocol (Nugen). Briefly, the resulting double stranded cDNA is used to produce single stranded DNA using SPIA® technology. This cDNA  is fragmented and biotin labelled before hybridization.

growth_protocol: Muscle cells were cultivated on plastic dishes coated by 1mg/mL matrigel in growth medium ((DMEM/F12, 2% UltroserG, 20% fetal calf serum) for 24 , and induced to differentiate in differentiation medium (DMEM/F12, 2% horse serum)

extract_protocol: Qiagen RNEasy minikit  and DNAse treatment

treatment_protocol: Muscle cells  are transduced  twice with adenoviruses Ad-GFP (Srf WT)  and Ad-Cre-GFP (Srf KO. ). Two days after the first transduction, GFP-positive cells were sorted with BD FACSAriaIII. Cells were cultivated on plastic dishes coated with 1 mg/mL matrigel in  growth medium (DMEM/F12, 2% UltroserG, 20% fetal calf serum) for 24 h. Total mRNA were purified using Qiagen RNeasy minikit and DNAse treatment from cells at Day 0 (before changing the cell medium to differentiation medium) and at day 1 and 3, after the differentiation induction with 2% horse serum-supplemented medium. The experiments were done in triplicate

value: muscle cells

tag: transduced with

value: adenoviruses Ad-GFP (Srf WT)

tag: timepoint

value: day 3 (J3) of differentiation


title: HaCaT cells_DMSO_3 h_rep1

tag: treatment

value: 0.3% DMSO for 3 h


title: HaCaT cells_30 μM apratyramide_12 h_rep1


title: J1_KO_2

description: 11_J1_2c VR_(MoGene-2_0-st).CEL

tag: cell type

value: adenoviruses Ad-Cre-GFP (Srf KO)

value: day 1 (J1) of differentiation


title: HaCaT cells_DMSO_3 h_rep2


title: J1_KO_1

description: 10_J1_1c VR_(MoGene-2_0-st).CEL


title: HaCaT cells_DMSO_12 h_rep1


title: J3_KO_2

description: 17_J3_2c VR_(MoGene-2_0-st).CEL


title: J3_KO_1

description: 16_J3_1c VR_(MoGene-2_0-st).CEL


title: J3_KO_3

description: 18_J3_3c VR_(MoGene-2_0-st).CEL


title: J3_WT_1

description: 13_J3_1g VR_(MoGene-2_0-st).CEL


title: J3_WT_2

description: 14_J3_2g VR_(MoGene-2_0-st).CEL


title: J1_WT_3

description: 9_J1_3g VR_(MoGene-2_0-st).CEL


title: J0_KO_3

description: 6_J0_3c VR_(MoGene-2_0-st).CEL

value: day 0 (J0) of differentiation


title: J1_WT_1

description: 7_J1_1g VR_(MoGene-2_0-st).CEL


title: F1-GDM4

city: Hangzhou

first: Jun

last: Ren

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
bcl2fastq  version 2.1 software used for basecalling with default parameters
Raw reads were filtered by trim_galore version 0.3.7,with parameters:-q 25，--stringency 5，--length 50
reads were aligned to the mm10 genome assembly using Bsmap，version 2.74，with parameters：-r 0，-p 8，-v 0.02
Differential Methylation was indentied by DSS version 2.10.0, with parameters, delta=0.05, p.threshold=0.05,minlen=50, minCG=3 , dis.merge=50, pct.sig=0.5
Genome_build: mm10
Supplementary_files_format_and_content: compressed tab-delimited text files include each CpGs information: chromosome,pos,strain,C context type,C context details,mC reads,non-mC reads, The binomial distribution expected value, p-value,corrected q-value

source_name: primordial germ cells

extract_protocol:
at day 13.5 of pregnancy, pregnant mice were sacrificed, fetus were dissected under anatomical lens to get male genital ridge, PGCs were released by puncturing genital ridge.
Briefly, 5 μg genomic DNA was digested with the methylation insensitive restriction enzyme MspI (New England Biolabs, Beverly, MA, USA). The QIAGEN Mini Purification kit was used to purify the digested products. Ends of each restriction fragment were filled in and a 3’-adenosine was added. Methylated paired-end Illumina adapters were ligated to the ends of the DNA fragments using T4 DNA Ligase. Fragments between 170 bp and 340 bp were purified by agarose gel extraction. The purified fragments were treated with sodium bisulfite and then amplified by PCR. The final PCR products were sequenced on HiSeq2500 (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Normal virgin female ICR mice at 8 week of age were mated with normal males overnight. Onset of pregnant was determined by the presence of a vaginal plug at the following morning and defined as D0.5 of gestation. Gestational mice were randomly divided into control group and intrauterine hyperglycemia group (GDM group). After 8-h fasting, GDM group mice were treated with a single intraperitoneal injection of streptozotocin (STZ; Sigma, St. Louis, MO) in 0.1 mmol/L citrate buffer (pH 4.5) at a dose of 150 mg/kg body weight. Mice in the control group received an equal volume of citrate buffer. On D3.5 of pregnancy, blood glucose concentration was measured via the tail vein using a glucometer (Roche Diagnostics Accu-Chek, Mannheim, Germany). Diabetes was defined as a glucose level between 14 and 19 mM.

tag: genotype/variation

tag: development stage

value: day 13.5 fetal mice

value: ICR


title: F1-GDM1


title: F1-GDM3


title: F1-GDM2


title: control4

value: control


title: J0_KO_2

description: 5_J0_2c VR_(MoGene-2_0-st).CEL


title: J0_KO_1

description: 4_J0_1c VR_(MoGene-2_0-st).CEL


title: J1_KO_3

description: 12_J1_3c VR_(MoGene-2_0-st).CEL


title: J1_WT_2

description: 8_J1_2g VR_(MoGene-2_0-st).CEL


title: J0_WT_3

description: 3_J0_3g VR_(MoGene-2_0-st).CEL


title: control3


title: control2


title: control1


title: Huh7.5 - HCV - BA - bio rep 3

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

description: BA 3

hyb_protocol: RNA were hybridized in a Advalytix Slidebooster SB400 hybridization station at 56°C overnight

scan_protocol: The arrays were scanned on a GenePix 4200A Scanner (Molecular Devices).

data_processing: Data extraction and image analysis were performed using GenePix Pro Software (Molecular Devices).  Replicate spots from same array were averaged.  Missing spots or high background portions of arrays were flagged manually and omitted from downstream analysis.  Quantile normalization was performed using the preprocessCore library of the Bioconductor package in the R environment on solely the human microRNA probe-associated signal intensities.

label: 550 Oyster

source_name: Huh7.5 hepatoma cells

label_protocol: Total RNA (3 μg) was labelled using the Oyster-550 based Flashtag RNA labelling kit (Genisphere)

growth_protocol: Huh7.5 cells were grown in DMEM supplemented with 5% FCS, and pen/strep.

extract_protocol: mirVana miRNA isolation kit (Ambion) was used to extract total RNA, in accordance with the manufacturer's instructions.

treatment_protocol: Huh7.5 cells were mock infected or infected with JFH1T HCV (MOI = 0.1).  48 hours post-transfection, cells were treated with 25 μM 2-chloro-5-nitro-N-(pyridyl)benzamide .  24 hours post-treatment, total RNA was isolated from cells.

tag: cell line

value: Huh7.5 hepatoma cells

tag: infection

value: JFH1 strain (JFH-1T; MOI = 0.1) of hepatitis C virus

value: BA


title: Huh7.5 - HCV - BA - bio rep 2 - tech rep 1

description: BA 2-1


title: Huh7.5 - HCV - BA - bio rep 1

description: BA 1


title: miR-7 mimic

description:
Gene expression data from Huh7.5 cells transfected with miR-7 mimic
miR-7-1

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed with the Affymetrix Expression Console using Affymetrix default analysis settings (RMA) and Affymetrix Transcriptome Analysis Console.

source_name: Huh7.5 cells transfected with miR-185 mimic

label_protocol: Biotinylated cDNA were prepared from 400 ng RNA using the Affymetrix WT Plus Kit.

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% FBS, 1X non essential amino acids, and pen/strep.

extract_protocol: 72 hours post-transfection, total RNA was isolated using Qiagen RNeasy Kit, as per manufacturer's protocol.

treatment_protocol: Huh7.5 cells were transfected with 100 nM control or miR-7-5p mimics (Ambion) using Lipofectamine RNAiMax, as per manufacturer's instructions.

tag: transfection

value: miR-7 mimic


title: Ctrl mimic

description:
Gene expression data from Huh7.5 cells transfected with control mimic
Ctrl1


title: J0_WT_1

description: 1_J0_1g VR_(MoGene-2_0-st).CEL


title: aSTAT1_STAT1WT_STIM_1_CHIP

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)

source_name: splenic NK cells

extract_protocol:
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: chip antibody

value: anti-STAT1 (Santa Cruz, sc-592, clone M-22, lot# F1312)

tag: condition

value: IFNa

value: splenic NK cells


title: aSTAT1_STAT1WT_STIM_2_CHIP


title: Huh7.5 - HCV - BA - bio rep 2 - tech rep 2

description: BA 2-2


title: FC(IV:XV:V:VII)CEN4_rep1

city: Barcelona

first: Marco

last: Di Stefano

address: Carrer Baldiri Reixac, 4

country: Spain

institute: CNAG-CRG

data_processing:
The file with the ORF orf_coding_all.fasta was downloaded from http://downloads.yeastgenome.org/sequence/S288C_reference/orf_dna/
The index was obtained using Kallisto with the command kallisto index -i orf_coding_all.idx orf_coding_all.fasta
The quantification was done using Kallisto with the command kallisto quant -i orf_coding_all.idx -o output -b 100 read1_file.fastq.gz read2_file.fastq.gz
Genome_build: S288C
Supplementary_files_format_and_content: TAB-separated values. Headers: target_id length eff_length est_counts tpm

organism: Saccharomyces cerevisiae

source_name: yeast culture

extract_protocol:
total RNA was extracted from fresh pellets using a RiboPure Yeast Kit (Ambion). RNA concentrations were determined using a NanoDrop 1000 (Thermo Scientific), while quality and integrity was checked using a Bioanalyzer 2100 (Agilent Technologies).
llumina TruSeq Stranded mRNA Sample Prep kit

treatment_protocol: cells were grown in YPD and harvested in mid-log phase.

tag: strain

value: Strain 1788

tag: batch

value: Batch 2

tag: tissue

value: yeast culture


title: FC(IV:XV:V:VII)CEN4_rep3

value: Batch 3


title: FC(IV:XV:V:VII)CEN4_rep2


title: FC(IV:XV:V:VII)CEN7_rep3

value: Strain 1793


title: FC(IV:XV:V:VII)CEN7_rep2


title: FC(IV:XV:V:VII)CEN7_rep1


title: FC(IV:XV:XVI)CEN16_rep2

value: Strain 1380


title: FC(IV:XV:XVI)CEN4_rep3

value: Strain 1388


title: FC(IV:XV:XVI)CEN16_rep4


title: FC(IV:XV:XVI)CEN4_rep1

value: Batch 1


title: tumor from HN1L siRNA-treated mouse #4814 [mRNA]

city: Houston

first: Jenny

last: Chang

address: 6670 Bertner Ave.

department: Houston Methodist Cancer Center

institute: Houston Methodist Hospital

description: mRNA expression data from TNBC tumor sample of HN1L-siRNA treated mouse model BCM2665

hyb_protocol: Affymetrix Hybridization,cocktail assembly and Fluidics protocol for Standard Array( 49 format) with minor modifications provided by NUGEN's FL-Ovation cDNA biotin module V2 protocol

scan_protocol: Genechips were scanned using Affymetrix Genechip Scanner model 7G, Genechip command console (AGCC)software provided instrument control, data acquisition and first order data anaylsis

data_processing: The array data were evaluated using the commercial software suite, Partek Genomics Suite. Specifically, data were normalized by using the RMA (robust multichip averaging) method. Gene-expression levels were analyzed on a logarithmic scale. ANOVA was used to identify differentially expressed genes. Genes with P value less than 0.05 in each comparison were selected for further functional and pathway analyses by Ingenuity Pathway Analysis (IPA) tools.

source_name: patient-derived xenograft tumor from HN1L siRNA-treated mouse #4814

label_protocol: Biotinylated cDNA were prepared according to Ovation Pico WTA system V2 and FL-Ovation cDNABtiotin Module V2 from NUGEN Technologies

growth_protocol: In docetaxel-resistant BCM2665 PDX xenografts, tumors were transplanted into the mammary fat pad of SCID-Beige mice. Mice were randomized into 5 groups when tumor volume reached 150-200mm3: (0)scrambled siRNA, (1)HN1L siRNA.

extract_protocol: Extraction of total RNA from each frozen tumor sample was performed using RNeasy Mini kit from Qiagen following manufacturer instruction.

treatment_protocol: Groups (0) and (1) (n=10) were treated with 5 µg/mouse DOPC nanoliposomal siRNA IP injection twice a week for 3 weeks. Mice were sacrificed on day 21. Tumors were harvested and snap frozen.

value: breast cancer tumor tissue

value: Triple-negative breast cancer

tag: xenograft type


title: tumor from HN1L siRNA-treated mouse #4810 [mRNA]

source_name: patient-derived xenograft tumor from HN1L siRNA-treated mouse #4810

tag: genotype


title: FC(IV:XV:XVI)CEN16_rep3


title: FC(IV:XV:XVI)CEN4_rep4


title: tumor from scrambled siRNA-treated mouse #4959 [mRNA]

description: mRNA expression data from TNBC tumor sample of scramble-siRNA treated mouse model BCM2665

source_name: patient-derived xenograft tumor from scrambled siRNA-treated mouse #4959


title: J0_WT_2

description: 2_J0_2g VR_(MoGene-2_0-st).CEL

value: muscle cells

value: adenoviruses Ad-GFP (Srf WT)

value: day 0 (J0) of differentiation


title: tumor from HN1L siRNA-treated mouse #4950 [mRNA]

source_name: patient-derived xenograft tumor from HN1L siRNA-treated mouse #4950


title: tumor from scrambled siRNA-treated mouse #4989 [mRNA]

source_name: patient-derived xenograft tumor from scrambled siRNA-treated mouse #4989


title: tumor from HN1L siRNA-treated mouse #4809 [mRNA]

source_name: patient-derived xenograft tumor from HN1L siRNA-treated mouse #4809


title: tumor from scrambled siRNA-treated mouse #4967 [mRNA]

source_name: patient-derived xenograft tumor from scrambled siRNA-treated mouse #4967


title: FC(IV:XV:XVI)CEN16_rep1


title: tumor from scrambled siRNA-treated mouse #4817 [mRNA]

source_name: patient-derived xenograft tumor from scrambled siRNA-treated mouse #4817


title: tumor from HN1L siRNA-treated mouse #4984 [mRNA]

source_name: patient-derived xenograft tumor from HN1L siRNA-treated mouse #4984


title: tumor from scrambled siRNA-treated mouse #4819 [mRNA]

source_name: patient-derived xenograft tumor from scrambled siRNA-treated mouse #4819


title: FC(IV:XV:V)CEN4_rep2

value: Strain 1387


title: FC(IV:XV:XVI)CEN4_rep2


title: FC(IV:XV:V)CEN4_rep4


title: FC(IV:XV:V)CEN4_rep1


title: FC(IV:XV:V)CEN5_rep3

value: Strain 1379


title: FC(IV:XV:V)CEN4_rep3


title: FC(IV:XV)CEN15_rep3

value: Strain 1138


title: FC(IV:XV)CEN15_rep2


title: FC(IV:XV:V)CEN5_rep4


title: FC(IV:XV:V)CEN5_rep1


title: FC(IV:XV)CEN15_rep4


title: FC(IV:XII)CEN12_rep1

value: Strain 524


title: FC(IV:XV)CEN4_rep2

value: Strain 1228


title: FC(IV:XII)CEN4_rep3

value: Strain 527

value: Batch 2


title: FC(IV:XII)CEN12_rep3

value: yeast culture


title: FC(IV:XV)CEN15_rep1


title: wildtype_rep3

value: Strain 409


title: FC(IV:XII)CEN12_rep4

value: Batch 3


title: FC(IV:XV:V)CEN5_rep2


title: FC(IV:XII)CEN4_rep1


title: FC(IV:XV)CEN4_rep4


title: FC(IV:XII)CEN4_rep2


title: FC(IV:XII)CEN12_rep2


title: FC(IV:XV)CEN4_rep3


title: FC(IV:XV)CEN4_rep1


title: FC(IV:XII)CEN4_rep4


title: wildtype_rep2


title: wildtype_rep1


title: wildtype_rep4


title: tumor from HN1L siRNA-treated mouse #4814 [miRNA]

description: miRNA expression data from TNBC tumor sample of HN1L-siRNA treated mouse model BCM2665

hyb_protocol: hybridization,washing and staining were done following Affymetrix protocol for Genechip miRNA 4.0 arrays.

scan_protocol: Scanning was done on Affymetrix Genechip Scanner model 7G, Affymetrix Genechip command console(AGCC) software was used for instrument control, data acquisition and quality control.

data_processing: Expression values were processed and normalized using the affy library in R statistical software. Only human probes were isolated, from the multispecies miRNA profiling by the miRNA array 4.0, for the purpose of the analysis. Differential expression analysis was then performed using limma package in R.  The most significantly differentially expressed miRNAs were selected based on a cut off log fold change > 1 and FDR < 0.2.

label_protocol: Biotinylated miRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Extraction of miRNA from each frozen tumor sample was performed using miRNeasy Mini kit from Qiagen following manufacturer instruction.


title: tumor from HN1L siRNA-treated mouse #4984 [miRNA]


title: tumor from HN1L siRNA-treated mouse #4950 [miRNA]


title: tumor from HN1L siRNA-treated mouse #4810 [miRNA]


title: tumor from scrambled siRNA-treated mouse #4819 [miRNA]

description: miRNA expression data from TNBC tumor sample of scramble-siRNA treated mouse model BCM2665


title: tumor from scrambled siRNA-treated mouse #4989 [miRNA]


title: tumor from scrambled siRNA-treated mouse #4967 [miRNA]


title: tumor from scrambled siRNA-treated mouse #4959 [miRNA]


title: tumor from HN1L siRNA-treated mouse #4809 [miRNA]


title: tumor from scrambled siRNA-treated mouse #4817 [miRNA]


title: Uninfected AGS cells_1_mRNA

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

description: mRNA expression of uninfected AGS cells

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242 was used

scan_protocol: Scanned Using Agilent Scanner

data_processing: Percentile Shift Normalization to the 75th percentile

source_name: Uninfected AGS cells, mRNA, replicate 1

label_protocol: Agilent’s Quick-Amp labeling Kit (p/n5190-0442) was used. The labeling method uses T7 promoter based-linear amplification to generate labeled complementary   RNA (One-Color Microarray-Based Gene Expression Analysis)

growth_protocol: The human gastric epithelial cell line AGS was obtained from the National Centre of Cell Science (Pune, India) and maintained in Ham’s F-12 (Invitrogen) medium supplemented with 10% heat-inactivated FBS, 100U/ml penicillin and 100 µg/ml streptomycin at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from 106 AGS cells using the mirVana miRNA isolation kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: AGS cells were infected with H. pylori 26695 at 100 MOI for 4 h,  washed and RNA was isolated from the cells. Uninfected cells were also maintained for the same time point, following which cells were harvested for RNA.

value: Gastric epithelial cell line, AGS

tag: infected with

value: Uninfected


title: AGS cells infected with H. pylori at 100 MOI_2_mRNA

description: mRNA expression of infected AGS cells

source_name: AGS cells infected with H. pylori at 100 MOI, mRNA, replicate 2

value: H. pylori 26695 at 100 MOI, for 4 hrs


title: BRAF lung CD103 #2

first: Brandon

last: Hogstad

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: tissue dissection, FACS Aria sorted

hyb_protocol: Expression Analysis, Inc standard protocol using Hybridization, Wash and Stain kit (Affymetrix)

scan_protocol: Expression Analysis, Inc standard protocol using Affymetrix GeneChip Scanner

data_processing:
Immgen.org data QC protocol: http://www.immgen.org/Protocols/ImmGen%20QC%20Documentation_ALL-DataGeneration_0612.pdf
Expression normalized across the entire group according to Immgen data QC protocol: http://www.immgen.org/Protocols/ImmGen%20QC%20Documentation_ALL-DataGeneration_0612.pdf

source_name: BRAF lung CD103 #2

label_protocol: Expression Analysis, Inc standard biotin labeling protocol.

growth_protocol: Control and CD11c-Cre/BRAFV600E(flox) mice were aged to 14 weeks old before harvesting organs. BMDCs were derived from bone marrow obtained from femur bones of 5 week old control and CD11c-Cre/BRAFV600E(flox) mice.

extract_protocol: Immgen.org standard protocol for total RNA extraction with Trizol

treatment_protocol: Control and CD11c-Cre/BRAFV600E(flox) mice were unmanipulated before organ harvest. BMDCs cultures were untreated before harvest.

tag: braf status

tag: organ of origin

value: Lung


title: Uninfected AGS cells_2_mRNA

description: mRNA expression of uninfected AGS cells

source_name: Uninfected AGS cells, mRNA, replicate 2


title: NS-GFP1+_LSK3

city: Kanazawa

first: Atsushi

last: Hirao

address: kakuma

department: Division of Molecular Genetics

institute: kanazawa university

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Expression data was processed with GeneSpring 12.6GX, using quantile normalization with no baseline transformation.

source_name: sorted murine LSK cells from bone marrow

label_protocol: Samples were processed by Hokkaido System Science Co.,Ltd.(Japan), and run on Agilent SurePrint G4 mouse gene expression arrays (single color).

extract_protocol: Total RNA from 1x 10E4 each fractionated LSK cells based on NS-GFP level  was isolated by using TRIzol (Invitrogen).

tag: strain background

value: bone marrow

value: sorted NS-GFP1+ LSK cells


title: NS-GFP4+_LSK1

tag: cell type

value: sorted NS-GFP4+ LSK cells


title: BRAF lung CD103 #1

description: tissue dissection, FACS Aria sorted

source_name: BRAF lung CD103 #1


title: NS-GFP1+_LSK1


title: NS-GFP2+_LSK3

value: sorted NS-GFP2+ LSK cells


title: NS-GFP1+_LSK2


title: BRAF lung CD11b #2

description: tissue dissection, FACS Aria sorted

source_name: BRAF lung CD11b #2


title: NS-GFP3+_LSK3

value: sorted NS-GFP3+ LSK cells


title: BRAF BMDC #3

description: FACS Aria sorted (live CD11c+CD11b+ BMDC)

source_name: BRAF BMDC #3

value: BMDC


title: BRAF lung CD11b #1

description: tissue dissection, FACS Aria sorted

source_name: BRAF lung CD11b #1


title: BRAF liver CD11b #2

description: tissue dissection, FACS Aria sorted

source_name: BRAF liver CD11b #2

value: Liver


title: NS-GFP4+_LSK2


title: AGS cells infected with H. pylori at 100 MOI_1_mRNA

description: mRNA expression of infected AGS cells

source_name: AGS cells infected with H. pylori at 100 MOI, mRNA, replicate 1


title: NS-GFP2+_LSK1


title: NS-GFP3+_LSK1


title: BRAF liver CD11b #3

description: tissue dissection, FACS Aria sorted

source_name: BRAF liver CD11b #3


title: NS-GFP3+_LSK2


title: BRAF BMDC #2

source_name: BRAF BMDC #2