title: PD76_PROCAP

data_processing:
Library strategy: PRO-CAP
Index: an alignment index was constructed using BWA (command bwa index -a bwtsw) from a FASTA file which excluded alt/unassembled contigs and which included sequence U13369.1 (human rDNA) or BK000964.3 (mouse rDNA) as a separate contig so that tags aligning to it could be removed later.
Alignment: PRO-seq/cap data were aligned to the NCBI v37 (ENSEMBL release 75) assembly of the human genome (hg19) or the GRCm38 (ENSEMBL release 75) assembly of the mouse genome (mm10) using ProSeq 2.0 (Danko lab, https://github.com/Danko-Lab/proseq2.0) (component software versions used for this pipeline were bwa v0.7.10, fastx toolkit v0.0.14, samtools v1.1, seqtk v1.3-r115-dirty, cutadapt v2.10, prinseq-lite.pl v0.20.4, and bedtools v2.27.1-65-gc2af1e7-dirty). Paired-end data were aligned in mode -PE with parameters --RNA5=R1_5prime --RNA3=R2_5prime --ADAPT1=GATCGTCGGACTGTAGAACTCTGAAC --ADAPT2=TGGAATTCTCGGGTGCCAAGG.
Filtering: output BAM files were processed to remove unmapped reads using samtools view -F 4 and data were converted to BED format using bamToBed. Data sequenced on the Illumina NextSeq platform were then pooled across lanes. Tags containing adapter dimers were flagged in unaligned data using DimerRemover (https://github.com/royludo/DimerRemover) then removed from aligned data. All tags aligning to rDNA sequences were removed from aligned data using grep -v. Strands were reversed for single-end PRO-cap data. A and B replicates from PROCAP were pooled.
Track creation: bigWig files were made by splitting BED files by strand and then converting to a bedGraph using BEDtools genomeCoverageBed -bg. Tag pile-ups were multiplied by the RPM scalar then bedGraphs were sorted using UCSC Genome Browser tools bedSort and converted to bigWig with bedGraphToBigWig.
Peak calling: to call PRO-cap peaks in human IMR90 cells, we used HOMER's findPeaks method with -style tss.
Differential peaks: to obtain a stringent list of new PRO-cap peaks in the senescence condition, this initial list was further filtered to retain only those peaks that have a signal >4rpm (HOMER normalized tag counts) for human or >10rpm for mouse and >10-fold enrichment versus the opposite condition (e.g., sen > 10*pro) in an area-under-the-curve analysis. A pseudocount of 0.01 was added for fold change calculation to avoid division by zero. Any peak from this list that intersected (BedTools) with an RPM-passing peak from the other condition was removed.
Cryptic peak refinement: all peaks within 3.5 Kb of the nearest TSS (RefSeq hg19 or GENCODE hg19) and peaks which did not fall in the 3' half of a gene body were also removed. The 3.5 Kb distance cutoff was chosen by assessing the distribution of distances of all ENCODE Broad chromHMM elements29 in state 1 or 2 (promoters) to the nearest RefSeq TSS; roughly 2/3 of elements are within 3.5 Kb. Peaks in PRO-cap replicate 1 were deemed to be reproduced if a peak in PRO-cap replicate 2 was identified within 5kb.
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs are strand-specific tracks of aligned PRO-seq/CAP tags (minus/M or plus/P with respect to the genomic reference strand).
Supplementary_files_format_and_content: BEDs are coordinates for condition-specific cryptic peaks from the PRO-CAP experiment.

tag: cell line

value: Fibroblast cell line

tag: senescent

value: Yes


title: RRBS_ESC_WT_single_cell_sorted_cl3

status: Public on Jan 02 2023

type: SRA

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Bisulfite-converted DNA

library_source: genomic

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter), followed by NuGEN diversity adapter trimming (https://github.com/nugentechnologies/NuMetRRBS).
The trimmed reads were aligned to the mouse genome (mm10) using BSMAP (version 2.90; parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG).
Aligned reads were deduplicated based on unique molecular identifiers (UMIs) using NuDup (https://github.com/nugentechnologies/nudup; parameters: --start 6 --length 6). Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
All analyses were restricted to autosomes and only CpGs covered by at least 10 and at maximum 150 reads were considered for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing methylation rates for CpGs covered by at least 10 and at most 150 reads: <chr> <start> <end> <methylation rate>

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESC (clone 3) wild type cells were cultured in Knockout DMEM (Thermo, #10829018, 15% fetal bovine serum (PAN, #P30-2602), 1X GlutaMAX supplement (Thermo, #35050-038), 1X non-essential amino acids (Thermo, #11140-035), 100 µM 2-mercaptoethanol (Thermo, #21985023), 1X Penicillin/Streptomycin (Thermo, #15140122) and leukemia inhibitory factor (LIF)

extract_protocol:
The DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermo, #K182002) according to manufacturer’s instructions.
Concentration of genomic DNA (gDNA) was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng gDNA of each sample using the NuGen Ovation® RRBS Methyl-Seq System (Tecan, #0353) following the manufacturer’s recommendations with the following modifications (6). After the final repair step, the bisulfite conversion of DNA was conducted using the Qiagen EpiTect Fast Bisulfite Conversion kit (Qiagen, #59824) following the manufacturer’s recommendations, eluting the bisulfite converted DNA in 23 µl EB. Libraries were amplified with 12 cycles of PCR. Amplified library purification with Agencourt RNAclean XP beads (Beckman Coulter, #A63987) was performed twice (1X). The purified libraries were quality-assessed on an Agilent 4150 Tape-Station HS D1000 ScreenTape and sequenced for 100-bp single-end reads on the NovaSeq6000 (Illumina).

treatment_protocol: ESC (clone 3) wild type cells were sorted as single cells onto gelatin and MEF-coated 96-well plates containing ESC medium. Cells were expanded and MEF-depleted for methylation analysis by RRBS.

tag: condition

value: WT


title: CK5_02428_1

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

country: China

institute: 江西农业大学

library_source: transcriptomic

data_processing:
Illumina Hiseq4000 software used for basecalling.
The quality of sequenced reads were checked, and masked for low-complexity or low-quality sequence, then Hisat is used to compare the preprocessed Valid Data with reference genomes, and statistics are made separately according to the gene position information specified by the genome annotation file gtf.
Genome_build: Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt: Matrix table with FPKM values for every gene and every sample.

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: seedlings

growth_protocol: Thirty germinative seeds were placed in each dish, and the treatment groups (Cd) were treated with 200mg/L CdCl2 while the control groups (CK) with distilled water. Seedlings were maintained in the incubator at 28℃/25℃ for 16/8 h light/dark condition.

extract_protocol:
RNA was isolated using Trizol reagent Kit.
RNA libraries were prepared for sequencing using Illumina Hiseq4000 protocols.

treatment_protocol: After three days of cultivation, the seedlings of two rice varieties treated with cadmium and control were sampled respectively.

tag: developmental stage

value: germination stage

tag: tissue

value: seedlings

tag: treatment

value: control


title: TP309_panicle_mRNA_replicate1

city: Nanjing

first: Lili

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

description: TP309_panicle_rep1 mRNA-seq

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: MSU version 7.0

source_name: panicle

growth_protocol: Rice plants grown in soil in Jiangsu province

extract_protocol:
RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT).  2.Adding reagent in Thermomixer to interrupt mRNA into short fragments.  3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand.  4.Purified by using the kit, and repaired the adhesive termination, added the base "A" and adapter in the CDNA 3'end, then selected 200-300bp fragments and performed PCR amplification.   5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.

value: panicle

tag: cultivar

tag: genotype

value: wildtype


title: PD23_PROCAP

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

organism: Homo sapiens

source_name: IMR90 fibroblasts

growth_protocol: IMR90 cells, obtained from Coriell Institute for Medical Research, Camden, NJ, were grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin/streptomycin; Invitrogen) at 3% oxygen.

extract_protocol:
PRO-seq/CAP was performed on proliferating and senescent IMR90 cells as described in Mahat, D.B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 11, 1455-76 (2016). Briefly, ~12e6 trypsinized cells were permeabilized and stored in storage buffer (10mM Tris-HCl pH 8.0, 25% glycerol, 5mM MgCl2, 0.1mM EDTA, 5mM DTT) at -80°C until use. The permeabilized cells were then resuspended in 1X nuclear run-on reaction mix containing biotin-11-rCTP and unlabeled rATP, rGTP and rUTP for 3 minutes at 37°C. RNA was extracted, fragmented and subjected to biotin enrichment.
The enriched nascent RNA population was ligated to a 3’ adapter sequence and subjected to a second round of biotin enrichment. The 5’ ends of the RNA were decapped, phosphorylated, ligated to 5’ adapter and subjected to a third biotin enrichment. The RNA was then reverse transcribed and PCR amplified with appropriate index primers. The libraries were purified by extraction from an 8% polyacrylamide gel, quantified by Bioanalyzer (Agilent) and qPCR (Kapa Biosystems). The PRO-seq/CAP run was performed on the NextSeq 500 platform (Illumina).

treatment_protocol: Senescence was induced by replicative exhaustion. Briefly, for each passage, cells were washed with PBS, trypsinized at 37 °C for 5 minutes, and plated on fresh 10 cm plates at 0.5-1e6/plate or fresh 15cm plates at 1-2e6/plate. Cells were counted with a Countess automated cell counter (Life Technologies), and the numbers were recorded for growth curve generation. Cell viability record was maintained via Trypan Blue staining. Cells were maintained in dishes for 2 weeks to ensure growth termination/senescence at endpoint. Markers such as p16 expression and β-gal were tested to confirm senescence.

tag: cell type

value: No


title: TP309_seedling_mRNA_replicate3

description: TP309_seedling_rep3 mRNA-seq

source_name: seedling

value: seedling


title: RRBS_ESC_WT_single_cell_sorted_cl12

description: Bisulfite-converted DNA

growth_protocol: ESC (clone 12) wild type cells were cultured in Knockout DMEM (Thermo, #10829018, 15% fetal bovine serum (PAN, #P30-2602), 1X GlutaMAX supplement (Thermo, #35050-038), 1X non-essential amino acids (Thermo, #11140-035), 100 µM 2-mercaptoethanol (Thermo, #21985023), 1X Penicillin/Streptomycin (Thermo, #15140122) and leukemia inhibitory factor (LIF)

treatment_protocol: ESC (clone 12) wild type cells were sorted as single cells onto gelatin and MEF-coated 96-well plates containing ESC medium. Cells were expanded and MEF-depleted for methylation analysis by RRBS.


title: Cd5_02428_3

value: cadmium


title: TP309_seedling_mRNA_replicate2

description: TP309_seedling_rep2 mRNA-seq


title: Cd5_02428_1


title: PD20_PROseq

data_processing:
Library strategy: PRO-Seq
Index: an alignment index was constructed using BWA (command bwa index -a bwtsw) from a FASTA file which excluded alt/unassembled contigs and which included sequence U13369.1 (human rDNA) or BK000964.3 (mouse rDNA) as a separate contig so that tags aligning to it could be removed later.
Alignment: PRO-seq/cap data were aligned to the NCBI v37 (ENSEMBL release 75) assembly of the human genome (hg19) or the GRCm38 (ENSEMBL release 75) assembly of the mouse genome (mm10) using ProSeq 2.0 (Danko lab, https://github.com/Danko-Lab/proseq2.0) (component software versions used for this pipeline were bwa v0.7.10, fastx toolkit v0.0.14, samtools v1.1, seqtk v1.3-r115-dirty, cutadapt v2.10, prinseq-lite.pl v0.20.4, and bedtools v2.27.1-65-gc2af1e7-dirty). Paired-end data were aligned in mode -PE with parameters --RNA5=R1_5prime --RNA3=R2_5prime --ADAPT1=GATCGTCGGACTGTAGAACTCTGAAC --ADAPT2=TGGAATTCTCGGGTGCCAAGG.
Filtering: output BAM files were processed to remove unmapped reads using samtools view -F 4 and data were converted to BED format using bamToBed. Data sequenced on the Illumina NextSeq platform were then pooled across lanes. Tags containing adapter dimers were flagged in unaligned data using DimerRemover (https://github.com/royludo/DimerRemover) then removed from aligned data. All tags aligning to rDNA sequences were removed from aligned data using grep -v. Strands were reversed for single-end PRO-cap data. A and B replicates from PROCAP were pooled.
Track creation: bigWig files were made by splitting BED files by strand and then converting to a bedGraph using BEDtools genomeCoverageBed -bg. Tag pile-ups were multiplied by the RPM scalar then bedGraphs were sorted using UCSC Genome Browser tools bedSort and converted to bigWig with bedGraphToBigWig.
Peak calling: to call PRO-cap peaks in human IMR90 cells, we used HOMER's findPeaks method with -style tss.
Differential peaks: to obtain a stringent list of new PRO-cap peaks in the senescence condition, this initial list was further filtered to retain only those peaks that have a signal >4rpm (HOMER normalized tag counts) for human or >10rpm for mouse and >10-fold enrichment versus the opposite condition (e.g., sen > 10*pro) in an area-under-the-curve analysis. A pseudocount of 0.01 was added for fold change calculation to avoid division by zero. Any peak from this list that intersected (BedTools) with an RPM-passing peak from the other condition was removed.
Cryptic peak refinement: all peaks within 3.5 Kb of the nearest TSS (RefSeq hg19 or GENCODE hg19) and peaks which did not fall in the 3' half of a gene body were also removed. The 3.5 Kb distance cutoff was chosen by assessing the distribution of distances of all ENCODE Broad chromHMM elements29 in state 1 or 2 (promoters) to the nearest RefSeq TSS; roughly 2/3 of elements are within 3.5 Kb. Peaks in PRO-cap replicate 1 were deemed to be reproduced if a peak in PRO-cap replicate 2 was identified within 5kb.
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs are strand-specific tracks of aligned PRO-seq/CAP tags (minus/M or plus/P with respect to the genomic reference strand).
Supplementary_files_format_and_content: BEDs are coordinates for condition-specific cryptic peaks from the PRO-CAP experiment.


title: RRBS_ESC_WT_single_cell_sorted_cl11

description: Bisulfite-converted DNA

growth_protocol: ESC (clone 11) wild type cells were cultured in Knockout DMEM (Thermo, #10829018, 15% fetal bovine serum (PAN, #P30-2602), 1X GlutaMAX supplement (Thermo, #35050-038), 1X non-essential amino acids (Thermo, #11140-035), 100 µM 2-mercaptoethanol (Thermo, #21985023), 1X Penicillin/Streptomycin (Thermo, #15140122) and leukemia inhibitory factor (LIF)

treatment_protocol: ESC (clone 11) wild type cells were sorted as single cells onto gelatin and MEF-coated 96-well plates containing ESC medium. Cells were expanded and MEF-depleted for methylation analysis by RRBS.


title: TP309_seedling_mRNA_replicate1

description: TP309_seedling_rep1 mRNA-seq


title: PD76_PROseq


title: F1 hybrid leaf 19mm, top, rep 1

status: Public on Jan 01 2023

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
Illumina reads were aligned to a coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of biological triplicates group were calculated.
Differential gene expression between each of the leaf segments of A. prostrata vs. A. rosea.was analyzed with DeSeq2 (Love et al., 2010).
Genome_build: TAIR 10 release of the Arabidopsis thaliana genome
Supplementary_files_format_and_content: Comma-separated table (.txt) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw  counts, rpm for each sample and mean of rpm for biological triplicates, DeSeq2 results of differential gene expression (log2-fold change and qValue) comparing each of the leaf segments between A. prostrata and A. rosea

organism: Atriplex prostrata x Atriplex rosea

source_name: F1 hybrid leaf 19mm, top

growth_protocol: All plants were grown in controlled growth chambers at 27 ˚C day temperature and 22 ˚C night temperature at 17 hour daylength under light levels of ~500 µmol m^12 s^-1. Plants were watered daily, and fertilized biweekly with Hoagland's fertilizer.

extract_protocol:
Leaves, stem, and roots were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end (100 bp read length) or paired-end mode (100 bp or 150 bp read length) on an Illumina HiSeq platform.

treatment_protocol: Developmental stages

tag: hybrid info.

value: C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid

tag: leaf segment

value: Top half of leaf

tag: tisse info.

value: 19mm length, top, leaf plastochron index = 0.8


title: F1 hybrid leaf 34mm, bottom, rep 1

source_name: F1 hybrid leaf 34mm, bottom

value: Bottom half of leaf

value: 34mm length, bottom, leaf plastochron index = 1.5


title: F1 hybrid leaf 19mm, top, rep 2


title: F1 hybrid leaf 34mm, top, rep 2

source_name: F1 hybrid leaf 34mm, top

value: 34mm length, top, leaf plastochron index = 1.5


title: F1 hybrid leaf 34mm, bottom, rep 3


title: F1 hybrid leaf 34mm, top, rep 1


title: F1 hybrid leaf mature, middle rep 3

source_name: F1 hybrid leaf mature, middle

value: Mature leaf, middle


title: F1 hybrid leaf 34mm, bottom, rep 2


title: F3003 hybrid leaf mature, middle rep1

source_name: F3003 hybrid leaf mature, middle

value: C3 Atriplex prostrata x C4 Atriplex rosea F3 hybrid F3003


title: F3036 hybrid leaf mature, middle rep2

source_name: F3036 hybrid leaf mature, middle

value: C3 Atriplex prostrata x C4 Atriplex rosea F3 hybrid F3036


title: F1 hybrid leaf mature, middle rep 2


title: F3036 hybrid leaf mature, middle rep3


title: Cd5_02428_2

value: germination stage


title: F1 hybrid leaf mature, middle rep 1


title: F1 hybrid leaf 19mm, bottom, rep 2

source_name: F1 hybrid leaf 19mm, bottom

value: 19mm length, bottom, leaf plastochron index = 0.8


title: F1 hybrid leaf 12mm, top, rep 3

source_name: F1 hybrid leaf 12mm, top

value: 12mm length, top, leaf plastochron index = 0.3


title: F1 hybrid leaf 19mm, bottom, rep 1


title: F1 hybrid leaf 19mm, bottom, rep 3


title: F1 hybrid leaf 12mm, top, rep 2


title: F3036 hybrid leaf mature, middle rep1


title: F3003 hybrid leaf mature, middle rep2


title: F1 hybrid leaf 12mm, bottom, rep 1

source_name: F1 hybrid leaf 12mm, bottom

value: 12mm length, bottom, leaf plastochron index = 0.3


title: F1 hybrid leaf 12mm, bottom, rep 2


title: F1 hybrid leaf 7mm rep 3

source_name: F1 hybrid leaf 7mm

value: Whole leaf

value: 7mm length, leaf plastochron index = -0.35


title: F1 hybrid leaf 12mm, bottom, rep 3


title: RRBS_ESC_WT_single_cell_sorted_cl10

description: Bisulfite-converted DNA

growth_protocol: ESC (clone 10) wild type cells were cultured in Knockout DMEM (Thermo, #10829018, 15% fetal bovine serum (PAN, #P30-2602), 1X GlutaMAX supplement (Thermo, #35050-038), 1X non-essential amino acids (Thermo, #11140-035), 100 µM 2-mercaptoethanol (Thermo, #21985023), 1X Penicillin/Streptomycin (Thermo, #15140122) and leukemia inhibitory factor (LIF)

treatment_protocol: ESC (clone 10) wild type cells were sorted as single cells onto gelatin and MEF-coated 96-well plates containing ESC medium. Cells were expanded and MEF-depleted for methylation analysis by RRBS.

value: WT


title: F3003 hybrid leaf mature, middle rep3


title: F1 hybrid leaf 19mm, top, rep 3


title: F1 hybrid leaf 7mm rep 1


title: F1 hybrid leaf 7mm rep 2


title: F1 hybrid leaf 34mm, top, rep 3


title: F1 hybrid leaf 12mm, top, rep 1


title: A. rosea leaf 13mm, top, rep 3

organism: Atriplex rosea

source_name: A. rosea leaf 13mm, top

value: 13mm length, top, leaf plastochron index = 0.8


title: A. rosea leaf 15mm, bottom, rep 3

source_name: A. rosea leaf 15mm, bottom

value: 15mm length, bottom, leaf plastochron index = 1.5


title: F1 hybrid leaf 5mm rep 2

source_name: F1 hybrid leaf 5mm

value: C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid

value: 5mm length, leaf plastochron index = -0.7


title: A. rosea leaf mature, primary branch, middle, rep 1

value: Middle of leaf

value: Mature leaf from primary branch, middle


title: A. rosea leaf 15mm, bottom, rep 1

value: Bottom half of leaf


title: A. rosea root rep 3

source_name: A. rosea root

value: Root


title: A. rosea root rep 1


title: F1 hybrid leaf 1mm rep3

source_name: F1 hybrid leaf 1mm

value: 1mm length, leaf plastochron index = -1.3


title: A. rosea stem rep 3

source_name: A. rosea stem

value: Stem


title: A. rosea leaf mature, primary branch, middle, rep 3


title: A. rosea leaf mature, main stem, middle, rep 1

source_name: A. rosea leaf mature, main stem, middle

value: Mature leaf from main stem, middle


title: A. rosea stem rep 2


title: A. rosea leaf 15mm, bottom, rep 2


title: A. rosea root rep 2


title: F1 hybrid leaf 1mm rep2


title: A. rosea leaf mature, main stem, middle, rep 3


title: A. rosea leaf mature, primary branch, middle, rep 2


title: F1 hybrid leaf 5mm rep 3


title: A. rosea leaf 13mm, top, rep 1

value: Top half of leaf


title: A. rosea leaf 15mm, top, rep 3

source_name: A. rosea leaf 15mm, top

value: 15mm length, top, leaf plastochron index = 1.5


title: A. rosea stem rep 1


title: F1 hybrid leaf 5mm rep 1


title: A. rosea leaf 15mm, top, rep 2


title: A. rosea leaf mature, main stem, middle, rep 2


title: F1 hybrid leaf 1mm rep1


title: A. rosea leaf 13mm, bottom, rep 2

source_name: A. rosea leaf 13mm, bottom

value: 13mm length, bottom, leaf plastochron index = 0.8


title: A. rosea leaf 13mm, bottom, rep 3


title: A. rosea leaf 15mm, top, rep 1


title: A. rosea leaf 13mm, bottom, rep 1


title: A. rosea leaf 13mm, top, rep 2


title: A. rosea leaf 11mm, top, rep 2

source_name: A. rosea leaf 11mm, top

value: 11mm length, top, leaf plastochron index = 0.3


title: A. rosea leaf 11mm, top, rep 3


title: A. rosea leaf 11mm, bottom, rep 2

source_name: A. rosea leaf 11mm, bottom

value: 11mm length, bottom, leaf plastochron index = 0.3


title: A. rosea leaf 10 - 7.5mm rep 3

source_name: A. rosea leaf 10 - 7.5mm

value: Whole leaf

value: 7.5mm length, leaf plastochron index = -0.35


title: A. rosea leaf 10 - 7.5mm rep 2


title: A. rosea leaf 11mm, bottom, rep 1


title: A. rosea leaf 11mm, bottom, rep 3


title: A. rosea leaf 9 - 7.5mm rep 5

source_name: A. rosea leaf 9 - 7.5mm


title: A. rosea leaf 5mm rep 2

source_name: A. rosea leaf 5mm


title: A. prostrata root rep 3

organism: Atriplex prostrata

source_name: A. prostrata root


title: A. rosea leaf 1mm rep 1

source_name: A. rosea leaf 1mm


title: A. rosea leaf 5mm rep 3


title: A. rosea leaf 11mm, top, rep 1


title: A. rosea leaf 1mm rep 3


title: A. rosea leaf 5mm rep 1


title: A. prostrata root rep 1


title: A. prostrata stem rep 3

source_name: A. prostrata stem


title: A. rosea leaf 9 - 7.5mm rep 4


title: A. rosea leaf 9 - 7.5mm rep 3


title: A. rosea leaf 10 - 7.5mm rep 1


title: A. prostrata root rep 2


title: A. prostrata leaf mature, main stem, middle, rep 1


title: A. prostrata leaf mature, primary branch, middle, rep 3


title: A. prostrata leaf mature, primary branch, middle, rep 2


title: A. prostrata stem rep 2


title: A. rosea leaf 1mm rep 2


title: A. prostrata leaf mature, primary branch, middle, rep 1


title: A. prostrata leaf 25mm, bottom, rep 3

source_name: A. prostrata leaf 25mm, bottom

value: 25mm length, bottom, leaf plastochron index = 1.5


title: A. prostrata stem rep 1


title: A. prostrata leaf 25mm, top, rep 2

source_name: A. prostrata leaf 25mm, top

value: 35mm length, top, leaf plastochron index = 1.5


title: A. prostrata leaf mature, main stem, middle, rep 2


title: A. prostrata leaf 25mm, bottom, rep 2


title: A. prostrata leaf 25mm, bottom, rep 1


title: A. prostrata leaf mature, main stem, middle, rep 3


title: A. prostrata leaf 18mm, top rep 2

source_name: A. prostrata leaf 18mm, top

value: 18mm length, top, leaf plastochron index = 0.8


title: A. prostrata leaf 18mm, top rep 3


title: A. prostrata leaf 25mm, top, rep 1


title: A. prostrata leaf 25mm, top, rep 3


title: A. prostrata leaf 18mm, bottom, rep 3

source_name: A. prostrata leaf 18mm, bottom

value: 18mm length, bottom, leaf plastochron index = 0.8


title: A. prostrata leaf 18mm, bottom, rep 2


title: A. prostrata leaf 18mm, top rep 1


title: A. prostrata leaf 15mm, top, rep 3

source_name: A. prostrata leaf 15mm, top

value: 15mm length, top, leaf plastochron index = 0.3


title: A. prostrata leaf 15mm, top, rep 1


title: A. prostrata leaf 15mm, bottom, rep 1

source_name: A. prostrata leaf 15mm, bottom

value: Bottom half of leaf

value: 15mm length, bottom, leaf plastochron index = 0.3


title: A. prostrata leaf 10 - 7.5mm rep 3

source_name: A. prostrata leaf 10 - 7.5mm


title: A. prostrata leaf 15mm, bottom, rep 3


title: A. prostrata leaf 9 - 7.5mm rep 3

source_name: A. prostrata leaf 9 - 7.5mm


title: A. prostrata leaf 10 - 7.5mm rep 1


title: A. prostrata leaf 5mm rep 2

source_name: A. prostrata leaf 5mm

value: 5mm length, leaf plastochron index = -0.7


title: A. prostrata leaf 9 - 7.5mm rep 4


title: A. prostrata leaf 10 - 7.5mm rep 2


title: A. prostrata leaf 9 - 7.5mm rep 5


title: A. prostrata leaf 5mm rep 1


title: A. prostrata leaf 1mm rep 3

source_name: A. prostrata leaf 1mm

value: 1mm length, leaf plastochron index = -1.3


title: A. prostrata leaf 18mm, bottom, rep 1


title: MA48_54h_IR28_Shoot_salt_R3

data_processing:
Illumina Casava-1.9software used for basecalling.
The software kallisto (v 0.45.0) was used for quantification with the MSU Rice Ref 7 Nipponbare genome reference. The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses.
Kallisto was run with 50 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
Means and standard deviation of tpm of biological triplicates group were calculated.
Genome_build: MSU Rice Ref 7 Nipponbare (MSU Rice Ref 7 Nipponbare)
Supplementary_files_format_and_content: Comma-separated table (.txt) file including Oryz sativa locus ID, brief annotation, interproscan annotation (all annotation from http://rice.plantbiology.msu.edu/), raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each salinity treatment against control within the respective species, tissue and time

growth_protocol: After germination, the seedlings of the tolerant and sensitive genotypes were transferred and grown in Yoshida hydroponic medium for 14 days under controlled conditions

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 16 libraries per lane and sequenced in single-end mode (150 bp read length) on an Illumina HiSeq 3000 platform.

treatment_protocol: For salinity stress half of the seedlings were under 150 mM NaCl and after 6 and 54 h the treated and untreated samples were harvested in three replications from roots and shoots separately

tag: duration of treatment

value: salinity

value: Shoot

tag: biological replicate


title: A. prostrata leaf 1mm rep 1


title: A. prostrata leaf 15mm, top, rep 2

value: Top half of leaf


title: MA45_54h_IR28_Root_salt_R3

value: Root


title: MA47_54h_IR28_Shoot_salt_R2


title: MA46_54h_IR28_Shoot_salt_R1


title: MA42_54h_IR28_Shoot_ctrl_R3

value: control


title: A. prostrata leaf 1mm rep 2


title: A. prostrata leaf 15mm, bottom, rep 2


title: MA38_54h_IR28_Root_ctrl_R2


title: A. prostrata leaf 5mm rep 3


title: MA41_54h_IR28_Shoot_ctrl_R2


title: MA37_54h_IR28_Root_ctrl_R1


title: MA40_54h_IR28_Shoot_ctrl_R1


title: MA33_54h_CSR28_Root_salt_R3


title: MA36_54h_CSR28_Shoot_salt_R3


title: MA34_54h_CSR28_Shoot_salt_R1


title: MA32_54h_CSR28_Root_salt_R2


title: MA35_54h_CSR28_Shoot_salt_R2


title: MA44_54h_IR28_Root_salt_R2


title: MA29_54h_CSR28_Shoot_ctrl_R2


title: MA28_54h_CSR28_Shoot_ctrl_R1


title: MA26_54h_CSR28_Root_ctrl_R2


title: MA27_54h_CSR28_Root_ctrl_R3


title: MA25_54h_CSR28_Root_ctrl_R1


title: MA43_54h_IR28_Root_salt_R1


title: MA24_6h_IR28_Shoot_salt_R3


title: MA21_6h_IR28_Root_salt_R3


title: MA23_6h_IR28_Shoot_salt_R2


title: MA20_6h_IR28_Root_salt_R2


title: MA22_6h_IR28_Shoot_salt_R1


title: MA39_54h_IR28_Root_ctrl_R3


title: MA16_6h_IR28_Shoot_ctrl_R1


title: MA19_6h_IR28_Root_salt_R1


title: MA18_6h_IR28_Shoot_ctrl_R3


title: MA17_6h_IR28_Shoot_ctrl_R2


title: MA14_6h_IR28_Root_ctrl_R2


title: MA13_6h_IR28_Root_ctrl_R1


title: MA15_6h_IR28_Root_ctrl_R3


title: MA12_6h_CSR28_Shoot_salt_R3


title: MA31_54h_CSR28_Root_salt_R1


title: MA11_6h_CSR28_Shoot_salt_R2


title: MA10_6h_CSR28_Shoot_salt_R1


title: MA30_54h_CSR28_Shoot_ctrl_R3


title: MA04_6h_CSR28_Shoot_ctrl_R1


title: MA06_6h_CSR28_Shoot_ctrl_R3


title: MA09_6h_CSR28_Root_salt_R3


title: MA07_6h_CSR28_Root_salt_R1


title: MA08_6h_CSR28_Root_salt_R2


title: MA01_6h_CSR28_Root_ctrl_R1


title: MA03_6h_CSR28_Root_ctrl_R3


title: UV6 rep2

city: shanghai

first: yongp

last: li

address: shanghai

institute: shanghai jiaotong university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to txid35608 whole genome using Hisat2 version 2.1.0 with default parameters
Normalized gene expression levels were estimated using TPM (transcripts per million) value using Salmon software and differential expression levels were analyzed using the DESeq R package.
Genome_build: txid35608; https://www.ncbi.nlm.nih.gov/assembly/GCA_003112345.1
Supplementary_files_format_and_content: TPM values for each Sample

organism: Artemisia annua

growth_protocol: Artemisia annua used in this study is a high-artemisinin cultivar, ‘Huhao 1’, which has been selected and developed in Shanghai for several years. A. annua and Nicotiana benthamiana seeds were sown in pots filled with a 3:7 mixture of peat soil and vermiculite and placed in a greenhouse under the growth condition of 16-hour light/8-hour dark photoperiod at 23 ± 2°C and supplemented with regular water and fertilizer.

extract_protocol:
Total RNA was isolated from three independent pools of leaves using RNAprep pure Plant Kit (Tiangen, Beijing, China), according to the manufacturer’s instructions. The concentration and integrity of each RNA sample was detected using a NanoDrop 2000 (Thermo Scientific, Waltham, MA, USA) and 1% agarose gels. The quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For UV-B treatment, six-week-old A. annua seedlings growing under normal growth condition were supplemented with extra narrowband UV-B lamps (Philips TL20W/01RS; 1.5 μmol·m-2·s-1). The most recently expanded leaf for each A. annua seedling was collected at 0, 2, 4 and 6 hours after exposure to UV-B radiation and named as UV0, UV2, UV4 and UV6, respectively according to their harvest time. All samples were separately harvested from three independent individual seedlings as mix. Three biological repeats for each sample were measured.

value: high-artemisinin cultivar, Huhao 1

tag: developmetal stage/age

value: six-week-old A. annua seedlings

value: leaf

value: wild type

tag: treatment/time point

value: 6h after exposure to UV-B radiation


title: UV4 rep1

value: 4h after exposure to UV-B radiation


title: UV4 rep2


title: UV6 rep1


title: MA02_6h_CSR28_Root_ctrl_R2


title: UV0 rep3

value: 0h after exposure to UV-B radiation


title: UV0 rep2


title: UV2 rep2

value: 2h after exposure to UV-B radiation


title: UV4 rep3


title: UV0 rep1


title: UV2 rep3


title: HEK293 cell, Doxycyline 250 ng/ml, rep2

city: Gainesville

first: Joseph

middle: Anthony

last: Ellis

state: FL

address: 1200 Newell Drive

department: Biochemistry and Molecular Biology

institute: University of Florida

data_processing:
Alignment to hg38 genome using STAR v2.7.9a
alternative splicing analysis using aligned bam files using rMATS turbo v4.1.2
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing skipped exon alternative splicing event coordinate information and triplicate inclusion level values with associate statistics obtained from rMATS

growth_protocol: cultured as a monolayer in DMEM (Corning) supplemented with 10 % FBS (Corning), 10 μg/mL blasticidin (Gibco), 150 μg/mL hygromycin (Gibco), and 2 μg/mL puromycin (Gibco) at 37 °C under 5 % CO2.

extract_protocol:
Total RNA from ddHEKs were harvested utilizing the Aurum Total RNA Mini kit (Bio-Rad, Hercules, CA, USA) and DNase treated on-column
manufcaturer specified protocols for NEBNext Ultra II Directional RNA Library Kit (NEB #E7760) with the NEBNExt rRNA Depletion Kit (NEB #E6310) were followed as specified except for 40X adaptor dilutions were utilized, 4X lower concentrations of index primers were used, all bead incubations were performed at room temperature, and 10 cycles of library amplification were performed.

treatment_protocol: fresh doxycycline was prepared at 1 mg/mL, diluted, and then added to the cells at the appropriate concentrations to induce a range of HA-MBNL1 protein expression

value: embyonic kidney

value: Doxycycline 250 ng/mL


title: HEK293 cell, Doxycyline 250 ng/ml, rep3


title: HEK293 cell, Doxycyline 1000 ng/ml, rep3

value: Doxycycline 1000 ng/mL


title: HEK293 cell, Doxycyline 0 ng/ml, rep3

value: Doxycycline 0 ng/mL


title: HEK293 cell, Doxycyline 1000 ng/ml, rep2


title: HEK293 cell, Doxycyline 280 ng/ml, rep3

value: Doxycycline 280 ng/mL


title: HEK293 cell, Doxycyline 170 ng/ml, rep3

value: Doxycycline 170 ng/mL


title: HEK293 cell, Doxycyline 100 ng/ml, rep3

value: Doxycycline 100 ng/mL


title: MA05_6h_CSR28_Shoot_ctrl_R2

value: Shoot


title: UV6 rep3


title: HEK293 cell, Doxycyline 100 ng/ml, rep2


title: HEK293 cell, Doxycyline 170 ng/ml, rep2


title: HEK293 cell, Doxycyline 280 ng/ml, rep1


title: HEK293 cell, Doxycyline 1000 ng/ml, rep1


title: HEK293 cell, Doxycyline 0 ng/ml, rep2


title: HEK293 cell, Doxycyline 170 ng/ml, rep1


title: HEK293 cell, Doxycyline 0 ng/ml, rep1


title: HEK293 cell, Doxycyline 100 ng/ml, rep1


title: UV2 rep1


title: HEK293 cell, Doxycyline 280 ng/ml, rep2


title: 21

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

description: Female

data_processing:
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Assembly: Sus Scrofa 11.1

organism: Sus scrofa domesticus

source_name: Cholecalciferol + 25(OH)D_Increased dose_muscle

extract_protocol:
Collected tissues were stored at -80°C. RNA was isolated using Trizol reagent. QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) with 100ng/ul total RNA was used to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cholecalciferol + 25(OH)D

tag: dose

value: Increased dose

tag: Sex

value: Female

value: Muscle


title: 5

description: Female


title: 7

description: Female

source_name: 25(OH)D_Standard dose _muscle

value: Standard dose


title: 61

description: Female


title: 38

description: Castrated male

value: male


title: HEK293 cell, Doxycyline 250 ng/ml, rep1

tag: cell line


title: 17

description: Female

source_name: Cholecalciferol _Standard dose _muscle

value: Cholecalciferol


title: 36

description: Castrated male

source_name: Cholecalciferol_Increased dose_muscle


title: 30

description: Castrated male


title: M_frozen_16C

type: genomic

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

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

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

data_processing: Sesame R package

label: Cy3, Cy5

source_name: Term placenta

label_protocol: Standard Illumina Protocol

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol: Genomic DNA was extracted and purified from Placentas samples using Phenol:Chloroform according to lab protocols. Then samples were Bisulfite-treated using Qiagen EpiTect Bisulfite Conversion Kit.

treatment_protocol: Placentas were collected at E18.5, snap frozen in liquid nitrogen and stored at -80C for DNA extraction.

value: placenta

tag: fetal gender

value: Male

tag: group

value: frozen


title: 10

description: Castrated male

tag: tissue


title: 2

description: Castrated male

tag: treatment


title: 59

description: Female


title: F_control_C4B

tag: developmental stage

value: control


title: M_fresh_8A

value: fresh


title: 53

description: Female


title: M_frozen_17B


title: 22

description: Castrated male


title: 20

description: Castrated male


title: F_frozen_2A


title: M_fresh_4A


title: M_fresh_3A


title: 51

description: Female


title: 19

description: Female


title: 11

description: Female


title: M_frozen_10B


title: 14

description: Castrated male


title: M_frozen_20A


title: M_control_C3B


title: 44

description: Castrated male


title: 4

description: Castrated male


title: 43

description: Female


title: 16

description: Castrated male


title: M_fresh_11A


title: M_control_C1B


title: M_control_C2F


title: F_frozen_18B


title: F_fresh_9A


title: 63

description: Female


title: M_control_C4A


title: 49

description: Female

source_name: Cholecalciferol_Standard dose _muscle


title: 56

description: Castrated male


title: F_frozen_14B


title: F_control_C1A


title: F_fresh_12A


title: F_fresh_14D


title: 24

description: Castrated male


title: 15

description: Female


title: F_control_C2A


title: 9

description: Female


title: 33

description: Female


title: F_control_C3A


title: F_fresh_6B


title: 18

description: Castrated male


title: F_frozen_19A


title: 8

description: Castrated male


title: 100 mGy/h, 8 days, rep 4

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description:
G84
Processed file_raw_counts_8d_mRNAGene.txt

data_processing:
Sequence reads filtering: the BGI software SOAPnuke to filter the low quality reads
Genome mapping: HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)
Dose-responsive gene identification: Dromics R package
Assembly: NCBI genome assembly: ASM399081v1
Supplementary files format and content: tab-delimited files with counts and annotations for each gene in the files

organism: Daphnia magna

source_name: Whole organism

growth_protocol: Daphnia magna were cultured in the M7 medium, pH 7.8-8.2, dissolved oxygen >8 mg/L and temperature 19-21, according to the standard toxicity testing guideline OECD TG211

extract_protocol:
Total RNA was extracted using the Zymo Tissue & Insect Micro Prep kit. The quantity and purity of the RNA were measured using an ND-1000 Nanodrop and integrity assessed using an Agilent Bioanalyzer.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: Daphnia magna were exposed to 7 dose-rates (0, 0.4, 1, 4, 10, 40, 100 mGy/h) of gamma radiation in a static system (50 mL plastic beaker filled with 45 mL culture medium) for 8 days. Samples were taken after 4 and 8 days exposure for RNA-seq.

value: Whole organism

value: Juvenile, 8 days old

tag: genotype

value: WT

value: 100 mGy/h gamma radiation

tag: time point

value: 8 days exposure


title: 100 mGy/h, 8 days, rep 3

description:
G83
Processed file_raw_counts_8d_mRNAGene.txt


title: 40 mGy/h, 8 days, rep 4

description:
F84
Processed file_raw_counts_8d_mRNAGene.txt

value: 40 mGy/h gamma radiation


title: 100 mGy/h, 8 days, rep 2

description:
G82
Processed file_raw_counts_8d_mRNAGene.txt


title: 40 mGy/h, 8 days, rep 2

description:
F82
Processed file_raw_counts_8d_mRNAGene.txt


title: 40 mGy/h, 8 days, rep 3

description:
F83
Processed file_raw_counts_8d_mRNAGene.txt


title: 10 mGy/h, 8 days, rep 3

description:
E83
Processed file_raw_counts_8d_mRNAGene.txt

value: 10 mGy/h gamma radiation


title: 100 mGy/h, 8 days, rep 1

description:
G81
Processed file_raw_counts_8d_mRNAGene.txt

value: Female


title: 40 mGy/h, 8 days, rep 1

description:
F81
Processed file_raw_counts_8d_mRNAGene.txt


title: 10 mGy/h, 8 days, rep 2

description:
E82
Processed file_raw_counts_8d_mRNAGene.txt


title: 4 mGy/h, 8 days, rep 4

description:
D84
Processed file_raw_counts_8d_mRNAGene.txt

value: 4 mGy/h gamma radiation


title: 10 mGy/h, 8 days, rep 1

description:
E81
Processed file_raw_counts_8d_mRNAGene.txt


title: 4 mGy/h, 8 days, rep 3

description:
D83
Processed file_raw_counts_8d_mRNAGene.txt


title: 3

description: Female

value: Increased dose

value: Muscle


title: 1 mGy/h, 8 days, rep 4

description:
C84
Processed file_raw_counts_8d_mRNAGene.txt

value: 1 mGy/h gamma radiation


title: 4 mGy/h, 8 days, rep 1

description:
D81
Processed file_raw_counts_8d_mRNAGene.txt


title: 1 mGy/h, 8 days, rep 3

description:
C83
Processed file_raw_counts_8d_mRNAGene.txt


title: 1 mGy/h, 8 days, rep 1

description:
C81
Processed file_raw_counts_8d_mRNAGene.txt


title: 0.4 mGy/h, 8 days, rep 3

description:
B83
Processed file_raw_counts_8d_mRNAGene.txt

value: 0.4 mGy/h gamma radiation


title: 0.4 mGy/h, 8 days, rep 2

description:
B82
Processed file_raw_counts_8d_mRNAGene.txt


title: 1 mGy/h, 8 days, rep 2

description:
C82
Processed file_raw_counts_8d_mRNAGene.txt


title: 0.4 mGy/h, 8 days, rep 4

description:
B84
Processed file_raw_counts_8d_mRNAGene.txt


title: 10 mGy/h, 8 days, rep 4

description:
E84
Processed file_raw_counts_8d_mRNAGene.txt


title: 0 mGy/h, 8 days, rep 4

description:
A84
Processed file_raw_counts_8d_mRNAGene.txt

value: 0 mGy/h gamma radiation


title: 0 mGy/h, 8 days, rep 2

description:
A82
Processed file_raw_counts_8d_mRNAGene.txt


title: 0.4 mGy/h, 8 days, rep 1

description:
B81
Processed file_raw_counts_8d_mRNAGene.txt


title: 0 mGy/h, 8 days, rep 3

description:
A83
Processed file_raw_counts_8d_mRNAGene.txt


title: 100 mGy/h, 4 days, rep 1

description:
G41
Processed file_raw_counts_4d_mRNAGene.txt

value: Juvenile, 4 days old

value: 4 days exposure


title: 0 mGy/h, 8 days, rep 1

description:
A81
Processed file_raw_counts_8d_mRNAGene.txt


title: 100 mGy/h, 4 days, rep 4

description:
G44
Processed file_raw_counts_4d_mRNAGene.txt


title: 40 mGy/h, 4 days, rep 4

description:
F44
Processed file_raw_counts_4d_mRNAGene.txt


title: 100 mGy/h, 4 days, rep 2

description:
G42
Processed file_raw_counts_4d_mRNAGene.txt


title: 40 mGy/h, 4 days, rep 3

description:
F43
Processed file_raw_counts_4d_mRNAGene.txt


title: 10 mGy/h, 4 days, rep 3

description:
E43
Processed file_raw_counts_4d_mRNAGene.txt


title: 40 mGy/h, 4 days, rep 1

description:
F41
Processed file_raw_counts_4d_mRNAGene.txt


title: 10 mGy/h, 4 days, rep 4

description:
E44
Processed file_raw_counts_4d_mRNAGene.txt


title: 10 mGy/h, 4 days, rep 1

description:
E41
Processed file_raw_counts_4d_mRNAGene.txt


title: 4 mGy/h, 4 days, rep 4

description:
D44
Processed file_raw_counts_4d_mRNAGene.txt


title: 4 mGy/h, 8 days, rep 2

description:
D82
Processed file_raw_counts_8d_mRNAGene.txt


title: 4 mGy/h, 4 days, rep 2

description:
D42
Processed file_raw_counts_4d_mRNAGene.txt


title: 10 mGy/h, 4 days, rep 2

description:
E42
Processed file_raw_counts_4d_mRNAGene.txt


title: 4 mGy/h, 4 days, rep 3

description:
D43
Processed file_raw_counts_4d_mRNAGene.txt


title: 4 mGy/h, 4 days, rep 1

description:
D41
Processed file_raw_counts_4d_mRNAGene.txt


title: 1 mGy/h, 4 days, rep 4

description:
C44
Processed file_raw_counts_4d_mRNAGene.txt


title: 1 mGy/h, 4 days, rep 3

description:
C43
Processed file_raw_counts_4d_mRNAGene.txt


title: 0.4 mGy/h, 4 days, rep 4

description:
B44
Processed file_raw_counts_4d_mRNAGene.txt


title: 1 mGy/h, 4 days, rep 1

description:
C41
Processed file_raw_counts_4d_mRNAGene.txt


title: 42

description: Castrated male

value: Cholecalciferol

value: Standard dose

value: male


title: 0.4 mGy/h, 4 days, rep 1

description:
B41
Processed file_raw_counts_4d_mRNAGene.txt

value: Whole organism

value: WT


title: 0.4 mGy/h, 4 days, rep 3

description:
B43
Processed file_raw_counts_4d_mRNAGene.txt


title: 0.4 mGy/h, 4 days, rep 2

description:
B42
Processed file_raw_counts_4d_mRNAGene.txt


title: 1 mGy/h, 4 days, rep 2

description:
C42
Processed file_raw_counts_4d_mRNAGene.txt


title: 100 mGy/h, 4 days, rep 3

description:
G43
Processed file_raw_counts_4d_mRNAGene.txt

value: 100 mGy/h gamma radiation


title: 0 mGy/h, 4 days, rep 3

description:
A43
Processed file_raw_counts_4d_mRNAGene.txt


title: 40 mGy/h, 4 days, rep 2

description:
F42
Processed file_raw_counts_4d_mRNAGene.txt

value: 40 mGy/h gamma radiation


title: 0 mGy/h, 4 days, rep 4

description:
A44
Processed file_raw_counts_4d_mRNAGene.txt


title: 0 mGy/h, 4 days, rep 2

description:
A42
Processed file_raw_counts_4d_mRNAGene.txt


title: 0 mGy/h, 4 days, rep 1

description:
A41
Processed file_raw_counts_4d_mRNAGene.txt


title: SisLAL14/1, control, 6hpi [Control.6h-2]

city: København N

first: Laura

last: Martínez Alvarez

state: Please select

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

description:
FeatureCountsNAR.txt
EdgeR-0v0.txt
DESeq.6-12h.txt

data_processing:
Reads were trimmed using the tool bbduk from the BBTools package (ktrim=r, k=23, mink=11, hdist=1, tpe, tbo, qtrim=r, trimq=25)
Removal of rRNA was done usinb bbsplit from the BBTools package using the rRNAs of SisLAL14/1 as reference
Optical duplicates were removed using the tool clumpify from the BBTools package (optical distance=40 spantiles=f)
Trimmed reads were mapped to SisLAL14 using bowtie2
Read counts mapping to genes were calculated using Feature Counts
Normalization of data and statistical analysis was done using DESeq2 (comparison of control vs. gp21 samples at 6+12 hpi) and/or EdgeR (comparison of control vs gp21 samples at 0 hpi)
Assembly: CP003928.1
Supplementary files format and content: tab-delimited text files include read counts mapping to each genomic feature or log2 fold change and p-values of the differential expression of each feature

organism: Saccharolobus islandicus LAL14/1

growth_protocol: S. islandicus LAL14/1 cell cultures were grown in SCV medium at 78° C under agitation

extract_protocol:
RNA was extracted using TRI Reagent according to the instructions by the manufacturer
Libraries were constructed using the services of Novogen

treatment_protocol: Protein expression was induced by the addition of 0.2% D-arabinose

tag: alternative name

value: Saccharolobus islandicus LAL14/1

tag: strain

value: Darrays

tag: cell type

value: cell culture

value: 0.2% D-arabinose

tag: time

value: 6 hours post-induction


title: SisLAL14/1, p.SIRV2gp21, 0hpi [SIRV2gp21.0h-1]

source_name: Sis/pGE2-SIRV2 gp21

value: Sis/pGE2-SIRV2 gp21

value: 0 hours post induction


title: SisLAL14/1, control, 0hpi [Control.0h-2]


title: SisLAL14/1, p.SIRV2gp21, 12hpi [SIRV2gp21.12h-2]

value: 12 hours post-induction


title: SisLAL14/1, p.SIRV2gp21, 6hpi [SIRV2gp21.6h-2]


title: SisLAL14/1, control, 0hpi [Control.0h-1]


title: SisLAL14/1, p.SIRV2gp21, 12hpi [SIRV2gp21.12h-1]


title: Nectary postsecretory replicate 2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description: L-C-S77 normalized read counts

data_processing:
Assembly with Trinity 2.12.0
Transcript read counts by kallisto 0.46.1
Protein predictions with Transdecoder 5.5
Arabidopsis thaliana associations with Blast+
Assembly: Araport 11
Supplementary files format and content: Mminor_Atmapped_GEO.xlsx A.thaliana-mapped normalized counts and statistics
Supplementary files format and content: Mminor_contigs.fa.gz assembled contigs

organism: Melianthus elongatus

source_name: Nectary

extract_protocol:
RNA was isolated from pre-secretory, secretory, and post-secretory nectaries (stages described above), as well as leaves, with the RNAqueous Micro Kit (Invitrogen cat. no. AM1931). The total RNA was treated with the TURBO DNA-free kit (Invitrogen Cat# AM1907) according to the manufacturer’s protocol.
Barcoded library creation and sequencing was performed via NovaSeq 6000 using via paired-end 150 bp runs using rapid chemistry

value: Nectary

value: postsecretory


title: SisLAL14/1, p.SIRV2gp21, 6hpi [SIRV2gp21.6h-1]


title: SisLAL14/1, p.SIRV2gp21, 0hpi [SIRV2gp21.0h-2]


title: SisLAL14/1, control, 12hpi [Control.12h-1]


title: SisLAL14/1, control, 6hpi [Control.6h-1]


title: Nectary postsecretory replicate 0

description: L-A-S75 normalized read counts


title: Nectary presecretory replicate 2

description: 2-A-S72 normalized read counts

value: secretory


title: Nectary secretory replicate 2

description: 2-C-S74 normalized read counts


title: Nectary secretory replicate 1

description: 2-B-S73 normalized read counts


title: Nectary presecretory replicate 0

description: 1-B-S70 normalized read counts

value: presecretory


title: Nectary presecretory replicate 1

description: 1-C-S71 normalized read counts


title: Leaf sample replicate 1

description: 0-B-S67 normalized read counts

source_name: Leaf

value: Leaf

value: mature


title: Leaf sample replicate 2

description: 1-A-S69 normalized read counts


title: SisLAL14/1, control, 12hpi [Control.12h-2]


title: MDS_E_19

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
All reads assigned to a particular miRNA or piRNA were counted and the associated UMIs were aggregated to count unique molecules.
A matrix of the UMI counts of miRNA or piRNA was subjected to downstream analyses using StrandNGS 3.4 software (Agilent Technologies, Santa Clara, CA).
The UMI counts were quantified using a Trimmed Mean of M-value (TMM) method (1).
miRNAs were annotated against miRBase (Robinson and Oshlack, 2010).

source_name: Extracellular vesicles

extract_protocol:
EVs were collected from peripheral blood serum by ultracentrifugation.
the sequencing libraries were constructed using the QIAseq™ miRNA Library Kit (Cat#331505, Qiagen, Hilden, Germany) according to the manufacturer’s protocols. The pooled libraries of the samples were sequenced using NextSeq 500 (Illumina, Inc., San Diego, CA) in 76-base-pair (bp) single-end reads.

value: Serum

tag: disease state

value: MDS


title: MDS_E_18


title: MDS_E_17


title: MDS_E_15


title: MDS_E_16


title: MDS_E_14


title: MDS_E_11


title: MDS_E_8


title: MDS_E_9


title: MDS_E_7


title: MDS_E_2


title: MDS_E_5


title: MDS_E_6


title: Nectary postsecretory replicate 1

description: L-B-S76 normalized read counts


title: MDS_E_10


title: MDS_E_12


title: Control_E_6

value: healthy


title: Control_E_5


title: Control_E_2


title: Control_E_7


title: Control_E_3


title: Leaf sample replicate 0

description: 0-A-S66 normalized read counts


title: Control_E_8


title: Control_E_4


title: Control_E_1


title: Leading Edge G

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioma

extract_protocol:
Fresh glioma samples were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.  RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3, 10x Genomics).

tag: seizure status

value: seizure

tag: location

value: Leading Edge

value: glioma


title: Core G

description: 10x Genomics

value: Core


title: Core E

description: 10x Genomics


title: Core F

description: 10x Genomics


title: Core D

description: 10x Genomics


title: Leading Edge E

description: 10x Genomics


title: MDS_E_13


title: MDS_E_4


title: MDS_E_3


title: MDS_E_1


title: Leading Edge C

description: 10x Genomics

value: No seizure


title: Core C

description: 10x Genomics


title: Leading Edge B

description: 10x Genomics


title: Core A

description: 10x Genomics


title: Leading Edge A

description: 10x Genomics


title: Core B

description: 10x Genomics


title: ChIPseq_PROLIF_G_H3K4me1

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo

description: Proliferating ASCs (gluteofemoral)

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1
For histone ChIPs with replicates, bams files were merged.  For LMNA ChIPs, replicates were merged after peak calling.
Duplicate reads were removed using picard MarkDuplicates.  For histone ChIPs multi-mapping reads and alignments with a mapping quality below 10 were also filtered out.
For histone modification ChIPseq, peaks were called using macs2 2.2.7.1.  For H3K27me3, H3K36me3 and H3K4me1 option --broad was used.
For LMNA ChIPseq, peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings before a final run with optimized settings.
Assembly: hg38
Supplementary files format and content: Bed EDD peak file - 4th column is EDD score.
Supplementary files format and content: bigwig (.bw) files are regular bigwig files are log2ratio of filtered ChIP/Input files, generated using bamCompare from deeptools 3.5.1 if the extension is ".grep.norm.bw".  Else if the tracks ends "_pileup.norm.bw" the track is generated from macs output files as the log 10 ratio of treat/control lamba pileup files.
Supplementary files format and content: .narrowPeak and .broadPeak files are modified bed files created by macs2 callpeaks

source_name: Adipose (gluteofemoral)

growth_protocol: Human normal ASCs purifed from adipose tissue were cultured in proliferating state in DMEM/F12 containing 10 % fetal calf serum and 20 ng/ml basic fibroblast growth factor.

extract_protocol:
For ChIP, cells were sonicated to produce chromatin fragments of 200 base-pairs, lysates were clarified by sedimentation and histone-DNA or lamin-DNA complexes were isolated from supernatants by ChIP using specific antibodies. RNA was purified from cell lysates using the RNEasy mini kit (Qiagen).
ChIP sequencing libraries were prepared according to Illumina protocols for sequencing at the Norwegian Sequencing Center.

treatment_protocol: Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. On Day 0, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1 µM dexamethasone and 0.5 µM 3-isobutyl-1-methylxanthine.  Cells were collected at indicated timepoints for protein, RNA and chromatin preparations and analyses.

value: Human primary adipose stem cells

value: Adipose (gluteofemoral)

value: Day minus 2 (proliferating)

tag: chip antibody

value: H3K4me1 (Diagenode c15410037)

tag: replicate


title: ChIPseq_PROLIF_G_H3K27me3

description: Proliferating ASCs (gluteofemoral)

value: H3K27me3 (Diagenode C15410069)


title: ChIPseq_PROLIF_G_H3K27ac

description: Proliferating ASCs (gluteofemoral)

value: H3K27ac (Diagenode c15410174)


title: ChIPseq_PROLIF_G_H3K4me3

description: Proliferating ASCs (gluteofemoral)

value: H3K4me3 (Diagenode c15410003)


title: SKNMC_shFLI1_NFIB_del_DBD_V5

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using bwa v.0.7.12 with default settings.
Duplicate reads were removed using picard-tools v.1.95. Aligned reads were extended to 150 bp to approximate fragment sizes
Assembly: hg19
Supplementary files format and content: bigwig files were generated using bedtools; scores show fragments normalized to 10M mapped fragments.

source_name: Ewing sarcoma cells

growth_protocol: SKNMC was grown in RPMI-1640 (Gibco, 11875). All media were supplemented with 10% FBS and cells were cultured at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the specified antibodies using standard protocol.
Precipitated DNA samples were used to prepare sequencing libraries with Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, 0344NB-A01), and DNA samples were sequenced with the Nextseq 500 Illumina genome analyzer.

treatment_protocol: untreated

value: Ewing sarcoma cells

value: untreated

value: anti-V5 (Cell Signaling, Cat#13202)


title: SKNMC_shGFP_NFIB_del_DBD_V5


title: ChIPseq_PROLIF_G_INPUT

description: Proliferating ASCs (gluteofemoral)


title: SKNMC_shFLI1_EV_V5


title: SKNMC_shGFP_NFIB_WT_V5


title: SKNMC_shFLI1_NFIB_WT_V5


title: Sample MM13 control (s015)

city: Utrecht

first: Victor

last: Peperzak

state: Utrecht

address: Heidelberglaan 100

department: Center for Translational Immunology

country: Netherlands

institute: UMC Utrecht

description: SORT-seq

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for the identification of the Illumina library barcode, cell barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables were automated using the MapAndGo script[1] .
Assembly: Hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Bone marrow aspirates from muliple myeloma (MM) patients containing CD38+CD138+ myeloma plasma cells were cultured in the presence of growth factors IL-6 and APRIL (100 ng/mL each).

extract_protocol:
After treatment, CD38+CD38+ myeloma plasma cells were FACS sorted directly into 384-well plates. Plates were shipped on dry ice to Single Cell Discoveries, where single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016) with primers described in van den Brink et al., 2017). Cells were heat-lysed at 65°C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT).
Library preparation was done following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1×75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles).

treatment_protocol: MM bone marrow samples were treated for 72 hours with a combination of 20 μM tankyrase inhibitor (TNKSi) XAV939 and 5 μM porcupine inhibitor (PORCi) C59.

value: Bone marrow

value: CD38+CD138+ myeloma plasma cells

value: no


title: Sample MM13 +WNTi (s016)

description: SORT-seq

value: 20 uM XAV939 & 5 uM C59 for 72h


title: SKNMC_shGFP_EV_V5


title: 23

description: Female

tag: dose

value: Standard dose

tag: Sex

value: Female

value: Muscle


title: Sample MM10 +WNTi (s022)

description: SORT-seq


title: Sample MM10 control (s021)

description: SORT-seq


title: Sample MM11 +WNTi (s024)

description: SORT-seq


title: Sample MM12 control (s013)

description: SORT-seq


title: Sample MM09 +WNTi (s020)

description: SORT-seq


title: Sample MM09 control (s019)

description: SORT-seq


title: Sample MM12 +WNTi (s014)

description: SORT-seq


title: Sample MM11 control (s023)

description: SORT-seq


title: hs20151130-SC3-89

city: Los Angeles

first: David

last: Cobrinik

state: CA

address: 4546 Sunset Blvd

institute: Children's Hospital Los Angeles

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to grch38 using HISAT2
Transcript assembly and quantitation were performed using StringTie
Read count extraction was performed using tximport
Assembly: GRCh38

source_name: fetal retina

extract_protocol:
Retinae were dissected from fetal eyes in ice-cold PBS, dissociated in 2 ml 10 u/ml papain at 37o C for 10 min, followed by gentle pipetting with a 1,000 ul tip to dissociate larger pieces every 5-10 min (at 37o C for an additional 20-30 min total) to obtain a mostly single-cell suspension. ~ 2 volumes of retina culture media [IMDM, 10% fetal bovine serum (FBS), 0.28 u/ml insulin, 55 uM β-mercaptoethanol, 1% by volume penicillin-streptomycin] was used to halt dissociation. Cells were centrifuged at 300 x g for 10 min, resuspended for counting, then recentrifuged and resuspended at 10,000 cell/ul in PBS with 5% FBS and CD133-PE, CD44-FITC, and CD49b FITC antibodies. After 1 h at room temperature, samples were diluted in PBS + 5% FBS, centrifuged, and resuspended in PBS with 1% FBS and 10 ug/ml DAPI. Forward and side scatter and CD133+/CD44,CD49b-low gating was used to enrich for cone photoreceptors. Single cells were either i) directly collected from FACS into 1.2 ul lysis buffer droplets on a parafilm-covered glass slide and transferred to low-adherence tubes for subsequent processing or ii) collected in bulk for isolation with the Fluidigm C1 microfluidics system.
Full-length single cell cDNA transcripts were generated using SMARTer (Sequencing #1- 2) or SMART-SeqV4 chemistry (Sequencing #3 - 6) from Clontech (now Takara Bio) at ~ 0.1x scale using a Mantis liquid handler. Library preparation was performed using the Nextera XT DNA Library Preparation Kit at reduced volume using Mantis liquid handler and otherwise as per the manufacturer instructions.

value: fetal retina

tag: sequencing run

tag: post fertilization_week

tag: collection method

value: LM

tag: pfw-retina id

tag: final dataset

value: Y

tag: removal reason


title: hs20151130-SC3-84

tag: tissue

value: iPRP


title: hs20151130-SC3-86

value: ER

value: TR


title: hs20151130-SC3-92


title: hs20151130-SC3-85


title: hs20151130-SC3-90


title: hs20151130-SC3-83


title: hs20151130-SC3-82

value: N


title: hs20151130-SC3-81


title: hs20151130-SC3-79


title: hs20151130-SC3-75


title: hs20151130-SC3-74


title: hs20151130-SC3-76

value: S


title: hs20151130-SC3-78


title: hs20151130-SC3-72


title: hs20151130-SC3-77


title: hs20151130-SC3-70

value: RPC/MG

value: MG


title: hs20151130-SC3-7


title: hs20151130-SC3-69


title: hs20151130-SC3-9


title: hs20151130-SC3-67


title: hs20151130-SC3-64


title: hs20151130-SC3-62


title: hs20151130-SC3-63


title: hs20151130-SC3-61


title: hs20151130-SC3-6


title: hs20151130-SC3-59


title: hs20151130-SC3-55

value: cRPC


title: hs20151130-SC3-53


title: hs20151130-SC3-56


title: hs20151130-SC3-52


title: hs20151130-SC3-54


title: hs20151130-SC3-5


title: hs20151130-SC3-71


title: hs20151130-SC3-49


title: hs20151130-SC3-58


title: hs20151130-SC3-43


title: hs20151130-SC3-44


title: hs20151130-SC3-42


title: hs20151130-SC3-48


title: hs20151130-SC3-4


title: hs20151130-SC3-40


title: hs20151130-SC3-66


title: hs20151130-SC3-39


title: hs20151130-SC3-38


title: hs20151130-SC3-36


title: hs20151130-SC3-34


title: hs20151130-SC3-31


title: hs20151130-SC3-30


title: hs20151130-SC3-25


title: hs20151130-SC3-3


title: hs20151130-SC3-24


title: hs20151130-SC3-45


title: hs20151130-SC3-46


title: hs20151130-SC3-2


title: hs20151130-SC3-22


title: hs20151130-SC3-41


title: hs20151130-SC3-19


title: hs20151130-SC3-13


title: hs20151130-SC3-18


title: hs20151130-SC3-16


title: hs20151130-SC3-17


title: hs20151130-SC3-12


title: hs20151130-SC3-37


title: hs20151130-SC2-96


title: hs20151130-SC2-94


title: hs20151130-SC2-95


title: hs20151130-SC2-85


title: hs20151130-SC2-83


title: hs20151130-SC3-1


title: hs20151130-SC2-82


title: hs20151130-SC2-80


title: hs20151130-SC2-79


title: hs20151130-SC2-78


title: hs20151130-SC3-32


title: hs20151130-SC3-23


title: hs20151130-SC2-89


title: hs20151130-SC2-76


title: hs20151130-SC2-77


title: hs20151130-SC3-14


title: hs20151130-SC2-72


title: hs20151130-SC2-69


title: hs20151130-SC2-75


title: hs20151130-SC2-71


title: hs20151130-SC2-70


title: hs20151130-SC2-93


title: hs20151130-SC2-68


title: hs20151130-SC2-63


title: hs20151130-SC2-66


title: hs20151130-SC2-65


title: hs20151130-SC2-60


title: hs20151130-SC2-59


title: hs20151130-SC2-61


title: hs20151130-SC2-62

value: LR


title: hs20151130-SC2-81


title: hs20151130-SC2-57


title: hs20151130-SC2-56


title: hs20151130-SC2-53


title: hs20151130-SC2-52


title: hs20151130-SC2-54


title: hs20151130-SC2-45


title: hs20151130-SC2-51


title: hs20151130-SC2-50


title: hs20151130-SC2-43


title: hs20151130-SC2-49


title: hs20151130-SC2-39


title: hs20151130-SC2-41


title: hs20151130-SC2-47


title: hs20151130-SC2-58


title: hs20151130-SC2-67


title: hs20151130-SC2-36


title: hs20151130-SC2-35


title: hs20151130-SC2-29


title: hs20151130-SC2-33


title: hs20151130-SC2-32


title: hs20151130-SC2-24


title: hs20151130-SC2-17


title: hs20151130-SC1-95


title: hs20151130-SC2-12


title: hs20151130-SC2-15


title: hs20151130-SC2-26


title: hs20151130-SC1-93


title: hs20151130-SC1-77


title: hs20151130-SC1-67


title: hs20151130-SC1-58


title: hs20151130-SC1-65


title: hs20151130-SC1-94


title: hs20151130-SC1-29


title: hs20151130-SC1-41


title: hs20151130-SC1-26


title: hs20151130-SC2-74


title: MDS_E_38

value: Serum

value: MDS


title: MDS_E_37


title: MDS_E_36


title: MDS_E_34


title: hs20151130-SC1-53


title: MDS_E_33


title: MDS_E_31


title: MDS_E_32


title: MDS_E_27


title: MDS_E_29


title: MDS_E_26


title: hs20151130-SC1-75


title: hs20151130-SC1-87


title: MDS_E_30


title: MDS_E_24


title: MDS_E_28


title: hs20151130-SC1-28


title: MDS_E_25


title: MDS_E_21


title: MDS_E_20


title: WB_pChRO_SL1_1910

city: Ithaca

first: Hojoong

last: Kwak

state: NY

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Library strategy: pChRO-seq
Fastq data is pre-processed to extract unique molecular identifier (UMI) sequence from the first 8mer using UNIX text tools (bash scripts, awk).
Sequence reads were aligned to the human genome using STAR aligner.
Aligned SAM files are processed to collapse duplicate reads with the same UMIs using UNIX text tools (bash scripts, awk, sort)
De-duplicated reads were processed into bedgraph files using Bedtools for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files of strand specific read counts

source_name: Whole blood chromatin

extract_protocol:
For chromatin preparation, 1 ml of frozen blood sample is thawed and lysed in 10 ml of the NUN buffer (0.3M NaCl, 1M Urea, 1% NP-40, 20mM HEPES, pH 7.5, 7.5mM MgCl2, 0.2mM EDTA, 1x protease inhibitor cocktail, 1 mM DTT, 4 u/ml RNase inhibitor) with gentle mixing. Blood chromatin is pelleted by centrifugation at 15,000 g for 20 min, 4°C, and resuspended in Wash buffer (50 mM Tris pH 7.5). After brief centrifugation, the pellet is washed once more in Buffer D (50 mM Tris-HCl, pH 8.0, 25% glycerol, 5 mM Mg Acetate, 0.1 mM EDTA, 5 mM DTT), then homogenized using short sonication cycles in 50 μl of Buffer D. For peripheral leukocyte isolation, 5-10 ml of peripheral whole blood is sampled from brachial veins. A final concentration of 1.5 mM EDTA is added to the whole blood to prevent clotting. To isolate PBMC and PMNL from the peripheral blood, 3 ml of Poly Cell Separation Media, 4 ml of Human Cell Separation Media, and 5 ml of blood are carefully layered consecutively with minimal mixing. Separation occurs with a centrifugation of 450-500 g for 30-35 minutes at 18-22°C. 3 interface layers should be visible. The top interface is PBMC and the middle interface including the layer right below is PMN. 5ml of each PBMC and PMN layers are collected in 1.7 ml microcentrifuge tubes. PBMC and PMN are pelleted by centrifugation at 4,000 for 4 min, 4°C, and washed in PBS. Centrifugation and wash is repeated once more. After brief centrifugation, the pellet is washed in Buffer D (50 mM Tris-HCl, pH 8.0, 25% glycerol, 5 mM Mg Acetate, 0.1 mM EDTA, 5 mM DTT), then resuspended in 50 μl of Buffer D.
Chromatin or cells were incubated in the nuclear run-on reaction condition (5 mM Tris-HCl pH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5% Sarkosyl, 0.4 units / μl of RNase inhibitor) with biotin-NTPs and rNTPs supplied (18.75 μM rATP, 18.75 μM rGTP, 1.875 μM biotin-11-CTP, 1.875 μM biotin-11-UTP for uPRO; 18.75 μM rATP, 18.75 μM rGTP, 18.75 μM rUTP, 0.75 μM CTP, 7.5 μM biotin-11-CTP for pChRO) for 5 min at 37°C. Run-On RNA was extracted using TRIzol, and fragmented under 0.2 N NaOH for 15 min on ice. Fragmented RNA was neutralized, and buffer exchanged by passing through P-30 columns (Biorad). 3′ RNA adaptor (/5Phos/NNNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT/) is ligated at 5 μM concentration for 1 hours at room temperature using T4 RNA ligase (NEB), followed by 2 consecutive streptavidin bead bindings and extractions. Extracted RNA is converted to cDNA using template switch reverse transcription with 1 μM RP1-short RT primer (GTTCAGAGTTCTACAGTCCGA), 3.75 μM RTP-Template Switch Oligo (GCCTTGGCACCCGAGAATTCCArGrGrG), 1x Template Switch Enzyme and Buffer (NEB) at 42°C for 30 min. After a SPRI bead clean-up, the cDNA is PCR amplified up to 20 cycles using primers compatible with Illumina Small RNA sequencing.
smallRNA-seq

value: Peripheral blood leukocytes

tag: fraction

value: nascent RNA


title: WB_pChRO_HK3_1910

tag: cell type


title: WB_pChRO_HK4_1910


title: MDS_E_22


title: WB_pChRO_HK2_1910


title: MDS_E_35


title: WB_pChRO_EK6_2003


title: WB_pChRO_EK55_2003


title: WB_pChRO_HK1_1910


title: WB_pChRO_EK54_2003


title: WB_pChRO_EK53_2003


title: hs20151130-SC2-27


title: WB_pChRO_EK52_2003


title: WB_pChRO_EK45_2003


title: WB_pChRO_EK46_2003


title: MDS_E_23


title: WB_pChRO_EK36_2003


title: hs20151130-SC2-37


title: LCL PRO GM19239

data_processing:
Library strategy: PRO-seq
Fastq data is pre-processed to extract unique molecular identifier (UMI) sequence from the first 8mer using UNIX text tools (bash scripts, awk).
Sequence reads were aligned to the human genome using STAR aligner.
Aligned SAM files are processed to collapse duplicate reads with the same UMIs using UNIX text tools (bash scripts, awk, sort)
De-duplicated reads were processed into bedgraph files using Bedtools for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files of strand specific read counts

value: Lymphoblastoid cells

tag: cell line


title: LCL PRO GM19238 rep


title: MDM_uPRO_C_2010

data_processing:
Library strategy: uPRO-seq
Fastq data is pre-processed to extract unique molecular identifier (UMI) sequence from the first 8mer using UNIX text tools (bash scripts, awk).
Sequence reads were aligned to the human genome using STAR aligner.
Aligned SAM files are processed to collapse duplicate reads with the same UMIs using UNIX text tools (bash scripts, awk, sort)
De-duplicated reads were processed into bedgraph files using Bedtools for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files of strand specific read counts

source_name: Monocyte derived macrophage

value: Macrophages


title: MDM_uPRO_A_2010


title: PBMC_uPRO_1911

source_name: PBMC

value: Peripheral blood monoculear cells


title: LCL PRO GM19222 rep


title: PMNL_uPRO_1911

source_name: PMNL

value: Polymorphonuclear leukocytes


title: LCL PRO GM19222


title: MDM_uPRO_B_2010


title: LCL PRO GM19238


title: LCL PRO GM18520


title: LCL PRO GM18522


title: LCL PRO GM19193


title: LCL PRO GM19131


title: LCL PRO GM19099 rep


title: LCL PRO GM18522 rep


title: WB_pChRO_EK33_2003


title: LCL PRO GM18517 rep


title: LCL PRO GM18520 rep


title: LCL PRO GM18505


title: LCL PRO GM18517


title: HAP1 uPRO

value: Chronic meyloid leukemia derived haploid cells


title: HeLa uPRO RepS

source_name: HeLa

value: Cervical cancer cells

value: HeLa


title: HeLa PRO


title: HeLa uPRO repA


title: LCL PRO GM19239 rep


title: bcdummy10

city: Abbasia

first: Yahia

middle: Ahmad

last: Yahia

state: Cairo

address: Faculty of Medicine Ain Shams University

country: Egypt

institute: Faculty of Medicine Ain Shams Research Institute (MASRI)

data_processing:
RNA counts were retrieved from the sequencer using RNASeqAnalysis (version 5.2.0.5) plugin
Assembly: RNA counts were obtained from the sequencer using RNASeqAnalysis (version 5.2.0.5) plugin

source_name: WHOLE BLOOD

extract_protocol: Library preparation was made using the Ion Total RNA-Seq Kit v2 (ThermoFisher, Waltham, MA, United States). The libraries were sequenced on the Ion Chef using Ion PI™ Hi-Q™ Chef Kit and Ion Proton using Ion PI™ Chip.

value: WHOLE BLOOD

tag: disease

value: Acute Coronary Syndrome


title: bcdummy9


title: HAP1 PRO


title: bcdummy11

value: healthy


title: bcdummy8


title: bcdummy5


title: bcdummy7


title: LCL PRO GM19193 rep


title: bcdummy6


title: bcdummy4


title: bcdummy1


title: bcdummy3


title: p2080 no doxycyline + gamma interferon, replicate 2

city: Murfreesboro

first: Rebecca

middle: L

last: Seipelt-Thiemann

state: TN

address: 1301 E Main St Box 60

department: Biology

institute: Middle Tennessee State University

data_processing:
quality check using fastQC (version 0.11.5)
STAR alignment (version 2.5.3a) using mouse ENSEMBL genome 38 and genome annotation 39.9
FeatureCount, multi-join, EdgeR to generate feature count table and MDS plot
cuffDiff (version 2.2.1) to generate differentially expressed genes among sample groups
Assembly: 38
Supplementary files format and content: text file of cuffdiff output including genes/comparisons/foldchange

source_name: macrophage-like cell line RAW 264.7

growth_protocol: RAW264.7 macrophage-like cells were obtained from ATCC (Manassas, VA) and were cultured in DMEM supplemented with 10% FBS, 25 mM HEPES, 1% penicillin and streptomycin, and 50 μg/mL gentamicin (all from Sigma Aldrich). Lenti-X 293T packaging cells were obtained from Takara-Clontech and were cultured in DMEM supplemented with 10% tetracycline-free FBS (Takara-Clontech), 200 mM L-glutamine, 1 mM sodium pyruvate, and 100 units/mL penicillin and streptomycin. All cell lines were maintained at 37 ºC in a humidified 5% CO2 atmosphere.

extract_protocol:
Macrophages were homogenized in lysis reagent (RLT buffer, Qiagen, Germantown, MD) using a 20-gauge needle and remaining intact Cn were removed by centrifugation at 750 x g for 5 min at 4 °C. RNA was extracted from the lysates using an RNeasy® Mini Kit (Qiagen), according to the manufacturer’s instructions. Genomic DNA was then removed from the total RNA using a Message Clean kit (GenHunter, Nashville, TN) per the manufacturer’s instructions. Clean RNA was resuspended in 10 µL diethyl pyrocarbonate (DEPC)-treated water and RNA integrity and quality was appraised using a Qubit 2 fluorometer (ThermoFisher Scientific).
The cDNA libraries for RNA sequencing were prepared from 1 µg of isolated RNA using the NEBNext UltraTM Directional RNA Library Prep Kit for Illumina, the NEBNext Multiplex Oligos for Illumina Index Primers, and the NEBNext Poly(A) Magnetic Isolation Module (all from New England BioLabs, Ipswich, MA) in accordance with the manufacturer’s instructions.

treatment_protocol: For all western blotting, qRT-PCR, and RNA sequencing experiments, cells were seeded in 6-well plates (Thermo Fisher Scientific) at a density of 1.5×105 cells/well in 2 mL of medium and grown to ~80% confluency prior to treatment with the indicated reagents. Unless specified otherwise, recombinant murine IFNγ (Biolegend, San Diego, CA) was used at a final concentration of 200 U/mL, doxycycline at 100 ng/mL. For treatments lasting longer than 24 hours, the medium, cytokines, and compounds were replaced at 24-hour intervals. The pINDUCER20-mCITED1 lentiviral construct was produced by amplifying the full-length murine CITED1 coding sequence from pCDNA3-FlagmCITED1 (a kind gift from Dr. Mark P. de Caestecker (VUMC)) and recombining it into the pENTR Gateway donor vector (Addgene, USA) using an In-Fusion ligase-independent cloning kit (Takara-Clontech). The mCITED1 sequence was then subcloned into the pINDUCER20 lentiviral vector (a kind gift from the Weissmiller lab, MTSU; originally sourced from the Elledge Lab; (88)) using an LR Clonase® II reaction (Life Technologies).  The fidelity of all plasmid constructs was verified using by  Sanger sequencing (Eurofins Genomics) prior to use in experiments.

tag: inducible cited1 present

value: yes

tag: inducer present

value: no

tag: stimulated with gamma interferon


title: p2080 no doxycyline + gamma interferon, replicate 3


title: p2080 + doxycyline + gamma interferon, replicate 2


title: p2080 + doxycyline, replicate 1


title: p2080 no doxycyline + gamma interferon, replicate 1


title: p2080 + doxycyline + gamma interferon, replicate 3


title: p2080 no doxycyline, replicate 3


title: p2080 + doxycyline, replicate 2


title: bcdummy2


title: p2080 no doxycyline, replicate 2


title: p2080 no doxycyline, replicate 1


title: RAW cells + doxycyline, replicate 3


title: RAW cells + doxycyline, replicate 2


title: Scramble_3

data_processing:
quality check using fastQC (version 0.11.5)
STAR alignment (version 2.5.3a) using mouse ENSEMBL genome 38 and genome annotation 39.9
FeatureCount, multi-join, EdgeR to generate feature count table and MDS plot
cuffDiff (version 2.2.1) to generate differentially expressed genes among sample groups
Assembly: mouse ENSEMBL genome 38
Supplementary files format and content: text file of cuffdiff output including genes/comparisons/foldchange

treatment_protocol: For all western blotting, qRT-PCR, and RNA sequencing experiments, cells were seeded in 6-well plates (Thermo Fisher Scientific) at a density of 1.5×105 cells/well in 2 mL of medium and grown to ~80% confluency prior to treatment with the indicated reagents. Unless specified otherwise, recombinant murine IFNγ (Biolegend, San Diego, CA) was used at a final concentration of 200 U/mL, doxycycline at 100 ng/mL. For treatments lasting longer than 24 hours, the medium, cytokines, and compounds were replaced at 24-hour intervals. Lentiviral constructs 460 encoding the Cas9 enzyme and a gRNA were obtained from VectorBuilder, USA. The sequences (5’ to 3’) of gRNAs targeting murine genes were as follows: Cited1 TACCCCGGGGTCACCGCAAA, Stat1 GTTGGGCGGTCCCCCGATGC, and non-targeting “scramble” gRNA GTGTAGTTCGACCATTCGTG. Lentiviral transductions – Lentiviral constructs were packaged by transfection in to Lenti-X 293T cells using a Lenti-X™ Packaging Single Shots kit. Viral supernatants were concentrated and tested for the presence of viral particles using Lenti-X GoStix. The concentrated lentiviral supernatants were used to transduce RAW264.7 cells by spinoculation in the presence of polybrene. Transduced cells were selected by growth in 500 μg/mL G418, and then clonal lineswere produced by dilution plating. Loss of gene expression was confirmed using a combinationof western blotting and RT-PCR. All Lenti-X products were obtained from Takara-Clontech.

value: macrophage-like cell line

tag: genotype

value: wild-type

tag: treatment

value: scramble guide RNA


title: Scramble_2


title: CITED1 KO Clone 9_2

value: CITED1 guide RNA (clone 9)


title: CITED1 KO Clone 9_1


title: CITED1 KO Clone 9_3


title: Scramble_1


title: RAW cells no doxycyline, replicate 3


title: RAW cells + doxycyline, replicate 1


title: RAW cells no doxycyline, replicate 2


title: RAW cells no doxycyline, replicate 1


title: 4T1_MKL1_OE_replicate_2

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

description:
RNA with polyA+ selection
MKL1-5_145_048_S34

data_processing:
After quality control, the clean reads were mapped to human genome (hg38) or mouse genome (mm10) using STAT.
Genes expression level were quantitated with featureCounts.
Differentially expressed genes (DEGs) were identified with DESeq2. An absolute log2 fold change >1 and the adjusted p-value (FDR) significance score <0.05 were used as thresholds to identify DEGs.
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

growth_protocol: We performed bulk RNA-seq of control, MKL1 overexpressed (OE)  and caMKL1 OE in LM2 and 4T1 cell lines . We also performed bulk RNA-seq of control, low and high expression of LifeAct in LM2 cell line.

extract_protocol:
Total RNA with polyA+ selection or rRNA depletion was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.
RNA-seq was performed at Illumina Hiseq 2500 platform that included quality control, library preparation, fragmentation and PCR enrichment of target RNA according to standardized procedures.
150 bp paired-end raw reads were initially processed to obtain clean reads by removing adaptor sequences, low quality sequences, empty reads.

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.

value: breast cancer

value: WT

value: WT MKL1 OE


title: 4T1_caMKL1_OE_replicate_3

description:
RNA with polyA+ selection
caMKL1-6_097_096_S38

value: caMKL1 OE


title: 4T1_caMKL1_OE_replicate_2

description:
RNA with polyA+ selection
caMKL1-5_109_084_S37


title: 4T1_MKL1_OE_replicate_3

description:
RNA with polyA+ selection
MKL1-6_133_060_S35


title: p2080 + doxycyline, replicate 3


title: 4T1_caMKL1_OE_replicate_1

description:
RNA with polyA+ selection
caMKL1-4_121_072_S36


title: 4T1_MKL1_OE_replicate_1

description:
RNA with polyA+ selection
MKL1-4_157_036_S33


title: 4T1_control_replicate_3

description:
RNA with polyA+ selection
Ctrl-6_169_024_S32

value: control


title: 4T1_control_replicate_2

description:
RNA with polyA+ selection
Ctrl-5_181_012_S31


title: WT_iPSCs_replicate_2

data_processing:
After quality control, the clean reads were mapped to mouse genome (mm10) using STAT.
Genes expression level were quantitated with TEtranscripts.
Differentially expressed genes (DEGs) were identified with DESeq2. An absolute log2 fold change >1 and the adjusted p-value (FDR) significance score <0.05 were used as thresholds to identify DEGs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: iPSCs

growth_protocol: Mouse iPSCs with SRFΔ/Δ (KO) and SRFf/f (WT) were generated and cultured in serum containing medium follow our previous work (Hu et al., 2019).

extract_protocol:
Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of SRF KO and three replicates of WT.
RNA-seq was performed at Illumina Hiseq 2500 platform that included quality control, library preparation, fragmentation and PCR enrichment of target RNA according to standardized procedures.
150 bp paired-end raw reads were initially processed to obtain clean reads by removing adaptor sequences, low quality sequences, empty reads.

value: iPSCs

value: WT iPSCs


title: WT_iPSCs_replicate_3

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of SRF KO and three replicates of WT.


title: SRF_KO_iPSCs_replicate_3

value: SRF KO iPSCs


title: 4T1_control_replicate_1

description:
RNA with polyA+ selection
Ctrl-4_098_095_S30


title: WT_iPSCs_replicate_1


title: Mitral valves - FhetCko_2

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were trimmed to remove adapter and low quality sequences using Trim Galore and Cutadapt, then aligned to the reference mouse genome version GRCm38/mm10 with the program STAR.
Aligned reads were stripped of duplicate reads with the program sambamba.
Read counting was done with the program featureCounts from the Rsubread package. Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab separated file with raw read counts for all samples
Supplementary files format and content: tab separated file with TPM for all samples

source_name: Mitral valves

extract_protocol:
The mitral valve from each mouse was dissected under the microsope in RNAlaterTM stabilization solution (Thermo Fisher Scientific; AM7021) and quickly frozen in liquid nitrogen. The mitral valve was subsequently processed individually and RNA extracted using a RNeasy Micro Kit (Qiagen; 74004).
The RNA that passed quality control by the Agilent 2100 Bioanalyzer was amplified using Ovation RNA-Seq System v2 and DNA libraries were then generated using the Nextera XT DNA Library Preparation Kit. Subsequently, the samples were subjected to paired-end sequencing on an Illumina HiSeq 2500 system to a depth of 35-40 million mapped reads.

tag: strain

value: Mitral valves

value: Fbn1 C1039G/+; CCR2 RFP/RFP

tag: age

value: 2 months


title: Mitral valves - FhetChet_2

value: Fbn1 C1039G/+; CCR2 RFP/+


title: Mitral valves - FhetCko_3


title: Mitral valves - FhetCko_1


title: SRF_KO_iPSCs_replicate_2


title: Mitral valves - FhetChet_4


title: Mitral valves - FhetChet_1


title: SRF_KO_iPSCs_replicate_1


title: p2080 + doxycyline + gamma interferon, replicate 1

value: yes


title: Mitral valves - Cko_4

value: CCR2 RFP/RFP


title: Mitral valves - Cko_3


title: Mitral valves - Cko_2


title: 32_Adult

city: Rockville

first: Julian

last: Lui

state: MD

address: 605 WATTS BRANCH PKWY, 10 Center Drive

institute: NICHD

data_processing:
RNA-Seq reads were trimmed with cutadapt (-AAGATCGGAAGAGCACACGTCTGAACTCCAGTCA  -AAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -overlap 6 -q 20 -minimum-length 25) and aligned using STAR (2 pass alignment) to mouse mm10 reference genome sequences.
Assembly: mm10

source_name: Adult

extract_protocol:
PNday10-old mice were killed (n=10 per exposure group) and the lungs excised. A 3mm×3mm tip of the left lung were snap frozen in liquid nitrogen and kept at -80°C. RNA extraction on the lung tissue was carried out utilizing magnetic beads technology, on a chemagic Prepito® (Perkin Elmer, Waltham, Massachussets), as recommended by the manufacturers. Concentration and purity were measured with a NanoDrop1000 spectrophotometer, with all samples showing an A260/280 ratio between 1.9 and 2.1. RNA integrity was analyzed using a 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 Pico Kit (Agilent Technologies) as recommended by manufacturer. All samples used for RNAseq displayed RNA integrity number (RIN) above 7.
Sequencing libraries were prepared using a TruSeq Stranded mRNA Prep Kit (Illumina), without the polyA selection step. Sequencing was performed via a paired end 75 cycle on Illumina HiSeq 2500.

treatment_protocol: Pregnant BALB/c germ-free mice were kept in separate germ-free isolators until either (a) no exposure (GF), (b) exposure to either Bifidobacterium animalis ssp. Lactis (BI04) or to (c) full cecum content harvested from female SPF mice (Cecum). Subsequently, perinatally exposed offspring were used for the analyses. Lung tissue transcriptomics analysis was done at postnatal day 10 (PNday10) at first phase of lung alveolar development. RNA were extracted for bulk RNA-sequencing.

value: lung

value: adult

tag: time


title: Mitral valves - Chet_2

value: CCR2 RFP/+


title: Mitral valves - Chet_1


title: Mitral valves - Chet_4


title: Mitral valves - FhetChet_3


title: 31_Male PN10 C

source_name: Male PN10 C

value: innoculated caecium

tag: Sex

value: male

value: 10day old


title: 28_Male PN10 BI04

source_name: Male PN10 BI04

value: WT

value: innoculated Bifidobacterium


title: 27_Male PN10 BI04


title: 25_Male PN10 GF

source_name: Male PN10 GF

value: untreated


title: 26_Adult


title: 20_Male PN10 C


title: 19_Male PN10 C


title: Mitral valves - FhetCko_4


title: 24_Female PN10 GF

source_name: Female PN10 GF

value: female


title: 22_Adult


title: 17_Male PN10 BI04


title: 21_Male PN10 C


title: 15_Male PN10 BI04


title: Mitral valves - Cko_1


title: 11_Adult


title: 14_Female PN10 GF


title: 23_Female PN10 GF


title: 16_Female PN10 BI04

source_name: Female PN10 BI04


title: Mitral valves - Chet_3


title: 9_Female PN10 C

source_name: Female PN10 C


title: 8_Female PN10 C


title: 30_Male PN10 C


title: 13_Female PN10 GF


title: 12_Female PN10 GF


title: 29_Adult


title: 3_Male PN10 GF


title: 10_Male PN10 C


title: 18_Female PN10 C


title: 6_Male PN10 BI04


title: 5_Female PN10 BI04


title: 2_Female PN10 GF


title: 4_Female PN10 BI04


title: Control_3

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the GRCm39 refSeq refFlat GTF file.
Genes with P-value < 0.05 and foldChange >1.2 were defined as differentially expressed genes (DEGs).
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Testis

extract_protocol:
The total RNA of mouse testis in each group was isolated using RNAiso Plus (TakaRa, 9108) and stored at -80℃. The concentration and purity of RNA were determined using a NanoPhotometer (ThermoFisher Scientific Intertek, Cat. 3100668).
RNA purification, cDNA synthesis and RNA-Seq of each group (n = 3) were performed by Oebiotech company (Shanghai, China). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 was subjected to the following analysis. The cDNA libraries were constructed through TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).Shanghai

value: ICR

value: Testis

value: 8 week

value: PBS injection


title: KO_HA3

city: Guangzhou

first: Haiqiong

last: Liu

state: Guangdong

address: Gongye Avenue 253

institute: Zhujiang Hospoital, Southern Medical University

data_processing:
data filering use fastp 0.21.0
data QC(fastqc and multiqc)
data aligment:bowtie2-2.3.5.1
Genetic quantitative : RSEM v1.3.1
diff gene Expression :DESeq2
Genome_build: ref genome:Mus_musculus gencode.vM27
Supplementary_files_format_and_content: geneExpression matrix,include all geneExpression of each sample

source_name: neonatal mouse heart cell

growth_protocol: Neonatal hearts were isolated from 1-3-day-old new-born C57BL/6J mice(WT and ATF3-KO) as previously described and cultured in DMEM (Gibco; Thermo Fisher Scientific, Inc.) with 100 U/ml penicillin–streptomycin and 10% fetal bovine serum (FBS; Gibco; Thermo Fisher Scientific, Inc.) at 37℃ with 5% CO2 for follow-up experiments.

extract_protocol:
Cells were removed, flash frozen on dry ice, and 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 libraies were prepared for sequencing using standard illumina protocols

treatment_protocol: Control: with no treatment; H/R: PBS was used to replace the former medium, and cells were cultured in a triple gas incubator with 95% N2 and 5% CO2 at 37 ℃ for 3 h under hypoxia. Reoxygenation was then initiated by medium change to replace PBS, and cells were placed back into incubated in a normal incubator at 37℃.Before H/R, cells were transfectied with Adv-GFP(KO_HG) or ATF3(KO_HA).

value: Heart

value: KO cells transfected with Ad-ATF3 for H/R model


title: AZ82_1

value: 1uM AZ82 injection


title: AZ82_3


title: CW069_1

value: 50uM CW069 injection


title: Control_1


title: CW069_2


title: CW069_3


title: KO_HA2


title: AZ82_2


title: 7_Female PN10 BI04

value: lung


title: KO_HR3

value: KO cells for H/R model


title: KO_HR1


title: KO_CT2

value: ATF3-KO control


title: KO_CT3


title: WT_CT3

value: wild type control


title: WT_CT2


title: KO_HA1


title: WT_CT1


title: WT_HR3

value: wt cells for H/R model