title: RNA-Seq of Helianthus annuus SF009_SF342: stress R3

value: Stressed plants - water status FTSW = 0.1.


title: S18-EBNA2Dox10ug-H3K27ac-rep1

status: Public on Sep 22 2020

type: SRA

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

country: China

institute: Southern Medical University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq rawdata were filtered by fastp(version 0.19.6) with default parameters.
ChIP-seq reads were mapped to the hg38 genome assembly using bowtie2 (version 2.20.8) with parameters (-p 6, --sensitive);
Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (version version 2.20.8) and samtools (version 1.3.1);
RPKM normalized BigWig files of  ChIP-seq were generated by bedtools (version 2.29.2);
Bed files of ChIP-seq were got from Bam file by using HOMER (version 4.10.4) with parameters (-style histone).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks.

molecule: genomic DNA

organism: Homo sapiens

source_name: CNE2 cells (S18)

growth_protocol: CNE2 cells (S18) were cultured at 37℃ and 5% CO2 in  complete medium: RPMI 1640 medium  supplemented with 10% fetal bovine serum, 100U ml-1 penicillin/streptomycin.

extract_protocol: 1 x 10e6 S18 cells were washed by 1x PBS. Discard supernatant and try to remove residue，and then the cells were Resuspended by 500μL Cell lysis buffer.After incubation on ice for 10 mins，cells were centrifuged at 2000rpm for 5min at 4℃. Resuspend the cells by 100μL digestion buffer，and then incubate in 37℃ 5mins. Add 4μl of 0.2M EDTA/EGTA to stop digestion. After adding 500μL IP dilution buffer，chromatin were precipitated by antibody and rotated for 12 hours. Followed by washing buffer, protein G beads were added to samples. Samples were eluted by 50ul ChIP-elution buffer.

treatment_protocol: Two replicate was Doxycycline 10ug/ml treated for 24 hours.

tag: cell line

tag: cell type

value: Human  nasopharyngeal carcinoma cells

tag: chip antibody

value: H3K27ac (Abcam, ChIP Grade ab4729)

tag: treatment


title: RNA-Seq of Helianthus annuus SF092: stress R2

city: Castanet-Tolosan

first: Ludovic

last: Legrand

address: 24 Chemin de Borde Rouge

country: France

institute: INRA/CNRS

library_source: transcriptomic

data_processing: The transcriptomic study was performed with the EdgeR package version 3.16.5 on R version 3.3.3 (Another Canoe).CPM were computed with the cpm function from the edgeR package. 30,831 genes were found with at least 3 CPM in 3 libraries. Count normalization was performed as described in the edgeR user guide with the calcNormFactors function using the TMM method (Trimmed Mean normalization).

molecule: total RNA

organism: Helianthus annuus

source_name: leaves

growth_protocol: For the Heliaphen phenotyping platform experiment conducted from May 31st to July 16th. Bleach-sterilized seeds were germinated on Petri dishes with Apron XL and Celeste solutions (Syngenta, Basel, Switzerland) for 3 days at 28C. Germinated plantlets were transplanted in individual pots, and each pot contained two or three plants. Pots were filled with 15 L of P.A.M.2 potting soil (Proveen distributed by Soprimex, Chateaurenard, Bouches-du-Rhone, France) and covered with a 3-mm-thick polystyrene sheet to prevent evaporation. On June 17th, plants were thinned to keep one plant per pot representative of the genotype. Plants were fertilized with 500ml of Peter's Professionnal 17-07-27 (0,6g/l) and Hortilon (0,46g/l) solution. On June 21st, Polyaxe at 5mg/l was applied on foliage against thrips. The XRQ plants were part of a larger experimental design that will not be completely studied in this article. In total, 144 plants, corresponding to 24 genotypes, two drought stress conditions and three replicates were arranged in a split-split-plot design with three blocks. The stress intensity (i.e., FTSW) was the main factor within the block, the genotype was the second factor. Each pot was fertilized and irrigated as in Rengel et al., (2012) before the beginning of the water stress application. For this study, we retained only the six XRQ plants (three irrigated and three non-irrigated plants). Pots were saturated with water on July 5th 2013, 35 days after germination. The following morning, excessive water was drained for two hours and pots were weighed to obtain the saturation mass. On July 8th, irrigation was stopped for stressed plants. Both control and stressed plants were weighed three or four times per day by the Heliaphen robot to estimate evapotranspiration. The water lost was added back automatically by the robot to control plants. Pairs of stressed and control plants were harvested when the FTSW of the stressed plant reached 0.1 which happened between July 12th to 16th. Leaves were harvested between 11:00 and 13:00. To select the leaf to harvest, the total leaf number was estimated, and leaves at the rank position corresponding to two thirds of the total leaf number from the bottom were tagged and termed the nth leaf. For transcriptomic studies, we selected the n+1 leaves.

extract_protocol: Leaves were cut without their petiole and immediately frozen in liquid nitrogen (greenhouse) or in dry ice (field). Grinding was performed using a ZM200 grinder (Retsch, Haan, Germany) with a 0.5-mm sieve. Total RNA was extracted using QIAzol Lysis Reagent following the manufacturers instructions (Qiagen, Dusseldorf, Germany). The RNA quality was checked by electrophoresis on an agarose gel and quality and quantity were assessed using the Agilent RNA 6000 nano kit (Agilent, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq 2000 by DNAVision (Charleroi, Belgium) as paired-end libraries (2*100 bp, oriented) using the TruSeq sample preparation kit (Illumina San Diego, CA, USA) according to manufacturers instructions.

treatment_protocol: Stressed plants have water status FTSW = 0.1.

tag: cultivar

tag: tissue

value: leaves


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PAL

tag: Sex

value: male

tag: age

tag: strain


title: S18-EBNA2Dox10ug-input-rep2

value: Doxycycline 10ug/ml treated for 24 hours


title: S18-EBNA2Con-H3K27ac-rep2

value: untreated


title: Ctr_siRNA_rep1

city: Chuo-ku, Kumamoto

first: Mitsuyoshi

last: Nakao

state: Kumamoto

address: 2-2-1 Honjo

department: Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

data_processing:
Basecalls and conversion to FASTQ files were performed using MiSeq Control Software(MCS) /Real Time Analysis (RTA) (Illumina).
Low quality reads were trimmed out using Trimmmomatic (Galaxy v.0.36.3).
Reads were alignmened onto the human reference genome hg19 using HISAT2 algorithm (Galaxy v.2.1.0) with gene annotation file obtained from iGenomes (Illumina).
Uniquely mapped reads were extracted using SAMTOOLS Filter SAM or BAM, output SAM or BAM (Galaxy v.1.8).
Gene expression levels were calculated using featureCounts (Galaxy v.1.6.2) with gene annotation file obtained from iGenomes (Illumina).
Genome_build: hg19
Supplementary_files_format_and_content: Differentially expressed genes in NSD2-KD cells were calculated using DESeq2 algorithm (Galaxy v.2.11.40.2) compared with Ctr-KD cells.

source_name: Growing IMR-90 cells

growth_protocol: IMR-90 cells were cultured in Dulbecco-modified eagle’s medium (DMEM)/F12 supplemented with 10% (v/v) heat-inactivated fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol reagent.
Messenger RNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were synthesized using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cells were transfected with siRNA for 24 h.

value: Human fibroblasts

tag: sirna

value: Ctr


title: GX-S-3

first: dayong

last: liang

state: Guangdong

address: 604, Huangpu Avenue West, Tianhe District

institute: Jinan University

description: replicate 3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right  files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the  left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all  other parameters set default.
RSEM was used for readcount value and FPKM.
Genome_build: de novo transcriptome assembly, FASTA of unigene sequences is available on the series record.
Supplementary_files_format_and_content: abundance measurements

organism: Phaeocystis globosa

source_name: Single cell stage

extract_protocol:
the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 -mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: phaeocystis

value: Exponential growth period

tag: phenotype

value: Single cell stage


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad007


title: RNA-Seq of Helianthus annuus SF009_SF342: stress R1


title: RNA-Seq of Helianthus annuus SF009_SF342: stress R2


title: GX-S-1

description: replicate 1


title: RNA-Seq of Helianthus annuus SF009_SF342: control R3

treatment_protocol: Control plants have water status FTSW = 1.

value: Control plants - water status FTSW = 1.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad010


title: S18 -Dox10ug-H3K27ac_rep2


title: GX-S-2

description: replicate 2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad012


title: S18-EBNA2Con-H3K27ac-rep1


title: S18 -Dox10ug-H3K27ac_rep1


title: GX-C-2

description: replicate 2

source_name: colony stage

value: colony stage


title: RNA-Seq of Helianthus annuus SF009_SF342: control R2


title: S18-Dox10ug-input_rep2


title: RNA-Seq of Helianthus annuus SF009_SF326: stress R3


title: GX-C-1

description: replicate 1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad002


title: RNA-Seq of Helianthus annuus SF009_SF326: stress R2


title: S18-Dox10ug-input_rep1


title: GX-C-3

description: replicate 3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad010


title: T-cell_RNA_seq_rep2

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl, Memphis, TN

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: RNA-seq

data_processing:
gene expression profile was quantified using kallisto quant
Genome_build: hg38
Supplementary_files_format_and_content: gene expression table (tsv)

source_name: Human primary CD4/CD8 T cells

growth_protocol: Human primary CD4+/CD8+ T-cells were cultured in X-Vivo 15 media (Lonza) supplemented with 5% human heat-inactivated serum (Fisher), 10 ng/ml IL-7 (Miltenyi), and 10 ng/ml IL-15 (Miltenyi). T-cells were stimulated with MACS GMP T-cell TransAct polymeric nanomatrix (Miltenyi) for 3 days according to the manufacturer’s instructions prior to transfection.

extract_protocol: RNA extraction was performed using the RNeasy Mini Kit (Qiagen). RNA quality was checked by Agilent High Sensitivity RNA ScreenTape, and the two samples with the highest RNA Integrity Number equivalent were chosen (RINe = 9.9). RNA libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep, including ribosomal RNA removal using Ribo-Zero. Libraries were sequenced with 75-bp paired-end reads using Illumina NovaSeq 6000.

tag: tag

value: Human primary CD4/CD8 T cells


title: EdU-seq-WT rep1

city: Pasadena

first: Akiko

last: Kumagai

state: California

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

description: EdU-seq: released into S-phase

data_processing:
Library strategy: EdU-seq
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

source_name: colorectal adenocarcinoma

extract_protocol:
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.
EdU-seq:  Cells were labeled with 10 µM EdU for 3 hr.  Cells were fixed with 70% ice-cold ethanol, washed, and incubated in click-reaction buffer containing 100 µM biotin-dPEG11-azide (Quanta Biodesign), 2 mM CuSO4, and 10 mM sodium ascorbate in TBS for 15 min.  Genomic DNA was isolated and sonicated to 300-500 bp with a Branson 450 sonifier.  Biotinylated DNA was collected on 20 µl of Dynabeads MyOne Streptavidin T1 magnetic beads.

value: colorectal adenocarcinoma

tag: genotype/variation

value: MTBP-mAID/MTBP-WT-FLAG

tag: molecule subtype

value: EdU-labeled DNA


title: EdU-seq-deltaC rep1

description:
EdU-seq: released into S-phase
processed data file: EdU_seq_deltaC.bw
RO0613_3_USPD16101116_H33FJCCX2_L5

data_processing:
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

extract_protocol:
EdU-seq: Cells were labeled with 10 µM EdU for 3 hr. Cells were fixed with 70% ice-cold ethanol, washed, and incubated in click-reaction buffer containing 100 µM biotin-dPEG11-azide (Quanta Biodesign), 2 mM CuSO4, and 10 mM sodium ascorbate in TBS for 15 min. Genomic DNA was isolated and sonicated to 300-500 bp with a Branson 450 sonifier. Biotinylated DNA was collected on 20 µl of Dynabeads MyOne Streptavidin T1 magnetic beads.
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.

value: MTBP-mAID/MTBP-deltaC-FLAG


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad004


title: RNA-Seq of Helianthus annuus SF009_SF326: control R3

value: leaves


title: T-cell_RNA_seq_rep1

description: RNA-seq


title: EdU-cont rep1

description: EdU-seq: G1-arrested


title: Bdistachyon_+Pf_-Fe_rep5

city: Corvallis, OR

first: Rene

middle: M

last: Boiteau

state: OR

address: 104 CEOAS Administration Building

institute: Oregon State University

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Brachypodium reads were aligned using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). using parameters -local, --sensitive-local
Pseudomonas reads were aligned using TMAP (https://github.com/iontorrent/TS/tree/master/Analysis/TMAP) using the 'map4' command with parameters --softclip-type 0, --aln-output-mode 1
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Genome_build: Brachypodium distachyon 3.1: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Bdistachyon
Genome_build: Pseudomonas fluorescens: https://www.ncbi.nlm.nih.gov/genome/150?genome_assembly_id=154324
Supplementary_files_format_and_content: read counts per gene

organism: Brachypodium distachyon

source_name: Roots

growth_protocol: Brachypodium distachyon was grown in sterile conditions in a light box operating at 14:10 sunlight at 50% relative humidity and 20C. Plants were watered with 1/4 strength Hoagland solution containing every 3-4 days. After 28 days of growth, plants were cut between the roots and shoots and immediately frozen in natural craft bags in liquid nitrogen and stored at -80°C prior to RNA extraction. Two plants from the same container were pooled to obtain 5 biological replicates for each condition. Then the nutrient solution was agitated to wash bacterial cells off of the bead matrix, transferred to a 15mL centrifuge tube, and centrifuged at 4500rpm for 5 minutes at 4°C to obtain a bacterial pellet for RNA analysis (5 biological replicates for +Fe and -Fe conditions with bacterial inoculation).

extract_protocol:
RNA from Brachypodium roots was extracted using Qiagen Mini RNeasy kits, followed by genomic DNA removal using Qiagen RNase-Free DNase Set kit. Integrity of the RNA samples was assessed using an Agilent 2100 Bioanalyzer. TruSeq stranded mRNA was used to generate cDNA libraries for sequencing (Illumina NextSeq550 sequencer). RNA from the bacterial pellet was extracted using Trizol followed by clean-up using Qiagen Mini RNeasy kits and Qiagen RNase-Free Dnase sets.
For Brachypodium, TruSeq Stranded Total RNA (cat#20020596) is used to generate the cDNA library for illumina NextSeq550 platform according to the manufacturer's protocol. Single-read sequencing of the cDNA libraries with a read length of 150 is performed on NextSeq 550 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles
For Pseudomonas, the SMARTerR Universal Low RNA kit was used to generate full length cDNA template library according to the instruction manual, follow by the Ion Plus fragment library kit (Thermo Fisher Scientific) to fragment cDNA and barcode adapter ligation for template prep.  The template library was quantified using the Ion Library TaqMan Quantitation kit (Thermo Fisher Scientific). Emulsion clonal bead amplification was used to generate bead templates for the Ion Torrent platform using the Ion PI™ Hi-Q™ Chef Kit with Ion PI™ Chip Kit v3 on the Ion Chef System (Thermo Fisher Scientific).

treatment_protocol: After 14 days of establishing growth under the same conditions, each container received one of four treatments: (1) no change in watering conditions (sterile, +Fe), (2) Fe deprivation by exclusion of Fe-EDTA from the watering solution (sterile, -Fe ), (3) inoculation with P. fluorescens ( +Fe), (4) inoculation with Pseudomonas fluorescens and Fe deprivation ( -Fe). Plants that were inoculated with P. fluorescens were watered one time with bacteria containing Hoagland solution on day 14 of growth. For -Fe treatments, Fe was omitted from the 1/4 strength Hoagland watering solution beginning on day 16 of growth for the remainder of the experiment.

tag: bacterial treatment

value: Pseudomonas fluorescens

tag: iron

value: no


title: RNA-Seq of Helianthus annuus SF009_SF342: control R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad006

value: PAL

value: male


title: RNA-Seq of Helianthus annuus SF009_SF326: control R2


title: CUT&RUN: MTBP-deltaC-FLAG rep1

description: CUT&RUN with FLAG antibody

data_processing:
Library strategy: CUT&RUN
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genome coverage).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

extract_protocol:
Sequencing libraries were prepared using NEBNext Ultra DNA library preparation kit.  In brief, the DNA was end-repaired, adaptor-ligated, and PCR-amplified.
CUT&RUN: After the CUT&RUN procedure, MNase-digested DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB).

tag: cell line

value: CUT&RUN released DNA


title: RNA-Seq of Helianthus annuus SF009_SF326: control R1


title: Bdistachyon_+Pf_-Fe_rep4


title: CUT&RUN: MTBP-WT-FLAG rep1

description: CUT&RUN with FLAG antibody


title: RNA-Seq of Helianthus annuus SF009_SF317: stress R3

value: Stressed plants - water status FTSW = 0.1.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A10_ad008


title: CUT&RUN: control rep1

description: CUT&RUN with FLAG antibody

data_processing:
Library strategy: CUT&RUN
Sequence reads were processed using Trim Galore to remove adapter and low-quality reads (q < 20).
Reads were mapped to the human hg38 genome assembly using Bowtie2 with options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10.
MACS2 was used to call peaks on the reads for CUT&RUN experiments using options:  --keep-dup 1 -f BAMPE --nolambda -q 0.01.  Summits were also called in MACS2 and the highest summit for each peak was identified.
Peaks of EdU-seq were called using HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).
Genome_build: hg38
Supplementary_files_format_and_content:
MTBP_WT.bw, MTBP_deltaC.bw, and MTBP_cont.bw files are the averages of three replicates.  The scores for MTBP_WT.bw represent RPGC (reads per genomic content).  The scores for MTBP_deltaC.bw and MTBP_cont.bw were normalized to MTBP_WT.bw using spike-in DNA.
MTBP_peaks.txt contains the locations of MTBP_peaks called using MACS2 in a tab-separated file.  The locations of summits of the peaks were also included.
H3K4me2.bw and Control_IgG.bw files are the averages of two replicates.   The scores for H3K4me2.bw represent RPGC (reads per genomic content).  The scores for Control_IgG.bw were normalized to H3K4me2.bw using spike-in DNA.
H3K4me2.bed file contains the locations of H3K4me2 peaks identified using MACS2.
EdU_seq_WT.bw and EdU_seq_deltaC.bw are the average of three replicates.  The scores represent  log2 ratio of EdU_seq reads over control reads.
Initiation_zones.txt contains the initiation zones (peaks of EdU-seq-WT) called by HOMER findPeaks (region -size 6000 -minDist 12000 -F 2).

value: MTBP-mAID/MTBP-mAID


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad012


title: RNA-Seq of Helianthus annuus SF009_SF317: stress R2


title: tie1 WT_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (available online at http://www.bioinformatics.babraham.ac.uk/ projects/fastqc).
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (6).  Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (8).  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded.
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

extract_protocol:
Hearts from 48 hpf tie mutant embryos and siblings were manually dissected using insulin needles, pooled in 1.5 ml tubes with TRIzol and frozen in -80°C. Total RNA was isolated using the miRNeasy micro kit (Qiagen).  For exclusion of genomic DNA contamination, the samples were treated by on-column DNase digestion (DNase-Free DNase Set, Qiagen).  Total RNA and library integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
2 ng of total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Clontech).

value: Hearts

tag: developmental stage

value: 48 hpf

tag: genotype

value: tie1 WT


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad002


title: Bdistachyon_+Pf_-Fe_rep1


title: RNA-Seq of Helianthus annuus SF009_SF317: stress R1

tag: treatment


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad010


title: tie1 WT_1


title: RNA-Seq of Helianthus annuus SF009_SF326: stress R1

tag: cultivar


title: Bdistachyon_+Pf_+Fe_rep5

value: yes


title: RNA-Seq of Helianthus annuus SF009_SF317: control R3

tag: tissue

value: Control plants - water status FTSW = 1.


title: tie1 KO_2

value: tie1 KO


title: RNA-Seq of Helianthus annuus SF009_SF317: control R2


title: Bdistachyon_+Pf_+Fe_rep4


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad006

tag: brain region


title: tie1 KO_1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad001

tag: Sex


title: Bdistachyon_+Pf_-Fe_rep3


title: RNA-Seq of Helianthus annuus SF009_SF317: control R1


title: Bdistachyon_+Pf_+Fe_rep3


title: miR9-124-Ascl1_day28_3

city: Aarhus C

first: Mette

last: Habekost

state: Midtjylland

address: HØEGH-GULDBERGSGADE 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

description: iN day 28-3

data_processing:
Total RNA was subjected to oligo dT based mRNA enrichment. 100 bp single-end read sequencing was performed on BGISEQ-500.
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. More than 20 million clean reads were obtained per sample.
Reads were trimmed using Trimmomatic to remove the first 10 bases from the start of the read.
Reads were aligned to the porcine genome build Sscrofa11.1 using HISAT2 aligner (v2.1.0).
Transcript quantification was performed using featureCounts (v1.6.3) and the read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM).
Genome_build: Sscrofa11.1 (Ensemble release 98)
Supplementary_files_format_and_content: TSV file of raw counts or TPM values for all genes per sample

organism: Sus scrofa

source_name: Induced neurons from fibroblasts

growth_protocol: Neurobasal media and DMEM/F12 mixed at a 1:1 ratio containing glucose, Pen/Strep, Glutamax, ITS-A, B27 and N2.

extract_protocol:
RNA was extracted using an automated RNA purification system, Maxwell® RSC simplyRNA Tissue Kit (Promega).
BGISeq-500 Library contruction protocol

tag: breed

value: Gottingen minipig

tag: age of pig at fibroblast-biopsy date

value: 19 weeks

value: Wild-type

value: Treated with miR9/9*-124 and Ascl1 and small molecules:CHIR99021, SB-431542, LDN-193189, A-83, Forskolin and growth factors:LM-22A4, GDNF, NT3, db-cAMP and epigenetics regulator:valproic acid.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A1_ad007

tag: age

tag: strain


title: RNA-Seq of Helianthus annuus SF009_SF279: stress R3

value: leaves


title: Bdistachyon_+Pf_-Fe_rep2

value: Pseudomonas fluorescens

value: no


title: Bdistachyon_+Pf_+Fe_rep2


title: RNA-Seq of Helianthus annuus SF009_SF279: stress R2


title: miR9-124-Ascl1_day28_2

description: iN day 28-2

tag: phenotype


title: Bdistachyon_+Pf_+Fe_rep1


title: miR9-124-Ascl1_day10_3

description: iN day 10-3


title: RNA-Seq of Helianthus annuus SF009_SF279: stress R1


title: Bdistachyon_sterile_-Fe_rep5


title: Bdistachyon_sterile_-Fe_rep4


title: RNA-Seq of Helianthus annuus SF009_SF279: control R3


title: miR9-124-Ascl1_day10_2

description: iN day 10-2


title: RNA-Seq of Helianthus annuus SF009_SF279: control R2


title: Bdistachyon_sterile_-Fe_rep2


title: miR9-124-Ascl1_day10_1

description: iN day 10-1


title: RNA-Seq of Helianthus annuus SF009_SF279: control R1


title: miR9-124-Ascl1_day28_1

description: iN day 28-1


title: miR9-124-Ascl1_day4_3

description: iN day 4-3


title: RNA-Seq of Helianthus annuus SF009: stress R3


title: Bdistachyon_sterile_-Fe_rep1


title: miR9-124-Ascl1_day4_2

description: iN day 4-2


title: ascending.194LDLR.HO_mRNA

type: RNA

city: Shanghai

first: Zhen

last: Sheng

address: F13, Building 2, 4560 Jinke Road

institute: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd

description: gene expression of ascending aorta tissue from mouse 194 with homozygous-mutated LDLR (mRNA)

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

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

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: ascending aorta tissue from mouse 194 with homozygous mutated LDLR

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

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) |following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: ascending aorta tissue

value: mutated


title: ascending.184LDLR.HO_mRNA

description: gene expression of ascending aorta tissue from mouse 184 with homozygous-mutated LDLR (mRNA)

source_name: ascending aorta tissue from mouse 184 with homozygous mutated LDLR


title: ascending.158LDLR.WT_mRNA

description: gene expression of ascending aorta tissue from mouse 158 with widetype LDLR (mRNA)

value: wild type


title: ascending.187LDLR.WT_mRNA

description: gene expression of ascending aorta tissue from mouse 187 with widetype LDLR (mRNA)


title: Bdistachyon_sterile_+Fe_rep5


title: RNA-Seq of Helianthus annuus SF009: stress R1

value: Stressed plants - water status FTSW = 0.1.


title: porcine_fibroblast_3

source_name: Fibroblast

growth_protocol: DMEM containing 10% FBS, Pen/Strep, Glutamine and bFGF.


title: HAEC_oxLDL_Rep2

description: gene expression of HAEC cells with treatment of oxLDL

hyb_protocol: Each slide was hybridized with 100 ng of this Cy3-labeled miRNA in a hybridization oven (Agilent technologies, G2545A) at 55°C and at 20 rpm for 20 h. After hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit (Agilent Technologies, 5188-5327).

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent Technologies) and analyzed using Feature Extraction software v10.7 (Agilent Technologies).

data_processing: Probes were detected in all samples (P for present, A for absent), and at least one group was kept for further analysis (Table S3). Genes and miRNA expression profiles from all samples were quantile-normalized after a log2-normalization.

source_name: human aorta endothelial cells, treated with oxLDL, replicate 2

label_protocol: Total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, 5190-2305). Individual miRNA obtained from the total RNA were labelled with Cy3 using a miRNA Complete Labelling and Hyb Kit (Agilent Technologies, 5190-0456). Labelled miRNA was then purified using a RNeasy mini kit (Qiagen, 74106).

growth_protocol: Human aortic endothelial cells (HAECs) were purchased from the American Type Culture Collection (ATCC, PCS-100-011) and cultured in Vascular Cell Basal Medium (ATCC, PCS-100-030) supplemented with Endothelial Cell growth kit (ATCC, PCS-100-041) and 0.1% penicillin/streptomycin (ATCC, PCS-999-002) at 37°C in an incubator with 5% CO2.

extract_protocol: Total RNA was separately extracted from aorta endothelial cells and mouse aorta tissue and purified using a mirVanaTM miRNA isolation kit without phenol (Ambion, AM1561).

treatment_protocol: HAECs were treated with oxLDL 100 μg/ml for 48 h.

tag: cell

value: human aorta endothelial cells

value: oxLDL


title: HAEC_oxLDL_Rep3

source_name: human aorta endothelial cells, treated with oxLDL, replicate 3


title: Bdistachyon_sterile_+Fe_rep4


title: Bdistachyon_sterile_-Fe_rep3


title: RNA-Seq of Helianthus annuus SF009: control R3


title: ascending.179LDLR.HO_mRNA

description: gene expression of ascending aorta tissue from mouse 179 with homozygous-mutated LDLR (mRNA)

source_name: ascending aorta tissue from mouse 179 with homozygous mutated LDLR


title: HAEC_oxLDL_Rep1

source_name: human aorta endothelial cells, treated with oxLDL, replicate 1


title: porcine_fibroblast_2


title: miR9-124-Ascl1_day4_1

description: iN day 4-1


title: Bdistachyon_sterile_+Fe_rep3


title: Bdistachyon_sterile_+Fe_rep1


title: HAEC_Untreated_Rep2

description: gene expression of HAEC cells without treatment of oxLDL

source_name: human aorta endothelial cells, untreated, replicate 2

value: Vehicle


title: HAEC_Untreated_Rep3

source_name: human aorta endothelial cells, untreated, replicate 3


title: Bdistachyon_sterile_+Fe_rep2

value: yes


title: RNA-Seq of Helianthus annuus SF009: control R2

source_name: leaves

value: Control plants - water status FTSW = 1.


title: ascending.133LDLR.WT_mRNA

description: gene expression of ascending aorta tissue from mouse 133 with widetype LDLR (mRNA)


title: RNA-Seq of Helianthus annuus SF009: stress R2


title: RNA-Seq of Helianthus annuus SF009: control R1


title: HAEC_Untreated_Rep1

source_name: human aorta endothelial cells, untreated, replicate 1


title: mESCs, C1

status: Public on Sep 21 2020

city: Hohhot

first: Yuting

last: Fu

address: university west road

institute: Inner Mongolia University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary_files_format_and_content: Matrix table with clean gene counts for every gene and every sample

source_name: mouse embryonic stem cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: female 129/sv mouse mated with GOF/GFP male mouse

value: advanced embryonic stem cells (ASCs)


title: mESCs, C3


title: mESCs, C2


title: mESCs, KO3


title: mESCs, KO1


title: mESCs, KO2


title: porcine_fibroblast_1

value: Gottingen minipig

value: 19 weeks


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H7_ad007

source_name: C57BL/6J Male P56 Mouse Brain

value: DG

value: male


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H9_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H9_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H8_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H9_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H9_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H8_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H8_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H7_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H8_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H6_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H7_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H6_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H7_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H6_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H6_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H5_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H5_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H4_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H5_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H4_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H2_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H2_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H3_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H2_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H12_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H11_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H11_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H11_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H12_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H12_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H10_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H1_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H1_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H5_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H3_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H11_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H1_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H10_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G9_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_H1_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G8_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G7_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G5_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G6_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G2_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad008


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G2_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G2_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G2_ad004


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad006


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad007


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G4_ad010


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G12_ad002


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G3_ad001


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G11_ad012


title: CEMBA190716_8J_3_CEMBA190716_8J_4_G2_ad012


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title: CEMBA190716_8J_1_CEMBA190716_8J_2_C8_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_D11_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_D10_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_D10_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C8_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C7_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C7_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C8_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C6_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C7_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C6_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C6_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C6_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C7_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C5_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C5_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C5_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C5_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C4_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C5_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C8_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C3_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C3_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C4_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C4_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C2_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C12_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C2_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C3_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C11_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C2_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C2_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C12_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C12_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C10_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C10_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C12_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C11_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C11_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C3_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C1_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C10_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C1_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C10_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C12_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C1_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B8_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C1_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B9_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B8_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B7_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B7_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_C11_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B8_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B7_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B6_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B6_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B4_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B5_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B5_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B5_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B4_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B4_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B3_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B6_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B9_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B5_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B3_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B3_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B2_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B3_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B2_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B8_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B2_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B2_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B12_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B12_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B7_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B12_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B11_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B11_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B12_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B11_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B11_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B11_ad006


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B1_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B1_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B1_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B1_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B10_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A9_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B10_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A8_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_B10_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A8_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A9_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A9_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A8_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A5_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A6_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A4_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A8_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A3_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A5_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A2_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A7_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A5_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A4_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A4_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A12_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A3_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A9_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A3_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A2_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A3_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A2_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A12_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A12_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A12_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A1_ad001


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A1_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A1_ad007


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A4_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad006


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A10_ad012


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A10_ad010


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad008


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A10_ad002


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A11_ad002


title: 033_17: Sample 17

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

data_processing:
The STAR aligner v. 2.7.3a was used to align RNA-seq read against the mm10 mouse genome assembly and GENCODE vM22 mouse transcripts.
The software program featureCounts v. 1.6.4 was used to summarize reads onto genes.
Testing for differential expression was performed using edgeR v. 3.26.8 using the quasi-likelihood framework with a fitted model of the form ~ 0 + group where group encoded both genotype and treatment. Contrasts were constructed as described in the edgeR manual.
Gene Ontology and Reactome enrichments were found using the CAMERA function which is part of the edgeR package. Only gene ontologies with between 5 and 500 genes were investigated.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with read counts for GENCODE vM22 genes

molecule: polyA RNA

source_name: Soleus muscle

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), the DNA fragments were amplified using PCR followed by a final clean-up.
Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 51-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 1.07 billion reads was generated.

value: TRa1 KO

value: Male

value: Soleus muscle

value: vechicle


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A10_ad001


title: 033_16: Sample 16

value: T3 treatmant


title: 033_20: Sample 20


title: CEMBA190716_8J_1_CEMBA190716_8J_2_A1_ad010


title: 033_19: Sample 19

value: WT


title: 033_18: Sample 18


title: 033_15: Sample 15


title: 033_22: Sample 22


title: 033_12: Sample 12


title: 033_10: Sample 10


title: 033_13: Sample 13


title: 033_14: Sample 14


title: 033_7: Sample 7


title: 033_5: Sample 5


title: 033_6: Sample 6


title: 033_21: Sample 21


title: 033_3: Sample 3


title: 033_2: Sample 2


title: 033_4: Sample 4


title: 033_1: Sample 1


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad012

value: PAL


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad004


title: 033_11: Sample 11


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad012


title: 033_9: Sample 9


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H7_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H9_ad010


title: 033_8: Sample 8


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H8_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H4_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H6_ad007


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad004


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H5_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H3_ad006


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad002


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad012


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H12_ad008


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad010


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H12_ad001


title: CEMBA181015_5H_3_CEMBA181015_5H_4_H2_ad007