title: Wild-type-replicate 4

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

description: Summary of RPKM mean values for all genes

data_processing:
Raw sequence data in Fastq format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content. NovoAlign version 2.08 (Novocraft, http://novocraft.com) was used to align reads to the reference genome.
Alignments were combined to create clusters of reads (or patches), which represent nonredundant genomic regions in the reference genome sequence. Cluster boundaries are created by taking all samples into account during the cluster generation to define the leftmost and right-most end coordinates of each cluster. Only uniquely mapping reads are taken into consideration. While clusters represent expressed loci regardless of genomic location, clusters overlapping known genes (as defined by the reference genome assembly annotation), they were labeled as such for downstream analysis. After clusters are created in this way, they undergo linear normalization by multiplying each sample’s locus coverage by the total reads of the lowest read-count sample divided by the respective sample's total reads.
normalized expression data is the basis for the expression comparison. The comparative expression approach steps through each cluster and compares every possible pairing of samples and generates a log2(A/B), where A and B are the two normalized average coverage of each sample, A and B. Pairwise P-values were determined among the samples using Welch's t-test for unequal variance.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing average RPKM of gene transcripts for each experimental group

source_name: Testis

extract_protocol:
Hypothalami were harvested, frozen on dry ice and total RNA extracted using RNAse kit from Qiagen
Performed using protocols for Illumina platform

tag: genetic background

value: Postnatal day 5

value: Testis

tag: genotype/variation

value: wild type


title: SaOS+As_IgG_Rep3

status: Public on Aug 01 2019

type: SRA

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

country: United Kingdom

institute: University of Warwick

library_source: transcriptomic

data_processing:
Sequence data were aligned to Ensemble release GRCh38 of the human genome using Tophat release 2.1.1. incorporating Bowtie 2.2.5.
Read counts against individual genes were obtained using HTSeq against the Ensemble reference annotation GRCh38.84.gtf
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file gives read counts for each gene for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: HeLa, U2OS and SaOS-2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% foetal calf serum (FCS) (Biosera) at 37 °C in a humidified environment containing 5% carbon dioxide.

extract_protocol:
Cells were washed four times in PBS and then suspended in polysome lysis buffer (0.5% v/v NP40, 100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH7.0) then incubated on ice for 5 min before being transferred to -80 °C for a period of no less than 8 h
Finally, the raw lysates were thawed on ice, centrifuged at 15000 x g at 4 °C for 15 min, then the supernatants collected and the pelleted debris discarded. The lysate was further purified by a second centrifugation at 15000 x g at 4 °C to separate the aqueous lysate from unwanted lipids.
To precipitate UNR and associated molecules, Protein A-conjugated Dynabeads (Life Technologies) were firstly incubated with either an antibody against UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914) or a control IgG (Invitrogen 10500C) in PBS containing 0.01% (v/v) Tween-20 (PBST) in tubes attached to a rotating mixer for 1 h at room temperature.
Following this, the beads were similarly blocked at 4 °C in 0.1% (w/v) bovine serum albumin (BSA) in PBS. The beads were then washed twice in ice-cold PBST and then once in ice-cold NT2 buffer (50 mM Tris-HCl, pH 7.4; 150 mM NaCl; 1mM MgCl2; 0.05% [v/v] NP-40) before resuspension in NT2 containing 0.5 % (v/v) RNase OUT, 400 μM VRC and 1 mM DTT. Cleared lysate  was then added at 1 part to 9 parts bead suspension and mixed by rotation for 4 h at 4 °C.
The beads were then washed five times in ice cold NT2 and each sample divided, 4 parts for RNA analysis
RNA was extracted from immune complex-loaded beads using Trizol (Life Technologies) according to the manufacturer’s instructions. RNA-Seq cDNA libraries were then made using the low sample protocol from the Illumina TruSeq RNA sample preparation v2 guide, except that the oligo-dT selection step was omitted, where possible 100 ng of RNA was used per sample, and libraries were quantified using Qubit Fluorometry.  The libraries were normalised to 10 nM.

treatment_protocol: Oxidative stress was applied by adding growth medium containing 0.5 mM sodium arsenite (S7400, Sigma); control untreated cells were similarly re-fed with fresh medium alone.

tag: cell line

tag: disease state

value: Osteosarcoma

tag: stress

value: oxidative stress (0.5mM sodium arsenite)

tag: rip antibody (pulldown)

value: control IgG (Invitrogen 10500C)

tag: replicate


title: Wild-type-replicate 3

country: USA

organism: Mus musculus

tag: age

tag: tissue


title: SaOS+As_IgG_Rep2


title: AD, CBL sample 03--07

type: genomic

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

institute: Arizona State University

description:
Alzheimer's CBL sample
CBL 03--07

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: iScan System according to user protocol

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: CBL sample 03--07

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: plate

tag: bead chip

tag: well position

value: brain

tag: brain region

value: CBL

tag: gender

value: M

tag: diagnosis

value: AD


title: Wild-type-replicate 2


title: SaOS+As_IgG_Rep1


title: 4c Hepatocytes [Hep_4c_30]

type: RNA

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

label: FAM

organism: Rattus norvegicus

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

label_protocol: Single cell capture, lysis and RT pre-amplification experiments were performed using C1 Auto Prep System (Fluidigm) according to the manufacturer's instructions. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer.

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.

tag: strain

value: Wistar

value: 6 week old

tag: Sex

value: Female


title: AD, CBL sample 07--49

description:
Alzheimer's CBL sample
CBL 07--49

source_name: CBL sample 07--49

value: F


title: Wild-type-replicate 1

tag: genetic background


title: Dio3KO-replicate 4

tag: genotype/variation


title: AD, CBL sample 02--28

description:
Alzheimer's CBL sample
CBL 02--28

source_name: CBL sample 02--28


title: 4c Hepatocytes [Hep_4c_31]


title: AD, CBL sample 08--89

description:
Alzheimer's CBL sample
CBL 08--89

source_name: CBL sample 08--89


title: AD, CBL sample 03--30

description:
Alzheimer's CBL sample
CBL 03--30

source_name: CBL sample 03--30


title: 4c Hepatocytes [Hep_4c_28]


title: 4c Hepatocytes [Hep_4c_29]


title: AD, CBL sample 04--54

description:
Alzheimer's CBL sample
CBL 04--54

source_name: CBL sample 04--54


title: SaOS-As_UNR_Rep1

tag: cell line

value: Control

value: UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914)


title: SaOS-As_UNR_Rep2

tag: disease state


title: Dio3KO-replicate 3


title: 4c Hepatocytes [Hep_4c_27]


title: H3K27ac_LPS-1h_rep2

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against H3K27ac on Mnase-digested chromatin

library_source: genomic

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with the following parameters: --gsize=mm --nomodel --nolambda --bw=100 --shiftsize=75.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of peaks (MACS)

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP-seq libraries were prepared for HiSeq2000 sequencing following standard protocols.

tag: cell type

value: BMDM cells (7th day of differentiation)

tag: treatment

value: LPS (10 ng/ml) for 1hrs

tag: antibody

value: Chromatin IP against H3K27ac


title: Dio3KO-replicate 2

tag: age

value: Postnatal day 5

value: Testis


title: SaOS-As_IgG_Rep3

value: Osteosarcoma

tag: stress

tag: rip antibody (pulldown)

tag: replicate


title: AD, CBL sample 96--04

description:
Alzheimer's CBL sample
CBL 96--04

source_name: CBL sample 96--04

tag: plate

tag: bead chip

tag: well position

tag: tissue


title: Dio3KO-replicate 1


title: AD, CBL sample 97--15

description:
Alzheimer's CBL sample
CBL 97--15

source_name: CBL sample 97--15

tag: brain region

tag: gender

tag: diagnosis


title: 4c Hepatocytes [Hep_4c_26]

tag: strain

tag: Sex


title: SaOS-As_IgG_Rep2

tag: cell line

tag: disease state

value: control IgG (Invitrogen 10500C)


title: HF-3

data_processing:
Raw sequence data in Fastq format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content. NovoAlign version 2.08 (Novocraft, http://novocraft.com) was used to align reads to the reference genome.
Alignments were combined to create clusters of reads (or patches), which represent nonredundant genomic regions in the reference genome sequence. Cluster boundaries are created by taking all samples into account during the cluster generation to define the leftmost and right-most end coordinates of each cluster. Only uniquely mapping reads are taken into consideration. While clusters represent expressed loci regardless of genomic location, clusters overlapping known genes (as defined by the reference genome assembly annotation), they were labeled as such for downstream analysis. After clusters are created in this way, they undergo linear normalization by multiplying each sample’s locus coverage by the total reads of the lowest read-count sample divided by the respective sample's total reads.
normalized expression data is the basis for the expression comparison. The comparative expression approach steps through each cluster and compares every possible pairing of samples and generates a log2(A/B), where A and B are the two normalized average coverage of each sample, A and B. Pairwise P-values were determined among the samples using Welch's t-test for unequal variance.
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing average RPKM of gene transcripts for each experimental group

source_name: HF

tag: background strain

value: Postnatal day 15

value: hypothalamus

tag: experimental group

value: HF


title: SaOS-As_IgG_Rep1


title: AD, CBL sample 97--01

description:
Alzheimer's CBL sample
CBL 97--01

source_name: CBL sample 97--01

value: brain

value: CBL

tag: age

value: AD


title: SaOS-As_UNR_Rep3

tag: stress


title: HF-2


title: H3K4me1_LPS-1h_rep2

description: Chromatin IP against H3K4me1 on Mnase-digested chromatin

tag: cell type

tag: treatment

tag: antibody

value: Chromatin IP against H3K4me1


title: HeLa+As_UNR_Rep3

value: HeLa

value: Cervical Carcinoma

value: oxidative stress (0.5mM sodium arsenite)

tag: rip antibody (pulldown)

tag: replicate


title: AD, CBL sample 96--43

description:
Alzheimer's CBL sample
CBL 96--43

source_name: CBL sample 96--43

tag: plate

tag: bead chip

tag: well position

tag: tissue

value: F


title: HF-1


title: 4c Hepatocytes [Hep_4c_23]

tag: strain

value: Wistar

value: 6 week old

value: Female


title: HeLa+As_UNR_Rep2

value: UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914)


title: HeLa+As_UNR_Rep1


title: 4c Hepatocytes [Hep_4c_22]

tag: Sex


title: Control-2

source_name: Control

value: Control


title: AD, CBL sample 03--53

description:
Alzheimer's CBL sample
CBL 03--53

source_name: CBL sample 03--53

tag: brain region

tag: gender

value: M

tag: diagnosis


title: Control-3

tag: background strain

value: Postnatal day 15

tag: experimental group


title: AD, CBL sample 05--37

description:
Alzheimer's CBL sample
CBL 05--37

source_name: CBL sample 05--37

tag: age


title: 4c Hepatocytes [Hep_4c_21]


title: AD, CBL sample 04--55

description:
Alzheimer's CBL sample
CBL 04--55

source_name: CBL sample 04--55


title: Control-1

value: hypothalamus


title: HeLa+As_IgG_Rep3

tag: cell line

tag: disease state

tag: stress

value: control IgG (Invitrogen 10500C)


title: HeLa+As_IgG_Rep2

tag: rip antibody (pulldown)


title: 4c Hepatocytes [Hep_4c_19]


title: HM-3

source_name: HM

value: HM


title: HM-2


title: 4c Hepatocytes [Hep_4c_25]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: 4c Hepatocytes [Hep_4c_18]


title: HeLa+As_IgG_Rep1

tag: replicate


title: 4c Hepatocytes [Hep_4c_24]


title: HeLa-As_UNR_Rep3


title: AD, CBL sample 06--26

description:
Alzheimer's CBL sample
CBL 06--26

source_name: CBL sample 06--26

tag: plate

value: brain

value: CBL


title: AD, CBL sample 07--02

description:
Alzheimer's CBL sample
CBL 07--02

source_name: CBL sample 07--02

tag: bead chip

value: AD


title: HM-1


title: 4c Hepatocytes [Hep_4c_17]


title: PGF-3

source_name: PGF

value: PGF


title: HeLa-As_UNR_Rep1

value: HeLa

value: Cervical Carcinoma


title: AD, CBL sample 98--44

description:
Alzheimer's CBL sample
CBL 98--44

source_name: CBL sample 98--44

tag: well position


title: 4c Hepatocytes [Hep_4c_16]


title: PGF-2

tag: tissue


title: AD, CBL sample 04--22

description:
Alzheimer's CBL sample
CBL 04--22

source_name: CBL sample 04--22


title: HeLa-As_IgG_Rep3


title: AD, CBL sample 03--03

description:
Alzheimer's CBL sample
CBL 03--03

source_name: CBL sample 03--03


title: 4c Hepatocytes [Hep_4c_20]

tag: strain


title: PGF-1


title: HeLa-As_IgG_Rep1


title: 4c Hepatocytes [Hep_4c_15]

tag: Sex


title: AD, CBL sample 99--48

description:
Alzheimer's CBL sample
CBL 99--48

source_name: CBL sample 99--48

tag: brain region

value: F


title: 4c Hepatocytes [Hep_4c_13]

value: Wistar


title: AD, CBL sample 01--22

description:
Alzheimer's CBL sample
CBL 01--22

source_name: CBL sample 01--22

tag: gender


title: PGM-3

source_name: PGM

value: PGM


title: HeLa-As_UNR_Rep2


title: 4c Hepatocytes [Hep_4c_14]

value: 6 week old

value: Female


title: PGM-2


title: AD, CBL sample 04--06

description:
Alzheimer's CBL sample
CBL 04--06

source_name: CBL sample 04--06

tag: diagnosis


title: AD, CBL sample 03--18

description:
Alzheimer's CBL sample
CBL 03--18

source_name: CBL sample 03--18


title: 4c Hepatocytes [Hep_4c_12]


title: 4c Hepatocytes [Hep_4c_11]


title: AD, CBL sample 01--28

description:
Alzheimer's CBL sample
CBL 01--28

source_name: CBL sample 01--28


title: PGM-1

tag: background strain


title: HML58-3 treated with OR-2100

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

description: Gene expression in OR2100-treated cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1xAgilent fragmentation buffer and 2xAgilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2xAgilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: A derivative cell line of HCT116, HML58-3, was maintained in McCoy's 5A medium with 10% FBS.

extract_protocol: Total RNA was extracted using the ReliaPrep™ RNA Cell Miniprep System (Promega, Madison, WI).

treatment_protocol: Cells were seeded at a density of 3 × 10^5 cells/10-cm dish on Day 0. On Day 1, the medium was replaced with a medium containing 1 µM of drugs, which was freshly dissolved in DMSO and filtered through a 0.2-µ filter. On Day 5, the cells were collected for total RNA extraction.


title: IGFBP7_KO_3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Mouse liver

growth_protocol: adult liver tissues directly for RNA extraction

extract_protocol:
Total RNA is extracted using Qiagen miRNAeasy mini kit (Qiagen, Valencia, CA) from livers
RNASeq library was prepared using Illumina TruSeq RNA sample preparation kit and were pooled together to aim about 25-40M read passed filtered reads per sample

treatment_protocol: Igfbp-7-/- mouse was created in a pure C57BL/6 background using a Cre-loxP strategy

value: adult liver

tag: genotype/variation

value: IGFBP7 knock-out


title: 4c Hepatocytes [Hep_4c_10]

tag: age


title: AD, CBL sample 07--29

description:
Alzheimer's CBL sample
CBL 07--29

source_name: CBL sample 07--29


title: HML58-3 treated with OR-2003

description: Gene expression in OR2003-treated cells

tag: cell line


title: HeLa-As_IgG_Rep2

tag: disease state

value: Control


title: IGFBP7_KO_2


title: 4c Hepatocytes [Hep_4c_9]


title: AD, CBL sample 07--21

description:
Alzheimer's CBL sample
CBL 07--21

source_name: CBL sample 07--21


title: 4c Hepatocytes [Hep_4c_8]


title: HML58-3 treated with mock

description: Gene expression in mock-treated cells


title: AD, CBL sample 07--57

description:
Alzheimer's CBL sample
CBL 07--57

source_name: CBL sample 07--57


title: 4c Hepatocytes [Hep_4c_7]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: AD, CBL sample 08--82

description:
Alzheimer's CBL sample
CBL 08--82

source_name: CBL sample 08--82

value: M


title: 4c Hepatocytes [Hep_4c_6]


title: WT_3

value: wild type


title: AD, CBL sample 08--22

description:
Alzheimer's CBL sample
CBL 08--22

source_name: CBL sample 08--22


title: WT_2


title: WT_1


title: AD, CBL sample 03--27

description:
Alzheimer's CBL sample
CBL 03--27

source_name: CBL sample 03--27


title: 4c Hepatocytes [Hep_4c_3]


title: 4c Hepatocytes [Hep_4c_5]


title: 4c Hepatocytes [Hep_4c_4]


title: AD, CBL sample 02--22

description:
Alzheimer's CBL sample
CBL 02--22

source_name: CBL sample 02--22


title: AD, CBL sample 03--05

description:
Alzheimer's CBL sample
CBL 03--05

source_name: CBL sample 03--05


title: US10353831_252116914326_S01_GE1_107_Sep09_1_2: inoculated with Mucor sp. 10 days after inoculation

city: Kraków

first: Piotr

last: Rozpądek

address: Gronostajowa 7a

department: Małopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

description: Gene expression

hyb_protocol: Gene Expression Hybridization Kit was used for fragmentation and hybridization and Gene Expression Wash Buffer Kit was used for washing slides after hybridization following the manufacturers instructions.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C.

data_processing: Data were extracted and background subtracted using the standard procedures from the Agilent Feature Extraction (FE) Software version 10.7.3.1

organism: Arabidopsis thaliana

source_name: shoot

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from frozen in liquid nitrogen, ground leaves (from 3 plants per sample) with the Total RNA Mini Kit (Biorad, US). RNA purity and quantity was determined by Biospec-Nano (SHIMADZU) The integrity of RNA was assessed with the Agilent 2100 Bioanalyzer (USA) and RNA 6000 Nano Kit (Agilent, Germany).

treatment_protocol: Seedlings were inoculated in vitro, in MSR. Plants were cultivated for 5 days in a Panasonic MLR-352H-PE, JPN chamber with a 16h photoperiod, 100-120 μmol·m-2·s-1 PAR,  21/17°C day/night temperature and 50% humidity.

value: shoot


title: US10353831_252116914326_S01_GE1_107_Sep09_1_1: inoculated with Mucor sp. 10 days after inoculation

description: Gene expression


title: 4c Hepatocytes [Hep_4c_2]


title: US10353831_252116914325_S01_GE1_107_Sep09_1_2: noninoculaed control 10 days

description: Gene expression


title: AD, CBL sample 05--27

description:
Alzheimer's CBL sample
CBL 05--27

source_name: CBL sample 05--27

value: brain


title: US10353831_252116914325_S01_GE1_107_Sep09_1_1: noninoculaed control 10 days

description: Gene expression


title: AD, CBL sample 92--17

description:
Alzheimer's CBL sample
CBL 92--17

source_name: CBL sample 92--17

value: CBL


title: US10353831_252116914323_S01_GE1_107_Sep09_1_4: inoculated with Mucor sp.5 days after inoculation

description: Gene expression


title: AD, CBL sample 95--15

description:
Alzheimer's CBL sample
CBL 95--15

source_name: CBL sample 95--15

value: AD


title: IGFBP7_KO_1


title: 2c Hepatocytes [Hep_2c_92]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes

value: 5 week old


title: US10353831_252116914323_S01_GE1_107_Sep09_1_3: inoculated with Mucor sp. 5 days after inoculation

description: Gene expression


title: 187271-F_D14

description: Gene expression

hyb_protocol: For each hybridization, 0.60 μg of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID: 72363).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software, which performs background subtractions.

source_name: Lot 187271 APHHs cultured for 14 days without AC

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA)

extract_protocol: RNA was extracted using the miRNAeasy mini kit (QIAGEN).

treatment_protocol: Primary human hepatocytes were cultured for 2 weeks in SHM supplemented with 10%FBS in the presence or absence of 0.5 microM A83-01 and 3 microM CHIR99021.

value: Male

value: 26 years


title: 187271-FAC_D7

description: Gene expression

source_name: Lot 187271 APHHs cultured for 7 days with AC


title: HML58-3 treated with decitabine

description: Gene expression in decitabine-treated cells


title: 187271-F_D7

description: Gene expression

source_name: Lot 187271 APHHs cultured for 7 days without AC


title: 187271-F_D1

description: Gene expression

source_name: Lot 187271 APHHs cultured for 1 day without AC


title: AD, CBL sample 95--18

description:
Alzheimer's CBL sample
CBL 95--18

source_name: CBL sample 95--18

value: F


title: 187271-FAC_D14

description: Gene expression

source_name: Lot 187271 APHHs cultured for 14 days with AC


title: HC5-25-FAC_D14

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 14 days with AC

value: 56 years


title: 187271-FAC_D1

description: Gene expression

source_name: Lot 187271 APHHs cultured for 1 day with AC


title: 2c Hepatocytes [Hep_2c_91]

value: Wistar


title: HC5-25-F_D14

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 14 days without AC


title: US10353831_252116914323_S01_GE1_107_Sep09_1_2: noninoculaed control 5 days

description: Gene expression


title: 2c Hepatocytes [Hep_2c_89]


title: 2c Hepatocytes [Hep_2c_87]


title: US10353831_252116914323_S01_GE1_107_Sep09_1_1: noninoculaed control 5 days

description: Gene expression


title: HC5-25-F_D7

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 7 days without AC


title: 4c Hepatocytes [Hep_4c_1]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

value: 6 week old


title: AD, CBL sample 95--10

description:
Alzheimer's CBL sample
CBL 95--10

source_name: CBL sample 95--10


title: 2c Hepatocytes [Hep_2c_88]

value: Female


title: 2c Hepatocytes [Hep_2c_90]


title: 2c Hepatocytes [Hep_2c_86]


title: 2c Hepatocytes [Hep_2c_83]


title: AD, CBL sample 04--49

description:
Alzheimer's CBL sample
CBL 04--49

source_name: CBL sample 04--49


title: HC5-25-FAC_D7

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 7 days with AC


title: 2c Hepatocytes [Hep_2c_85]


title: HC5-25-FAC_D1

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 1 day with AC


title: AD, CBL sample 04--36

description:
Alzheimer's CBL sample
CBL 04--36

source_name: CBL sample 04--36


title: AD, CBL sample 04--47

description:
Alzheimer's CBL sample
CBL 04--47

source_name: CBL sample 04--47


title: 2c Hepatocytes [Hep_2c_84]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes


title: FCL-FAC_batch2_D14

description: Gene expression

source_name: Lot FCL IPHHs cultured for 14 days with AC

value: 12 months


title: FCL-F_batch2_D14

description: Gene expression

source_name: Lot FCL IPHHs cultured for 14 days without AC


title: AD, CBL sample 03--38

description:
Alzheimer's CBL sample
CBL 03--38

source_name: CBL sample 03--38


title: FCL-FAC_batch2_D7

description: Gene expression

source_name: Lot FCL IPHHs cultured for 7 days with AC


title: 2c Hepatocytes [Hep_2c_82]


title: AD, CBL sample 06--12

description:
Alzheimer's CBL sample
CBL 06--12

source_name: CBL sample 06--12


title: AD, CBL sample 06--09

description:
Alzheimer's CBL sample
CBL 06--09

source_name: CBL sample 06--09


title: 2c Hepatocytes [Hep_2c_81]


title: Zone III (Right): BB/PF region (Right Ventricle)

city: San Francisco

first: William

middle: Rowland

last: Goodyer

state: CA

address: 386A Noe Street

department: Medicine

institute: Stanford University

description: oligodTs were used to reverse transcribe the single-cell derived mRNAs

data_processing:
The single cell library was sequenced with illumina hiseq 4000 platform
Sequencing reads were aligned to mouse MM10 reference genome with CellRanger

source_name: Microdissected regions from embryonic day 16.5 (E16.5) mouse hearts

growth_protocol: Embryonic heart regions microdissected from E16.5 wild-type (CD1) mice

extract_protocol:
This step was done by following the 10x genomics singel cell preparation protocol
This step was done by following the 10x genomics single cell library preparation protocol
Only the 3' end of mRNA fragements were used to make library. One end of the fragements were added P5, read1 illumina sequencing primer, 16 base pairs of 10x barcode, and UMI sequences; The other end ligated with P7, sample index sequences, and illumina read2 sequencing primer sequences.

tag: developmental stage

value: BB/PF region (Right Ventricle)

value: mouse heart


title: HC5-25-F_D1

description: Gene expression

source_name: Lot HC5-25 APHHs cultured for 1 day without AC


title: Zone III (Left): BB/PF region (Left Ventricle)

value: BB/PF region (Left Ventricle)


title: AD, CBL sample 97--24

description:
Alzheimer's CBL sample
CBL 97--24

source_name: CBL sample 97--24


title: AD, CBL sample 01--12

description:
Alzheimer's CBL sample
CBL 01--12

source_name: CBL sample 01--12

value: M


title: Zone II: AVN/His region

value: AVN/His region


title: 2c Hepatocytes [Hep_2c_80]


title: AD, CBL sample 06--48

description:
Alzheimer's CBL sample
CBL 06--48

source_name: CBL sample 06--48

value: brain


title: 2c Hepatocytes [Hep_2c_79]


title: AD, CBL sample 99--07

description:
Alzheimer's CBL sample
CBL 99--07

source_name: CBL sample 99--07

value: CBL


title: AD, CBL sample 98--18

description:
Alzheimer's CBL sample
CBL 98--18

source_name: CBL sample 98--18

value: AD


title: AD, CBL sample 00--47

description:
Alzheimer's CBL sample
CBL 00--47

source_name: CBL sample 00--47


title: 2c Hepatocytes [Hep_2c_77]

value: 5 week old


title: 2c Hepatocytes [Hep_2c_76]


title: 2c Hepatocytes [Hep_2c_75]


title: FCL-F_batch2_D1

description: Gene expression

source_name: Lot FCL IPHHs cultured for 1 day without AC


title: AD, CBL sample 99--41

description:
Alzheimer's CBL sample
CBL 99--41

source_name: CBL sample 99--41


title: AD, CBL sample 01--45

description:
Alzheimer's CBL sample
CBL 01--45

source_name: CBL sample 01--45


title: 2c Hepatocytes [Hep_2c_74]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes


title: AD, CBL sample 99--06

description:
Alzheimer's CBL sample
CBL 99--06

source_name: CBL sample 99--06


title: 2c Hepatocytes [Hep_2c_73]


title: FCL-FAC_batch2_D1

description: Gene expression

source_name: Lot FCL IPHHs cultured for 1 day with AC


title: FCL-F_batch2_D7

description: Gene expression

source_name: Lot FCL IPHHs cultured for 7 days without AC


title: AD, CBL sample 08--01

description:
Alzheimer's CBL sample
CBL 08--01

source_name: CBL sample 08--01


title: 2c Hepatocytes [Hep_2c_72]


title: 2c Hepatocytes [Hep_2c_78]


title: Zone I: SAN region

value: SAN region


title: NIH3T3 H3.1K36A

city: shanghai

first: Jin

last: Sun

department: life science and technology

country: China

institute: Tongji University

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-20h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and  was used for background subtraction and LOWESS normalization.

label_protocol: 0.5 µg genomic DNA was directly labeled by Klenow random priming with Cy3 nonamers and cy5 Nonamers， per agilent manufacturer's protocol

growth_protocol: mouse ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer. NIH3T3 cells were cultured with standard protocol in DMEM medium and 10% FBS.

extract_protocol: Genomic DNA was prepared using the  qiangen Mini kit following the manufacturer's recommendations.  DNA was quantified using a NanoDrop-2000 spectrophotometer.

treatment_protocol: stable cells lines of mESCs and NIH3T3 were produced by lenti-virus mediated infection and the positive clones were sorted by FACS.

tag: cell type

tag: treatment

value: histone H3.1K36A overexpression

value: control cells, empty


title: NIH3T3 H3.1K27A

value: histone H3.1K27A overexpression


title: NIH3T3 H3.1WT

value: histone H3.1WT overexpression


title: AD, CBL sample 97--39

description:
Alzheimer's CBL sample
CBL 97--39

source_name: CBL sample 97--39

tag: plate

value: F


title: 2c Hepatocytes [Hep_2c_71]

value: Wistar

value: Female


title: NIH3T3 H3.1K9A

value: histone H3.1K9A overexpression


title: DN replication2

source_name: mESCs

value: mESCs

value: Suv39h1/h2 double null repeat2


title: AD, CBL sample 08--59

description:
Alzheimer's CBL sample
CBL 08--59

source_name: CBL sample 08--59

tag: bead chip

value: M


title: AD, CBL sample 08--45

description:
Alzheimer's CBL sample
CBL 08--45

source_name: CBL sample 08--45

tag: well position


title: 2c Hepatocytes [Hep_2c_69]


title: AD, CBL sample 03--34

description:
Alzheimer's CBL sample
CBL 03--34

source_name: CBL sample 03--34

tag: tissue


title: 2c Hepatocytes [Hep_2c_70]

tag: strain


title: 2c Hepatocytes [Hep_2c_68]

tag: Sex


title: DN replication1

value: Suv39h1/h2 double null repeat1


title: shSuv39h2 replication1

source_name: mESCs, J1 strain

value: shRNA against Suv39h2 repeat1


title: 2c Hepatocytes [Hep_2c_67]


title: AD, CBL sample 00--04

description:
Alzheimer's CBL sample
CBL 00--04

source_name: CBL sample 00--04

value: brain

tag: brain region

value: CBL


title: 2c Hepatocytes [Hep_2c_66]

value: 5 week old


title: 2c Hepatocytes [Hep_2c_65]


title: 2c Hepatocytes [Hep_2c_64]


title: shSuv39h1 replication2

value: shRNA against Suv39h1 repeat2


title: 2c Hepatocytes [Hep_2c_63]

value: 6 week old


title: 6_RM1_replicate3

city: Houston

first: Filippo

last: Giancotti

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

data_processing:
Raw reads were quality-checked and subsequently mapped to the human genome (hg19) using Tophat2 (2.2.4) using default settings.
Differential gene expression was analyzed using the DESeq2 (1.8.1) package  in R using default settings
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: RNA-Seq of mus musculus prostate cancer

growth_protocol: Pten Smad4 cells are grown in DMEM 10% FBS.

extract_protocol:
Total RNA are extracted by Maxwell® RSC simplyRNA Cells Kit.
Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to doublestrand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end,  then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

value: Mouse prostate cancer primary site

value: 17 days

tag: genotype

value: ras + myc transformed mouse prostate carcinomas


title: 2c Hepatocytes [Hep_2c_62]


title: Con, biological rep3

city: Beer-Sheva

first: Yoram

last: Etzion

state: Please Select

address: 1st Ben-Gurion Street

department: Physiology and Cell Biology

country: Israel

institute: Ben-Gurion University, Israel

description: Gene expression data from left atria exposed to control pacing for 48 hours

hyb_protocol: The biotinylated Samples were hybridized to the GeneChip Rat Gene 1.0 ST arrays contains 722,254 probe sets (for estimated 27,342 genes).

scan_protocol: Following hybridization the arrays were washed and stained using FS450_0007 protocol, and fluorescent signals were scanned using the 3000 G7 Scanner (Affymetrix)

data_processing: CEL files were processed in Partek Genomics Suite® using Robust Multiarray Averaging (RMA, Irizarry et al 2003) with default parameters.

label: biotin

source_name: Control atrial pacing, pair #3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA from each sample

growth_protocol: Male Sprague-Dawley rats (250-320 gr)

extract_protocol: RNA samples were extracted from the left atrium with TRI-Reagent (MRC, Cincinnati, OH, USA)

treatment_protocol: Rats were subjected to either rapid atrial pacing (RAP, 70 ms Cycle length) or control pacing (Con, 140 ms Cycle length) for 48 hours. Ventricular rate was simillar in both groups

value: left atrium

tag: gender

value: Male

value: Sprague-Dawley

value: adult

value: exposed to control pacing for 48 hours


title: Con, biological rep2

source_name: Control atrial pacing, pair #2


title: RAP, biological rep2

description: Gene expression data from left atria exposed to rapid atrial pacing for 48 hours

source_name: Rapid atrial pacing, pair #2


title: RAP, biological rep3

source_name: Rapid atrial pacing, pair #3

value: exposed to rapid atrial pacing for 48 hours


title: 2c Hepatocytes [Hep_2c_61]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes

value: Wistar

value: Female


title: 5_RM1_replicate2


title: 4_RM1_replicate1


title: 2c Hepatocytes [Hep_2c_60]


title: Con, biological rep1

source_name: Control atrial pacing, pair #1


title: RAP, biological rep1

source_name: Rapid atrial pacing, pair #1


title: shSuv39h1 replication1

value: mESCs

value: shRNA against Suv39h1 repeat1

value: control cells, empty


title: H3.1K36M

value: histone H3.1K36M overexpression


title: EBC-211_0.1_48h_Rep4

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed according to standard Illumina protocols.

scan_protocol: Scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method. Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA). Expression values were normalized using quantile normalization with default settings.

source_name: HaCaT cells treated with 0.1 mg/ml EBC-211 for 48 hours

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

growth_protocol: HaCaTs were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 1% antibiotics/antimycotics (100 U/ml penicillin G sodium, 100 μg/ml streptomycin sulfate and 0.25 μg/ml amphotericin B), 2 mM L-glutamine and 10% fetal calf serum (all Thermo Fisher Scientific, Paisley, UK). HaCaTs were maintained at 37°C in a humidified 5% CO2/95% air atmosphere, with medium changes every 48 h. To determine epoxy-tigliane effects on HaCaT gene expression, HaCaTs were seeded into T-75 tissue culture flasks (VWR International, Lutterworth, UK), in 10% serum-containing DMEM at a density of 2x10e6 cells/flask for 24 h, followed by incubation in serum-free DMEM for a further 24 h.

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified. RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Serum-free media was subsequently replaced with 1% serum-containing DMEM with EBC-46 and EBC-211 (0 μg/ml, 0.001 μg/ml, 0.1 μg/ml or 10 μg/ml). Cultures were maintained at 37°C in a humidified 5% CO2/95% air atmosphere, for 24 h or 48 h. At 24 h and 48 h, culture medium was removed and immediately replaced with RNAprotect Cell Reagent (Qiagen Ltd, Manchester, UK)/culture medium (4.5 ml/flask).

value: HaCaT

value: normal keratinocyte cell line

tag: time

value: 48 hours


title: EBC-211_10_48h_Rep4

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 48 hours

value: 10 mg/ml EBC-211


title: shSuv39h2 replication2

value: shRNA against Suv39h2 repeat2


title: EBC-46_10_24h_Rep4

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 24 hours

value: 10 mg/ml EBC-46

value: 24 hours


title: H3.1K9A

value: histone H3.1K9A overexpression


title: EBC-211_10_24h_Rep4

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 24 hours


title: H3.1WT

value: histone H3.1WT overexpression


title: EBC-46_0.1_48h_Rep4

source_name: HaCaT cells treated with 0.1 mg/ml EBC-46 for 48 hours

value: 0.1 mg/ml EBC-46


title: H3.1K36A

value: histone H3.1K36A overexpression


title: EBC-46_10_48h_Rep4

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 48 hours


title: 2c Hepatocytes [Hep_2c_58]

value: Wistar

value: 6 week old


title: 2c Hepatocytes [Hep_2c_57]

value: Female


title: 2_Pten_Smad4_replicate2

description: RNASeq_PTEN Smad4.txt

value: Pten Smad4

value: FVB

value: Mouse prostate cancer primary site

value: 33 weeks


title: 1_Pten_Smad4_replicate1

description: RNASeq_PTEN Smad4.txt


title: H3.1K9M

value: mESCs

value: histone H3.1K9M overexpression

value: control cells, empty


title: 3_Pten_Smad4_replicate3

description: RNASeq_PTEN Smad4.txt


title: 2c Hepatocytes [Hep_2c_56]


title: 2c Hepatocytes [Hep_2c_55]


title: CHO-K1_9C

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina FASTQ Generation version 1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC. The FastQC results indicated that all sequences were of high quality.
The annotation file for CriGri_1.0 was downloaded from the pre-Ensembl ftp site.  This gtf contains annotations from a variety of sources which overlap.  Therefore, this gtf file was parsed to contain only homology to mouse Ensembl transcripts.
Sequences were directly aligned to the Cricetulus griseus reference genome assembly CriGri_1.0 downloaded from the pre-Ensembl ftp site using tophat2 (version 2.0.13), generating alignment files in bam format.
Differentially expressed genes (DEGs) were identified  for all three pairwise comparisons using Cuffdiff2 (v2.2.1).
Genome_build: CriGri_1.0
Supplementary_files_format_and_content: tab-delimted cuffnorm normalized FPKM files
Supplementary_files_format_and_content: gtf file containing mouse homologs from Ensembl

organism: Cricetulus griseus

source_name: CHO-K1 cell line Pre-miR-29a transfected replicate 3

growth_protocol: CHO-K1 cells were grown in triplicates in phenol red IMEM supplemented with 5% dextran-coated charcoal-stripped fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).

extract_protocol:
RNA was isolated using the Exiqon miRCURYTM RNA Isolation kit and its concentration and quality assessed using a NanoDrop spectrophotometer. Quantitative real-time PCR confirmed overexpression of miR-29b-1, miR-29a, or knockdown of miR-29b-1 and miR-29a in respective samples.
The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 2ug total RNA.  Libraries were confirmed on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems and the ABI7900HT real-time PCR instrument.  75-76 cycle single read sequencing was performed with the 500 High-output v2 (75 cycle) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: Cells were transfected with anit-miR-29a (Anti-miRTMs, Ambion), pre-miR-29a and pre-miuR-29b-1 (Pre-miRTMs, Ambion), using Lipofectamine RNAiMAX (Invitrogen) for 48 h.

tag: transfection


title: CHO-K1_9B

source_name: CHO-K1 cell line Pre-miR-29a transfected replicate 2


title: 2c Hepatocytes [Hep_2c_54]

tag: age


title: CHO-K1_9A

source_name: CHO-K1 cell line Pre-miR-29a transfected replicate 1

tag: cell line


title: CHO-K1_8C

source_name: CHO-K1 cell line Anti-miR-29a transfected replicate 3


title: 2c Hepatocytes [Hep_2c_53]


title: CHO-K1_8B

source_name: CHO-K1 cell line Anti-miR-29a transfected replicate 2


title: EBC-211_0.001_48h_Rep4

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 48 hours

value: HaCaT

value: normal keratinocyte cell line

value: 48 hours


title: CHO-K1_8A

source_name: CHO-K1 cell line Anti-miR-29a transfected replicate 1


title: 2c Hepatocytes [Hep_2c_51]


title: EBC-211_0.001_24h_Rep4

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 24 hours

value: 24 hours


title: CHO-K1_7C

source_name: CHO-K1 cell line pre-miR-29b-1 transfected replicate 3


title: EBC-46_0.001_24h_Rep4

source_name: HaCaT cells treated with 0.001 mg/ml EBC-46 for 24 hours


title: 2c Hepatocytes [Hep_2c_52]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes


title: Control_48h_Rep4

source_name: HaCaT cells treated with vehicle for 48 hours

value: vehicle


title: Control_24h_Rep4

source_name: HaCaT cells treated with vehicle for 24 hours


title: EBC-46_0.001_48h_Rep4

source_name: HaCaT cells treated with 0.001 mg/ml EBC-46 for 48 hours


title: CHO-K1_7B

source_name: CHO-K1 cell line pre-miR-29b-1 transfected replicate 2


title: CHO-K1_7A

source_name: CHO-K1 cell line pre-miR-29b-1 transfected replicate 1


title: EBC-211_10_24h_Rep3

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 24 hours

value: 10 mg/ml EBC-211


title: 2c Hepatocytes [Hep_2c_48]


title: 2c Hepatocytes [Hep_2c_47]


title: 2c Hepatocytes [Hep_2c_59]


title: 2c Hepatocytes [Hep_2c_46]


title: RNA A2

city: Yuseong-gu

first: Yoseb

last: Song

state: Daejeon

address: 291 Daehak-ro

country: South Korea

institute: KAIST

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The reads were aligned to the C.drakei genome (CP020953) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.8, and similarity fraction 0.8.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
Genome_build: CP020953
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for transcriptome result

organism: Clostridium drakei

source_name: cell culture in H2/CO2 replicate 2

growth_protocol: C. drakei SL1T was obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany) and cultivated anaerobically at 30 °C in 100 mL DSM 135 medium, which composed of 18.7 mM NH4Cl, 2.4 mM KH2PO4, 2.6 mM K2HPO4, 0.4 mM MgSO4 × 7 H2O, 0.2% (w/v) yeast extract, 119.0 mM NaHCO3, 2.8 mM L-cysteine-HCl × H2O, 4 µM resazurin, 20 mL trace element solution (DSMZ, media 141), and 10 mL vitamin solution (DSMZ, media 141) per liter medium,  supplemented with 5 g/L fructose or H2/CO2 (80:20) at a pressure of 200 kPa with 50 mL of headspace for the heterotrophic and the autotrophic growth conditions, respectively (see DSMZ, media 135 for more detail). The cultured cells were harvested by anaerobic centrifugation at 4000 g, washed with basal DSM 135 medium, and inoculated in 100 mL of new medium with 50 mL of headspace, adjusting initial optical density 600 nm to be around 0.05.

extract_protocol:
The cells were resuspended in 500 µL lysis buffer composed of 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, and 1% Triton X-100. Resuspended cells were frozen in liquid nitrogen and then ground with pestle and mortar. The powdered cells were thawed and the cell debris was removed by centrifugation at 4000 g for 15 min at 4 °C. Total RNA was then isolated using TRIzol (Thermo Scientific).
To remove residual genomic DNA in the RNA sample, 4 U of rDNase I (Ambion) was applied to the isolated RNA for 1 h at 37 °C, followed by incubation at 75 °C for 10 min. Ribosomal RNAs (rRNAs) were removed by using the Ribo-ZeroTM rRNA Removal Kit for Meta-bacteria (Epicentre), and the rRNA-depleted RNA quality was checked using the Agilent 2200 TapeStation system (Agilent Technologies). Using the TruSeq Stranded mRNA Library Prep Kit (Illumina), the rRNA-depleted RNAs were converted into RNA-Seq libraries, which were then sequenced by the 150 bp read recipe with an Illumina MiseqTM system.
The cells were resuspended in 500 µL lysis buffer composed of 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, and 1% Triton X-100. Resuspended cells were frozen in liquid nitrogen and then ground with pestle and mortar. The powdered cells were thawed and the cell debris was removed by centrifugation at 4000 g for 15 min at 4 °C. Total RNA was then isolated using TRIzol (Thermo Scientific).
To remove residual genomic DNA in the RNA sample, 4 U of rDNase I (Ambion) was applied to the isolated RNA for 1 h at 37 °C, followed by incubation at 75 °C for 10 min. Ribosomal RNAs (rRNAs) were removed by using the Ribo-ZeroTM rRNA Removal Kit for Meta-bacteria (Epicentre), and the rRNA-depleted RNA quality was checked using the Agilent 2200 TapeStation system (Agilent Technologies). Using the TruSeq Stranded mRNA Library Prep Kit (Illumina), the rRNA-depleted RNAs were converted into RNA-Seq libraries, which were then sequenced by the 150 bp read recipe with an Illumina MiseqTM system.

treatment_protocol: Cultured C. drakei in H2/CO2 (80:20) supplemented DSM135 media and cultured until the cell reached mid-exponential phase.


title: 2c Hepatocytes [Hep_2c_49]


title: RNA H2

source_name: cell culture in fructose replicate2

treatment_protocol: Cultured C. drakei in fructose (5 g/L) supplemented DSM135 media and cultured until the cell reached mid-exponential phase.


title: 2c Hepatocytes [Hep_2c_45]


title: RNA_H1

source_name: cell culture in fructose replicate1


title: 2c Hepatocytes [Hep_2c_44]


title: 2c Hepatocytes [Hep_2c_43]


title: EBC-46_10_24h_Rep3

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 24 hours

value: 10 mg/ml EBC-46


title: EBC-46_10_48h_Rep3

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 48 hours


title: EBC-211_10_48h_Rep3

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 48 hours


title: 2c Hepatocytes [Hep_2c_50]

value: Wistar


title: RNA A1

source_name: cell culture in H2/CO2 replicate 1


title: EBC-211_0.1_48h_Rep3

source_name: HaCaT cells treated with 0.1 mg/ml EBC-211 for 48 hours


title: 2c Hepatocytes [Hep_2c_42]

value: 6 week old


title: 2c Hepatocytes [Hep_2c_41]

value: Female


title: ATAC_UT_rep2

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v1.1.2 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Accessible regions were identified using MACS v1.4 (PMID: 18798982) with the following parameters: --gsize=mm --bw=300 --nomodel --nolambda --shiftsize=150.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of peaks (MACS)

source_name: Primary bone marrow-derived macrophages (BMDM)

extract_protocol: ATAC-seq libraries were prepared for HiSeq 4000 sequencing following standard protocols.

value: BMDM cells (7th day of differentiation)

value: No treatment


title: EBC-46_0.1_48h_Rep3

source_name: HaCaT cells treated with 0.1 mg/ml EBC-46 for 48 hours

value: 0.1 mg/ml EBC-46


title: EBC-211_0.001_48h_Rep3

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 48 hours


title: EBC-46_0.001_48h_Rep3


title: ATAC_UT_rep1


title: EBC-211_0.001_24h_Rep3

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 24 hours


title: EBC-46_0.001_24h_Rep3

source_name: HaCaT cells treated with 0.001 mg/ml EBC-46 for 24 hours


title: 2c Hepatocytes [Hep_2c_40]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes


title: ATAC_LPS-4h_rep3

value: LPS (10 ng/ml) for 4hrs


title: 2c Hepatocytes [Hep_2c_39]


title: ATAC_UT_rep3


title: ATAC_LPS-4h_rep2


title: C14

city: Boston

first: Katherine

last: Silkaitis

state: MA

address: 655 Huntington Ave, 2-237

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: In limma in R, we used normexp method for background correction, and the robustspline and aquantile methods for within- and between-array normalization, respectively.

organism: Drosophila melanogaster

source_name: Total RNA from Ycongo control

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

value: control

value: Ycongo

value: Male

value: 2 days old

value: whole flies

source_name: Total RNA from Ycongo CdCl2


title: 2c Hepatocytes [Hep_2c_38]


title: C13

source_name: Total RNA from Ycs CdCl2

value: Ycs


title: ATAC_LPS-4h_rep1


title: C12

source_name: Total RNA from Ycs control


title: C11


title: 2c Hepatocytes [Hep_2c_37]


title: 2c Hepatocytes [Hep_2c_36]


title: Control_24h_Rep3

source_name: HaCaT cells treated with vehicle for 24 hours

value: HaCaT

value: normal keratinocyte cell line

value: 24 hours


title: ATAC_LPS-30min_rep3

value: LPS (10 ng/ml) for 30'


title: Control_48h_Rep3

source_name: HaCaT cells treated with vehicle for 48 hours

value: vehicle

value: 48 hours


title: ATAC_LPS-30min_rep2


title: 2c Hepatocytes [Hep_2c_35]

value: Wistar

value: 6 week old

value: Female


title: 2c Hepatocytes [Hep_2c_34]


title: ATAC_LPS-30min_rep1

value: BMDM cells (7th day of differentiation)


title: Normal stroma  139_norm

city: Zurich

first: Enni

last: Markkanen

address: Winterthurerstr. 260

department: Institute of Veterinary Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

description: Normal stroma

data_processing:
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBLE (CanFam3.1). All other parameters were set to default when running kallisto.
Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.

organism: Canis lupus familiaris

source_name: canine simple mammary carcinoma

growth_protocol: spontaneous tumours from canine patients removed in the context of curative surgery

extract_protocol:
RNA was extracted using the optimised Covaris-FFPE RNA isolation procedure described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7
SMARTer Stranded Total RNA-seq Kit—Pico Input Mammalian from Clontech/ Takara Bio USA, using 4 ng total RNA per sample; details described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7

treatment_protocol: no treatment

value: female

tag: age of patient (years)

tag: subtype of simple carcinoma

value: cystic-papillary

tag: age of sample at analysis (months)

tag: breed

value: not disclosed


title: C8

tag: treatment

value: Ycongo

value: Male

value: control


title: Cancer-associated stroma 139_tumour

description: Cancer-associated stroma


title: C9

value: 2 days old

value: whole flies

value: Ycs


title: EBC-211_10_48h_Rep2

value: HaCaT

tag: cell type

value: normal keratinocyte cell line

value: 10 mg/ml EBC-211


title: EBC-211_10_24h_Rep2

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 24 hours

value: 24 hours


title: EBC-46_10_48h_Rep2

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 48 hours

value: 10 mg/ml EBC-46

value: 48 hours


title: ATAC_LPS-2h_rep3

value: LPS (10 ng/ml) for 2hrs


title: Cancer-associated stroma 138_tumour

description: Cancer-associated stroma

value: tubulo-papillary

value: Boxer


title: EBC-46_10_24h_Rep2

source_name: HaCaT cells treated with 10 mg/ml EBC-46 for 24 hours


title: C6


title: EBC-211_0.1_48h_Rep2

source_name: HaCaT cells treated with 0.1 mg/ml EBC-211 for 48 hours


title: ATAC_LPS-2h_rep2

source_name: Primary bone marrow-derived macrophages (BMDM)

value: BMDM cells (7th day of differentiation)


title: Normal stroma  138_norm

description: Normal stroma

value: female


title: EBC-46_0.1_48h_Rep2

source_name: HaCaT cells treated with 0.1 mg/ml EBC-46 for 48 hours

value: 0.1 mg/ml EBC-46


title: C7

value: Male

value: Ycongo


title: EBC-211_0.001_48h_Rep2

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 48 hours


title: 2c Hepatocytes [Hep_2c_31]

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

value: Wistar

value: 6 week old

value: Female


title: EBC-211_0.001_24h_Rep2

source_name: HaCaT cells treated with 0.001 mg/ml EBC-211 for 24 hours

value: HaCaT


title: ATAC_LPS-2h_rep1


title: Cancer-associated stroma 137_tumour

description:
Female, neutered
Cancer-associated stroma

value: tubular

value: Chihuahua


title: 2c Hepatocytes [Hep_2c_30]


title: ATAC_LPS-1h_rep3

value: LPS (10 ng/ml) for 1hrs


title: Normal stroma  137_norm

description:
Female, neutered
Normal stroma


title: 2c Hepatocytes [Hep_2c_29]


title: Cancer-associated stroma 136_tumour

value: Beagle


title: Normal stroma  136_norm

description:
Female, neutered
Normal stroma


title: EBC-46_0.001_24h_Rep2

source_name: HaCaT cells treated with 0.001 mg/ml EBC-46 for 24 hours

value: normal keratinocyte cell line

value: 24 hours


title: Control_48h_Rep2

value: vehicle

value: 48 hours


title: 2c Hepatocytes [Hep_2c_28]

source_name: Percoll-treated and FACS-sorted 2c hepatocytes


title: EBC-46_0.001_48h_Rep2

source_name: HaCaT cells treated with 0.001 mg/ml EBC-46 for 48 hours


title: ATAC_LPS-1h_rep2

value: BMDM cells (7th day of differentiation)


title: 2c Hepatocytes [Hep_2c_26]


title: GmSIN1 OE NaCl rep2

city: Jinan

first: Fengning

last: Xiang

state: Shandong

address: 27, Shandanan Road

department: School of life science

institute: Shandong University

data_processing:
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file (Cock P., et al., 2010).
Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011) computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.FPKM method is used in calculated expression level.
Genome_build: Glycine max Glycine_max_v2.0 from NCBI
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Glycine max

source_name: equal mix of root and leaf RNA

growth_protocol: For germination, seeds of soybean were laid on moistened filter paper for 2 d at 20°C. Seedlings of uniform size were transferred to a 16-h photoperiod regime (light/dark temperature 28 °C /20 °C) under 800 µmol m-2 s-1 illumination and a relative humidity of 60% and were grown hydroponically in half-strength Hoagland solution for two weeks.

extract_protocol:
Total RNA was extracted from mock treated and 150 mM NaCl treated 2-week old seedlings (WEI6823 and GmSIN1 OE) using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions. The total RNA from roots and leaves was isolated separately and mixtured equaly.
The mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: Addition of NaCl (final concentration is 150 mM) to the hydroponic solution for 6 hrs.

value: root, leaf

value: 2-week old

value: GmSIN1 over-expression

value: 150 mM NaCl treatment for 6 hrs


title: 2c Hepatocytes [Hep_2c_32]

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.

value: Wistar


title: EBC-211_10_48h_Rep1

source_name: HaCaT cells treated with 10 mg/ml EBC-211 for 48 hours

value: 10 mg/ml EBC-211


title: Normal stroma  135_norm

description: Normal stroma

value: female

value: Bassett


title: 2c Hepatocytes [Hep_2c_25]

value: 6 week old

value: Female


title: WT NaCl rep2

value: GmSIN1 wildtype


title: Cancer-associated stroma 135_tumour

description: Cancer-associated stroma

value: tubular


title: Cancer-associated stroma 134_tumour

description: Cancer-associated stroma

value: cystic-papillary

value: Viszla


title: EBC-46_10_48h_Rep1

value: HaCaT

value: normal keratinocyte cell line

value: 10 mg/ml EBC-46


title: 2c Hepatocytes [Hep_2c_24]


title: WT NaCl rep1

value: root, leaf


title: ATAC_LPS-1h_rep1

value: BMDM cells (7th day of differentiation)

value: LPS (10 ng/ml) for 1hrs


title: EBC-211_10_24h_Rep1

value: 24 hours


title: Normal stroma  134_norm

description: Normal stroma


title: GmSIN1 OE rep2

value: 2-week old

value: GmSIN1 over-expression

value: mock treatment for 6 hrs


title: 2c Hepatocytes [Hep_2c_23]

value: Wistar


title: 2c Hepatocytes [Hep_2c_27]

value: 6 week old


title: Control_24h_Rep2

value: vehicle


title: EBC-211_0.1_48h_Rep1

value: 48 hours


title: GmSIN1 OE NaCl rep1

value: 150 mM NaCl treatment for 6 hrs


title: EBC-46_10_24h_Rep1


title: GmSIN1 OE rep1


title: 2c Hepatocytes [Hep_2c_22]

value: Female


title: Normal stroma  132_norm

description:
Female, neutered
Normal stroma

value: female

value: tubular

value: Appenzell Mountain Dog


title: EBC-46_0.1_48h_Rep1

value: HaCaT

value: normal keratinocyte cell line

value: 0.1 mg/ml EBC-46


title: EBC-211_0.001_48h_Rep1


title: Cancer-associated stroma 131_tumour

value: cribriform

value: Bracke


title: WT rep1

value: root, leaf

value: 2-week old

value: GmSIN1 wildtype


title: Cancer-associated stroma 130_tumour

value: not disclosed


title: bin2-1 rep3

data_processing:
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before  downstream analysis to decrease data noise.Filtering steps are as follows:1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no  more than 5).  After filtering, the remaining reads are called "clean reads" and stored as FASTQ format
In general, the higher ratio of alignment, indicating that the closer the genetic relationship between sample and reference species. The lower rate may be due to low similarity with reference species or there are other pollutions.  We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome. Their alignment parameters change a little according different sequencing strategy (PE or SE):
Bowtie2 parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p  16 -k 200 Bowtie2 parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar  99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200  HISAT parameters for PE reads: -p 8 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000  HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: bin2-1_whole seedlings

growth_protocol: The seeds were treated at 4 ºC for 4 days and then germinated at 22 ºC under a 16-h light/8-h dark cycle.

extract_protocol:
Total RNA was extracted from 5-day-old light-grown seedlings (Col-0, MIR394A OE and bin2-1) using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions.
The mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).

tag: ecotype background

tag: genotype/variation

tag: developmental stage

value: whole seedlings


title: Normal stroma  131_norm

description:
Female, neutered
Normal stroma

tag: Sex


title: 2c Hepatocytes [Hep_2c_20]

tag: strain

value: Wistar

value: 6 week old


title: 2c Hepatocytes [Hep_2c_19]


title: Cancer-associated stroma 132_tumour


title: 2c Hepatocytes [Hep_2c_18]


title: Normal stroma  130_norm

description:
Female, neutered
Normal stroma


title: bin2-1 rep2

tag: tissue


title: EBC-211_0.001_24h_Rep1

value: 24 hours


title: EBC-46_0.001_48h_Rep1

value: 48 hours


title: 2c Hepatocytes [Hep_2c_17]

value: Female


title: Cancer-associated stroma 128_tumour

description: Cancer-associated stroma

value: female

value: tubulo-papillary

value: Chihuahua


title: WT rep2

tag: genotype

value: mock treatment for 6 hrs


title: bin2-1 rep1


title: 2c Hepatocytes [Hep_2c_16]


title: Control_48h_Rep1

value: HaCaT

value: normal keratinocyte cell line

value: vehicle

tag: time


title: Control_24h_Rep1

source_name: HaCaT cells treated with vehicle for 24 hours


title: MIR394 OE rep1

source_name: MIR394 OE_whole seedlings

value: MIR394A overexpression


title: Normal stroma  128_norm

description: Normal stroma

source_name: canine simple mammary carcinoma


title: 2c Hepatocytes [Hep_2c_21]


title: 2c Hepatocytes [Hep_2c_15]


title: Cancer-associated stroma 127_tumour

description: Cancer-associated stroma

value: tubular

value: Havanese


title: Col-0 rep3

source_name: Col-0_whole seedlings

value: wild type


title: Normal stroma  127_norm

description: Normal stroma


title: Col-0 rep2

value: whole seedlings


title: EBC-46_0.001_24h_Rep1


title: Cancer-associated stroma 126_tumour

description: Cancer-associated stroma

value: Tibetan Terrier


title: Col-0 rep1


title: Normal stroma  126_norm

description: Normal stroma


title: 2c Hepatocytes [Hep_2c_14]

value: Wistar

value: 6 week old


title: 2c Hepatocytes [Hep_2c_13]


title: MIR394 OE rep2


title: 2c Hepatocytes [Hep_2c_11]


title: 2c Hepatocytes [Hep_2c_10]


title: H358_ADAR B_1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: Gene expression data from H358 cells transfected with ADAR shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: Lung adenocarcinoma cell line


title: Cancer-associated stroma 123_tumour

description: Cancer-associated stroma

value: Maltese


title: Normal stroma  123_norm

description: Normal stroma

value: female


title: culture-Cont LC

city: Shanghai

first: Ajun

last: Geng

state: Shanghai

address: 320 Yue-Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: culture-Cont LC

data_processing:
Quality control using Illumina 1.5+
Basecalling usingHCS1.5.15.1+RTA1.13.48+OLB-1.9.4
Reads were aligned against the mm10 mouse reference genome with the UCSC Genes annotation (mm10 knownGene.txt) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -no-coverage-search -microexon-search -m 2). 80% of mapping rate.
Differential gene expression analysis using FDR≤0.001 AND |log2Ratio|≥1
Genome_build: mm10
Supplementary_files_format_and_content: Quantification of gene expression using RPKM algorithm and screening of differentially expressed genes using Poisson distribution model.

organism: Mus

source_name: cultured luminal cells in condition of DMSO

extract_protocol:
Total RNA from freshly isolated Lin-, CD24+, CD29lo, Sca1+and Sca1- cells were extracted with Trizol. Total RNA from cultured luminal cell  extracted with Trizol.
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2000 in BGI-tech, Beijing.

treatment_protocol: Cells were freshly sorted from mouse mammary gland.Cultured luminal cells were treated with either vehicle [DMSO] or [E2Pg, 1 mM E2, 2.5 mM Pg]

value: mammary gland

value: luminal cell

value: adult virgin

value: 8 weeks


title: culture-E2Pg LC

description: culture-E2Pg LC

source_name: cultured luminal cells in condition of E2Pg treatment


title: H358_ADAR B_2


title: Sca1- LC

description: Sca1- LC

source_name: Freshly sorted low-Sca1-expressing luminal cells in mouse mammary epithelial cells

treatment_protocol: Cells were freshly sorted from mouse mammary gland.FACS-sorted cells were resuspended at a density of 4x105cells per milliliter in chilled 100% growth factor-reduced Matrigel, and the mixture was allowed to polymerize before covering with culture medium (DMEM/F12; ITS [1:100; Sigma]; 50 ng mL1 EGF; plus either vehicle [0.01% DMSO in PBS], E2Pg[1 mM E2 and 2.5 mM Pg]. Culture medium was changed every 24 h.


title: H358_SC_1

source_name: Gene expression data from H358 cells transfected with scrambled


title: Cancer-associated stroma 121_tumour

description: Cancer-associated stroma

value: tubulo-papillary

value: Samoyed


title: H358_SC_2


title: Sca1+ LC

description: Sca1+ LC

source_name: Freshly sorted high-Sca1-expressing luminal cells in mouse mammary epithelial cells


title: Normal stroma  121_norm

description: Normal stroma


title: 2c Hepatocytes [Hep_2c_8]

city: Philadelphia

first: Takeshi

last: Katsuda

institute: University of Pennsylvania

value: Female


title: HDM D.p. RNA Band#3

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed by sickle available at https://github.com/najoshi/sickle. by Q20 and minimum-length>50
Trimmed Band#1, Band#2 and Band#3 reads were assembled de novo respectively by 'Trinity' with minimum contig length 150bp
The trimmed reads were aligned back to assembled contigs by 'bowtie2', and the bbmap/pileup.sh by Bushnell B available at https://sourceforge.net/projects/bbmap/ was used to count reads abundance for each contig.
Genome_build: Trinity_Band_*.fasta  file
Supplementary_files_format_and_content: Trinity assembled fasta and contig coverage/RPKM

organism: Dermatophagoides pteronyssinus

source_name: HDM D.p. RNA (Greer)

growth_protocol: Standard mite culture (Greer Lab)

extract_protocol:
Trizol RNA extraction from HDM
Approximately 100 ng RNA from each band #1, #2 and #3 was used for RNA-Seq library preparation by following the KAPA Total RNA-Seq Kit with RiboErase (HMR) sample preparation guide with some modifications.

tag: sample type

value: House Dust Mite (HDM) D.p. immunogenic RNA

tag: fraction

value: gel-extracted and purified RNA between 50-150bp


title: Cancer-associated stroma 109_tumour

value: tubular-solid

value: West Highland White Terrier


title: 2c Hepatocytes [Hep_2c_33]

tag: age


title: HDM D.p. RNA Band#2

value: gel-extracted and purifed RNA about 300bp


title: Aged single muscle fibers, biological replicate 2

first: Andrew

last: Brack

address: 35 Medical Center Way

department: Orthopaedic Surgery

institute: University of California San Francisco

description: Gene expression data from single muscle fibers of an aged mouse

hyb_protocol: 6 μg of the fragmented and labeled cDNA was hybridized to GeneChip Gene 1.0 ST mouse array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher)

data_processing: The data were analyzed with ExpressionFileCreator module at the Broad institute website using RMA method  and quantile normalization.

label: Biotin

source_name: Wild-type muscle fibers from an aged mouse

label_protocol: 1ng of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher)

extract_protocol: Wild-type EDL muscle was isolated and dissociated with Collagenase II for 90 minutes to yield single muscle fibers. The fibers were washed well to remove any contaminating cells. Total RNA was isolated from the purified single muscle fibers using Trizol, following  the manufaturer's instructions

value: Single muscle fibers from EDL muscle

value: Wild-type

value: 24-25 months


title: Aged single muscle fibers, biological replicate 1


title: P7 single muscle fibers, biological replicate 2

description: Gene expression data from single muscle fibers of a P7 pup

source_name: Wild-type muscle fibers from postnatal 7 day old pups

value: 7 day old


title: 2c Hepatocytes [Hep_2c_9]

address: 421 Curie Blvd, BRB II/III Rm531

source_name: Percoll-treated and FACS-sorted 2c hepatocytes

value: Wistar

value: 6 week old


title: HDM D.p. RNA Band#1

value: gel-extracted and purified RNA>500bp


title: Adult single muscle fibers, biological replicate 1

description: Gene expression data from single muscle fibers of an adult mouse

source_name: Wild-type muscle fibers from an adult mouse

value: 3-4 months


title: C_3

city: Baotou

first: Yangming

last: Si

state: Inner Mongolia

address: Arding Street No.7

department: School of Life Science and Technology

institute: Inner Mongolia University of Science&Technology

data_processing:
Basecalls performed using CASAVA
Transcript splicing by Trinity( r20140413p1)
Gene function annotation by NCBI blast 2.2.28+, KAAS(r140224),hmmscan（HMMER 3 ），blast2go（b2g4pipe_v2.5）
Relative quantity by RSEM（v1.2.15）
Supplementary_files_format_and_content: tab-delimited text files include Read count, RPKM values for each Sample …

organism: Glycyrrhiza uralensis

source_name: cell

growth_protocol: The calli was induced from young explants of licorice aseptic seedlings on solid Murashige and Skoog (MS) medium, supplemented with 2,4-D (1.0 mg/L), NAA (0.5 mg/L) and 6-BA (0.5 mg/L) (Sigma，USA). After cultured to 20 generations on a solid medium, it is inoculated to a 100 mL MS liquid medium, which is supplemented by NAA (0.5 mg/L), 6-BA (0.5 mg/L) and 30g/L sucrose, 120 rpm, 3 weeks

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent protocol.
Total RNA was extracted and detected, mRNA was separated and purified from total RNA using poly-Toligo attached magnetic beads, and then broken into small fragments using divalent cations under conditions of elevated temperature. First-strand cDNA was synthesized using a random hexamer primer and M-MuLV Reverse Transcriptase (NEB), followed by second strand cDNA synthesis using buffer, deoxyribonucleotide triphosphates (dNTPs), DNA polymerase I, and Ribonuclease H (RNase H). Finally, PCR amplification was performed and the PCR product was purified with AMPure XP beads to obtain the final library. After the library quality was assessed on the Agilent Bioanalyzer 2100 System.

treatment_protocol: 0.5 ul/ml of MeJA and 0.4 ul/ml of absolute ethyl alcohol were added to the suspension cells, respectively, and cultured for 9 h.

value: suspended cell

value: uninduced by MeJA

tag: treated time

value: uninduced


title: Normal stroma  109_norm

description:
Female, neutered
Normal stroma

value: female

tag: age of patient (years)

tag: subtype of simple carcinoma


title: 2c Hepatocytes [Hep_2c_5]

department: Perelman School of Medicine

value: Female


title: 2c Hepatocytes [Hep_2c_4]


title: P3 single muscle fibers, biological replicate 1

description: Gene expression data from single muscle fibers of a P3 pup

source_name: Wild-type muscle fibers from postnatal 3 day old pups

value: 3 day old


title: 2c Hepatocytes [Hep_2c_6]


title: 2c Hepatocytes [Hep_2c_7]


title: Adult single muscle fibers, biological replicate 2


title: C_1


title: 2c Hepatocytes [Hep_2c_3]


title: P3 single muscle fibers, biological replicate 2


title: 2c Hepatocytes [Hep_2c_1]


title: E_3

value: induced by MeJA

value: induced 9h


title: P7 single muscle fibers, biological replicate 1


title: CV16_HetFasted_4

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: HetFasted

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc).   Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: Liver

value: Heterozygous

tag: diet

value: Fasting diet


title: E_2


title: CV14_HetFasted_2


title: BEC-enriched NPC [BEC_10]

source_name: Krt19-expressing cells

value: 7 week old


title: E_1


title: CV15_HetFasted_3


title: CV13_HetFasted_1


title: C_2


title: BEC-enriched NPC [BEC_7]


title: BEC-enriched NPC [BEC_9]


title: CV12_MutFasted_4

source_name: MutFasted

value: Mutant


title: 2c Hepatocytes [Hep_2c_2]

value: Wistar


title: BEC-enriched NPC [BEC_8]


title: BEC-enriched NPC [BEC_6]


title: BEC-enriched NPC [BEC_5]


title: BEC-enriched NPC [BEC_4]


title: BEC-enriched NPC [BEC_3]


title: BEC-enriched NPC [BEC_2]


title: BEC-enriched NPC [BEC_1]


title: CV11_MutFasted_3


title: NIKS18

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

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

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

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

source_name: NIKS (ATCC CRL-12191) transfected with whole genomes of HPV18

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

extract_protocol: RNeasy mini kit (QIAGEN)

value: Foreskin keratinocytes

tag: cell line

value: ATCC CRL-12191


title: NIKS

source_name: NIKS (ATCC CRL-12191)


title: End18

source_name: End1/E6E7 (ATCC CRL-2615) transfected with whole genomes of HPV18

value: Endocervix

value: ATCC CRL-2615


title: CV08_HetUnfasted_4

source_name: HetUnfasted

value: non-Fasting normal diet


title: W03_circRNA

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: processed data file: circRNA_SRPBM.txt

data_processing:
For miRNA library preparation, a total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. A total of three small libraries were constructed using ovaries of honey bee workers. The small RNA tags were mapped to reference sequence (Amel_4.5) by Bowtie. The characteristics of hairpin structure of miRNA precursor can be used to predict new miRNA. The available software miREvo60 and mirdeep261 were integrated to predict new miRNA. Predicting the target gene of miRNA was performed by miRanda.
A total amout of 3 μg total RNA per sample was used as input material for the mRNA and lncRNA library. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The libraries were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of three libraries were constructed using ovaries of honey bee workers. Index of reference genome (Amel_4.5) was built using Bowtie V2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (FPKM, expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For circRNA library preparation, a total amount of 5 μg RNA per sample was used as input material for RNA sample preparation. Firstly, ribosomal RNAs were depleted by using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) to get rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R (Epicentre, USA) and then were subjected to Trizol extraction. Subsequently, sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of three small libraries were constructed using ovaries of honey bee workers. Reference genome was Amel_4.5. For circRNA identification, unmapped reads were kept and 20-mers from 5’ and 3’ end of these reads were extracted and aligned independently to reference sequences by Bowtie. Anchor sequences were extended by find_circ such that the complete read aligned and the breakpoints were flanked by GU/AG splice sites. Then the back-spliced reads with at least two supporting reads were annotated as circRNAs.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: counts, count RPM

organism: Apis mellifera

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA, according to the manufacturer’s instructions. mRNA and lncRNA sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. CircRNA sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. miRNA sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: social caste

value: honey bee workers

value: ovaries

tag: molecule subtype

value: circRNA


title: CV06_HetUnfasted_2


title: NIKS16

source_name: NIKS (ATCC CRL-12191) transfected with whole genomes of HPV16


title: Nitroglycerin 4

city: Huaihua

first: Wei-hua

last: Wu

state: Hunan

address: Jingxi South Street, 492

department: School of Pharmaceutical Sciences

institute: Hunan University of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Rnor_6.0.83
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Aorta

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit. Approximately 10 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit.
The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit

treatment_protocol: Male Sprague Dawley rats (180~200 g) were given GTN (100 mg/kg subcutaneously) or its vehicle (ethanol) 3 times a day for 3 days. Thoracic aorta was excised and washed by normal saline and preserved in RNAlater.

value: Aorta

value: Sprague Dawley

value: 12 Weeks

value: wild type

tag: treatment

value: nitroglycerin


title: CV09_MutFasted_1

value: Liver

value: Fasting diet


title: Ect18

source_name: Ect1/E6E7 (ATCC CRL-2614) transfected with whole genomes of HPV18

value: Ectocervix

value: ATCC CRL-2614


title: W03_mRNA including lncRNA

description: processed data file: mRNA_FRKM.xlsx

source_name: workers_ovary_mRNA including lncRNA

value: mRNA including lncRNA


title: CV04_MutUnfasted_4

source_name: MutUnfasted

value: Mutant


title: End16

source_name: End1/E6E7 (ATCC CRL-2615) transfected with whole genomes of HPV16

value: Endocervix


title: Nitroglycerin 3


title: W02_circRNA

description: processed data file: circRNA_SRPBM.txt


title: Myo1A[ts]_ImdD30A gut, biological rep2 [M_D_2]

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

data_processing:
Basecalls performed using Cyberduck(FTP)
FASTQC was used to evaluate the quality of raw paired-end sequencing reads. Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic. Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0). The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR. In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6
Supplementary_files_format_and_content: counts and edgeR

source_name: Drosophila Myo1A[ts]>ImdD30A guts 10 days post activation

growth_protocol: Flies were raised on regular food (standard cornmeal food) at 18C befor eclosion. Adult flies were transferred to 29C for 10 days to get ImdD30A expression in gut progenitor cells or enterocytes.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Library construction and sequencing was performed by Novogen company.

treatment_protocol: After the 10 day heat shift, a total of 10 guts per sample (virgin female) were dissected into Trizol and used for RNA extraction.

tag: genotype/variation

value: w; Myo1AGal4/+; tubGAL80[ts], UASGFP/UASImdD30A

tag: timepoint

value: 10 days post activation

value: dissected midgut

tag: cell type

value: enterocytes


title: CV10_MutFasted_2

tag: tissue


title: Myo1A[ts]_ImdD30A gut, biological rep1 [M_D_1]


title: End

source_name: End1/E6E7 (ATCC CRL-2615)

value: ATCC CRL-2615


title: CV07_HetUnfasted_3

tag: genotype

value: Heterozygous

value: non-Fasting normal diet


title: CV02_MutUnfasted_2


title: CV05_HetUnfasted_1


title: CV01_MutUnfasted_1


title: Ect

source_name: Ect1/E6E7 (ATCC CRL-2614)


title: Myo1A[ts]_ImdD30A gut, biological rep3 [M_D_3]


title: Nitroglycerin 2

value: Aorta

tag: strain

value: Sprague Dawley

value: 12 Weeks


title: Myo1A[ts] gut, biological rep3 [M_3]

source_name: Drosophila Myo1A[ts] guts 10 days post activation

value: w; Myo1AGal4/+; tubGAL80[ts], UASGFP/+


title: CV03_MutUnfasted_3

value: Liver


title: W02_mRNA including lncRNA

description: processed data file: mRNA_FRKM.xlsx

value: honey bee workers

value: ovaries


title: Nitroglycerin 1

value: wild type

value: nitroglycerin


title: Myo1A[ts] gut, biological rep2 [M_2]


title: Ect16

source_name: Ect1/E6E7 (ATCC CRL-2614) transfected with whole genomes of HPV16

value: Ectocervix

value: ATCC CRL-2614


title: Con 4

value: control


title: W01_circRNA

description: processed data file: circRNA_SRPBM.txt

value: circRNA


title: Myo1A[ts] gut, biological rep1 [M_1]

value: 10 days post activation

value: dissected midgut

value: enterocytes


title: W01_mRNA including lncRNA

description: processed data file: mRNA_FRKM.xlsx

value: mRNA including lncRNA


title: Con 3

value: Aorta


title: Con 2

value: Sprague Dawley


title: esg[ts]_ImdD30A gut, biological rep3 [e_D_3]

source_name: Drosophila esg[ts]>ImdD30A guts 10 days post activation

value: w; esgGal4, tubGAL80[ts], UASGFP/+;UAS-ImdD30A/+

value: progenitor cells


title: esg[ts]_ImdD30A gut, biological rep2 [e_D_2]


title: Con 1

value: 12 Weeks


title: esg[ts]_ImdD30A gut, biological rep1 [e_D_1]


title: esg[ts] gut, biological rep2 [e_2]

source_name: Drosophila esg[ts] guts 10 days post activation

value: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+


title: L1

city: Indianapolis

first: Kok

middle: Lim

last: Kua

state: IN

address: RR208  PNEO  IN

department: PED-NEONATAL MEDICINE

institute: Indiana University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq 500.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featurecounts.txt (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC rn6
Supplementary_files_format_and_content: Raw counts.txt and normalized abundance measurement from edgeR

source_name: Islets

growth_protocol: RPMI with 5mM glucose

extract_protocol:
RNA was isolated using Qiagen RNEasy Plus micro kit.
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Islets were extracted from 2 fetal pancreata after 48 hours of 4mg/min glucose infusion and recovered 24hrs in culture media

value: Fetal (GD22)

value: High glucose infusion


title: R1

value: Control


title: esg[ts] gut, biological rep3 [e_3]


title: D20L


title: D20R2


title: esg[ts] gut, biological rep1 [e_1]


title: 614489R