title: lgl-hypomorph day 5 biorep 3

status: Public on Dec 18 2017

city: Tucson

first: Daniela

middle: C

last: Zarnescu

state: AZ

address: 1007 E Lowell St LSS 514

department: Molecular and Cellular Biology

institute: University of Arizona

description: All spots were in triplicate, they included 4 negative controls (anti-fixB, fixB, anti-gnd, gnd) 4 positive controls (U6-337, tRNA-M2, U6-296, 5S-rRNA) and 229 pre-miRNA, star-miRNAs and mature miRNAs. The entire array was 840 spots, including blanks.

hyb_protocol: probes were hybridized an array spotted with cDNA complementary to 147 published Drosophila miRNAs including precursors and star microRNAs.

scan_protocol: Fluorescence was imaged with a GenePix 4000B microarray scanner and measured using GenePix Pro 5.0.0.49 software.

data_processing:
Data was grouped and normalized according to the comparison being made (i.e. if lgl-hypomorph day 0 was being compared to wild-type day 0 then only those two groups were normalized together).  Thus the three Control Samples are each represented by three Samples in this Series and their corresponding raw data are provided on the Series record (to avoid duplication).
Quantile normalized values were computed using the normalizeBetweenArrays() function of the limma package of the statistical software environment, R. The log transformation is log base 2.

organism: Drosophila melanogaster

source_name: cephalic complexes

label_protocol: total RNA was shipped on dry ice to Genosensor (Phoenix, AZ) where it was subjected to quality testing and labeled with Cy5

extract_protocol: Cephalic complexes were dissected from 20 third instar larvae per genotype were pooled to create each time point sample. Three samples were collected per time point and total RNA was immediately extracted following dissection with a miRVana RNA extraction kit to conserve small RNA according to manufacturer’s protocols (Ambion, Austin, TX).  RNA was quantified and evaluated for integrity with a nanodrop spectrophotometer and denaturing agarose gels.

value: cephalic complexes

tag: developmental stage

value: 3rd instar

value: 5 days

tag: genotype


title: lgl-hypomorph day 5 biorep 1

type: RNA

country: USA

molecule: total RNA

tag: tissue

tag: age


title: wild-type day 0 biorep 3 (vs mut5)

value: 0 days

value: yw; lgl1 / lglU334 P[lgl+]; +/+


title: lgl-hypomorph day 5 biorep 2


title: PBMC_NonResponder_Patient1_6d

status: Public on Dec 19 2017

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description: Gene expression data from PBMCs of a non-responder patient six days after Sorafenib treatment.

hyb_protocol: Total RNA was hybridized to Affymetrix Clariom S arrays as described by the manufacturers (Affymetrix/Thermo Fisher Scientific, 168 Third Avenue, Waltham, MA USA 02451.)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

label: Biotin

organism: Homo sapiens

source_name: peripheral blood

label_protocol: RNA integrity was analyzed by capillary electrophoresis using a Fragment Analyser (Advanced Analytical Technologies, Inc. Ames, IA) and were further processed with the Affymetrix GeneChip Pico kit

extract_protocol: 2ug of total RNA from about 10^7 cells  per sample were incubated with DNaseI according the Qiagen manufacture and cleaned up with RNeasy Micro Kit (Qiagen, Hilden, Germany).

treatment_protocol: RNA from peripheral blood mononuclear cell of 8 patients at 2 different time points (3 days before and 6 days after Sorafenib treatment) were extractied from 8 ml of blood.

tag: cell type

value: peripheral blood mononuclear cell

tag: treatment response

value: non-responder

tag: timepoint

value: 6 days

tag: treatment

value: Sorafenib


title: PBMC_Responder_Patient1_6d

description: Gene expression data from PBMCs of a responder patient six days after Sorafenib treatment.

value: responder


title: wild-type day 0 biorep 2 (vs mut5)


title: PBMC_Responder_Patient2_-3d

description: Gene expression data from PBMCs of a responder patient three days before Sorafenib treatment.

value: -3 days


title: wild-type day 0 biorep 1 (vs mut5)


title: PBMC_Responder_Patient4_6d


title: 4-day lgl27S3/lglE2S31 3rd instar larvae, biorep 1

description: Gene expression data from cephalic complexes of 4-day 3rd instar lgl27S3/lglE2S31 larvae

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Raw data was processed, normalized and background-corrected using the rma() algorithm of the statistical software environment R.
Values are the result of the rma() algorithm.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen) protocol and cleaned up prior to template preparation using the Qiagen RNeasy mini kit

tag: stage of larval development

value: lgl27S3 / lglE2S31


title: Latent Tuberculosis IFNalpha Dendritic cells rep3

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

country: Italy

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

description: LTBI TB20_vet5

hyb_protocol: Combine 200pmol of Cy5-labeled sample is combined with 300 pmol of Cy3-labeled one. Then, samples are precipitated, dry pelleted and resuspended in 70 ul of Hybridization buffer made of SSC(5x), SDS (0.1%), ss-DNA (0.1 ug/ul), Formamide (25%). Finally resuspended samples are applied to slides, covered with glass cover slip and placed in sealed hybridization chamber in water bath at 48°C for 24h.

scan_protocol: Slides were scanned by Gene Pix 4200 (Molecular Devices); microarray images and data files were analysed by means of ScanArray Software.

data_processing: BRB-ArrayTools Version: 4.3.2 was used for normalization and analysis. In details, the following spot filters were applide:  If RED intensity is below 100, increase it to 100. If GREEN intensity is below 100, increase it to 100. Exclude the spot if RED intensity is below 100 AND GREEN intensity is below 100 .  Each array was normalized lowess smoother. Intensity ratios (and inverse ratios) greater than 64  were truncated. Genes were excluded under any of the following conditions: Percent of data missing or filtered out exceeds 15 %; Exclude the spot if the Spot Flag contains numeric values outside the range: 0 to 0 ; Exclude the spot if the Spot Size is less than: 25

label_protocol: cDNA obtained from 1 μg of total RNA (Amino Allyl MessageAmp II aRNA amplification kit, Ambion) was amplified in the presence of T7 RNA polymerase to obtain the aRNA. aRNAs from experimental samples were labeled with Cy5 and co-hybridized with a reference aRNA used as a control (Universal Human Reference RNA, Stratagene) onto made in-house microarray oligo-based human chips.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by density-gradient centrifugation using Lympholyte-H (Cedarlane).  CD14+ monocytes were isolated from PBMC by column magnetic immunoselection (MACS CD14 microbeads, Miltenyi Biotec), cultured at concentration of 2x106 cells/ml in RPMI-1640 supplemented with 10% LPS-free fetal calf serum and cultured for 3 days in presence of 500 U/ml GM-CSF (PeproTech) and 104 IU/ml IFNα2b (Intron A, Merck Sharp and Dohme)

extract_protocol: Total RNA was extracted from cells by RNeasy mini kit (Qiagen).

tag: disease classification

value: Latent Tuberculosis

value: IFNalpha Dendritic cells

tag: sample type

value: Universal Human Reference RNA


title: 4-day lgl27S3/lglE2S31 3rd instar larvae, biorep 3


title: Latent Tuberculosis IFNalpha Dendritic cells rep4

description: LTBI TB21_vet9

source_name: Universal Human Reference RNA, Stratagene


title: lgl-hypomorph day 3 biorep 2

value: 3 days


title: lgl-hypomorph day 3 biorep 3


title: 4-day lgl27S3/lglE2S31 3rd instar larvae, biorep 2


title: 0-day FRT82B 3rd instar larvae, biorep 2

description: Gene expression data from cephalic complexes of 0-day 3rd instar FRT82B larvae


title: 0-day FRT82B 3rd instar larvae, biorep 1


title: Latent Tuberculosis IFNalpha Dendritic cells rep5

description: LTBI TB28_vet29


title: Latent Tuberculosis IFNalpha Dendritic cells rep1

description: LTBI TB2_vet6


title: Latent Tuberculosis IFNalpha Dendritic cells rep2

description: LTBI TB19_vet30


title: wild-type day 0 biorep 2 (vs mut3)


title: lgl-hypomorph day 3 biorep 1


title: wild-type day 0 biorep 3 (vs mut3)


title: wild-type day 0 biorep 1 (vs mut3)


title: lgl-hypomorph day 0 biorep 2


title: lgl-hypomorph day 0 biorep 3


title: L6_pinosylvin_60microM_rep3

city: Kuopio

first: Tarja

last: Kokkola

address: Yliopistonranta 1 C

department: School of Medicine / Internal Medicine

country: Finland

institute: University of Eastern Finland

description:
Gene expression after 24h in pinosylvin-treated rat L6 myotubes.
Replicate 3

hyb_protocol: Samples (600 ng of cRNA) were mixed with blocking agent, fragmentation and hybridization buffer, and were hybridized to Agilent SurePrint G3 Rat GE 8 x 60K Microarrays for 17 hours at 65°C.

scan_protocol: Microarrays were washed and scanned with Agilent Scanner using manufacturer provided protocols (Agilent Scan Control version A.8.5.1).

data_processing: Agilent Feature Extraction software (version 12.0.0.7) was used to extract data from raw microarray image files. The data was processed with limma package of the Bioconductor software. The processing included background correction with normexp method, log2 transformation and normalization with quantile method. Next step was filtering which excluded probes that were less than 10% brighter than the 95% percentile of the negative control probes on at least 3 arrays, yielding 37670 probes representing 25848 genes. To obtain results with unique probe names, the data was condensed and values for within-array replicate probes were replaced by their average.

organism: Rattus norvegicus

source_name: L6 myotubes, 60 microM pinosylvin, 24h

label_protocol: 200 ng of total RNA was primed using oligo-dT(T7) promoter primers and converted to cDNA with AffinityScript RNase Block (Agilent). Primed cDNA was amplified and labeled using Cy3-labeled dNTPs and T7 RNA Polymerase.

growth_protocol: Rat L6 skeletal muscle cells (ATCC) were differentiated into myotubes in alpha-MEM containing 2% horse serum for 6 days.

extract_protocol: RNA was prepared using the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA quality was assessed with the Agilent Bioanalyzer 2100.

treatment_protocol: Myotubes were treated with 60 micromolar test compounds in DMSO or DMSO (control) for 24 hours.

tag: cell line

value: skeletal muscle myotubes

value: 60 microM pinosylvin

tag: time


title: lgl-hypomorph day 0 biorep 1

value: cephalic complexes

value: 3rd instar


title: Healthy Donor IFNalpha Dendritic cells rep 3

description: healthy TB23_vet25

source_name: Healthy Donor IFNalpha Dendritic cells

value: Healthy Donor


title: HGSOC Patient3 primary tumor cells

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

country: China

institute: cancer biology center

description: Gene expression data from primary tumor cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: PICR scanner 3000

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

source_name: HGSOC patient primary tumor

label_protocol: Label protocol was carried out according to the Eukaryotic Target Preparation protocol in the Affymetrix technical manual (701021 Rev. 5) for Genechip Expression analysis (Affymetrix).

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) and was purified using RNeasy spin columns (Qiagen) according to the manufacturers' protocols.

tag: tumor type

value: primary


title: L6_GR24_60microM_rep3

description:
Gene expression after 24h in GR24-treated rat L6 myotubes.
Replicate 3

source_name: L6 myotubes, 60 microM GR24, 24h

value: 60 microM GR24


title: Active Tuberculosis IFNalpha Dendritic cells rep1

description: active TB3_vet1

value: Active Tuberculosis


title: Healthy Donor IFNalpha Dendritic cells rep 5

description: healthy TB26_vet22


title: Healthy Donor IFNalpha Dendritic cells rep 4

description: healthy TB25_vet8


title: wild-type day 0 biorep 3 (vs mut0)

value: 0 days

value: yw; lgl1 / lglU334 P[lgl+]; +/+


title: Healthy Donor IFNalpha Dendritic cells rep 2

description: healthy TB22_vet5


title: Active Tuberculosis IFNalpha Dendritic cells rep4

description: active TB13_vet3


title: L6_Ctrl_rep3

description:
Gene expression after 24h in control-treated rat L6 myotubes.
Replicate 3

source_name: L6 myotubes, control, 24h

value: control


title: wild-type day 0 biorep 1 (vs mut0)

data_processing:
Data was grouped and normalized according to the comparison being made (i.e. if lgl-hypomorph day 0 was being compared to wild-type day 0 then only those two groups were normalized together).  Thus the three Control Samples are each represented by three Samples in this Series and their corresponding raw data are provided on the Series record (to avoid duplication).
Quantile Quantile normalized values were computed using the normalizeBetweenArrays() function of the limma package of the statistical software environment, R. The log transformation is log base 2. The log transformation is log base 2.


title: wild-type day 0 biorep 2 (vs mut0)


title: Active Tuberculosis IFNalpha Dendritic cells rep5

description: active TB27_vet4


title: Active Tuberculosis IFNalpha Dendritic cells rep3

description: active TB12_vet24


title: Healthy Donor IFNalpha Dendritic cells rep 1

description: healthy TB18_vet23


title: L6_resveratrol_60microM_rep3

description:
Gene expression after 24h in resveratrol-treated rat L6 myotubes.
Replicate 3

source_name: L6 myotubes, 60 microM resveratrol, 24h

value: 60 microM resveratrol


title: L6_resveratrol_60microM_rep2

description:
Gene expression after 24h in resveratrol-treated rat L6 myotubes.
Replicate 2


title: Active Tuberculosis IFNalpha Dendritic cells rep2

description: active TB10_vet27


title: L6_pinosylvin_60microM_rep1

description:
Gene expression after 24h in pinosylvin-treated rat L6 myotubes.
Replicate 1


title: L6_GR24_60microM_rep2

description:
Gene expression after 24h in GR24-treated rat L6 myotubes.
Replicate 2


title: L6_resveratrol_60microM_rep1

description:
Gene expression after 24h in resveratrol-treated rat L6 myotubes.
Replicate 1


title: L6_pinosylvin_60microM_rep2

description:
Gene expression after 24h in pinosylvin-treated rat L6 myotubes.
Replicate 2


title: L6_Ctrl_rep1

description:
Gene expression after 24h in control-treated rat L6 myotubes.
Replicate 1


title: L6_Ctrl_rep2

description:
Gene expression after 24h in control-treated rat L6 myotubes.
Replicate 2


title: embryonic kidney cells - b - treated with Mir 22-3p

status: Public on Dec 17 2017

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

data_processing: The data were normalized by RMA with Parteck Genomic Suit 6.6

source_name: human embryonic kidney cells

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

growth_protocol: Standard human embryonic kidney cells growth protocal

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

treatment_protocol: mRNA is obtained by Co-Ip with FLAG tagged PAB-1 expressed in seam cells and VPCs converted to cDNA and amplified using NuGEN pico amplification kit


title: embryonic kidney cells - c - negative control


title: embryonic kidney cells - a - treated with Mir 22-3p


title: siSF3B1-PacBio Iso-Seq

status: Public on Dec 16 2017

type: SRA

city: Amsterdam

first: Remond

middle: JA

last: Fijneman

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: Netherlands Cancer Institute

description:
siRNA mediated down-modulation of F3B1, RNA and proteins were harvested in 48hours, single experiment performed
ACH71_F

library_source: transcriptomic

data_processing:
Illumina RNA-seq: Low quality reads and adapter sequences were trimmed by Trimmomatic version 3 to average quality score for a 4-base wide sliding window of 20, both at the beginning and at the end of the sequences (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, LEADING:20, TRAILING:20, AVGQUAL:20, SLIDINGWINDOW:4:20). Due to the requirements of the further analysis reads were processed to match length of 120bp, shorter reads were discarded and longer reads were trimmed (CROP:120, MINLEN:120). Mapping was performed with the use of STAR aligner version 2.4.2a to the human genome (USCS RefSeq hg19 annotation, as STAR option genomeDir) with the following  parameters; outSAMtype: BAM SortedByCoordinate, readFilesCommand: zcat, runThreadN: 28, outSAMattributes: All. Read counts per transcript were obtained with featureCounts from the Subread package v1.5.0-p2 with the UCSC RefSeq hg19 GTF file as reference. Differential splice variants were identified with rMATS version 3.2.5 using UCSC RefSeq hg19 GTF file as annotation in the unpaired analysis type (parameters; len: 120, t: paired, analysis: U). Significant events were extracted (FDR≤0.05) and transformed to a bedGraph. For the Mono experiment additional rMATS analysis was performed with PacBio GFF file as reference (all_samples.chained.gff).
PacBio Iso-seq: Redundant transcripts were removed by first aligning them to the human genome (hg19) with GMAP and collapsing highly similar transcripts predicted across FASTA files from various size fractions with the software cupcake ToFU (v1.3). In these steps both BAM and GTF files were produced for each sample. Samples were chained, to standardize transcript IDs and merge the transcripts from both experiments (all_samples.chained.gff).
Genome_build: hg19
Supplementary_files_format_and_content: TXT files include expression matrix with raw RNA-seq read counts per sample, bed Graphs represent differential splice variants between conditions identified from Illuminna RNA-seq data, GFF files include all transcripts for samples measured by PacBio Iso-Seq

source_name: CRC cell line SW480

growth_protocol: SW480 cells cultured in Dulbecco's modified Eagle's medium (DMEM; Invitrogen, Bleiswijk, The Netherlands) containing 10% fetal bovine serum (FBS; Perbio Science, Etten-Leur, The Netherlands) were maintained in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was isolated from viable cells, 48 hours after siRNA transfection with siSF3B1 and the siNon-Targeting (siNT) control, and 72 hours after transfection with siSRSF1 and its siNT control using Trizol reagent (15596; Invitrogen, Breda, The Netherlands) and the miRNeasy Mini Kit (217004; Qiagen, Venlo, the Netherlands), following the manufacturer’s protocol. Concentrations and purities were measured on a Nanodrop ND-1000 spectrophotometer (Isogen, Ijsselstein, The Netherlands).
cDNA libraries were prepared with the TruSeq Stranded mRNA LT sample Prep kit (RS-122-2101, Illumina, San Diego, USA) according to the TruSeq Stranded mRNA sample preparation guide (Part# 15031047, Revision E, October 2013). cDNA library quality control was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Sample libraries were diluted and pooled to obtain a final concentration of 10 nM.
Sequencing was performed on an Illumina HiSeq V4 2500, using a 125 bases paired end run with an input of 16 pM cDNA
RNA isolated from siSF3B1- and siNT-treated SW480 cells was subjected to full-length RNA single molecule real time (SMRT) sequencing called Iso-Seq(34). Briefly, RNA (RIN score of ~9.0 assessed by Agilent Bioanalysis) was amplified using the ClonTech Switching Mechanism at 5’ end of RNA Template (SMART) technology which incorporates known sequence at both ends of the cDNA product in the first strand synthesis process without the need for conventional adapter ligation strategies. 408 ng of siSF3B1 and 352ng siNT cDNA were used as input to the SMART cDNA amplification process to capture full-length, intact isoforms to be reverse transcribed and amplified into full-length cDNA representing the full transcriptome where the known sequences are used to complete SMRTbell library preparation using the cDNA products. Once ample double stranded cDNA was synthesized, cDNA Iso-Seq sequencing libraries were prepared using the SMRTbell library preparation procedure resulting in a library containing molecular inserts that represent a single isoform per library molecule. These libraries were then size-selected to enrich for isoforms of interest by targeting a population of full-length transcripts to enhance coverage by loading individual size fractions on single SMRTcells. More specifically, the SageELF electrophoretic lateral fractionator instrument was used to separate independent fractions of library where isoforms that are 0 – 1kbp, 1kbp – 2kbp, 2kbp - 3kbp and 3kbp – 50kbp were split into independent SMRTbell libraries for sequencing so that larger isoforms weren’t detrimentally dominated by smaller isoform library molecules during the sequencing process. Finally, samples were sequenced using 6-hr movie collection on the PacBio RSII sequencer with two SMRTcells per cDNA size fraction.

treatment_protocol: 24 hours after seeding, cells were transfected in duplo with small interfering RNA (siRNA) pools against SF3B1 (siGENOME SF3B1 SMARTpool, M-020061-02; Thermo Fisher Scientific, Waltham, USA) and SRSF1 (siGENOME SRSF1 SMARTpool, M-018672-01), according to manufacturer’s recommendations. A final siRNA concentration of 30 nM was obtained using DharmaFECT3 reagent (1:1000 dilution; T-2003-02, Thermo Fisher Scientific). A non-targeting siRNA pool (siGENOME Non-Targeting pool #2, D-001206-14) was used as negative control.

tag: genotype/variation

value: case (siSF3B1)

tag: experiment

value: Mono


title: siSRSF1-3

description:
siRNA mediated down-modulation of SRSF1, RNA and proteins were harvested in 72hours, n=3
GK12

value: case (siSRSF1)

value: Triplicates


title: siNT_72-2

description:
siRNA mediated down-modulation of NonTargeting control for siSRSF1, RNA and proteins were harvested in 72hours, n=2
GK9

value: control (siNT)


title: siNT_48-4

description:
siRNA mediated down-modulation of NonTargeting control for siSF3B1, RNA and proteins were harvested in 48hours, single experiment performed
ACH71_H


title: siSF3B1-4


title: siNT_48-PacBio Iso-Seq


title: siSF3B1-3

description:
siRNA mediated down-modulation of SF3B1, RNA and proteins were harvested in 48hours, n=3
GK6


title: siNT_72-3

description:
siRNA mediated down-modulation of NonTargeting control for siSRSF1, RNA and proteins were harvested in 72hours, n=3
GK11


title: siNT_48-3

description:
siRNA mediated down-modulation of NonTargeting control for siSF3B1, RNA and proteins were harvested in 48hours, n=3
GK5


title: siSRSF1-2

description:
siRNA mediated down-modulation of SRSF1, RNA and proteins were harvested in 72hours, n=2
GK10


title: siSF3B1-2

description:
siRNA mediated down-modulation of SF3B1, RNA and proteins were harvested in 48hours, n=2
GK4


title: siNT_72-1

description:
siRNA mediated down-modulation of NonTargeting control for siSRSF1, RNA and proteins were harvested in 72hours, n=1
GK7


title: siSRSF1-1

description:
siRNA mediated down-modulation of SRSF1, RNA and proteins were harvested in 72hours, n=1
GK8


title: embryonic kidney cells - c - treated with Mir 22-3p


title: embryonic kidney cells - b - negative control


title: embryonic kidney cells - a - negative control


title: L6_GR24_60microM_rep1

description:
Gene expression after 24h in GR24-treated rat L6 myotubes.
Replicate 1

value: skeletal muscle myotubes


title: siNT_48-2

description:
siRNA mediated down-modulation of NonTargeting control for siSF3B1, RNA and proteins were harvested in 48hours, n=2
GK3


title: siSF3B1-1

description:
siRNA mediated down-modulation of SF3B1, RNA and proteins were harvested in 48hours, n=1
GK2


title: siRNA tgfbr3 rep 3

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

hyb_protocol: The total amount of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was hybridized to Agilent-046064 Human miRNA Release 19.0 8x60K Microarray (GPL18402) for 20 hours at 55°C in a rotating 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 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

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

extract_protocol: At 24h following siTgfbr3 transfection, hPASMC were rinsed with PBS and the total RNA was extracted with miRNeasy Mini Kit (Qiagen). RNA was frozen in liquid nitrogen and stored in -80°C prior to the shipping.

tag: sirna transfection

value: siRNA tgfbr3

value: pulmonary arterial smooth muscle cells (hPASMC) in P2


title: siRNA tgfbr3 rep 4

source_name: pulmonary arterial smooth muscle cells (hPASMC)


title: siRNA tgfbr3 rep 2


title: Scramble rep 3

value: Scramble


title: siRNA tgfbr3 rep 1


title: Scramble rep 4


title: Scramble rep 2


title: Scramble rep 1


title: siNT_48-1

description:
siRNA mediated down-modulation of NonTargeting control for siSF3B1, RNA and proteins were harvested in 48hours, n=1
GK1


title: Normoxia-21% O2 6 h rep 4

description: microRNA expression after 6 h in normoxia

hyb_protocol: The total amount of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) hybridized to Agilent-035430 8x60K Mouse miRNA Rel17 Microarray (GPL15547) for 20 hours at 55°C in a rotating 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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 035430_D_F_20111226 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

organism: Mus musculus

source_name: lung alveolar type II cells

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

extract_protocol: miRNeasy Mini Kit (50) QIAGEN (Cat. No. 217004)

tag: strain

value: Lung

value: primary murine Alveolar type II cells


title: Hyperoxia-85% O2 24 h rep 2

description: microRNA expression after 24 h in hyperoxia


title: Hyperoxia-85% O2 24 h rep 1


title: Lhx6 Null Replicate 2

city: London

first: Guilherme

last: Neves

address: New Hunt's House, 4th Floor, Guy's Hospital Campus

department: MRC - Center for Neurodevelopmental Disorders

country: United Kingdom

institute: King's College London

data_processing:
GTF file was parsed to remove non-exonic and non-primary-assembly features.
Exonic GTF was used to build an index of transcripts using the RSEM rsem-prepare-reference command (version 1.2.31) and Bowtie2 (version 2.2.9).
FASTQ files were trimmed to remove occurrences of illumina adapter sequence (AGATCGGAAGAGC) and poor quality sequence (score threshold of 10) using CutAdapt (version 1.9.1).
FASTQ files were aligned to transcript index using and expected genes counts were extracted using a combination of Bowtie2 (version 2.2.9) and RSEM (version 1.2.31).
Expected counts were rounded and used as input in a differential expression analysis using DESeq2
Genome_build: Genome and annotation downloaded from Ensembl. Genome build GRCm38. Annotation release 84.
Supplementary_files_format_and_content: Mus_musculus.GRCm38.84.primary_assembly_exon.gtf. GTF file used to generate transcript indices,
Supplementary_files_format_and_content: gene_counts.txt. Gene counts generated by RSEM
Supplementary_files_format_and_content: dese2_results.txt. Results of the DESeq2 differential expression analysis.

source_name: Forebrain

extract_protocol:
Total RNA was extracted from freshly dissected forebrain of P15 mice. Forebrains were immediately harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols. The only deviation from the protocol was to use the e-gel clone well system (Invitrogen) for fragment size selection.

tag: developmental stage

value: post natal day 15

tag: genotype

tag: rin

tag: genders of mice

value: 2 females


title: Normoxia-21% O2 6 h rep 3

tag: tissue

tag: cell type


title: Normoxia-21% O2 24 h rep 1

description: microRNA expression after 24 h in normoxia


title: Normoxia-21% O2 24 h rep 2


title: Normoxia-21% O2 6 h rep 2


title: Hyperoxia-85% O2 6 h rep 2

description: microRNA expression after 6 h in hyperoxia


title: Hyperoxia-85% O2 6 h rep 4


title: Lhx6 Null Replicate 3

value: 1 male + 1 female


title: Normoxia-21% O2 24 h rep 3


title: Lhx6 Null Replicate 1


title: Hyperoxia-85% O2 6 h rep 3


title: Lhx6 Het Replicate 3


title: Lhx6 Het Replicate 2

value: 2 males


title: Lhx6 Het Replicate 4


title: Lhx6 Het Replicate 1


title: Normoxia-21% O2 6 h rep 1


title: Hyperoxia-85% O2 24 h rep 4


title: Hyperoxia-85% O2 24 h rep 3


title: Liver_ZT16_PPARaLWT_Fasted_rep2

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 33980 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31356 rows each corresponding to a unique ProbeName (provided as data Matrix). The data of technical replicates were averaged for sample s18 (s18a and s18b) and s15 (s15a and s15b). The Matrix template contains the resulting averaged data values for each replicate.

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a Safe 04 chow diet.

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. RNA amounts were determined by NanoDrop®ND-1000 and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

tag: gender

value: male

value: PPARaLWT

tag: diet

value: Fasted

tag: animal

tag: replicate


title: Liver_ZT16_PPARaLKO_Fed_rep6

value: PPARaLKO

value: Fed


title: Liver_ZT16_PPARaLKO_Fasted_rep2


title: Liver_ZT16_PPARaLWT_Fasted_rep3


title: Liver_ZT16_PPARaLKO_Fed_rep2


title: Liver_ZT16_PPARaLWT_Fed_rep3a

description:
technical replicate of s15
s15a


title: Hyperoxia 85% O2 6 h rep 4

description: exp. hyperoxia 6 h (Group 4)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (GPL10787) for 18 hours at 65°C in a rotating 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.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20121126 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

extract_protocol: peqGOLD Total RNA Kit (Order No. 12-6834-01)


title: Liver_ZT16_PPARaLKO_Fasted_rep4


title: Liver_ZT16_PPARaLWT_Fed_rep5


title: Hyperoxia 85% O2 6 h rep 3

description: exp. hyperoxia 6 h (Group 4)


title: Normoxia 21% O2 6 h rep 3

description: control normoxia 6 h (Group 3)


title: Hyperoxia 85% O2 6 h rep 2

description: exp. hyperoxia 6 h (Group 4)


title: Hyperoxia 85% O2 6 h rep 1

description: exp. hyperoxia 6 h (Group 4)


title: Liver_ZT16_PPARaLWT_Fasted_rep4


title: Liver_ZT16_PPARaLKO_Fasted_rep5


title: Normoxia 21% O2 6 h rep 1

description: control normoxia 6 h (Group 3)


title: Liver_ZT16_PPARaLKO_Fasted_rep6


title: Normoxia 21% O2 6 h rep 2

description: control normoxia 6 h (Group 3)


title: Liver_ZT16_PPARaLWT_Fed_rep3b

description:
technical replicate of s15
s15b


title: Hyperoxia 85% O2 24 h rep 4

description: exp. hyperoxia 24 h (Group 2)


title: Liver_ZT16_PPARaLWT_Fed_rep2


title: Liver_ZT16_PPARaLWT_Fasted_rep1b

description:
technical replicate of s18
s18b


title: Liver_ZT16_PPARaLKO_Fasted_rep1


title: Normoxia 21% O2 6 h rep 4

description: control normoxia 6 h (Group 3)


title: siRNA Tgfbr3 rep4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (GPL14550) for 18 hours at 65°C in a rotating 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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

source_name: pulmonary arterial endothelial cells (hPASMC)

extract_protocol: At 24h following transfection hPAEC were rinsed with PBS and the total RNA was extracted with peqGOLD TOTAL RNA Kit (VWR). RNA was frozen in liquid nitrogen and stored in -80°C prior to the shipping.

value: siRNA Tgfbr3

value: pulmonary arterial endothelial cells (hPAEC) in P2


title: Liver_ZT16_PPARaLKO_Fed_rep4


title: Liver_ZT16_PPARaLKO_Fed_rep5


title: Liver_ZT16_PPARaLKO_Fed_rep1


title: Hyperoxia 85% O2 24 h rep 3

description: exp. hyperoxia 24 h (Group 2)


title: Gel+metastatasis cancer cells H460

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

country: Japan

institute: Kurume Universuty

hyb_protocol: Labeled miRNA was hybridized to a 60K oligomicroarray (Human miRNA Microarray Kit Release 16.0, 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Gel, metastatasis cancer cells H460

label_protocol: miRNA was labelled using a miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from cells using an AllPrep DNA/RNA Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: cell line

tag: type

value: micro RNA


title: Liver_ZT16_PPARaLWT_Fed_rep4

tag: time


title: Hyperoxia 85% O2 24 h rep 2

description: exp. hyperoxia 24 h (Group 2)


title: siRNA Tgfbr3 rep1


title: HBEC3_SnailOEr_miRNA

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description:
Sample name: H3S1
microRNA

hyb_protocol: As recommended by manufacturer. Arrays used are: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno

scan_protocol: GenePix Personal 4100A Scanner and its software (GenePix Pro 6.0.1.25) were used for scanning, and image processing.

data_processing: Data was normalized by rmaMicroRna function in AgiMicroRna package (R/Bioconductor) which returned the data in log2 scale for individual probes

source_name: HBEC3, retroviral vector with SNAI1 cDNA

label_protocol: As recommended by manufacturer

growth_protocol: Grown in Keratinocyte medium supplemented with 30ug/ml Bovine Pituitary Extract (BPE) and 0.2ng/ml recombinant Epidermal Growth Factor (EGF), all from Invitrogen (#17005-042).

extract_protocol: Total RNA was extracted using Qiagen's Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Transduced cells underwent two weeks of antibiotic selection (100ug/ml hygromycin). They were then passaged three times in plain growth medium and harvested upon reaching 75% confluency.

value: Human bronchial epithelial cells immortalized with hTERT and hCDK4

tag: patient age

tag: patient gender

value: Female

tag: patient smoking status

value: Smoker

tag: patient diagnosis

value: No lung cancer as cells isolated from large airway

tag: snail oe

value: yes


title: HBEC4_SnailOEr_miRNA

description:
Sample name: H4S2
microRNA

source_name: HBEC4, retroviral vector with SNAI1 cDNA

value: With lung cancer as cells isolated from large airway


title: siRNA Tgfbr3 rep3

tag: sirna transfection


title: Normoxia 21% O2 24 h rep 3

description: control normoxia 24 h (Group 1)

value: primary murine Alveolar type II cells

tag: strain

value: Lung


title: siRNA Tgfbr3 rep2


title: scr rep4

value: scramble


title: scr rep3


title: Liver_ZT16_PPARaLWT_Fasted_rep1a

description:
technical replicate of s18
s18a

value: male

tag: genotype


title: Liver_ZT16_PPARaLWT_Fasted_rep5

value: PPARaLWT


title: Hyperoxia 85% O2 24 h rep 1

description: exp. hyperoxia 24 h (Group 2)

tag: tissue


title: HBEC4_vector_miRNA

description:
Sample name: H4V1
microRNA

source_name: HBEC4, empty retroviral vector

tag: cell type

value: no


title: Liver_ZT16_PPARaLKO_Fasted_rep3

tag: gender

value: PPARaLKO

value: Fasted


title: Biological replicate 88

status: Public on Dec 15 2017

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Paired-end 101bp length output reads were aligned to the human reference genome (UCSC hg19) with TopHat v.2.0.2 (PMID: 19289445) using Bowtie v.0.12.8 (PMID: 19261174). The TopHat parameters explicitly used are tophat -p 30 -G genes.gtf --library-type fr-unstranded -r 100 -F 0.05 --microexon-search.
The annotated RefSeq GTF transcript and fasta genome files were from UCSC and were downloaded from http://cufflinks.cbcb.umd.edu/igenomes.html.Gene expression was measured as the normalized sum of expression of all its exons. The dexseq_count python script (PMID: 22722343) was used by counting uniquely mapped reads in each exon.
Gene and exon expression normalizations were then performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene or exon length respectively.
In addition, only the genes and exons that had reads mapped to them in at least 5% of the samples were kept.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM gene values normalized for each Sample (and also normalized by gene length). The processed files also include the genomic start site of the genes annotated.

source_name: pancreatic islets

extract_protocol:
Pancreatic islets were isolated according to the isolation protocol described from Nordic Islet Transplantation Programme (http://www.nordicislets.org). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets


title: Biological replicate 84


title: Biological replicate 87


title: Biological replicate 85


title: HBEC3_vector_miRNA

description:
Sample name: H3V1
microRNA

source_name: HBEC3, empty retroviral vector


title: Biological replicate 86


title: scr rep1

value: pulmonary arterial endothelial cells (hPAEC) in P2


title: Biological replicate 83


title: Normoxia 21% O2 24 h rep 2

description: control normoxia 24 h (Group 1)


title: scr rep2


title: Normoxia 21% O2 24 h rep 1

description: control normoxia 24 h (Group 1)


title: Liver_ZT16_PPARaLWT_Fed_rep1

tag: diet

value: Fed


title: Biological replicate 81


title: Biological replicate 82


title: Biological replicate 79


title: Biological replicate 80


title: Biological replicate 78


title: Biological replicate 77


title: Liver_ZT16_PPARaLKO_Fed_rep3

tag: animal


title: Biological replicate 74


title: Biological replicate 76


title: Biological replicate 70


title: Biological replicate 71


title: Normoxia 21% O2 24 h rep 4

description: control normoxia 24 h (Group 1)


title: Gel+metastatasis cancer cells H460+endothelial cells

source_name: Gel, metastatasis cancer cells H460, endothelial cells

value: micro RNA


title: Biological replicate 69


title: Biological replicate 67


title: Biological replicate 65


title: Biological replicate 62


title: Biological replicate 59


title: Biological replicate 64


title: Biological replicate 66


title: Biological replicate 63


title: Biological replicate 58


title: Biological replicate 60


title: Biological replicate 55


title: Biological replicate 57


title: Biological replicate 56


title: Biological replicate 54


title: Biological replicate 51


title: Biological replicate 73


title: Biological replicate 49


title: Biological replicate 53


title: Biological replicate 72


title: Biological replicate 52


title: Biological replicate 50


title: Biological replicate 48


title: Biological replicate 46


title: Biological replicate 68


title: Biological replicate 45


title: Biological replicate 44


title: Biological replicate 61


title: Biological replicate 41


title: Biological replicate 43


title: Biological replicate 42


title: Biological replicate 39


title: Biological replicate 37


title: Biological replicate 38


title: Biological replicate 33


title: Biological replicate 31


title: Biological replicate 29


title: Gel+metastatasis cancer cells H460+stem cells

source_name: Gel, metastatasis cancer cells H460, stem cells


title: Biological replicate 34


title: Biological replicate 32


title: Biological replicate 30


title: Biological replicate 28


title: Biological replicate 25


title: Biological replicate 26


title: Biological replicate 47


title: Biological replicate 24


title: Biological replicate 40


title: Biological replicate 27


title: Biological replicate 35


title: Biological replicate 36


title: Biological replicate 20


title: Biological replicate 21


title: Biological replicate 16


title: Biological replicate 23


title: Biological replicate 19


title: Biological replicate 18


title: Biological replicate 14


title: Biological replicate 15


title: Biological replicate 17


title: Biological replicate 13


title: Biological replicate 12


title: Biological replicate 22


title: Biological replicate 9


title: Biological replicate 4


title: Biological replicate 10


title: Biological replicate 5


title: Biological replicate 11


title: Biological replicate 3


title: Biological replicate 2


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 3

type: genomic

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

description:
545071
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt

hyb_protocol: For analysis of DNA methylation levels, the Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used. This array has a density of 2.1 million probes (50-75 oligonucleotides long, median probe spacing 100 bp) that represent all annotated human promoters (~ 26,210), 27,867 CpG islands, and 750 miRNA promoters per slide. The promoters and CpG islands largely overlap with transcription start sites of well characterized RefSeq genes, covering, on average, 8 kb upstream and 3 kb downstream. Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000. Thirty-four microgram of Cy3 Input and 34 µg of Cy5 MeDIP DNA were pooled and completely dried by using a speed vac. The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing, the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing: Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen. PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR corrected p- value < 0.01) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment i.e. exposed versus control. Peaks were identified in the DMR by searching for regions containing at least 8 significant consecutive probes (p<0.01).   Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (20) and CpG islands of genes using the NimbleScan v2.6 software. A control corrected median log2 ratio was calculated for each peak. Log2 ratio’s > 0 indicate hyper methylation and log2 ratio’s < 0 indicate hypo methylation.

molecule: genomic DNA

source_name: input DNA from human primary hepatocytes

label_protocol: Genomic DNA was sonicated to obtain fragments ranging from 200 bp to 600 bp, cleaned up using silica columns (Zymo Research) and eluted in TE buffer. MeDIP was performed using the MagMeDIP kit (Diagenode, Liège, Belgium) according to the manufacturer’s protocol. In brief, IP incubation mix (containing magbuffer A, magbuffer B, 1.5 µg methylated DNA positive control, 1.5 µg non-methylated DNA negative control) was added to 1.2 µg of sonicated sample and denatured at 95 °C. 10% of this was kept aside as Input sample and stored at 4°C. Beads were washed 3 times with ice-cold diluted magbuffer A and collected in 20 µl of diluted magbuffer A. The remaining sample was immunoprecipitated using 5µl of antibodymix (containing an antibody against 5’-methylcytidine (provided in the kit) magbuffer A and magbuffer C) and 20 µl of magnetic beads solution. Immunoprecipitation was performed overnight at 4 °C on a rotating wheel. The following day, magnetic beads were washed twice with wash buffer 1 and once with wash buffer 2 and kept on ice. Next, DNA isolation was performed using the IPure kit (Diagenode, Liège, Belgium). Fifty ul of elution buffer was added to the MeDIP-bead pellet and 92.5 µl to the Input sample and incubated for 15 min at room temperature on a rotating wheel. Supernatant was transferred to a new Eppendorf tube using a magnet. Samples were subsequently incubated with 2 µl of glycogen carrier, 100 µl of 100% isopropanol and 15 µl of magnetic beads and incubated for 1 hour at room temperature on a rotating wheel. Magnetic beads were washed using wash buffer 1 and wash buffer 2 for 5 minutes. The DNA was eluted twice by using 75 µl of buffer C and incubated for 15 min at room temperature on a rotating wheel. All the samples were precipitated with sodium acetate and ethanol with glycogen as a carrier for 30 min at -80 °C and centrifuged at max speed for 30 min at 4°C. The cell pellet was washed using 70% ethanol and after air drying suspended in 20µl MQ. Eight µl of both Input and MeDIP samples were used for amplification by whole genome amplification (WGA) using the WGA2 kit (Sigma Aldrich) following the manufacturer’s instruction, without performing the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water. Methylation enrichment in the paired samples MeDIP/Input was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCq method using the primers included in the kit.

extract_protocol: Cells were lysed in 500 µl of digestion buffer (containing 0.5 M EDTA; 1 M Tris–HCl, pH 8.0; 10% SDS) and incubated for 1 hour at 55 °C. Next, 25 µl of proteinase K (20mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated for 10 minutes at 80 °C. RNAse A (2 µl; 100mg/ml) (Qiagen) and collagenase (25 µl; 1%) (Sigma) treatment was performed for 1 hour at 37 °C. Thereupon, 500 µl of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added. The mixture was shaken manually for 5 min, and centrifuged for 5 minutes at maximum speed. The upper phase was transferred to a new Eppendorf and the step with PCI was repeated. The upper phase was collected and precipitated using 50 µl of 3M NaAc pH 5.6 and 1250 µl of cold 100% ethanol for 30 min. at -80°C. After centrifugation for 30 minutes at maximum speed, the DNA pellet was washed using cold 70% ETOH, dried in a speed vac and dissolved in 50µl of nuclease free water. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 12 DNA samples were prepared. DNA was used for MeDIP-Chip analyses.

value: Human primary hepatocytes

tag: treatment

value: exposed to 15 mM valproic acid for 5 days daily and subsequently to 3 days medium

source_name: medip DNA from human primary hepatocytes

tag: antibody

value: antibody against 5'-methylcytidine


title: Biological replicate 7


title: Biological replicate 8


title: Biological replicate 6


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 2

description:
545020
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt


title: Primary human hepatocyte 8 days control replicate 3

description:
544669
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt

value: exposed to 1% ethalnol for 5 days daily and subsequently to 3 days medium


title: Biological replicate 1


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 1

description:
545077
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt


title: Primary human hepatocyte 8 days control replicate 2

description:
545072
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt


title: Primary human hepatocyte 8 days control replicate 1

description:
545029
PHH_exposed_to_VPA_for_5_days_daily_including_3_days_washout.txt


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 2

description:
544485
PHH_exposed_to_VPA_for_5_days_daily.txt

value: exposed to 15 mM valproic acid for 5 days daily


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 1

description:
544488
PHH_exposed_to_VPA_for_5_days_daily.txt


title: Primary human hepatocyte 5 days control replicate 2

description:
545035
PHH_exposed_to_VPA_for_5_days_daily.txt

value: exposed to 1% ethanol for 5 days daily


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 3

description:
545026
PHH_exposed_to_VPA_for_5_days_daily.txt


title: Primary human hepatocyte 5 days control replicate 1

description:
545106
PHH_exposed_to_VPA_for_5_days_daily.txt


title: Primary human hepatocyte 5 days control replicate 3

description:
545075
PHH_exposed_to_VPA_for_5_days_daily.txt


title: 11827

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: MEF PSEN1&2-/- +hARF6 vs. MEF Wild-type

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 825 ng; Cy5 label: 825 ng) was hybridised on Agilent's Mouse Whole Genome v2 oligo microarray (Cat # G2519F-026655, Agilent) followed by (manual) washing, according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with SuresScan High-Resolution Technology. Probe signals were quantified using Agilent's Feature Extraction software (version 10.7.3.1).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal) from Agilent Feature Extraction software v10.7.3.1 and compute log2-(Cy5/Cy3)-ratios. We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the features gIsPosAndSignif and rIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-(Cy5/Cy3)-ratios are averaged.

source_name: S4b-MEF PSENdKO+hARF6

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

extract_protocol: Total RNA was extracted from 80% confluent monolayer of cells using TriPure reagent and chloroform extraction. (1) Homogenization: Culture cells in 10cm² dishes,  Use 1ml TriPure reagent/10cm² dish (when appending too little TriPure reagent, the chances are higher to contaminate the RNA with genomic DNA), Pass cell lysates several times through a pipet, To reduce viscosity, shear the genomic DNA with 2 passes through a 26 gauge needle prior to the addition of chloroform,  Let stand at RT until completely resolved ~5min, Vortex samples. (2) Phase separation: Add 0.2ml chloroform per 1ml TriPure reagent, Shake vigorously for 15sec by hand,  Incubate 2-3min at RT, Spin 15min at 12,000rpm at 4°C, Three layers are formed (top layer = aqueous phase containing RNA; white interphase layer = containing DNA and protein; bottom layer = red organic phase containing DNA and protein). (3) RNA precipitation: Mix aqueous phase (top layer) with 0.5ml isopropanol per 0.7-0.75ml TriPure reagent (new eppe), Incubate 10min at RT, Spin 10min at 12,000rpm at 4°C, The RNA precipitate forms a gel-like pellet (often invisible before centrifugation) on the side and bottom of the tube. (4) RNA wash: Remove supernatant, Wash RNA pellet with at least 1ml 75% EtOH per 1ml TriPure reagent used for the initial RNA isolation step, Vortex, Spin 5min at 7,500xg at 4°C. (5) Redissolve the RNA: Air-dry RNA pellet (5-10min) (Do not let RNA pellet dry out completely as this will greatly decrease its solubility), Redisolve in RNAse free water, Pass solution a few times through a pipet tip and incubate 10min at 55°C-60°C to avoid problems with partially dissolved RNA, Expected yield for fibroblasts: 5-7µg from 1*106 cells. (6) Store RNA samples at -80°C (1µg needed for complete exp)

tag: strain/background

value: C57B6/J black × 129Sv

value: mouse embryonic fibroblasts

tag: genetic modification

value: retroviral infection with human ARF6 (puromycin resistant)

source_name: S1b-MEF Wild-type

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

value: wild-type


title: 11829

description: MEF PSEN1&2-/- +hARF6 vs. MEF PSEN1&2-/- +hPSEN1 D257A/D385A

source_name: S4c-MEF PSENdKO+hARF6

source_name: S3c-MEF PSENdKO+hPSEN1 Asp

value: retroviral infection with human PSEN1 D257A/D385A mutant (puromycin resistant)


title: 11828

description: MEF Wild-type vs. MEF PSEN1&2-/- +hARF6

source_name: S1c-MEF Wild-type


title: 11830

description: MEF PSEN1&2-/- +hPSEN1 D257A/D385A vs. MEF PSEN1&2-/-

source_name: S2c-MEF PSENdKO


title: 11825

source_name: S3b-MEF PSENdKO+hPSEN1 Asp

source_name: S2b-MEF PSENdKO


title: 11822

source_name: S4a-MEF PSENdKO+hARF6

source_name: S3a-MEF PSENdKO+hPSEN1 Asp


title: 11820

description: MEF Wild-type vs. MEF PSEN1&2-/-

source_name: S1a-MEF Wild-type

source_name: S2a-MEF PSENdKO


title: 11823

description: MEF PSEN1&2-/- +hPSEN1 D257A/D385A vs. MEF Wild-type


title: 11831

description: MEF PSEN1&2-/- vs. MEF Wild-type


title: 11824

description: MEF Wild-type vs. MEF PSEN1&2-/- +hPSEN1 D257A/D385A


hyb_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

data_processing: The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies, which were imported in R 2.15.3 (http://www.r-project.org) for quality control with an in-house developed pipeline (26). Filtering and normalization was performed using AgiMicroRna (27), which applies a LIMMA approach for selection of differentially expressed microRNAs (DE-miRs). Total gene signals were log2-transformed and quantile-normalized. DE-miRs with an absolute FC of 1.5 or higher (i.e., average log2 ratio of < −0.58 or > 0.58) and an FDR-corrected p-value < 0.05 were considered statistically significant.

source_name: RNA from human primary hepatocytes exposed to 15 mM valproic acid for 5 days daily

growth_protocol: Cryopreserved primary human hepatocytes (PHH) and culture media were purchased from Life Technologies (Bleiswijk, The Netherlands), unless otherwise stated.PHH were cultured in pre-coated multi-well plates in a 2-layer collagen sandwich.PHH were thawed for 1 min at 37°C. Three vials (one per donor) were poured in 50 ml Thawing Medium (CHRM CM7000) and centrifuged at 4°C for 10 min at 100g. The cell pellet was dissolved in plating medium (CM9000) at a concentration of 1*10E6 cells/ml. After seeding, PHH were incubated in the pre-coated multi-well plates for 4 hours at 37°C. Next, debris was removed by shaking and washing the cells twice with Williams’ Medium E medium. Subsequently, PHH were covered by a collagen layer (containing DMEM, NaOH and rat tail Collagen type 1 (BD biosciences, Breda, The Netherlands)), incubated for 30 min at 37°C, and covered with incubation medium (CM600, CM4000).

extract_protocol: At the end of treatment, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment.

treatment_protocol: PHH were exposed to 15 mM of VPA in a 24 hour repeat-dose testing regime. Medium was changed daily thereby providing a new dose of VPA to the PHH each day. A bi-phasic treatment regime was applied, combining a 5-day VPA exposure with a subsequent 3-days washout period during which the PHH were exposed to medium only. 1% Ethanol was used as solvent control.

value: Primary human hepatocytes


scan_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

source_name: RNA from human primary hepatocytes exposed to 1% ethanol for 5 days daily and subsequently to 3 days medium


source_name: RNA from human primary hepatocytes exposed to 1% ethanol for 5 days daily

label_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).


value: exposed to 1% ethanol for 5 days daily and subsequently to 3 days medium


title: Biological replicate 75

source_name: pancreatic islets

value: pancreatic islets


source_name: RNA from human primary hepatocytes exposed to 15 mM valproic acid for 5 days daily and subsequently to 3 days medium


title: 11821

description: MEF PSEN1&2-/- vs. MEF PSEN1&2-/- +hARF6


title: SLX-9703_L-cells_92

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Upper small intestine

extract_protocol:
Tissue was prepared from 3 male mice, aged 20-21 weeks. Intestinal pieces were stripped of the outer muscle layers. Tissue was chopped into 1–2 mm pieces and digested to single cells with 1 mg/ml collagenase in calcium-free Hanks Buffered Salt Solution (HBSS). Single cell suspensions were separated by FACS using an InfluxCell Sorter (BD Bioscience, USA). Cells were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, Cat. no. 93443) and 2.3 U of SUPERase-In RNase Inhibitor (Ambion, Cat no. AM2694). cDNA was obtained and amplified following the described SMARTSEQ2 protocol (Picelli et al., 2014). Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit. Pooled libraries were run on the Illumina Hi-Seq 2500.
Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit.

value: L-cells


title: SLX-9703_L-cells_90


title: SLX-9703_L-cells_8


title: SLX-9703_L-cells_93


title: SLX-9703_L-cells_96


title: SLX-9703_L-cells_91


title: SLX-9703_L-cells_95


title: SLX-9703_L-cells_94


title: SLX-9703_L-cells_9


title: SLX-9703_L-cells_89


title: SLX-9703_L-cells_88


title: SLX-9703_L-cells_85


title: SLX-9703_L-cells_83


title: SLX-9703_L-cells_87


title: SLX-9703_L-cells_86


title: SLX-9703_L-cells_84


title: SLX-9703_L-cells_82


title: 11826

source_name: S4b-MEF PSENdKO+hARF6


title: SLX-9703_L-cells_81


title: SLX-9703_L-cells_80


title: SLX-9703_L-cells_7


title: SLX-9703_L-cells_77


title: SLX-9703_L-cells_78


title: SLX-9703_L-cells_75


title: SLX-9703_L-cells_76


title: SLX-9703_L-cells_79


title: SLX-9703_L-cells_74


title: SLX-9703_L-cells_72


title: SLX-9703_L-cells_71


title: SLX-9703_L-cells_73


title: SLX-9703_L-cells_64


title: SLX-9703_L-cells_66


title: SLX-9703_L-cells_63


title: SLX-9703_L-cells_68


title: SLX-9703_L-cells_70


title: SLX-9703_L-cells_65


title: SLX-9703_L-cells_67


title: SLX-9703_L-cells_6


title: SLX-9703_L-cells_69


title: SLX-9703_L-cells_62


title: SLX-9703_L-cells_60


title: SLX-9703_L-cells_61


title: SLX-9703_L-cells_5


title: SLX-9703_L-cells_56


title: SLX-9703_L-cells_55


title: SLX-9703_L-cells_58


title: SLX-9703_L-cells_52


title: SLX-9703_L-cells_57


title: SLX-9703_L-cells_53


title: SLX-9703_L-cells_4


title: SLX-9703_L-cells_48


title: SLX-9703_L-cells_49


title: SLX-9703_L-cells_51


title: SLX-9703_L-cells_45


title: SLX-9703_L-cells_46


title: SLX-9703_L-cells_54


title: SLX-9703_L-cells_59


title: SLX-9703_L-cells_3


title: SLX-9703_L-cells_47


title: SLX-9703_L-cells_40


title: SLX-9703_L-cells_50


title: SLX-9703_L-cells_37


title: SLX-9703_L-cells_31


title: SLX-9703_L-cells_42


title: SLX-9703_L-cells_43


title: SLX-9703_L-cells_36


title: SLX-9703_L-cells_29


title: SLX-9703_L-cells_39


title: SLX-9703_L-cells_41


title: SLX-9703_L-cells_26


title: SLX-9703_L-cells_27


title: SLX-9703_L-cells_44


title: SLX-9703_L-cells_33


title: SLX-9703_L-cells_32


title: SLX-9703_L-cells_34


title: SLX-9703_L-cells_35


title: SLX-9703_L-cells_30


title: SLX-9703_L-cells_38


title: SLX-9703_L-cells_25


title: SLX-9703_L-cells_1


title: SLX-9703_L-cells_20


title: SLX-9703_L-cells_24


title: SLX-9703_L-cells_2


title: SLX-9703_L-cells_23


title: SLX-9703_L-cells_19


title: SLX-9703_L-cells_17


title: SLX-9703_L-cells_15


title: SLX-9703_L-cells_14


title: SLX-9703_L-cells_18


title: SLX-9703_L-cells_16


title: SLX-9703_L-cells_11


title: SLX-9703_L-cells_10


title: SLX-11179_L-cells_9


title: SLX-9703_L-cells_13


title: SLX-9703_L-cells_28


title: SLX-11179_L-cells_94


title: SLX-11179_L-cells_96


title: SLX-11179_L-cells_95


title: SLX-11179_L-cells_93


title: SLX-11179_L-cells_91


title: SLX-11179_L-cells_90


title: SLX-9703_L-cells_22


title: SLX-11179_L-cells_92


title: SLX-11179_L-cells_8


title: SLX-9703_L-cells_21


title: SLX-11179_L-cells_89


title: SLX-11179_L-cells_85


title: SLX-11179_L-cells_84


title: SLX-11179_L-cells_87


title: SLX-11179_L-cells_86


title: SLX-11179_L-cells_83


title: SLX-9703_L-cells_12


title: SLX-11179_L-cells_79


title: SLX-11179_L-cells_7


title: SLX-11179_L-cells_75


title: SLX-11179_L-cells_77


title: SLX-11179_L-cells_72


title: SLX-11179_L-cells_88


title: SLX-11179_L-cells_71


title: SLX-11179_L-cells_74


title: SLX-11179_L-cells_69


title: SLX-11179_L-cells_65


title: SLX-11179_L-cells_68


title: SLX-11179_L-cells_81


title: SLX-11179_L-cells_6


title: SLX-11179_L-cells_70


title: SLX-11179_L-cells_66


title: SLX-11179_L-cells_64


title: SLX-11179_L-cells_63


title: SLX-11179_L-cells_80


title: SLX-11179_L-cells_5


title: SLX-11179_L-cells_59


title: SLX-11179_L-cells_58


title: SLX-11179_L-cells_61


title: SLX-11179_L-cells_62


title: SLX-11179_L-cells_60


title: SLX-11179_L-cells_76


title: SLX-11179_L-cells_73


title: SLX-11179_L-cells_57


title: SLX-11179_L-cells_78


title: SLX-11179_L-cells_56


title: SLX-11179_L-cells_55


title: SLX-11179_L-cells_52


title: SLX-11179_L-cells_54


title: SLX-11179_L-cells_50


title: SLX-11179_L-cells_53


title: SLX-11179_L-cells_4


title: SLX-11179_L-cells_51


title: SLX-11179_L-cells_49


title: SLX-11179_L-cells_45


title: SLX-11179_L-cells_67


title: SLX-11179_L-cells_48


title: SLX-11179_L-cells_44


title: SLX-11179_L-cells_42


title: SLX-11179_L-cells_46


title: SLX-11179_L-cells_47


title: SLX-11179_L-cells_41


title: SLX-11179_L-cells_3


title: SLX-11179_L-cells_43


title: SLX-11179_L-cells_39


title: SLX-11179_L-cells_40


title: SLX-11179_L-cells_37


title: SLX-11179_L-cells_35


title: SLX-11179_L-cells_38


title: SLX-11179_L-cells_36


title: SLX-11179_L-cells_34


title: SLX-11179_L-cells_82


title: SLX-11179_L-cells_30


title: SLX-11179_L-cells_33


title: SLX-11179_L-cells_2


title: SLX-11179_L-cells_32


title: SLX-11179_L-cells_31


title: SLX-11179_L-cells_26


title: SLX-11179_L-cells_27


title: SLX-11179_L-cells_29


title: SLX-11179_L-cells_24


title: SLX-11179_L-cells_21


title: SLX-11179_L-cells_23


title: SLX-11179_L-cells_1


title: SLX-11179_L-cells_20


title: SLX-11179_L-cells_28


title: SLX-11179_L-cells_22


title: SLX-11179_L-cells_18


title: SLX-11179_L-cells_15


title: SLX-11179_L-cells_16


title: SLX-11179_L-cells_17


title: SLX-11179_L-cells_12


title: SLX-11179_L-cells_13


title: SLX-11179_L-cells_11


title: SLX-11179_L-cells_10


title: SLX-11175_L-cells_96


title: SLX-11175_L-cells_95


title: SLX-11175_L-cells_93


title: SLX-11175_L-cells_94


title: SLX-11175_L-cells_92


title: SLX-11179_L-cells_25


title: SLX-11175_L-cells_91


title: SLX-11175_L-cells_90


title: SLX-11175_L-cells_87


title: SLX-11179_L-cells_19


title: SLX-11175_L-cells_8


title: SLX-11175_L-cells_89


title: SLX-11175_L-cells_86


title: SLX-11175_L-cells_85


title: SLX-11175_L-cells_84


title: SLX-11175_L-cells_83


title: SLX-11179_L-cells_14


title: SLX-11175_L-cells_81


title: SLX-11175_L-cells_82


title: SLX-11175_L-cells_7


title: SLX-11175_L-cells_77


title: SLX-11175_L-cells_79


title: SLX-11175_L-cells_78


title: SLX-11175_L-cells_75


title: SLX-11175_L-cells_9


title: SLX-11175_L-cells_72


title: SLX-11175_L-cells_73


title: SLX-11175_L-cells_74


title: SLX-11175_L-cells_66


title: SLX-11175_L-cells_71


title: SLX-11175_L-cells_6


title: SLX-11175_L-cells_69


title: SLX-11175_L-cells_88


title: SLX-11175_L-cells_70


title: SLX-11175_L-cells_68


title: SLX-11175_L-cells_67


title: SLX-11175_L-cells_65


title: SLX-11175_L-cells_62


title: SLX-11175_L-cells_63


title: SLX-11175_L-cells_64


title: SLX-11175_L-cells_80


title: SLX-11175_L-cells_60


title: SLX-11175_L-cells_61


title: SLX-11175_L-cells_58


title: SLX-11175_L-cells_59


title: SLX-11175_L-cells_57


title: SLX-11175_L-cells_55


title: SLX-11175_L-cells_76


title: SLX-11175_L-cells_54


title: SLX-11175_L-cells_5


title: SLX-11175_L-cells_53


title: SLX-11175_L-cells_4


title: SLX-11175_L-cells_50


title: SLX-11175_L-cells_52


title: SLX-11175_L-cells_51


title: SLX-11175_L-cells_48


title: SLX-11175_L-cells_47


title: SLX-11175_L-cells_45


title: SLX-11175_L-cells_46


title: SLX-11175_L-cells_41


title: SLX-11175_L-cells_43


title: SLX-11175_L-cells_44


title: SLX-11175_L-cells_56


title: SLX-11175_L-cells_3


title: SLX-11175_L-cells_38


title: SLX-11175_L-cells_39


title: SLX-11175_L-cells_36


title: SLX-11175_L-cells_37


title: SLX-11175_L-cells_34


title: SLX-11175_L-cells_28


title: SLX-11175_L-cells_33


title: SLX-11175_L-cells_30


title: SLX-11175_L-cells_35


title: SLX-11175_L-cells_2


title: SLX-11175_L-cells_32


title: SLX-11175_L-cells_49


title: SLX-11175_L-cells_29


title: SLX-11175_L-cells_42


title: SLX-11175_L-cells_40


title: SLX-11175_L-cells_18


title: SLX-11175_L-cells_21


title: SLX-11175_L-cells_24


title: SLX-11175_L-cells_19


title: SLX-11175_L-cells_25


title: SLX-11175_L-cells_26


title: SLX-11175_L-cells_20


title: SLX-11175_L-cells_31


title: SLX-11175_L-cells_23


title: SLX-11175_L-cells_1


title: SLX-11175_L-cells_16


title: SLX-11175_L-cells_15


title: SLX-11175_L-cells_12


title: SLX-11175_L-cells_14


title: SLX-11175_L-cells_27


title: SLX-11175_L-cells_11


title: SLX-11175_L-cells_22


title: SLX-11175_L-cells_17


title: 29

city: New York

first: Diego

last: Scerbo

state: NY

institute: Columbia University Medical Center

data_processing:
Initially, FASTQC was performed on raw files to ensure proper quality reads before beginning data processing.  The reads were then aligned against the mm10 UCSC reference genome/transcriptome utilizing the tophat/2.0.9 aligner.  Subsequent gene counting of each sample was performed utilizing HTSeq-count/0.9.1.  Differential gene expression analysis was calculated using DESeq2/3.5, an R Bioconductor package.  Genes with an adjusted p value less than 0.05 were considered to be significantly differentiated.  DAVID/6.8 analysis was performed using the genes considered differentiated as the input.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample and pathway analysis.

source_name: Kidney

growth_protocol: Mice were kept on a 12 hour light dark cycle and fed a chow diet throughout the study.

extract_protocol:
Total RNA was purified from approximately a 50 mg piece of kidney cortex using TRIzol reagent (Invitrogen) according to the instructions of the manufacturer.
Libraries were prepared using TruSeq. RNA library prep according to the  instructions of the manufactuer.  RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were either fed adlibitum or fasted for 16 hours before sacrifice

tag: Sex

value: Male

value: Fasted


title: 25


title: 34

value: Fed


title: 32


title: SLX-11175_L-cells_10


title: 27


title: 23


title: siRNA Tgfbr3 24h rep4

source_name: human pulmonary artery smooth muscle cell

extract_protocol: At 24 and 48h following transfection cells were rinsed with PBS and the total RNA was extracted with peqGOLD TOTAL RNA Kit (VWR). RNA was frozen in liquid nitrogen and stored in -80°C prior to the shipping.

value: hPASMC

tag: transfection

value: 200nM siRNA


title: siRNA Tgfbr3 48h rep2


title: SLX-11175_L-cells_13


title: siRNA Tgfbr3 48h rep3


title: 20


title: 22


title: siRNA Tgfbr3 24h rep2


title: scramble 48h rep4

value: scrambled control


title: siRNA Tgfbr3 48h rep4


title: siRNA Tgfbr3 24h rep1


title: scramble 48h rep2


title: scramble 48h rep1


title: scramble 24h rep4


title: Knock down Tgfbr3-24h (timepoint 4)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (GPL14550) for 18 hours at 65°C in a rotating 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.

source_name: Human pulmonary arterial smooth muscle cells (hPASMC)

extract_protocol: At 6, 12, 18 and 24h following transfection cells were rinsed with PBS and the total RNA was extracted with peqGOLD TOTAL RNA Kit (VWR). RNA was frozen in liquid nitrogen and stored in -80°C prior to the shipping.

value: pulmonary artery smooth muscle


title: 18


title: scramble 24h rep1


title: scramble 48h rep3


title: Knock down Tgfbr3-18h (timepoint 3)


title: SCA3 transgenic mouse 9083514 LUM0373

city: Leiden

first: Lodewijk

last: Toonen

address: einthovenweg 20

department: human genetics

institute: LUMC

description: globin depleted RNA

data_processing:
Primary processing and base calling was performed with Illumina’s HCS and RTA. Demultiplexing and generation of FASTQ files was done with Illumina scripts (bcl2fastq v1.8).
Analysis of sequencing data was performed using the BIOPET Gentrap in-house pipeline (http://biopet-docs.readthedocs.io/en/v0.7.0/pipelines/gentrap/) The fastqc toolkit (v0.11.2) was used to evaluate sequencing quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sickle (v1.33 with default settings) and Cutadapt (v1.10, with default settings except for “-m 20”) were used to clean up reads.
Cleaned reads were aligned to the mouse reference genome build 10 (GRCm38/mm10) using STAR aligner version 2.3.0e
The non-default settings used by STAR are “--outFilterMultimapNmax 1 –outFilterMismatchNmax 10 –outSJfilterReads Unique”.
Gene raw read counts are generated using HTSeq (v0.6.1) with the Refseq gene annotation extracted from UCSC on 11-09-2015. The non-default settings used by HTSeq are “--format bam –stranded no”. Gene expression analysis was performed using edgeR (v 3.14.0). GC-content correction was first performed using the conditional quantile normalization (CQN) package as previously described (Hansen KD, Irizarry RA, Wu Z: Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (Oxford, England) 2012, 13:204-216.)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file (counts_sca3_blood_min4cpm.txt) include CPM values for each Sample. Only genes exceeding 4 counts per million (CPM) across all samples are listed.

source_name: blood

growth_protocol: MJD84.2 transgenic SCA3 mice and wild-type C57BL/6 mice were obtained from Jackson Laboratories (Bar Harbor, Maine, USA) and bred at the Leiden University Medical Center. Only male mice were used. Mice were group housed in individually ventilated cages with food and drinking water available ad libitum. Mice were aged to 17.5 months of age.

extract_protocol:
For RNA sequencing, 200 µl of blood was obtained by tail cut at 40 and 75 weeks of age. Blood samples for RNA sequencing were collected in RNAprotect animal blood tubes (Qiagen) following manufacturer’s instructions, stored overnight at 4°C and subsequently frozen at -80°C until RNA isolation. After thawing, filled blood tubes were incubated for 4 hours at 25°C to ensure proper cell lysis. Isolation of RNA was subsequently performed using the RNeasy protect animal blood kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions for total RNA isolation including DNAse treatment, resulting in isolation of RNA molecules longer than approximately 200 nucleotides. Reduction of alpha and beta globin mRNA was performed on RNA samples using the GLOBINclear magnetic bead kit for mouse/rat (Qiagen) following manufacturer’s instructions. RNA was shipped to DeCode Genetics (Reykjavik, Iceland) for RNA sequencing.
quality of RNA was assessed with the LabChip GX using the 96-well RNA kit (Perkin Elmer). Non strand-specific sample preparation was performed using the TruSeq Poly-A v2 kit (Illumina, San Diego, USA) following manufacturer’s instructions. In brief, mRNA was captured using magnetic poly-T oligo-attached magnetic beads, RNA molecules were fragmented, and cDNA synthesis was performed using SuperScript II (Invitrogen, Carlsbad CA, USA) with random hexamer primers. Subsequently, 2nd strand cDNA synthesis was performed in conjunction with RNAse-H treatment. End repair was performed to generate blunt ends and 3′ adenylation was performed, followed by ligation of indexing adapters to the ds-cDNA. PCR was performed to amplify the fragments. Quality of sequencing libraries was determined through pool sequencing on a MiSeq instrument (Illumina) to assess insert size, sample diversity and optimize cluster densities. Pooled samples (4 samples/pool) were clustered on paired-end (PE) flowcells (1 pool per lane) using a cBot instrument (Illumina). The sequencing was performed using a HiSeq 2500 with v4 SBS sequencing kits (read lengths 2x125 cycles).

treatment_protocol: Mice were not treated in this study, but aged naturally to 17.5 months of age. All mice were exposed to behavioral tests (beamwalk and rotarod) at 4, 6, 7.5, 9 and 12 months of age, but the ataxic phenotype was not detected in the SCA3 mice.

value: SCA3 transgenic mouse

tag: age in weeks

tag: group

value: D

tag: rin value


title: SCA3 transgenic mouse 9083515 LUM0374

description: globin depleted RNA


title: SCA3 transgenic mouse 9083513 LUM0372

description: globin depleted RNA


title: SCA3 transgenic mouse 7267054 LUM0369

description: globin depleted RNA


title: SCA3 transgenic mouse 9082853 LUM0371

description: globin depleted RNA


title: WT infected with VSV

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

description:
Cell line
WTvsWTVSV.DiffExpGene.anno.xls

data_processing:
The raw reads were filtered by removing reads containing adapter, poly-N and low quality reads for subsequent analysis. The steps of sequencing data filtering: 1) removing reads containing adapter; 2) removing reads containing poly-N (i.e., unrecognized bases), reads with a ratio greater than 5%; 3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read).
The mapped reads of each sample were assembled using Cufflinks (v2.2.1) with a reference-based approach. This method employed spliced reads to determine exon connectivity. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression levels of a minimal set of isoforms, which provides a maximum likelihood explanation of the expression data in a given locus.
Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample. Gene FPKMs were computed by summing the FPKMs of the transcripts in each gene group. FPKM stands for “fragments per kilobase of exon per million fragments mapped”, and it is calculated based on the length of the fragments and the reads count mapped to each fragment.
Cuffdiff (v2.2.1) provides statistical routines for determining differential expression in digital transcript or gene expression datasets using a model based on a negative binomial distribution. Genes with corrected p values less than 0.05 and the absolute value of log2 (fold change) < 1 were assigned as significantly differentially expressed.
The reference genome and gene model annotation files were downloaded directly from the genome website. The reference genome index was built using Bowtie2 (v2.2.9)[1], and paired-end clean reads were aligned to the reference genome using TopHat (v2.1.1).
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: *.anno.xls: Excel files include FPKM values.

source_name: iBMDM, WT, VSV

extract_protocol:
Immortalized bone marrow-derived macrophages (iBMDM), with or without VSV infection, were prepared, and RNA was harvested using Trizol reagent.
A total amount of 1 μg qualified RNA per sample was used as input material for the library preparation. The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s recommendations.

tag: genotype/variation

value: wild type

value: immortalized bone marrow-derived macrophages (iBMDM)

tag: infection

value: vesicular stomatitis virus (VSV)


title: HIPK2-/- replication1

description:
Cell line
HIR1vsHIR1VSV.DiffExpGene.anno.xls

source_name: iBMDM, HIPK2-/-


title: HIPK2-/- infected with VSV replication1

source_name: iBMDM, HIPK2-/-, VSV


title: HIPK2-/- infected with VSV replication2

description:
Cell line
HIR2vsHIR2VSV.DiffExpGene.anno.xls


title: HIPK2-/- replication2


title: WT

source_name: iBMDM, WT


title: C57BL/6 wildtype mouse 9083373 LUM0367

description: globin depleted RNA

tag: strain

value: C57BL/6 wildtype mouse

value: C


title: C57BL/6 wildtype mouse 9083375 LUM0368

description: globin depleted RNA


title: scramble 24h rep3

tag: tissue


title: Scrambled – 12h (timepoint 2)


title: Scrambled – 6h (timepoint 1)


title: Scrambled – 24h (timepoint 4)


title: Knock down Tgfbr3 -6h (timepoint 1)


title: C57BL/6 wildtype mouse 9083372 LUM0366

description: globin depleted RNA


title: Scrambled – 18h (timepoint 3)


title: Granta-519

city: Aarhus

first: Lasse

middle: Sommer

last: Kristensen

address: CF Møllers Allé 3

country: Denmark

institute: Aarhus University

description: Cells grown in culture

data_processing:
Basecalling performed with Illumina Casava1.7 at BGI-Shenzhen
Quality (Phred score: 20) and adapter trimmed using Trim Galore.
Filtered data were mapped to the human genome (HG19) using TopHat2
Detection of circRNA was done with find_circ and CIRI2 pipelines. The find_circ pipeline was run as suggested by the developers, except for an increased filtering stringency, requiring that both anchor segments map to the genome with mapping scores of 40. Only circRNAs with two or more supporting reads within single samples were kept. CircRNAs were normalized as the number of back-splice junction spanning reads per million raw reads (RPM). The CIRI2 pipeline was run as suggested by the developers, and circRNAs were normalizedthe number of back-splice junction spanning reads per million raw reads (RPM).
Genome_build: HG19
Supplementary_files_format_and_content: Excel files with detected circular RNAs (.xlsx)

source_name: Cell line (Mantle Cell Lymphoma)

growth_protocol: Cell lines were cultured according to standard protocols. More specifically, MCL cell lines REC-1 and UPN2 were grown in RPMI-1640 with 10% FBS, and Z138 and Granta-519 in IMDM with 10% HS and in DMEM with 10% FBS, respectively. The MM cell line H929 was cultured in RPMI-1640 with 1 mM sodium pyruvate, 50 µM 2-mercaptoethanol and a medium containing 40% IMDM.

extract_protocol:
Cells from cell lines were harvested following confirmation of a cell viability above 95% using the NucleoCounter NC-250 instrument (Chemometec, Alleroed, Denmark). RNA was isolated using the Allprep DNA/RNA/miRNA universal kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. on-column DNase treatment was performed using 10 µL lyophilized DNase I (1500 kU) in 70 µL buffer RDD and incubated at 15 min. at room temperature.
One µg of total RNA was rRNA depleted using the Ribo-Zero rRNA Removal Kit (Human, Mouse, Rat) (Epicentre, Madison, WI, USA) according to the manufacturer's instructions followed by a purification step using AMPure XP Beads (Beckman Coulter, Brea, CA, USA). Sequencing libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer's instructions with 12 PCR cycles for amplification. Purification was performed using AMPure XP Beads (Beckman Coulter). The final library was quality controlled on the 2100 Bioanalyzer (Agilent Technologies) and quantified using the KAPA library quantification kit (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer's protocol. High-throughput sequencing was performed on the HiSeq 4000 system (Illumina, San Diego, CA, USA) at the Beijing Genomics Institute (BGI) using the 100 paired-end sequencing protocol. Nine samples were pooled for each lane on the HiSeq 4000.

tag: cell type

value: Mantle Cell Lymphoma

tag: cell line


title: C57BL/6 wildtype mouse 9082857 LUM0364

description: globin depleted RNA


title: UPN2

description: Cells grown in culture


title: H929

description: Cells grown in culture

source_name: Cell line (Multiple Myeloma)

value: Multiple Myeloma


title: Knock down Tgfbr3-12h (timepoint 2)


title: REC-1

description: Cells grown in culture


title: C57BL/6 wildtype mouse 7267059 LUM0363

description: globin depleted RNA


title: C57BL/6 wildtype mouse 7267055 LUM0361

description: globin depleted RNA


title: Z138

description: Cells grown in culture


title: siRNA Tgfbr3 24h rep3


title: SCA3 transgenic mouse 7267057 LUM0340

description: globin depleted RNA

value: B


title: SCA3 transgenic mouse 9083514 LUM0343

description: globin depleted RNA


title: SCA3 transgenic mouse 7267056 LUM0339

description: globin depleted RNA


title: C57BL/6 wildtype mouse 9083375 LUM0337

description: globin depleted RNA

value: A


title: SCA3 transgenic mouse 9082854 LUM0341

description: globin depleted RNA


title: MGL_M

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Library strategy: SuperSAGE
GAPipeline1.4.0
Raw data was analyzed with GenXPro's SuperSAGE data processing pipeline. Distinct libraries were sorted out from the bulked sequencing data according to their respective indices.
Followed by elimination of PCR-derived tags identified by TrueQuent technology. 26bp SuperTAGSs were extracted from the remaining sequences.
The remaining reads were mapped on the Gallus gallus genome Galgal4 from ENSEMBL with novoalign allowing one mismatch.
Genome_build: Gallus_gallus.Gallus_gallus-4.0
Supplementary_files_format_and_content: Microsoft Excel Table with TPM values and statistics

organism: Gallus gallus

source_name: left gonad

growth_protocol: Chicken embryos were bred 19 days until section in a ThermoStar 100 egg incubator. Incubation was performed at 37.6 degrees Centigrade and 60% humidity, eggs were turned once every 2 hours. Embryos were decapitated 2 days before anticipated hatching and dissected under a microscope. Gonads were extracted and separated from embedding tissue.

extract_protocol:
Total RNA from right and left gonads (ten individuals of each group) was extracted with the SV Total RNA Isolation System Kit according to manual 048 (Promega). Deviating from the protocol, on-column DNAseI digestion of genomic DNA was elongated from original 15 min to 30 min. A second DNaseI digestion of genomic DNA was carried out in solution. Sequencing was performed on Illumina's Genome Analyzer Iix, subsequent base calling carried out by Illumina's GAPipeline.
DNase-treated total RNA was subjected to oligo(dT)-based reverse transcription using SuperScript III Reverse Transcriptase (Invitrogen) and an anchored, 5’ biotinylated oligo(dT) primer comprising the recognition site for EcoP15I. 3’ cDNA fragments were enriched via binding to streptavidin-coated paramagnetic beads (Dynabeads M-270 Streptavidin, Invitrogen) subsequent to cleavage of 5’-CATG sites in reverse-transcribed cDNAs by NlaIII (NEB). An adaptor comprising a known barcoding sequence and a second recognition site of EcoP15I was ligated to the enriched fragments using T4 DNA Ligase (Fermentas). The adaptor-ligated cDNA fragments were released from the beads via digestion by EcoP15I (NEB), end-repaired by KOD DNA Polymerase (Blunting High Kit, Toyobo), and subsequently ligated to a second barcoding adaptor using the T4 Ligase reagent provided with the Ligation high Ver. 2 Kit (Toyobo). Barcoding sequences of the adaptor-ligated cDNA fragments were extended during subsequent PCR-amplification employing Phusion Hot Start High-Fidelity DNA Polymerase (Fermentas) according to the manufacturer’s recommendations.

treatment_protocol: Gonads were immediately stored at -80 degrees C in RNA lysis buffer until RNA isolation.

value: gonad

tag: position

value: left

value: male

tag: substance

value: Methyltestosterone 30pg/g BW

tag: developmental stage


title: MGR_T

source_name: right gonad

value: right

value: Tributyltin 10 pg SN/g BW


title: C57BL/6 wildtype mouse 9083372 LUM0335

description: globin depleted RNA


title: C57BL/6 wildtype mouse 9083373 LUM0336

description: globin depleted RNA


title: MGL_S

value: Sesame oil


title: C57BL/6 wildtype mouse 9082857 LUM0333

description: globin depleted RNA


title: FGL_T

value: female


title: FGR_S


title: C57BL/6 wildtype mouse 7267059 LUM0332

description: globin depleted RNA


title: C57BL/6 wildtype mouse 9083371 LUM0334

description: globin depleted RNA


title: MGR_M


title: MGL_T


title: MGR_C


title: FGR_M


title: MGR_S


title: FGL_S


title: MGL_C


title: FGR_C


title: FGL_C


title: FGL_M


title: SCA3 transgenic mouse 9083515 LUM0344

description: globin depleted RNA

value: SCA3 transgenic mouse


title: FGR_T