title: Roots, total RNA - replicate 2

city: Prague 6

first: David

last: Honys

state: CZ

address: Rozvojova 263

institute: IEB ASCR

description:
Fraction: total RNA
Gene expression profile of microspores

hyb_protocol: 1650 ng of Cy3-labeled cRNA was hybridized to Agilent Tobacco Gene Expression Microarray 4x44K for 17 h at 65 °C in a rotating Agilent hybridization oven (Agilent).

scan_protocol: The slides were scanned on the Agilent High Resolution Microarray Scanner using default parameters for 4x44K microarray formats (Agilent). Background-subtracted and spatially-detrended Processed Signal intensities were obtained by Feature Extraction Software 11.0.1.1 (Agilent) used with default parameters (Protocol GE1_1100_Jul11 and Grid 21113_D_F_20130122).

data_processing: All transcriptomic data sets were normalized using publicly available dChip 1.3 software (http://www.dchip.org). The reliability and reproducibility of the analyses were ensured by the use of duplicates in each experiment, the normalization of all arrays to the median probe intensity level, and the use of normalized intensities of all arrays for the calculation of model-based gene expression values based on the Perfect Match-only model (Li C and Wong WH: Proc Natl Acad Sci U S A 98: 31-36, 2001).

organism: Nicotiana tabacum

source_name: Roots, total RNA

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 66 ng of total RNA by Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instruction. Cy3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen). NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) was used to evaluate the cRNA yield and labeling efficiency. Cy3-labeled cRNA was then fragmented in a 30-minute incubation at 60 °C.

growth_protocol: Wild-type Nicotiana tabacum (cv. Samsun) seeds were sown in a greenhouse under 22-25°C and short-day conditions. Adult plants with fully developed roots were transplanted to an outdoor greenhouse to compost soil. There the plants were grown under the natural day-night photoperiod in spring and summer. Immature pollen grains at three stages of development were collected from August to September. The appropriate developmental stage was determined by the total length of flower buds including calyx as published previously by (Tupý J, Süss J, Hrabětová E and Říhová L: Biol Plant 25: 231-237, 1983). Flower bud lengths were as follows: uninuclear microspores (stage 1), 15-16 mm; early bicellular pollen (stage 3), 25-27 mm, late bicellular pollen (stage 5), 46-49 mm. After flower collection, the freshly isolated anthers were immediately processed by gentle mashing in a chilled mortar with 5% sucrose in sterile water. The mixture containing released pollen was filtered through an ordinary gauze to remove the anther debris. The pollen was then sedimented by centrifugation (2,000 g, 5 min, 4°C) and stored in -80°C.

extract_protocol: Total and subcellular fraction RNA was isolated from 100 mg of pollen using the Qiagen RNeasy Plant Kit according to the manufacturer’s instructions and treated with DNaseI (Promega). RNA was quantified using NanoDrop (Thermo Scientific). RNA concentration, purity and integrity (RIN) were assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment

value: roots

tag: cultivar

value: Samsun


title: Leaves, total RNA - replicate 1

status: Public on May 24 2018

type: RNA

country: Czech Republic

molecule: total RNA

source_name: Leaves, total RNA

tag: tissue

value: leaves


title: 24h pollen tubes, RNA from RNP complexes - replicate 1

description:
Fraction: RNA RNA from RNP complexes
Gene expression profile of microspores

value: 24h pollen tubes


title: Leaves, total RNA - replicate 2


title: Roots, total RNA - replicate 1


title: MM34_75

type: SRA

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

library_source: transcriptomic

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher) and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
hg19
In 10X genomics data, Cellranger-2.1 was generated UMI count and modified matrix by Seurat.
Genome_build: hg19/GRCh38(10X)
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 173 single cells and the UMI count for 1,339 single cells (from 10X).

organism: Homo sapiens

extract_protocol:
Plasma cells were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).
In CD138-negative samples, starting with 100-500ng of input RNA, sequencing libraries were constructed with the Truseq RNA Sample Prep Kit v2-setA,B (Illumina). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies) then pooled without index overlapping. Finally pooled libraries were sequenced using the HiSeq2500 (Illumina) as 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit.

tag: cell type

value: Multiple myeloma

tag: prep-site

value: Bone marrow

tag: facs sorting

value: CD138 positive

tag: heavy chain

value: IgG

tag: light chain

value: kappa

tag: iss

value: III


title: 24h pollen tubes, RNA from RNP complexes - replicate 2


title: 24h pollen tubes, polysomal RNA - replicate 2

description:
Fraction: polysomal RNA
Gene expression profile of microspores

source_name: 24h pollen tubes, polysomal RNA


title: MM34_17


title: 4h pollen tubes, RNA from EPP complexes - replicate 1

description:
Fraction: RNA RNA from EPP complexes
Gene expression profile of microspores

source_name: 4h pollen tubes, RNA from EPP complexes

value: 4h pollen tubes


title: 4h pollen tubes, total RNA - replicate 2

source_name: 4h pollen tubes, total RNA


title: Mature pollen, RNA from EPP complexes - replicate 2

source_name: Mature pollen, RNA from EPP complexes

value: mature pollen


title: 4h pollen tubes, RNA from RNP complexes - replicate 2

source_name: 4h pollen tubes, RNA from RNP complexes


title: 24h pollen tubes, RNA from EPP complexes - replicate 2


title: 24h pollen tubes, RNA from EPP complexes - replicate 1


title: 4h pollen tubes, RNA from RNP complexes - replicate 1


title: 24h pollen tubes, polysomal RNA - replicate 1


title: 24h pollen tubes, total RNA - replicate 2

source_name: 24h pollen tubes, total RNA


title: 4h pollen tubes, total RNA - replicate 1


title: 24h pollen tubes, total RNA - replicate 1


title: 4h pollen tubes, RNA from EPP complexes - replicate 2


title: 4h pollen tubes, polysomal RNA - replicate 1

source_name: 4h pollen tubes, polysomal RNA


title: Mature pollen, RNA from RNP complexes - replicate 2

source_name: Mature pollen, RNA from RNP complexes


title: Mature pollen, RNA from RNP complexes - replicate 1


title: Mature pollen, polysomal RNA - replicate 1

source_name: Mature pollen, polysomal RNA


title: MM16R_73

value: I


title: 4h pollen tubes, polysomal RNA - replicate 2


title: Mature pollen, polysomal RNA - replicate 2


title: MM34_18


title: MM34_23


title: Late bicellular pollen, RNA from RNP complexes - replicate 2

value: late bicellular pollen


title: Late bicellular pollen, polysomal RNA - replicate 2

source_name: Late bicellular pollen, polysomal RNA


title: Mature pollen, total RNA - replicate 2

source_name: Mature pollen, total RNA


title: Late bicellular pollen, RNA from EPP complexes - replicate 2


title: Mature pollen, RNA from EPP complexes - replicate 1


title: Late bicellular pollen, RNA from EPP complexes - replicate 1


title: Late bicellular pollen, RNA from RNP complexes - replicate 1


title: Early bicellular pollen, polysomal RNA - replicate 1

source_name: Early bicellular pollen, polysomal RNA

value: early bicellular pollen


title: Mature pollen, total RNA - replicate 1


title: Early bicellular pollen, RNA from RNP complexes - replicate 2


title: Late bicellular pollen, total RNA - replicate 2

source_name: Late bicellular pollen, total RNA


title: Early bicellular pollen, polysomal RNA - replicate 2


title: Early bicellular pollen, RNA from RNP complexes - replicate 1


title: Late bicellular pollen, total RNA - replicate 1


title: Early bicellular pollen, RNA from EPP complexes - replicate 1


title: Late bicellular pollen, polysomal RNA - replicate 1


title: Microspores, RNA from RNP complexes - replicate 2

source_name: Microspores, RNA from RNP complexes

value: microspores


title: Early bicellular pollen, total RNA - replicate 1

source_name: Early bicellular pollen, total RNA


title: Early bicellular pollen, total RNA - replicate 2


title: Microspores, RNA from RNP complexes - replicate 1


title: Microspores, polysomal RNA - replicate 1

source_name: Microspores, polysomal RNA


title: Early bicellular pollen, RNA from EPP complexes - replicate 2


title: Microspores, polysomal RNA - replicate 2


title: Microspores, RNA from EPP complexes - replicate 1

source_name: Microspores, RNA from EPP complexes


title: Microspores, RNA from EPP complexes - replicate 2


title: Replicate 1, RA-Tregs

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

description:
0 to RA
mlevings_Th1vsRAvsNeutralHumanTreg_ProcessedCounts.xlsx

data_processing:
The RNA-Seq Alignment App (version 1.1.0) on Illumina Basespace was used for data-processing and read quantification as follows:
Basecalls were made using RTA v2.1. Demultiplexing was achieved using bcl2fastq2.
Alignment: STAR aligners version 2.5.0a
Quantification of gene expression was done with RnaReadCounter which is part of the IsisRNA tool (Version 2.6.25.18) in the RNA-Seq Alignement App. The raw gene counts generated by RnaReadCounter are saved in the 'processed data file'.
DESeq2 version 1.16 for R was used for analysis of differential gene expression with the raw counts (from the 'processed data file') as input.
Genome_build: Homo sapiens (PAR-masked)/hg19 reference sequence
Supplementary_files_format_and_content: Excel spreadsheet for all 12 samples (mlevings_Th1vsRAvsNeutralTreg_ProcessedCounts.xlsx), raw counts of sequencing reads generated with RnaReadCounter

molecule: polyA RNA

source_name: Thymic Tregs

growth_protocol: Day 0: Stimulation with artificial antigen-presenting cells (L cells (mouse fibroblast cell line) which provide CD28 stimulation) + anti-CD3 (100ng/ml) + human recombinant IL-2 (1000U/ml) + 100ng/ml rapamycin, culture from day 0 to 7. Day 7: Stimulation with L cells + anti-CD3 + IL-2, culture from day 7 to 13. Cultured in T cell Optmizer media with serum free supplement.

extract_protocol:
Expanded cells were centrifuged, resuspended in RNAzol lysis reagent and further processed as per manufacturers instructions to obtain RNA for library preparation and subsequent NGS.
Qualifying samples (RIN>8) were prepared using the TruSeq stranded mRNA library kit (Illumina) on the Illumina Neoprep automated nanofluidic prep instrument.

treatment_protocol: Th1-conditions: 10ng/ml human recombinant IL-12 + 10ng/ml human recombinant IFN-gamma; added to culture during day 0 to 7 and/or day 7 to 13. RA-conditions: 20nM retinoic acid (RA) added to culture from day 7 to 13.

tag: subject id

tag: polarizing condition from day 0 to 7

tag: polarizing condition from day 7 to 13

value: RA


title: Replicate 3, control Tregs

description:
0 to 0
mlevings_Th1vsRAvsNeutralHumanTreg_ProcessedCounts.xlsx


title: Replicate 2, short-time Th1-Tregs

description:
Th1 to 0
mlevings_Th1vsRAvsNeutralHumanTreg_ProcessedCounts.xlsx


title: Replicate 3, short-time Th1-Tregs


title: Replicate 3, long-time Th1-Tregs

description:
Th1 to Th1
mlevings_Th1vsRAvsNeutralHumanTreg_ProcessedCounts.xlsx


title: Replicate 2, RA-Tregs


title: Replicate 3, RA-Tregs


title: Replicate 1, short-time Th1-Tregs


title: Replicate 1, control Tregs


title: P2_1

city: La Jolla

first: Aki

last: Daisuke

state: CA

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm9 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm9
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

organism: Mus musculus

source_name: splenic CD4+ T cell

extract_protocol:
extracted by RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard protocols of mRNA enrichment, reverse transcription, adaptor ligation and PCR amplification

treatment_protocol: PMA+ionomycin stimulation

value: splenic CD4+ T cell

tag: strain

tag: age

value: 6 weeks old

tag: genotype


title: DKO_1

value: DKO (Itch and WWP2)


title: WT_1

value: Wild type


title: Replicate 1, long-time Th1-Tregs


title: Microspores, total RNA - replicate 2

source_name: Microspores, total RNA

value: Samsun


title: CI_1

value: Itchf/f Cd4cre


title: C85 cell genome  vs. CCD 841 CoN cell genome

type: genomic

city: Warszawa

first: Magdalena

last: Dabrowska

address: 3 Pasteur

country: Poland

institute: Nencki Institute of Experimental Biology

hyb_protocol: Hybridization was performed according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol version 7.3.

scan_protocol: The slides were scanned using Agilent SureScan microarray scanner system 8.4. Images were quantified using Agilent Feature Extraction Software version 12.0.3.1.

data_processing: Genomic aberrations were analyzed using Agilent CytoGenomics software version 4.0.3.12.

molecule: genomic DNA

source_name: colorectal adenocarcinoma

label_protocol: Genomic DNAs were digested with Alu I and Rsa I endonucleases, and labeled with the use of Agilent SureTag complete DNA labeling kit.

growth_protocol: C85 cells were grown in RPMI 1640 medium supplemented with 10% FBS. CCD 841 CoN cells were grown in ATCC-modified EMEM medium supplemented with 10% FBS.

extract_protocol: Genomic DNAs were extracted using Qiagen DNeasy Blood and Tissue kit with implementation of Qiagen RNase A digestion step.

tag: cell line

tag: gender

value: female

tag: tumor stage

value: Dukes' stage D

source_name: colon epithelium

value: normal colon epithelium


title: C85 cell genome vs. Agilent Female Reference DNA

source_name: Agilent Reference DNA

value: unknown


title: X21d miRNA

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

description: 21 days

data_processing:
Custom program FastMicros identified miRNAs from miRBase (mouse species mm9) with 17+ base identities with two or fewer mismatches per read
DESeq was used to normalize miRNA counts
Genome_build: miRBase (www.mirbase.org) mouse (mm9) miRNAs used
Supplementary_files_format_and_content: Excel, normalized miRNA counts

source_name: tibialis anterior muscle

extract_protocol:
Frozen tissue thawed, homogenized, cells lysed
10 ng of isolated total RNA from satellite cells was used to produce cDNA libraries using the SmartSeq4 protocol (Clonetech)

treatment_protocol: Freeze injury was induced by applying a 6 mm diameter steel probe (cooled to the temperature of dry ice, −70C) to the belly of the TA muscle (directly below incision site) for 10 seconds

value: tibialis anterior muscle

tag: timepoint

value: 21 days


title: X14d miRNA

description: 14 days

tag: tissue

value: 14 days


title: X28d miRNA

description: 28 days

value: 28 days


title: X28dC miRNA

description: 28 days control


title: Replicate 2, long-time Th1-Tregs


title: Replicate 2, control Tregs


title: Dlk+ cells in collagen gel+TNFa_5 days_rep1

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Gene expression of hepatoblasts after differentiation induction towards cholangiocytes

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized to Agilent SurePrintG3 Mouse GE Microarrays for 17 hours at 65Â°C in a DNA Microarray Hybridization Oven (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The expression value (Signal) for each probe set was calculated using GeneSpring GX 12.0 (Agilent). The data were subjected to normalization using GeneSpring normalization algorithms (Agilent).

source_name: Cholangiocytes derived from Dlk+ cells_5 days_rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000

growth_protocol: Dlk+ cells were stained with anti-Dlk antibody (MBL) followed by anti-rat IgG-conjugated magnetic beads (Miltenyi Biotec) and corrected by magnetic activated cell sorting (Miltenyi Biotec).

extract_protocol: RNA extraction was performed using RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.

treatment_protocol: Dlk+ cells  were placed on collagen type I gel (Nitta Gelatin, Osaka, Japan) in the presence of tumor necrosis factor (TNF)-a (Peprotech, Rocky Hill, NJ, USA) to examine the potential to differentiate into cholangiocytes. Similarly,  cells were placed on an Engelbreth–Holm–Swarm (EHS) gel (Becton–Dickinson) in the presence of oncostatin M (OSM, R&D Systems, Minneapolis, MN, USA).

value: fetal liver

tag: origin

value: Hepatoblasts (Dlk+ cells)

tag: cell type

value: Cholangiocytes derived from Dlk+ cells


title: Dlk+ cells in EHS gel+OSM_5 days_rep1

description: Gene expression of hepatoblasts after differentiation induction towards hepatocytes

source_name: Hepatocytes derived from Dlk+ cells_5 days_rep1

value: Hepatocytes derived from Dlk+ cells


title: X7d miRNA

description: 7 days

value: 7 days


title: Dlk+ cells_purified_rep1

description: Gene expression of purified hepatoblasts

source_name: Hepatoblasts_0 day_rep1

value: Hepatoblasts


title: rTDSCs_loading_7d_rep3

city: Shanghai

first: Yiyun

last: Geng

address: 320 Yue Yang Rd, Xuhui District

country: China

institute: Chinese Academy of Sciences

description: miRNA expression after 7days mechanical loading in rTDSCs

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: tendon derived stem cells, mechanical loading, 7days, replicate 3

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: P0 rTDSCs were plated at optimal cell densities (~50 cells/cm2) and cultured at 37 °C, 5% CO2 to form colonies. At day 2 after initial plating, the cells were washed twice with PBS to remove the non-adherent cells. At day 7, they were trypsinized and mixed together as passage 0 (P0). Cells of passage 3 were used for all experiments.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: rTDSCs were plated at the density of 5×104 cells/cm2 in 2 ml of growth medium in six-well flexible silicone rubber UniFlex™ plates coated with collagen type I (Flexcell International Corporation, Hillsborough, NC). The cells were cultured for 24 hours to allow them to attach and reach 80% to 90% confluence, at which time the growth medium was replaced, and then uniaxial cyclic mechanical stretch at 0.5 Hz sinusoidal curve, 10% elongation was applied to the cells for 8h per day using an FX-5000T™ Flexercell® Tension Plus™ unit (Flexcell International Corporation, Hillsborough, NC). The cultures were incubated in a humidified atmosphere at 37°C and 5% CO2 while stretching or in the static state.

value: tendon

value: male


title: X3hC miRNA

description: 3 hours control

value: 3 hours


title: X10h miRNA

description: 10 hours

value: 10 hours


title: X3h miRNA

description: 3 hours


title: rTDSCs_loading_7d_rep2

source_name: tendon derived stem cells, mechanical loading, 7days, replicate 2


title: MAoECs RNA-seq

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

data_processing:
Paired-end reads were mapped against the GRCm38 (mm10) mouse genome with STAR (version 2.3.1)
intergenic regions were derived with an in-house tool from transcribed regions not annotated in the GRCm38.75 ENSEMBL version
Genome_build: mm10

source_name: murine aortic endothelial cells

growth_protocol: Primary murine aortic endothelial cells (MAoECs; passage 3; PELOBiotech GmbH, Planneg, Germany) were cultured using endothelial cell complete growth medium (Promocell) containing gentamicin (0.05 mg/mL; ThermoFisher)

extract_protocol:
Total RNA was isolated using the NucleoSpin microRNA Kit (Macherey-Nagel GmbH & Co. KG). RNA purity and integrity were assessed using the Fragment Analyzer™ Automated CE System (Advanced Analytical, Heidelberg, Germany). A RQN of 8.8 and a 28S/18S ratio of 2.2 were considered acceptable for next generation sequencing assay.
Five µg of DNase-treated RNA were used to prepare Massive Analysis of cDNA ends (MACE) libraries needed to perform a DNA-Methylation-Sequencing (Meth-Seq) PCR bias free quantification with TrueQuant Technology, followed by a high-throughput sequencing on the Illumina Genome Analyzer II system (GenXPro GmbH, Frankfurt, Germany).
The libraries are amplified by PCR, purified by SPRI beads and sequenced (2 x 100 bp Illumina HiSeq2000 TrueSeq, 2 x 20 Mio. Reads poly-A selected paired-end reads). Paired end sequencing of both DNA strands from each end is required for fragment strand specificity.

treatment_protocol: no treatment

value: murine aortic endothelial cells

value: primary endothelial cells

tag: passage

value: cells at passage 4


title: rTDSCs_ctrl_7d_rep3

description: miRNA expression in untreated rTDSCs

source_name: tendon derived stem cells, untreated, 7days, replicate 3


title: rTDSCs_ctrl_7d_rep2

description: miRNA expression in untreated rTDSCs

source_name: tendon derived stem cells, untreated, 7days, replicate 2


title: X72h miRNA

description: 72 hours

value: tibialis anterior muscle

value: 72 hours


title: MCF-7 Vector

city: Commerce

first: Venugopalan

last: Cheriyath

state: TX

address: 2600 S Neal Street

department: Biological and Environmental Sciences

institute: Texas A&M University-Commerce

description: Direct hybridization

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and background substracted with Illumina Genomestudio V2011.1

label: Biotin

source_name: MCF-7 Cell line

label_protocol: Standard Illumina label protocol

growth_protocol: Both Vector and G1P3 expressing cells were maintained at standard cell culture cnonsitions (37oC and 5% CO2)

extract_protocol: RNA was extracted with E.Z.N.A Total RNA Kit 1 with DNase I treatment to remove DNA. Quality control was performed with Agilent Bioanalyser.

tag: vector

value: expresses pQCXIP


title: rTDSCs_loading_7d_rep1

source_name: tendon derived stem cells, mechanical loading, 7days, replicate 1


title: SGC_5_mRNA

status: Public on May 23 2018

city: Whitechapel

first: John

last: Bladen

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

description: Sebaceous gland carcinoma pagetoid sample

hyb_protocol: Labeling, hybridization and scanning carried out at UCL Genomics Core Facility.

data_processing: R/BioConductor with gcrma package

label: biotin

extract_protocol: Qiagen FFPE kit used for microRNA and messengerRNA

treatment_protocol: FFPE

value: Sebaceous gland carcinoma pagetoid


title: SGC_9_mRNA

description: Sebaceous gland carcinoma nodular sample

scan_protocol: Labeling, hybridization and scanning carried out at UCL Genomics Core Facility.

value: Sebaceous gland carcinoma nodular


title: Control_2_mRNA

description: Normal tissue sample

source_name: Control

label_protocol: Labeling, hybridization and scanning carried out at UCL Genomics Core Facility.

value: non-cancerous eyelid/tarsal plate


title: rTDSCs_ctrl_7d_rep1

description: miRNA expression in untreated rTDSCs

source_name: tendon derived stem cells, untreated, 7days, replicate 1


title: AGO2-RIP RNA from Dicer KO BMDMs

description: AGO2-immunoprecipitated RNA

hyb_protocol: Following cRNA clean-up and quantification, 530 to 600 ng of each Cyanine-3-labeled sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays (AMADID 028005). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescence signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction 10.7.3.1 software (Agilent Technologies) and the design files 028005_D_F_20131202.xml to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: AGO2-immunoprecipitated RNA  from Dicer KO macrophages

label_protocol: 500 ng cDNA of each sample were subjected to restriction digestion with a combination of Alu I and Rsa I. The digested cDNA samples were directly labeled with exo-Klenow fragment and random primers by incorporation of Cyanine-3 dUTP.

growth_protocol: mouse bone marrow-derived macrophages were cultured in DMEM-F12/10% FCS/10% L929-conditioned medium, at 37°C in a humidified atmosphere of 5% CO2

extract_protocol: Macrophages were washed with ice-cold PBS, subsequently incubated for 15 min on ice in lysis buffer (100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 7.0, 0.5% NP40, 5 mM DTT, 250 units/ml RNase OUT, 400 μM vanadyl ribonucleoside complexes, and 1 tablet per 10 ml protease inhibitors), and homogenized with a Dounce homogenizer. The lysates were centrifuged at 16,000 x g for 15 min at 4°C. The input RNA (without immunoprecipitation) was extracted from the supernatant with TRIzol. Prior to the immunoprecipitation, protein A/G-conjugated magnetic beads were incubated with a mouse monoclonal anti-AGO2 antibody or IgG control. The antibody-conjugated beads were subsequently incubated with the cell extracts in the supernatant for 7 hours at 4°C before immobilization of the precipitate with a magnetic separator. RNA was isolated from the precipitate with TRIzol, reverse-transcribed  and pre-amplified with Ovation PicoSL WTA System V2.

value: LysM-Cre/Dicerflox/flox/Apoe–/–

value: bone marrow

value: macrophage

value: 6-8 weeks

tag: Sex

value: Male

tag: antibody

value: EIF2C2 (AGO2) monoclonal antibody (clone 2E12-1C9, Abnova)


title: SGC_7_mRNA


title: Control_3_mRNA

description: Normal tissue sample


title: Control_5_mRNA

description: Normal tissue sample


title: IgG control-RIP RNA from Dicer WT BMDMs

description: IgG-immunoprecipitated RNA

source_name: IgG control-immunoprecipitated RNA from Dicer WT macrophages

value: LysM-Cre/Dicerwt/wt/Apoe–/–

value: IgG control


title: SGC_2_mRNA


title: SGC_1_mRNA


title: input RNA from Dicer WT BMDMs

description: total RNA

source_name: Total RNA before immunoprecipitation from Dicer WT macrophages

value: none (input)


title: Control_1_mRNA

description: Normal tissue sample


title: SGC_10_mRNA


title: SGC_3_mRNA


title: MCF-7G1P3

description: Direct hybridization

value: expresses pQCXIP-G1P3


title: IgG control-RIP RNA from Dicer KO BMDMs

description: IgG-immunoprecipitated RNA

source_name: IgG control-immunoprecipitated RNA from Dicer KO macrophages


title: Parp1-KO_0Gy_rep2

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4X44K v2 (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

source_name: whole blood 24h post mock irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at 24 hours post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: x-ray dose (gy)

value: male


title: input RNA from Dicer KO BMDMs

description: total RNA

source_name: RNA before immunoprecipitation from Dicer KO macrophages


title: SGC_11_mRNA


title: Parp1-KO_0Gy_rep5


title: Parp1-KO_0Gy_rep1


title: Parp1-KO_6Gy_rep5

source_name: whole blood 24h post irradiation


title: Parp1-KO_0Gy_rep4


title: AGO2-RIP RNA from Dicer WT BMDMs

description: AGO2-immunoprecipitated RNA

source_name: AGO2-immunoprecipitated RNA from Dicer WT macrophages


title: WT_0Gy_rep5

value: Wild Type


title: WT_0Gy_rep4


title: Parp1-KO_0Gy_rep3


title: WT_0Gy_rep3


title: Parp1-KO_6Gy_rep3


title: Parp1-KO_6Gy_rep4


title: RECTUM_BIOPSY_P0300

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

institute: UMG

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
Alignment was performed with STAR RNA-Seq aligner version 2.4.0h, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.19.
The transcriptome was generated with RSEM from Ensembl reference genome version GRCh38.76.
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include expected counts for each Sample

source_name: Pretherapeutic rectal cancer patient biopsy

extract_protocol:
RNA was isolated using Trizol reagent including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina.

value: rectal cancer

tag: event distant metastasis


title: WT_0Gy_rep2


title: WT_8.8Gy_rep4


title: WT_6Gy_rep5


title: WT_0Gy_rep1


title: Parp1-KO_6Gy_rep2


title: WT_8.8Gy_rep3


title: RECTUM_BIOPSY_P0294


title: WT_6Gy_rep3


title: WT_8.8Gy_rep2


title: AGS_control_2

city: Wuhan

first: Lianlian

last: Wu

state: Hubei

address: Jiefang Road 238

department: Department of Gastroenterology, Renmin Hospital of Wuhan University

institute: Wuhan University

description:
Gene_expression_data.txt
Trans_expression_data.txt
control2

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 hg38 whole genome.
Fragments per kilobase Million (FPKM) were calculated using the formula: (total exon reads)/[mapped reads(million)*exon length (kb)]
Genome_build: hg38
Supplementary_files_format_and_content: .txt files include FPKM values for each Sample

source_name: gastric cancer cell line AGS

growth_protocol: AGS cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: AGS cells were transfected with shRNA or shRNA-NC.

value: AGS

value: gastric cancer cell line

tag: shRNA

value: sh-control

value: control


title: Parp1-KO_6Gy_rep1

tag: strain


title: AGS_sh1_2

description:
Gene_expression_data.txt
Trans_expression_data.txt
sh2

value: MFAP2 silencing


title: AGS_sh1_1

description:
Gene_expression_data.txt
Trans_expression_data.txt
sh1


title: WT_6Gy_rep1


title: WT_8.8Gy_rep1


title: WT_6Gy_rep2


title: WT_6Gy_rep4


title: SW480_siAURKA_vs_siNT_rep2

city: Amsterdam

first: Beatriz

last: Carvalho

address: Plesmanlaan 121

country: Netherlands

institute: NKI

description: Biological replicate 1 of 2

hyb_protocol: For each microarray, 825-labeled and 825 Cy5-labeled cRNA was mixed with 10x Blocking agent and 25x Fragmentation Buffer in a total volume of 55 ul, and incubated at 6°C for 30 min to fragment RNA. Then, 55 ul 2x Gex Hybridization Buffer HI-RPM was added to stop the fragmentation reaction. 100 ul of hybridization sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was done at 65°C for 17 hours.After hybridization, slides were washed with GE Wash Buffer 1, GE Wash Buffer 2 and Acenotrile.

scan_protocol: Slides were scanned on an Agilent Technologies Scanner G2505C US22502676  with the following settings: Scan Area 61x21.6 mm, scan resolution 5 uM, Single Pass scanning mode,eXtended Dynamic range, Red and Green channel, Green PMT XDR Hi 100% XDR Lo 10%, Red PMT XDR Hi 100% XDR Lo 10%, Split and Rotate OFF.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1). Pre-processing and differential expression analysis (DEA) was done using the R-Bioconductor packages Limma (Ritchie et al, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, 2015) and SVA-combat (Leek and Storey, Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis, PLoS Genetics, 2007). Conventional background correction was applied, followed by within-array normalization using Loess. Subsequently, batch-effect removal was applied for the replicate experiments, after which between-array normalization was done using the quantile method.

source_name: SW480, AURKA siRNA

label_protocol: Firstly, in a total volume of 11.5 ul, 500 ng of total RNA was primed with 1.2 µl of T7 Promoter primer at 65°C for 10 min in the presence of  2 ul Spike A (Cy3) or Spike B (Cy5) mix. Secondly, a total volume of 8.3 cDNA Master mix (4 ul First Strand Buffer, 2 ul of 0.1 M DTT,  10 mM dNTP mix, 1 ul of MMLV-RT and 0.5 ul of RNaseOut) was added to each sample and incubated at 40°C for 2 h. Thirdly, a total volume of 58 ul Transcription Master mix ( 15.3 ul nuclease-free water, 20 ul of 4x Transcription Buffer, 6 ul of 0.1 M DTT, 8 ul of NTP mx, 6.4 ul of 50% PEG, 0.5 ul of RNaseOut, 0.6 ul of Inorganic Pyrophosphatase, 0.8 ul of T7 RNA Polymerase, 2.4 ul of Cy3-CTP or Cy5-CTP) was added to each sample and incubated at 40°C for 2 h

growth_protocol: SW480 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Lonza, Verviers, Belgium) containing 10% fetal bovine serum (FBS) (HyClone; Perbio Science, Etten-Leur, The Netherlands), and Caco2 cells were grown in RPMI 1640 (Lonza) containing 20% FBS. Both cell culture media were supplemented with 2 mM L-glutamine, 100 IU/ml sodium penicillin (Astellas Pharma B.V., Leiderdorp, the Netherlands), and 100 mg/ml streptomycin (Fisiopharma, Palomonta (SA), Italy).

extract_protocol: Total RNA was isolated using TriZol reagent (Invitrogen, Breda, the Netherlands) and subjected to purification using RNeasy Kit (Qiagen, Hilden, Germany). RNA concentrations and purities were measured on a Nanodrop ND-1000 spectrophotometer (Isogen, IJsselstein, the Netherlands). RNA quality was evaluated by generating an electropherogram on the Agilent Bioanalyzer 2100 using a RNA 6000 Nano-LabChip (Agilent Technologies, Santa Clara, CA, the Netherland). RNA integrity numbers (RIN) of > 9.0 were considered as good quality RNA.

treatment_protocol: Transfection with siRNA pools (SMARTpools) from Dharmacon (Lafayette, Colorado, USA) was performed 24 h after seeding according to the manufacturer’s recommendations. A final siRNA concentration of 30 nM was obtained using DharmaFECT3 reagent (1:1000 dilution) for both cell lines. A non-targeting control siRNA pool (Non-Targeting Pool 2; D-001206-14) was used as a negative control.

tag: tumor type

value: colorectal cancer

source_name: SW480, control (non-targeted) siRNA


title: Caco2_siAURKA_vs_siNT_rep2

description: Biological replicate 1 of 2

source_name: Caco2, AURKA siRNA

source_name: Caco2, control (non-targeted) siRNA


title: SW480_siAURKA_vs_siNT_rep1

description: Biological replicate 1 of 2


title: RECTUM_BIOPSY_P0311


title: AGS_control_1

description:
Gene_expression_data.txt
Trans_expression_data.txt
control1

tag: genotype


title: RECTUM_BIOPSY_P0160


title: RECTUM_BIOPSY_P0123


title: RECTUM_BIOPSY_P0112


title: RECTUM_BIOPSY_P0028


title: RECTUM_BIOPSY_P0291


title: RECTUM_BIOPSY_P0048


title: RECTUM_BIOPSY_P0022


title: Caco2_siAURKA_vs_siNT_rep1

description: Biological replicate 1 of 2

tag: cell line


title: Treated_day_3_replicate2

city: Manchester

first: Simon

middle: Roy

last: Turner

address: Oxford Road

department: Faculty of Biology, Medicine and Health Science, School of Biological Science

institute: University of Manchester

data_processing:
Demultiplexing of the output data (allowing one mismatch) and BCL-to-Fastq conversion was performed with CASAVA 1.8.3.
Post-sequencing libraries for the NGS experiment were assessed for read quality and adapter contamination using FastQC (version 0.11.3)
Reads were aligned to the A. thaliana genome using the STAR read aligner (version 2.5.0c Dobin et al., 2013).
Genome_build: Arabidopsis_thaliana.TAIR10
Supplementary_files_format_and_content: tab delimited csv file containing paired-end stranded and unstranded reads mapped to genome

organism: Arabidopsis thaliana

source_name: 5 pooled hypocotyls

growth_protocol: 35S::CO:GR co-2 tt4 plants (Coupland, 1997) were grown individually under long day conditions alongside co-2 tt4 control mutants. At 6 weeks of age, the 35S::CO:GR co-2 tt4 plants were watered with 25 ml of a 10 µM dexamethasone solution to induce flowering whilst the co-2 tt4 mutants were mock treated with water.  Hypocotyl tissue was harvested and frozen in liquid nitrogen 0, 1, 2, 3, 4, 6 and 14 days after induction for the 35S::CO:GR co-2 tt4 plants and days 0, 1, 3 and 4 for the co-2 tt4 controls.

extract_protocol:
Hypocotyl tissue was frozen in liquid nitrogen and ground using a mortar and pestle. RNA was extracted using TRIzol reagent (Life Technologies), as per the manufacturer's instructions.
RNA sequencing (RNA-seq) libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (0.1-4ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. The mRNA was then fragmented using divalent cations under elevated temperature and then reverse transcribed into first strand cDNA using random primers. Second strand cDNA was then synthesised using DNA Polymerase I and RNase H. Following a single 'A' base addition, adapters were ligated to the cDNA fragments, and the products then purified and enriched by PCR to create the final cDNA library. Adapter indices were used to multiplex libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (101 + 101 cycles, plus indices) on an Illumina HiSeq2500 instrument.

value: hypocotyls

tag: treatment

value: Treatment with 10 µM dexamethasone at day 3

tag: age at day 0

value: 6 weeks

tag: strain/line

value: 35S::CO:GR co-2 tt4


title: Treated_day_14_replicate2

treatment_protocol: At 6 weeks of age, the 35S::CO:GR co-2 tt4 plants were watered with 25 ml of a 10 µM dexamethasone solution to induce flowering whilst the co-2 tt4 mutants were mock treated with water.  Hypocotyl tissue was harvested and frozen in liquid nitrogen 0, 1, 2, 3, 4, 6 and 14 days after induction for the 35S::CO:GR co-2 tt4 plants and days 0, 1, 3 and 4 for the co-2 tt4 controls.

tag: tissue

value: Treatment with 10 µM dexamethasone at day 14


title: Treated_day_14_replicate3


title: Treated_day_4_replicate2

value: Treatment with 10 µM dexamethasone at day 4


title: Treated_day_6_replicate2

value: Treatment with 10 µM dexamethasone at day 6


title: Treated_day_3_replicate1


title: Treated_day_6_replicate3


title: Treated_day_2_replicate3

value: Treatment with 10 µM dexamethasone at day 2


title: Treated_day_3_replicate3


title: Treated_day_6_replicate1


title: Treated_day_2_replicate2


title: DNBS_GR159897 Rep1

city: East Lansing

first: Brian

middle: David

last: Gulbransen

state: MI

address: 567 Wilson Rd

department: Physiology

institute: Michigan State University

data_processing:
Low quality bases and adapter-contaminated reads were removed using Cutadapt v1.10 (Martin 2011) and LC sciences (Houston, TX) in-house perl scripts.
Sequence quality was confirmed using the web-based platform FastQC v 0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
HISAT2 v2.0 (Kim, Langmead, and Salzber 2015) was used to map reads to the mouse genome.
Reads were assembled using StringTie v1.3 (Pertea et al. 2015).
Transcriptomes of replicates were merged to a comprehensive transcriptome using perl scripts and gffcompare (Trapnell et al. 2010).
Genome_build: Transcript expression levels as FPKMs were estimated from the comprehensive transcriptome using StringTie v1.3 (Pertea et al. 2015).
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample in a single matrix table

source_name: distal colon myenteric glial cells

growth_protocol: All mice were maintained on a 12-hour light/dark cycle in a temperature-controlled environment with access to Teklad Global 19% protein extruded irradiated (2919) food and water ad libitum.

extract_protocol:
Distal colon myenteric plexi were dissected and flash frozen in liquid nitrogen. Tissue was homogenized and HA-tagged ribosomes were immunoprecipitated utilizing a protocol from Sanz et al., PNAS, 2009 with solution adjustments from Gabanyi et al., Cell, 2016 . RNA was extracted using the RNeasy micro kit (Qiagen). 1 ng mRNA was used to generate cDNA with the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories).
Paired-end libraries were constructed from 1ng cDNA utilizing Nextera DNA Library Preparation Kit (Ilumina, San Diego, CA) and sequenced on an Illumina Hiseq 4000 following manufacturer’s specification.

treatment_protocol: CreERT2 activity was induced by feeding the animals with chow containing tamoxifen citrate (400 mg/kg) for 2 weeks followed by 1 week of normal chow before use. 48 hours prior to euthanasia, mice under isoflurane anaesthesia were given an enema of 0.1 mL of either saline or a solution containing 5 mg di-nitrobenzene sulfonic acid (DNBS) dissolved in 50% ethanol. Mice received daily injections (i.p.) of either 0.5 mg/kg GR159897 (Tocris, Minneapolis, MN) in 0.1% dimethyl sulfoxide (DMSO) or 0.1% DMSO (vehicle) over 3 days beginning 24 hours prior to DNBS administration.

value: Sox10::CreERT2+/- / Rpl22tm1.1Psam/J

value: female

value: distal colon myenteric plexus glial cells

tag: treatment 1

value: 0.1mL of 5mg DNBS in 50% EtOH enema

tag: treatment 2

value: 0.5mg/kg GR159897 in 0.1% DMSO i.p. injection


title: Saline_GR159897 Rep3

value: saline enema


title: DNBS_GR159897 Rep2


title: DNBS_GR159897 Rep3

value: male


title: Saline_GR159897 Rep2


title: Saline_GR159897 Rep1


title: DNBS_Vehicle Rep3

value: 0.1% DMSO i.p. injection


title: Treated_day_14_replicate1


title: DNBS_Vehicle Rep2


title: Treated_day_2_replicate1


title: Treated_day_1_replicate3

value: Treatment with 10 µM dexamethasone at day 1


title: Treated_day_4_replicate3

value: hypocotyls


title: Treated_day_1_replicate2


title: Treated_day_1_replicate1


title: Microspores, total RNA - replicate 1

city: Prague 6

first: David

last: Honys

institute: IEB ASCR

description:
Fraction: total RNA
Gene expression profile of microspores

data_processing: All transcriptomic data sets were normalized using publicly available dChip 1.3 software (http://www.dchip.org). The reliability and reproducibility of the analyses were ensured by the use of duplicates in each experiment, the normalization of all arrays to the median probe intensity level, and the use of normalized intensities of all arrays for the calculation of model-based gene expression values based on the Perfect Match-only model (Li C and Wong WH: Proc Natl Acad Sci U S A 98: 31-36, 2001).

source_name: Microspores, total RNA

extract_protocol: Total and subcellular fraction RNA was isolated from 100 mg of pollen using the Qiagen RNeasy Plant Kit according to the manufacturer’s instructions and treated with DNaseI (Promega). RNA was quantified using NanoDrop (Thermo Scientific). RNA concentration, purity and integrity (RIN) were assessed using an Agilent 2100 Bioanalyzer.

value: microspores

tag: cultivar

value: Samsun


title: DNBS_Vehicle Rep1


title: Treated_day_4_replicate1

value: 6 weeks

value: 35S::CO:GR co-2 tt4


title: Saline_Vehicle Rep3


title: Treated_day_0_replicate3

value: Treatment with 10 µM dexamethasone at day 0


title: Treated_day_0_replicate1


title: Control_day_4_replicate2

value: Mock treatment with water at day 4

value: co-2 tt4


title: Saline_Vehicle Rep2

value: Sox10::CreERT2+/- / Rpl22tm1.1Psam/J


title: Control_day_4_replicate3


title: Wt Cranial Base 3

city: Aurora

first: Trevor

last: Williams

state: CO

address: 12801 East 17th Ave

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads generated were mapped to the mouse genome by gSNAP, expression derived by Cufflinks, and differential expressed analyzed by ANOVA in R, as described previously (Bradford et al., 2015).
Genome_build: Mm 10
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: cranial base

extract_protocol:
RNA was extracted from isolated tissue samples using the RNeasy Lipid Tissue Mini Kit (Qiagen Cat. NO 74804) following the manufacturer’s protocol.
Quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies, Santa Clara, CA) to ensure that it was of sufficient quality for library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA).
RNA-seq using the Illumina HiSeq4000 Platform and single end reads (1x151).

value: mixed

tag: developmental stage

value: wildtype

value: cranial base


title: Control_day_4_replicate1


title: Control_day_3_replicate3

value: Mock treatment with water at day 3


title: Treated_day_0_replicate2


title: Wt Cranial Base 2


title: Mutant Skull 2

source_name: cranial vault

value: Msx2Cre; CAGFgf8 mutant (MCAGF8)

value: cranial vault


title: Wt Skull 3


title: Control_day_3_replicate1


title: Control_day_1_replicate2

value: Mock treatment with water at day 1


title: Mutant Skull 1


title: Wt Skull 2


title: Wt Cranial Base 1


title: Mutant Skull 3


title: Control_day_1_replicate1


title: Control_day_1_replicate3


title: RN2_SETD2_6880_rep3

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
ChIP-Seq processing:
Quality-filtering and -trimming was done with PRINSEQ-lite (version 0.20.4)
Simultaneously mapped against the Mus musculus (GRCm38) and Drosophila melanogaster (dm6) reference genomes via BWA (version 0.7.15)
SAMtools (version 1.4) was used to split the alignments into mouse and Drosophila reads
Read normalization via the Drosophila melanogaster spike-in material was carried out with Deeptools (version 2.5.0.1)
RNA-Seq processing:
Pre-processing with PRINSEQ-lite (version 0.20.4)
Reads were mapped via STAR (version 2.5.0b) against the mouse (GRCm38) reference genome
Processing of the alignment results with SAMtools (0.1.19), counts per gene were obtained by HTSeq (version 0.6.0)
Normalization and differential expression analysis between two samples was carried out with DESeq2
Genome_build: mm10, dm6
Supplementary_files_format_and_content: bigWig files were generated using deeptools, txt files represent the DESeq2 output and HTSeq gene counts

source_name: AML cells; MLL-AF9/NrasG12D

growth_protocol: RNA-Seq/ChIP-Seq: Suspension cell line was maintained in RPMI1640 (Gibco) supplemented with 10% FBS, 100 U/ml penicilin an 100 µg/ml streptomycin

extract_protocol:
RNA-Seq: Total RNA was isolated using Qiagen Rneasy kit. ChIP-Seq: Lysates were clarified from sonicated nuclei and chromatine was isolated with indicated antibody.
RNA-Seq: TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer) ChIP-Seq: Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs)
ChIP-Rx (ChIP-seq, samples spiked in with Dropsophila Melanogaster Chromatin (S2 cell line))

treatment_protocol: RNA-Seq/ChIP-Seq: Cells were treated with Doxycyclin (1µg/ml) for 72 hours before the experiment to induce the expression of shRNAs

value: peripheral blood

tag: cell type

value: expected ckit+, Mac1-, Gr1- genotype:NRasG12D; MLL-AF9

value: Dox inducible knockdown of Setd2; shSetd2.6880


title: RN2_SETD2_1638_rep2

value: Dox inducible knockdown of Setd2; shSetd2.1638


title: Control_day_0_replicate3

value: hypocotyls

value: Mock treatment with water at day 0

value: 6 weeks


title: Control_day_3_replicate2


title: Saline_Vehicle Rep1

tag: Sex

value: male

value: distal colon myenteric plexus glial cells

value: saline enema

value: 0.1% DMSO intraperitoneal (i.p.) injection


title: RN2_SETD2_1638_rep1


title: Wt Skull 1

value: mixed

value: wildtype


title: Control_day_0_replicate2

value: co-2 tt4


title: RN2_SETD2_6880_rep1


title: Control_day_0_replicate1


title: RN2_SETD2_6880_rep2


title: RN2_Ren713_rep3

description:
DESeq2_output_REN_SETD2_1638.txt
DESeq2_output_REN_SETD2_6880.txt

value: Dox inducible knockdown of Renilla; shRen.713


title: Setd2_H3K79me2_2

library_source: genomic

tag: chip antibody


title: RN2_Ren713_rep1


title: RN2_Ren713_rep2


title: Setd2_H3K36me3_1


title: Setd2_H3K36me3_2


title: Setd2_H3K79me2_1


title: RN2_SETD2_1638_rep3


title: Setd2_H3K4me3_2


title: Ren_H3K4me3_2


title: Ren_H3K4me3_1


title: Ren_H3K79me2_2


title: Setd2_H3K4me3_1


title: Ren_H3K79me2_1


title: Ren_H3K36me3_2


title: Ren_H3K36me3_1


title: Setd2_H3K79me2_IN


title: Setd2_H3K36me3_IN


title: Setd2_H3K4me3_IN


title: Ren_H3K4me3_IN


title: Ren_H3K79me2_IN


title: Ren_H3K36me3_IN


title: Dicer KO BMDMs, Replicate 3

description:
Biological replicate 3. of 3 BMDMs from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Macrophage-KO3

data_processing:
The Applied Biosystems TaqMan Rodent miRNA A+B Cards Set v3.0  (catalog number 4444909) was used for this study. Taqman low density arrays were run on the 7900HT Fast Real-Time PCR System. The ABI TaqMan SDS v2.4 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software. Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRNAs from card A and B was used for analysis. Data were calculated using qBase software. Input data for analysis consisted of all samples. CT values were normalized to multiple endogenous controls (snoRNA202, snoRNA135 and MammU6 for Card A, snoRNA202, snoRNA135, MammU6 and snoRNA429 for Card B).
normalization: qBase-software computed signal (target gene signal normalized to endogenous controls and then scaled to WT group); Fold_Change: KO/WT

label: FAM

source_name: Dicer knockout bone marrow-derived macrophages

label_protocol: cDNA was obtained by TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems) and amplified by TaqMan PreAmp Master Mix (Applied Biosystems)

extract_protocol: mirVana miRNA Isolation Kit, see manufacturer's web site

value: bone marrow

value: macrophages

value: LysM-Cre/Dicerflox/flox/Apoe–/–

tag: age

value: 6-8 weeks

value: Male


title: SkM_Epi_Mem_28: Muscle_7wk_Loading_Participant_006_Rep1

city: Liverpool

first: Robert

middle: Arthur

last: Seaborne

address: Byrom Street

department: SCAMP

institute: Liverpool John Moores University

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

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing: Partek Genomic Suite V6.6 (manifest file B2 version)

label_protocol: Standard Illumina Protocol (Participant 001, Participant 002 etc. refer to the human participant number 1,2 etc.)

growth_protocol: Human muscle was obtained at baseline from previously untrained subjects, following the first single bout of resistance training (Acute_Resistance_Loading), after 7 weeks of resistance exercise loading (Resistance_Loading), 7 weeks exercise cessation (Unloading) and a final 7 weeks of resistance exercise loading (Resistance_Reloading).

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with manufacturers guidelines

value: vastus lateralis muscle

tag: gender

tag: weight

value: 74 kg

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: SkM_Epi_Mem_34: Muscle_7wk_Unloading_Participant_007_Rep1

value: 68 kg


title: SkM_Epi_Mem_21: Muscle_Baseline_Participant_005_Rep1

value: 79 kg


title: SkM_Epi_Mem_38: Muscle_7wk_Loading_Participant_008_Rep1


title: SkM_Epi_Mem_22: Muscle_Acute_Participant_005_Rep1


title: Dicer KO BMDMs, Replicate 2

description:
Biological replicate 2. of 3 BMDMs from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Macrophage-KO2

tag: genotype


title: SkM_Epi_Mem_26: Muscle_Baseline_Participant_006_Rep1


title: SkM_Epi_Mem_35: Muscle_7wk_Re-oading_Participant_007_Rep1


title: SkM_Epi_Mem_20: Muscle_7wk_Re-oading_Participant_004_Rep1


title: SkM_Epi_Mem_17: Muscle_Acute_Participant_004_Rep1


title: SkM_Epi_Mem_14: Muscle_7wk_Unloading_Participant_003_Rep1


title: Dicer KO BMDMs, Replicate 1

description:
Biological replicate 1. of 3 BMDMs from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Macrophage-KO1


title: SkM_Epi_Mem_32: Muscle_Acute_Participant_007_Rep1


title: SkM_Epi_Mem_12: Muscle_Acute_Participant_003_Rep1


title: SkM_Epi_Mem_40: Muscle_Baseline_Participant_001_Rep2


title: SkM_Epi_Mem_29: Muscle_7wk_Unloading_Participant_006_Rep1


title: SkM_Epi_Mem_36: Muscle_Baseline_Participant_008_Rep1


title: SkM_Epi_Mem_23: Muscle_7wk_Loading_Participant_005_Rep1


title: Dicer WT BMDMs, Replicate 2

description:
Biological replicate 2. of 3 BMDMs from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Macrophage-WT2

source_name: Dicer wide type bone marrow-derived macrophages

value: LysM-Cre/Dicerwt/wt/Apoe–/–


title: SkM_Epi_Mem_37: Muscle_Acute_Participant_008_Rep1


title: SkM_Epi_Mem_25: Muscle_7wk_Re-oading_Participant_005_Rep1


title: SkM_Epi_Mem_33: Muscle_7wk_Loading_Participant_007_Rep1


title: SkM_Epi_Mem_31: Muscle_Baseline_Participant_007_Rep1


title: SkM_Epi_Mem_27: Muscle_Acute_P006_Rep1


title: SkM_Epi_Mem_16: Muscle_Baseline_Participant_004_Rep1


title: SkM_Epi_Mem_19: Muscle_7wk_Unloading_Participant_004_Rep1


title: SkM_Epi_Mem_15: Muscle_7wk_Re-oading_Participant_003_Rep1


title: SkM_Epi_Mem_18: Muscle_7wk_Loading_Participant_004_Rep1


title: SkM_Epi_Mem_39: Muscle_7wk_Unloading_Participant_008_Rep1


title: SkM_Epi_Mem_13: Muscle_7wk_Loading_Participant_003_Rep1


title: Dicer WT BMDMs, Replicate 1

description:
Biological replicate 1. of 3 BMDMs from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Macrophage-WT1


title: SkM_Epi_Mem_30: Muscle_7wk_Re-oading_Participant_006_Rep1


title: H92N-017 smoke

city: Salt Lake City

first: Kenneth

middle: Ivan

last: Aston

state: Select

address: 675 Arapeen Dr Suite 201

institute: University of Utah

description:
Sample name:
X51

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

data_processing: BeadStudio software. matrix_processed.txt contains Average Beta

label: Cy5 and Cy3

source_name: sperm

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

extract_protocol: following somatic cell lysis,  genomic DNA was extracted and purified from sperm using Qiagen DNeasy Kit according to standard instructions, with the exception of cell lysis that was performed in buffer X2 (20 mM TrisHCl [pH 8.0], 20 mM EDTA, 200 mM NaCL, 80 mM DTT, 4% SDS, 250 ug/ml proteinase K)

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years

tag: sperm concentration (m/ml)


title: WD08-007 control

description:
Sample name:
X173

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

tag: tissue


title: UD8V-017 smoke

description:
Sample name:
X48


title: 3C5F-011 control

description:
Sample name:
X170


title: B11Z-013 control

description:
Sample name:
X171


title: 17RD017 smoke

description:
Sample name:
X81


title: 8FC4010 control

description:
Sample name:
X182


title: IM7G016 smoke

description:
Sample name:
X82


title: TS5.144_Inj_RNA-Seq

city: Lexington

first: Darrell

last: Ricke

institute: MIT Lincoln Laboratory

data_processing:
RNA data was pseudoaligned to the University of California, Santa Cruz, annotated Sus scrofa (pig) genome (build 9.2)
Transcript abundances were quantified using Kallisto with default parameters
R/Bioconductor DESeq 2 was used to calculate differential expression (DE) of transcripts
R was used to analyze expression data for set analysis (GAGE), principal component analysis, and correlation of inter-treatment gene expression
Cound data was log2 transformed, after adding a pseudocount of 0.5 to all measurements
Genome_build: Rattus norvegicus (rat) genome (build 6.0)
Supplementary_files_format_and_content: Excel format worksheet for genes

extract_protocol:
The muscles were thawed, minced and homogenized (Tissue Ruptor, Qiagen) for 30 seconds at room temperature and total RNA was isolated from the slurry using the miRNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
1 μg of isolated total RNA was used to produce cDNA libraries using the Truseq protocol (Illumina), as per the manufacturer’s instructions. Biological replicates or triplicates were produced from each condition and individual libraries were pooled and sequenced using 76 base-pair (bp) paired-end reads on a Hi-Seq. 2500 in high output mode to an average depth of 55 M reads per library.

treatment_protocol: while under isoflurane anesthesia a unilateral full-thickness VML injury was created using a 6 mm punch biopsy to the middle third of the TA muscle. On average, the tissue removed from the TA weighed 90.5 ± 3.2 mg.

tag: strain

value: Lewis rat

tag: injury

value: VML

tag: run

value: Run

tag: repair

value: MMG

tag: timepoint

value: day 14

value: tibialis anterior muscle


title: TS5.143_Inj_RNA-Seq

value: NoRun


title: BL2Baff-1 [Affymetrix]

hyb_protocol: Fragmentation and hybridization on Human ST1.0 Arrays were processed according to manufacturer's recommendations by the TAL (UMG, Germany)

scan_protocol: Affymetrix protocol

data_processing: R/Bioconductor

source_name: BL2 cells

label_protocol: RNA was labelled using Affymetrix GeneChip IVT Labelling Kit (Affymetrix)

growth_protocol: Cells were maintained in RPMI 160 supplemented with 10% fetal calf serum (FCS) and glutamine; peniciline; streptomycine at cell densities between 2x10^5 and 1x10^6 cells per ml.

extract_protocol: RNA was isolated with RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For stimulation studies, cells were cultured in cell culture medium supplemented with 10 mM HEPES at 1 x 10^6 cells/ml and incubated with B-cell activating factor (BAFF) for up to 24 hrs.

tag: agent

value: Baff stimulated

tag: cell line


title: GS00018 smoke

description:
Sample name:
X80


title: exGF-SI_7

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

description:
Processed data file 1 - HTSeq gene counts.xlsx
Processed data file 2 - DESeq2 results.xlsx

data_processing:
Base calling was achieved using standard Illumina CASAVA pipeline
Fastq-format reads were quality filtered and trimmed using Trimmomatic (v0.32)
Aligment to the mouse reference genome (GRCm38.p3) was achieved using the STAR aligner (v2.4.0f1 )
Ensembl database release 78 gene models were also used for counting mapped reads per gene using HTSeq-Count (v0.6.0)
Differential gene expression was calculated for pairwise comparisons using the DESeq2 R-package (v1.6.2) with default parameters. Genes with an FDR-adjusted p-value ≤ 0.1 were considered differentially regulated.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: .xlsx - tab delimited file with read counts for all samples (HTSeq)
Supplementary_files_format_and_content: .xlsx - Excel file with expression values, fold change, p-values and gene symbol (DESeq2) - multiple excel sheets in one excel workbook

source_name: Mouse brain amygdala handdissected hemisphere

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion/life technologies) and Dnase treated (Turbo DNA-free, Ambion/life technologies) according to the manufacturers recommendations. RNA concentrations and quality were determined using Nanodrop 1000 and Bioanalyzer.
TruSeq® Stranded ribodepleted RNA Sample preparation kit was performed externaly by Vertis, Germany and Beckmann-Coulter, USA

value: Swiss Webster

tag: treatment

value: germ-free colonized at weaning social interaction

tag: age

value: 10 weeks

tag: molecule

value: ribodepleted RNA


title: exGF-SI_8


title: BL2Baff-3 [Affymetrix]


title: TS5.142_Inj_RNA-Seq

value: NoRepair


title: BL2-3 [Affymetrix]

value: unstimulated


title: TS5.141_Inj_RNA-Seq


title: SkM_Epi_Mem_24: Muscle_7wk_Unloading_Participant_005_Rep1

value: vastus lateralis muscle

tag: gender

value: Male

tag: weight

value: 79 kg

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: BL2Baff-2 [Affymetrix]


title: BL2-2 [Affymetrix]


title: WI7K021 smoke

description:
Sample name:
X61

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years

tag: sperm concentration (m/ml)


title: exGF-SI_5

tag: strain

tag: tissue


title: SkM_Epi_Mem_11: Muscle_Baseline_Participant_003_Rep1


title: exGF-SI_6


title: insulin resistant [ID58_6072_SC]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to GeneChip Human Trancriptome Arrays 2.0 (HTA), and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction. Prior to further analysis,  collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetric probsets to mapped FANTOM-CAT IDs.

source_name: subcutaneous adipose tissue_insulin resistant

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies from the abdominal subcutaneous adipose tissue depot were obtained from the surgical incision. Samples were immediately frozen in liquid nitrogen and kept at -70C for subsequent DNA and RNA preparation.

tag: suject status

value: obese

value: female

tag: insulin sensitivity

value: insulin resistant

value: subcutaneous white adipose tissue


title: insulin resistant [ID60_6073_SC]


title: BL2-1 [Affymetrix]

tag: agent

tag: cell line


title: 94CK-015 control

description:
Sample name:
X172


title: 7DU9011 control

description:
Sample name:
X180


title: insulin resistant [ID56_6070_SC]

tag: age


title: T7GR-017 control

description:
Sample name:
X159


title: TS5.139_Inj_RNA-Seq

address: 244 Wood Street

value: Lewis rat

tag: injury

value: VML

tag: run

value: NoRun

tag: repair

value: MMG

tag: timepoint

value: day 14

value: tibialis anterior muscle


title: TS5.137_Inj_RNA-Seq

value: NoRepair


title: exGF-SI_2

value: Swiss Webster

tag: treatment

value: germ-free colonized at weaning social interaction

value: 10 weeks

tag: molecule

value: ribodepleted RNA


title: exGF-SI_4


title: TS5.138_Inj_RNA-Seq

value: Run


title: Dicer WT BMDMs, Replicate 3

city: Munich

first: Andreas

last: Schober

institute: Ludwig-Maximilians-University

description:
Biological replicate 3. of 3 BMDMs from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Macrophage-WT3

value: bone marrow

tag: cell type

value: macrophages

tag: genotype

value: LysM-Cre/Dicerwt/wt/Apoe–/–

value: 6-8 weeks

tag: Sex

value: Male


title: exGF-SI_3


title: YH7V-012 control

description:
Sample name:
X144

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years

tag: sperm concentration (m/ml)


title: exGF-SI_1

tag: strain

tag: tissue


title: insulin resistant [ID54_6055_SC]

tag: suject status

value: obese

tag: gender

value: female

tag: insulin sensitivity

value: insulin resistant

value: subcutaneous white adipose tissue


title: A93W-010 control

description:
Sample name:
X142


title: TS5.136_Con_RNA-Seq

value: Lewis rat

tag: injury

value: NoVML

tag: run

value: MMG

value: day 14

value: tibialis anterior muscle


title: GF-SI_12

value: Swiss Webster

value: germ-free social interaction

tag: age

value: 10 weeks

value: ribodepleted RNA


title: GF-SI_10

tag: treatment


title: insulin sensitive [ID50_6047_SC]

source_name: subcutaneous adipose tissue_insulin sensitive

value: insulin sensitive


title: insulin sensitive [ID46_6039_SC]


title: TS5.136_Inj_RNA-Seq

value: VML

value: Run

tag: repair

tag: timepoint


title: insulin resistant [ID48_6040_SC]


title: SkM_Epi_Mem_7: Muscle_Acute_Participant_002_Rep1

value: vastus lateralis muscle

value: Male

tag: weight

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: insulin resistant [ID44_6037_SC]

value: obese

value: female

value: insulin resistant

value: subcutaneous white adipose tissue


title: SkM_Epi_Mem_6: Muscle_Baseline_Participant_002_Rep1


title: K2SG019 smoke

description:
Sample name:
X32

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: insulin resistant [ID52_6051_SC]

tag: tissue


title: SkM_Epi_Mem_9: Muscle_7wk_Unloading_Participant_002_Rep1


title: TS5.135_Con_RNA-Seq

tag: strain

value: Lewis rat

value: NoVML

value: NoRun

value: MMG

value: day 14

value: tibialis anterior muscle


title: TS5.134_Con_RNA-Seq

value: NoRepair


title: GF-SI_8

value: Swiss Webster

value: germ-free social interaction

value: 10 weeks

tag: molecule

value: ribodepleted RNA


title: LG2Z012 control

description:
Sample name:
X193

tag: sperm concentration (m/ml)


title: U0QC-012 smoke

description:
Sample name:
X77


title: SkM_Epi_Mem_10: Muscle_7wk_Re-oading_Participant_002_Rep1

value: vastus lateralis muscle

tag: gender

value: Male

value: Untrained

value: Healthy


title: TS5.133_Inj_RNA-Seq

tag: injury

value: VML

tag: run


title: R3QB-015 smoke

description:
Sample name:
X45

value: sperm


title: SkM_Epi_Mem_3: Muscle_7wk_Loading_Participant_001_Rep1

tag: age


title: insulin resistant [ID158_6455_SC]

tag: suject status

value: obese

value: female

tag: insulin sensitivity

value: insulin resistant

value: subcutaneous white adipose tissue


title: TS5.135_Inj_RNA-Seq

value: Lewis rat

value: NoRun

tag: repair

value: MMG

tag: timepoint

value: day 14


title: GF-SI_11

value: Swiss Webster

tag: treatment

value: germ-free social interaction


title: GF-SI_6

value: 10 weeks

value: ribodepleted RNA


title: CB60010 smoke

description:
Sample name:
X43


title: insulin sensitive [ID156_6453_SC]

value: insulin sensitive


title: AA7E-010 control

description:
Sample name:
X143


title: TS5.133_Con_RNA-Seq

value: NoVML

value: NoRepair

value: tibialis anterior muscle


title: insulin resistant [ID154_6446_SC]


title: insulin resistant [ID42_6036_SC]


title: SkM_Epi_Mem_2: Muscle_Acute_Participant_001_Rep1

value: vastus lateralis muscle

value: Male

tag: weight

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: HK3B003 smoke

description:
Sample name:
X37

tag: tissue

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: IT9P017 smoke

description:
Sample name:
X36

tag: sperm concentration (m/ml)


title: SkM_Epi_Mem_1: Muscle_Baseline_Participant_001_Rep1

tag: gender


title: GF-SI_5

tag: strain

tag: molecule


title: TS5.132_Inj_RNA-Seq

value: Lewis rat

tag: injury

value: VML

tag: run

value: Run


title: SkM_Epi_Mem_5: Muscle_7wk_Re-oading_Participant_001_Rep1

tag: age


title: 9QC6020 control

description:
Sample name:
X184


title: TS5.132_Con_RNA-Seq

tag: repair

value: MMG

tag: timepoint

value: day 14


title: GF-SI_4

value: Swiss Webster

tag: treatment

value: germ-free social interaction


title: GF-SI_3

value: 10 weeks

value: ribodepleted RNA


title: TS5.131_Inj_RNA-Seq

value: NoRun


title: SL56004 smoke

description:
Sample name:
X27


title: insulin sensitive [ID160_6466_SC]

tag: suject status

value: obese

value: female

tag: insulin sensitivity

value: insulin sensitive

value: subcutaneous white adipose tissue


title: insulin resistant [ID150_6443_SC]

value: insulin resistant


title: GF-SI_9


title: insulin sensitive [ID148_6436_SC]


title: TS5.134_Inj_RNA-Seq

value: NoRepair

value: tibialis anterior muscle


title: insulin sensitive [ID152_6444_SC]


title: SkM_Epi_Mem_8: Muscle_7wk_Loading_Participant_002_Rep1

value: vastus lateralis muscle

value: Male

tag: weight

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: 47Q9-013 smoke

description:
Sample name:
X72

tag: tissue

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: GF-SI_1

tag: strain

value: Swiss Webster

tag: molecule


title: IE1C-012 control

description:
Sample name:
X129

tag: sperm concentration (m/ml)


title: TS5.130_Inj_RNA-Seq

value: Lewis rat

tag: injury

value: VML

tag: run

value: Run

value: day 14


title: TS5.130_Con_RNA-Seq

value: NoVML

tag: repair

tag: timepoint


title: CON-SI_8

tag: treatment

value: control social interaction

tag: age

value: 10 weeks

value: ribodepleted RNA


title: GF-SI_2

value: germ-free social interaction


title: CON-SI_7


title: CON-SI_6


title: TS5.129_Inj_RNA-Seq

value: NoRun

value: NoRepair


title: FT6X006 smoke

description:
Sample name:
X62


title: TS5.131_Con_RNA-Seq

value: MMG

value: tibialis anterior muscle


title: insulin resistant [ID144_6426_SC]

tag: suject status

value: obese

tag: gender

value: female

tag: insulin sensitivity

value: insulin resistant

value: subcutaneous white adipose tissue


title: TS5.129_Con_RNA-Seq

value: Lewis rat


title: insulin sensitive [ID146_6427_SC]

value: insulin sensitive


title: 42M5006 control

description:
Sample name:
X174

value: sperm


title: 2NN7-012 control

description:
Sample name:
X134


title: DZ35-013 control

description:
Sample name:
X136


title: CON-SI_5

value: Swiss Webster


title: CON-SI_4


title: TS5.128_Inj_RNA-Seq

value: VML

value: day 7


title: TS5.128_Con_RNA-Seq

value: NoVML


title: TS5.127_Inj_RNA-Seq


title: CON-SI_3

value: control social interaction

value: 10 weeks

value: ribodepleted RNA


title: SkM_Epi_Mem_4: Muscle_7wk_Unloading_Participant_001_Rep1

value: vastus lateralis muscle

value: Male

tag: weight

tag: height

tag: training history

value: Untrained

tag: health status

value: Healthy


title: EA8Q013 smoke

description:
Sample name:
X24

tag: tissue

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: 771A017 smoke

description:
Sample name:
X29

tag: sperm concentration (m/ml)


title: TS5.127_Con_RNA-Seq

tag: strain

tag: injury

tag: run

value: NoRun

value: MMG

value: tibialis anterior muscle


title: GF-SI_7

tag: treatment

value: germ-free social interaction

tag: molecule


title: insulin resistant [ID142_6424_SC]

tag: suject status

value: obese

value: female

tag: age

value: insulin resistant

value: subcutaneous white adipose tissue


title: insulin resistant [ID136_6401_OM]

tag: gender

tag: insulin sensitivity


title: insulin resistant [ID134_6304_SC]


title: CON-SI_1

value: Swiss Webster


title: GM16013 smoke

description:
Sample name:
X28

value: sperm


title: TS5.126_Inj_RNA-Seq

value: Lewis rat

value: VML

tag: repair

value: NoRepair

tag: timepoint

value: day 7


title: insulin sensitive [ID140_6409_SC]

value: insulin sensitive


title: exGF_4

value: germ-free colonized at weaning naive

value: 10 weeks

value: ribodepleted RNA


title: F5EV-001 control

description:
Sample name:
X131


title: insulin sensitive [ID138_6408_SC]


title: insulin resistant [ID132_6302_SC]


title: insulin sensitive [ID130_6295_SC]


title: J7VD009 smoke

description:
Sample name:
X16


title: exGF_3


title: TS5.126_Con_RNA-Seq

value: NoVML

value: NoRun


title: TS5.125_Inj_RNA-Seq

value: tibialis anterior muscle


title: 6K84-010 control

description:
Sample name:
X178


title: exGF_2


title: TS5.125_Con_RNA-Seq


title: CON-SI_2

value: control social interaction


title: insulin sensitive [ID128_6290_SC]

value: obese

value: female


title: TS5.108_Inj_RNA-Seq

value: MMG


title: GF_4

value: Swiss Webster

value: germ-free naive


title: 8VW3011 smoke

description:
Sample name:
X13

value: sperm


title: GF_3


title: TS5.108_Con_RNA-Seq

value: Lewis rat


title: TS5.107_Inj_RNA-Seq

value: VML


title: TS5.107_Con_RNA-Seq

value: day 7


title: 4AC8-012 control

description:
Sample name:
X127


title: TS5.140_Inj_RNA-Seq

value: Run

value: day 14


title: insulin resistant [ID124_6276_SC]

value: insulin resistant

value: subcutaneous white adipose tissue


title: insulin resistant [ID122_6272_SC]


title: GF_2

value: 10 weeks

value: ribodepleted RNA


title: GF_1


title: ZT4H014 control

description:
Sample name:
X123


title: exGF_1

value: germ-free colonized at weaning naive


title: TS5.106_Con_RNA-Seq

value: NoVML

value: NoRun

value: NoRepair

value: tibialis anterior muscle


title: CON_3

value: Swiss Webster

value: control naive


title: TS5.106_Inj_RNA-Seq


title: R03R017 smoke

description:
Sample name:
X58

value: sperm


title: CON_4


title: insulin sensitive [ID116_6232_SC]

value: obese

value: female

value: insulin sensitive


title: CON_2


title: insulin resistant [ID120_6268_SC]


title: insulin resistant [ID118_6247_SC]


title: insulin resistant [ID112_6221_SC]


title: 9ZV3013 smoke

description:
Sample name:
X7


title: insulin resistant [ID110_6220_SC]


title: insulin sensitive [ID108_6217_SC]


title: insulin resistant [ID114_6230_SC]


title: RR81-013 control

description:
Sample name:
X107


title: C9C0010 control

description:
Sample name:
X188


title: TS5.104_Inj_RNA-Seq

value: Lewis rat

value: VML

value: Run

value: MMG

value: day 3


title: CON_1

value: 10 weeks

value: ribodepleted RNA


title: TS5.103_Inj_RNA-Seq


title: TS5.105_Con_RNA-Seq

value: NoVML

value: day 7


title: insulin sensitive [ID106_6212_SC]

value: subcutaneous white adipose tissue


title: 4JL0-008 control

description:
Sample name:
X120


title: TS5.102_Inj_RNA-Seq

value: NoRepair

value: tibialis anterior muscle


title: TY0E010 smoke

description:
Sample name:
X6


title: TS5.105_Inj_RNA-Seq

value: NoRun


title: FB4U005 smoke

description:
Sample name:
X57

value: sperm


title: 6NW6015 smoke

description:
Sample name:
X8


title: ChIPseq for HP1a in Cbx1-/- Cbx3-/-  mES cells, replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on two independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
RNAseq: Sequenced reads were aligned using Bowtie 1.0.0 ( -m1 --best –strata) or STAR 2.5.0a (--outFilterMultimapNmax 20 --outMultimapperOrder Random --outSAMmultNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000)
ChIPseq: Sequenced reads were aligned using Bowtie 1.0.0 (-m 1 —best –strata) or STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within )
For RNAseq and ChIPseq, QuasR was used to count aligned reads (qCount) and to generate depth normalized bigWig files (qExportWig). Differential expression analysis was perfored using EdgeR on the raw gene count tables generated by QuasR.
ATACseq data was mapped using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType Local --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix  --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using QuasR. Read counts were binned in 50bp intervals and normalized to average sequencing depth. For ATACseq, data was not binned and the bigwig files display the full sequencing reads normalized to 1 mio genome mapping reads. Bed files containing peak positions were generated from the .narrowPeak output file from MACS2.

growth_protocol: Mouse ES cells were grown under standard conditions in 2i medium containing LIF.

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 1% of chromatin was set aside as Input control. The chromatin was incubated with Strapdavidin coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ostapcuk et al, 2017.
Libraries were prepared using the NEB Next DNA library prep kit according to manufacturers instructions. For barcodes, see sample characteristics.

tag: strain background

value: hybrid 129-C57BL/6

tag: genotype/variation

value: Cbx1 KO, Cbx3 KO

tag: cell type

value: embryonic stem (ES) cells

tag: antibody

value: Bio ChIP, Strepdavidin Dynabeads (Thermofisher)


title: ChIPseq for HP1a in Cbx1-/- Cbx3-/-  mES cells, replicate 1


title: TS5.101_Inj_RNA-Seq

value: Lewis rat

value: VML

tag: tissue


title: ZV9T-007 control

description:
Sample name:
X92

tag: # years smoking

tag: # cigarettes per day

tag: pack years

tag: sperm concentration (m/ml)


title: 8M65010 smoke

description:
Sample name:
X2


title: insulin resistant [ID104_6207_SC]

value: obese

value: female

value: insulin resistant


title: insulin resistant [ID102_6200_SC]


title: insulin resistant [ID100_6199_SC]


title: insulin resistant [ID098_6160_SC]


title: Input of ChIPseq for HP1a in Cbx1-/- Cbx3-/-  mES cells, replicate 1

tag: treatment


title: TS5.100_Inj_RNA-Seq

tag: strain

tag: injury

tag: run

value: MMG

value: day 3


title: ChIPseq for HP1a in Cbx1-/- mES cells, replicate 2

source_name: ChIPseq for HP1a in Cbx1-/- mES cells

value: Cbx1 KO, Cbx3 flox

value: no


title: AJ5T- 022 control

description:
Sample name:
X91


title: TS5.097_Inj_RNA-Seq

value: Run

value: NoRepair


title: TS5.098_Inj_RNA-Seq

value: tibialis anterior muscle


title: Input of ChIPseq for HP1a in Cbx1-/- Cbx3-/-  mES cells, replicate 2


title: Input of ChIPseq for HP1a in Cbx1-/- mES cells, replicate 2


title: B29T019 control

description:
This sample failed quality control. Thus there is no associated processed data.
Sample name:
X186

value: sperm


title: H4EB015 smoke

description:
Sample name:
X85


title: ChIPseq for HP1a in Cbx1-/- mES cells, replicate 1

value: hybrid 129-C57BL/6


title: Input of ChIPseq for HP1a in Cbx1-/- mES cells, replicate 1


title: TS5.091_Inj_1_RNA-Seq

value: NoRun


title: 9IO7014 smoke

description:
Sample name:
X84


title: TS5.088_Inj_RNA-Seq

value: day 28


title: insulin sensitive [ID094_6155_SC]

tag: suject status

tag: gender

tag: age

value: insulin sensitive

value: subcutaneous white adipose tissue


title: insulin sensitive [ID096_6156_SC]

tag: insulin sensitivity


title: Input of ChIpseq for H3K9me3 in wt mES cells, replicate 3

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and fragmented with micrococcal nuclease to mostly mono nuclesomes. 1% of chromatin was set aside as Input control. The chromatin was incubated with antibody over night, Protein A coupled Dynabeads were added for 2 hours and thereafter immunoprecipitated DAN was washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ostapcuk et al, 2017.
Libraries were prepared using the NEB Next DNA library prep kit according to manufacturers instructions. For barcodes, see sample characteristics.

tag: strain background

value: wt

value: embryonic stem (ES) cells


title: TS5.087_Inj_RNA-Seq

value: Lewis rat

value: VML

tag: repair

tag: timepoint


title: H961-009 smoke

description:
Sample name:
X88


title: ChIPseq for H3K9me3 in wt mES cells, replicate 3

source_name: ChIPseq for H3K9me3 in wt mES cells

tag: genotype/variation

tag: cell type

tag: antibody

value: anit H3K9me3 ab8898 (Abcam)


title: insulin resistant [ID090_6145_SC]

value: obese

value: female

value: insulin resistant

tag: tissue


title: insulin sensitive [ID092_6149_SC]


title: TS5.086_Inj_RNA-Seq

value: Run


title: J59I-001 control

description:
Sample name:
X99

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: Input of ChIpseq for H3K9me3 in wt mES cells, replicate 2

tag: treatment

value: no


title: insulin resistant [ID086_6125_SC]


title: TS5.084_Inj_RNA-Seq

tag: strain

tag: injury

value: MMG

value: tibialis anterior muscle


title: 4Z5Q009 control

description:
Sample name:
X175

value: sperm

tag: sperm concentration (m/ml)


title: XJ55-012 smoke

description:
Sample name:
X44


title: ChIPseq for H3K9me3 in wt mES cells, replicate 2

value: hybrid 129-C57BL/6


title: TS5.083_Inj_RNA-Seq

tag: run

value: NoRun

value: day 28


title: TS5.082_Inj_RNA-Seq

value: NoRepair


title: insulin sensitive [ID082_6113_SC]

tag: suject status

tag: gender

tag: age

value: insulin sensitive

value: subcutaneous white adipose tissue


title: insulin resistant [ID084_6123_SC]

tag: insulin sensitivity


title: insulin sensitive [ID088_6144_SC]


title: insulin sensitive [ID080_6107_SC]


title: TS5.081_Inj_RNA-Seq

value: Lewis rat

tag: repair

tag: timepoint


title: G9GD007 control

description:
Sample name:
X191


title: TS5.080.Ctrl_RNA-Seq

value: VML


title: CJ8K-009 control

description:
Sample name:
X158


title: TS5.085_Inj_RNA-Seq


title: TS5.080_Inj_RNA-Seq

value: NoVML


title: T5RK009 smoke

description:
Sample name:
X74


title: TS5.079.Ctrl_RNA-Seq


title: AN5H-013 control

description:
Sample name:
X96


title: insulin sensitive [ID076_6094_SC]

value: obese


title: insulin sensitive [ID078_6102_SC]

value: female


title: 81O2016 control

description:
Sample name:
X181


title: IF8A019 smoke

description:
Sample name:
X76


title: insulin sensitive [ID074_6093_SC]


title: insulin sensitive [ID072_6091_SC]


title: TS5.079_Inj_RNA-Seq


title: 7QU9-006 control

description:
Sample name:
X161


title: TS5.078.Ctrl_RNA-Seq


title: R9I2011 smoke

description:
Sample name:
X75


title: insulin resistant [ID070_6086_SC]

value: insulin resistant


title: WZ1R-006 smoke

description:
Sample name:
X79


title: TS5.078_Inj_RNA-Seq

value: Run


title: TS5.077.Ctrl_RNA-Seq


title: insulin resistant [ID066_6084_SC]


title: insulin sensitive [ID068_6085_SC]


title: TS5.077_Inj_RNA-Seq


title: 80EE019 smoke

description:
Sample name:
X42


title: TS5.076.Ctrl_RNA-Seq


title: TS5.076.Inj_RNA-Seq


title: TS5.075.Inj_RNA-Seq


title: KB2I-025 control

description:
Sample name:
X160


title: TS5.075.Ctrl_RNA-Seq


title: O557-012 control

description:
Sample name:
X157


title: TS5.074.Inj_RNA-Seq


title: JF98-018 smoke

description:
Sample name:
X78


title: 5X4F021 smoke

description:
This sample failed quality control. Thus there is no associated processed data.
Sample name:
X35


title: TS5.074.Ctrl_RNA-Seq


title: insulin sensitive [ID036_6025_SC]


title: insulin resistant [ID038_6028_SC]


title: VX90-007 control

description:
Sample name:
X155


title: insulin sensitive [ID030_5991_SC]


title: insulin sensitive [ID034_6000_SC]


title: insulin sensitive [ID064_6083_SC]


title: TS5.073.Inj_RNA-Seq


title: F063019 smoke

description:
Sample name:
X68


title: insulin sensitive [ID126_6285_SC]


title: TS5.073.Ctrl_RNA-Seq


title: LI6X009 smoke

description:
Sample name:
X40


title: J67U011 smoke

description:
Sample name:
X69


title: S4BI-009 control

description:
Sample name:
X167


title: insulin resistant [ID062_6080_SC]


title: TS5.031_Inj_RNA-Seq

value: day 7


title: insulin resistant [ID040_6032_SC]


title: TS5.032_Inj_RNA-Seq


title: LJ0W013 smoke

description:
Sample name:
X66


title: TS5.030_Inj_RNA-Seq

value: day 3


title: L95E-009 control

description:
Sample name:
X126


title: TS5.029_Inj_RNA-Seq

value: tibialis anterior muscle


title: 5R6J-007 control

description:
Sample name:
X177

value: sperm


title: HO70014 smoke

description:
Sample name:
X70


title: TS5.028_Inj_RNA-Seq

value: MMG


title: insulin resistant [ID026_5985_SC]


title: insulin resistant [ID028_5987_SC]


title: insulin sensitive [ID032_5999_SC]


title: insulin sensitive [ID022_5861_SC]


title: insulin resistant [ID024_5876_SC]


title: insulin sensitive [ID018_5857_SC]


title: insulin sensitive [ID016_5849_SC]


title: insulin sensitive [ID020_5859_SC]


title: TS5.027_Inj_RNA-Seq


title: TS5.025_Inj_RNA-Seq


title: 9SW8007 smoke

description:
Sample name:
X64


title: 9YW4-024 control

description:
Sample name:
X152


title: X46G-009 control

description:
Sample name:
X140


title: TS5.024_Inj_RNA-Seq

value: NoRun


title: insulin resistant [ID014_5834_SC]


title: insulin sensitive [ID010_5828_SC]


title: insulin sensitive [ID012_5829_SC]


title: 58ML014 smoke

description:
Sample name:
X65


title: OY3Y-006 control

description:
Sample name:
X156


title: TS5.023_Inj_RNA-Seq


title: TS5.026_Inj_RNA-Seq


title: AO4Z013 smoke

description:
Sample name:
X83


title: 8JT9007 control

description:
Sample name:
X183


title: C3BP-001 control

description:
Sample name:
X139


title: insulin sensitive [ID004_5803_SC]


title: insulin sensitive [ID002_5794_SC]


title: CP25_2h rep2

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

description: Experimental

data_processing:
Basecalls were performed with CASAVA version 1.8.2
75bp paired end reads were trimmed for adaptor sequence using trimmomatic 0.36, and aligned to the hg19 genome using Bowtie v 2.2.3 using default parameters.
Differential gene and transcript expression was analyzed following the protocol of Trapnell et al. Nat. Protoc.7, 562-578 (2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.  Files with differential expression are also included.

source_name: HEK293T cells

growth_protocol: HEK293T cells were routinely maintained in T25 flask on DMEM supplemented with 10% heat-inactivated FBS and 1% Pen/Strep.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Qiagen).
Poly(A) mRNA libraries were prepared for illumina sequencing using standard protocol.

treatment_protocol: HEK293T cells at 70% confluency were treated with 2 μM of CP25 or the same volume of vehicle for 18 h, and transcription was stopped by 5 μg/mL actinomycin D for 0 h and 2 h.

tag: cell line

tag: cell type

value: SV40 expressing stable kidney epithelial cell line

tag: passages

value: 2 microM CP25

tag: hours after transcription block


title: TS5.021_Inj_RNA-Seq

tag: tissue


title: CP25_2h rep3

description: Experimental


title: insulin resistant [ID006_5810_SC]


title: U1IF-008 control

description:
Sample name:
X150

tag: # years smoking

tag: # cigarettes per day

tag: pack years


title: Vehicle_2h rep3

description: Control

tag: treatment

value: Vehicle (peptide storage buffer)


title: TS5.020_Inj_2_RNA-Seq

tag: strain

tag: injury

value: NoRepair


title: CP25_2h rep1

description: Experimental


title: KH5H-015 control

description:
Sample name:
X141

tag: sperm concentration (m/ml)


title: KY4G-004 control

description:
Sample name:
X146


title: TS5.019_Inj_2_RNA-Seq

value: Lewis rat

tag: run


title: TS5.020_Inj_1_RNA-Seq

value: VML


title: Vehicle_2h rep1

description: Control


title: TS5.019_Inj_1_RNA-Seq


title: B04M014 control

description:
Sample name:
X185


title: CP25_0h rep2

description: Experimental


title: CP25_0h rep3

description: Experimental


title: 6AO7025 smoke

description:
Sample name:
X33


title: TS5.018_Inj_RNA-Seq


title: TS5.022_Inj_RNA-Seq


title: Vehicle_2h rep2

description: Control


title: TS5.017_Inj_RNA-Seq


title: CP25_0h rep1

description: Experimental


title: Y15S015 smoke

description:
Sample name:
X63


title: Vehicle_0h rep3

description: Control


title: TS5.016_Con_RNA-Seq

value: NoVML


title: TS5.017_Con_RNA-Seq


title: TS5.016_Inj_RNA-Seq


title: 75JA010 smoke

description:
Sample name:
X26


title: 7D07016 control

description:
Sample name:
X179


title: Vehicle_0h rep2

description: Control


title: WU9B-014 control

description:
Sample name:
X137


title: 9R8B-012 control

description:
Sample name:
X125


title: insulin sensitive [ID008_5811_SC]

tag: suject status

value: obese

tag: gender

tag: age

value: insulin sensitive

value: subcutaneous white adipose tissue


title: CO0C-014 smoke

description:
Sample name:
X52


title: TS5.015_Con_RNA-Seq

tag: repair

tag: timepoint


title: TS5.014_Inj_RNA-Seq


title: A33B012 smoke

description:
Sample name:
X23


title: R91C-009 control

description:
Sample name:
X138


title: TS5.014_Con_RNA-Seq


title: TS5.013_Inj_RNA-Seq


title: 2WC5-016 control

description:
Sample name:
X128


title: VL95011 smoke

description:
Sample name:
X56


title: TS5.013_Con_RNA-Seq


title: TS5.012_Inj_2_RNA-Seq


title: D98S-002 control

description:
Sample name:
X135


title: TS5.015_Inj_RNA-Seq


title: TS5.012_Inj_1_RNA-Seq


title: Vehicle_0h rep1

description: Control

tag: cell line

tag: cell type


title: TS5.012_Con_1_RNA-Seq


title: VI4I-016 control

description:
Sample name:
X124


title: TS5.011_Inj_RNA-Seq


title: GF_S_0004068

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data

hyb_protocol: Arrays were processed using the Affymetrix GeneChip Hybridization, Washing and Staining kit, using the Affymetrix Fluidics station 450 controlled by Affymetrix GeneChip Command Console (AGCC) Software.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000, 7G controlled by AGCC Software.

data_processing: Data were analyzed and normalized by the MAS5 algorithm as implemented by the ‘affy’ package version 1.56.0 under Bioconductor version 3.6 and R version 3.4.3. Default settings were used.

source_name: Primary AML sample, pretreatment

label_protocol: mRNA within the total RNA (100 ng) was amplified using the 3’ IVT Express kit from Affymetrix, starting with reverse transcription to synthesize first strand cDNA. This cDNA was then converted into double stranded DNA template for transcription to generate aRNA (cRNA) and incorporate a biotin conjugated nucleotide, then fragmented for hybridization on Human Gene U133_2.0 arrays.

growth_protocol: Samples were obtained from peripheral blood, in the case of patients with a substantial proportion of circulating blast cells, or bone marrow by aspiration

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (Qiagen).

treatment_protocol: Ficoll-Hypaque density gradient separation was performed to isolate mononuclear cells

tag: disease state

value: AML

value: peripheral blood

value: Mononuclear cells


title: GF_S_0004070

description: Gene expression data

tag: tissue


title: IB4N015 smoke

description:
Sample name:
X59

tag: # years smoking


title: 0U0S014 smoke

description:
Sample name:
X22

tag: # cigarettes per day


title: GF_S_0004071

description: Gene expression data


title: TS5.011_Con_2_RNA-Seq

value: day 7

value: tibialis anterior muscle


title: GF_S_0004065

description: Gene expression data


title: GF_S_0004067

description: Gene expression data


title: GF_S_0004066

description: Gene expression data


title: TS5.011_Con_1_RNA-Seq

value: day 3