title: Endoderm_RNA_seq_rep2

city: Guangzhou

first: Pang

last: Junjie

address: 132 Waihuan East Road, Beigang Village, Xiaoguwei Street, Panyu District, Guangzhou, Guangdong

institute: Sun Yat-sen University

data_processing:
For differential analysis, clean reads of each sample that mapped onto human genome (hg38) with clean ratios above 95.06% were obtained using Tophat (version 1.3.2) and Cufflinks (V1.1.0).
The HTSeq (version 0.6.0) was used to quantify mapped counts of human genes. Sequencing read counts were calculated using StringTie (v1.3.0).
The expression levels of different samples were normalized by the Trimmed Mean of M values (TMM) and converted into FPKM.
The edgeR package of R was used to analyze differential gene expression between samples. Significantly different genes were defined as those with ratios of FPKM greater than 1.5 and p-values less than 0.05.
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values for each Biological Sample

growth_protocol: Primed hESC cell lines were a gift from Dr. Jichang Wang at Sun Yat-sen University and cultured in mTeSR medium (STEMCELL Technologies) on Matrigel (BD Biosciences)-coated plates under 20% O2 and 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using the TRIzol reagent (TAKARA, 9109) and reversely transcribed using ABI StepOnePlus real-time PCR system.
The Agilent 2100 Bioanaylzer and ABI StepOnePlus real-time PCR system were used to analyze sample libraries, which were sequenced using the Illumina HiSeq2500 system in a mode of 150-bp paired-end read.

treatment_protocol: 10 mM crotonate for 12 days

value: derived from H9 embryonic stem cell

value: WT


title: Endoderm_RNA_seq_rep1

status: Public on Oct 03 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: H9_Cr_RNA_seq_rep1

value: embryonic stem cell

value: 10 mM crotonate for 12 days


title: H9_Cr_RNA_seq_rep2


title: hEPS_RNA_seq_rep2


title: H9_primed_RNA_seq_rep2


title: hEPS_Cr_RNA_seq_rep2


title: hEPS_RNA_seq_rep1


title: H9_primed_RNA_seq_rep1


title: hEPS_Cr_RNA_seq_rep1


title: Sample 1A_Rep1

status: Public on Oct 04 2022

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

country: USA

institute: University Of Miami

description: PAR-CLIP

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned using Bowtie 2
Read counts and variants were identified by using Naïve Variants Caller
Read counts and variants were counted by using Variants Annotator
Assembly: NC_000913.3
Supplementary files format and content: Base reads by genome coordinate

organism: Escherichia coli

source_name: FLAG-tagged Hfq strain

growth_protocol: Wild-type and mutant cells were grown at 37C in rich defined medium containing 4-thiouridine and harvested in mid log phase

extract_protocol:
Cells were lysed by sonication and cell extracts were incubated with anti-FLAG beads. After purification, proteins were gel-fractionated and transferred to nitrocellulose. RNA was released by using proteinase K treatment.
Libraries were constructed from the RNAs by using the NEBNext Small RNA prep kit (New England Biolabs).

value: MG1655 rph+

value: Bacteria

value: Growth at 37C with 4-thiouridine


title: PSPPH_0069-ChIP-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0069-CHIP-1_combined

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: narrowPeak files were generated from ChIP-seq, containing significant peaks. xlsx files were generated from RNA-seq, containing the differential expressional genes.

molecule: genomic DNA

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: liquid culture in KB (King's B)  medium

growth_protocol: ChIP-(KB with Rif and Spec) ; RNA-seq(KB or MM with Rif)

extract_protocol:
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
The ChIP assay was performed as previously described.For the FLAG-tagged plasmids, the open reading frame of each regulator coding gene was amplified by PCR from Psph1448A genome and cloned into pHM1 plasmid. Wild-type Psph1448A containing empty pHM1 or pHM1-RR-FLAG was cultured in 20 ml KB medium until mid-log phase (OD600 = 0.6). Cultured bacteria were then reated with 1% formaldehyde for 10 min at 28 ℃. Cross-linking was stopped by the addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl), re-suspended in 500 μl IP buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail (Roche), and then subjected to sonication to produce 100-300 bp DNA fragments. Insoluble cellular debris was removed by centrifugation at 4 ℃ and the supernatant was used as the input sample in IP experiments. Both control and IP samples were washed with protein A beads (General Electric) and then incubated with 50 μl agarose- conjugated anti-FLAG antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted. DNA fragments (150-250 bp) were selected for library construction and sequencing libraries were prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments. ChIP-seq reads were mapped to the Pseudomonas syringae pv. phaseolicola 1448A genome (NC_005773.3) using Bowtie2 (version 2.3.4.3). Uniquely mapped reads were retained for the subsequent analyses. Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0). Reproducible binding sites in both replicates were identified by BEDtools software (version 2.27.1)and used for the following analysis. Subsequently, the enriched loci for each regulator were annotated using the R package ChIPpeakAnno (version 3.18.2) . Target genes were annotated by peaks located in gene promoters defined as upstream of transcription start site (TSS), overlapping with TSS or encompassing the whole gene.
To examine the effect of histidine kinases on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures or 2 ml cultures of mid-log-phase induced in MM with 6 hours (Psph1448A and transcriptional regulator mutant strains) were collected by centrifugation (12,000 rpm, 4 ℃). A RNeasy mini kit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all RNA-seq experiments. For each RNA-seq sample, raw reads were mapped to the Pseudomonas sringae pv. phaseolicola 1448A genome (NC_005773.3) using STAR (version 2.6.1), and uniquely mapped reads were kept for further analyses. Differentially expressed genes were identified using DESeq2 (BH-adjusted P < 0.05 and log2 Fold Change| > 0.5).

treatment_protocol:
grow until mid-log phase in KB
grow until mid-log phase

tag: strain/genotype

tag: condition

value: virulence suppressing (King’s B medium, KB) condition

tag: chip antibody

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: SH-SY5Y WT 3

city: London

first: Paul

last: Chapple

address: Charterhouse Square

department: Faculty of Medicine & Dentistry

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Eurofins Genomics Europe performed primary data analysis using refernce genome hg19 / GRC37, UCSC.
RNA-Seq reads are aligned to the reference genome or reference transcriptome using Bowtie generating genome / transcriptome alignments.  RNA-Seq reads are aligned to the reference genome or reference transcriptome using Bowtie generating  genome / transcriptome alignments.
TopHat identifies the potential exon-exon splice junctions of the initial alignment. Then Cuffinks identifies and quantifies the transcripts from the pre-processed RNA-Seq alignment-assembly.
After this, Cuffmerge merges the identified transcript pieces to full length transcripts and annotates the transcripts based on the given annotations.
Finally, merged transcripts from two or more samples / conditions are compared using Cuffdiff to determine the differential expression levels at transcript and gene level including a measure of significance between samples / conditions.
Assembly: hg19

growth_protocol: SH-SY5Y cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kits following manufacturer's protocol. RNA was quantified using a Nanodrop spectophotometer and assessed for quality by measuring the 28S/18S ratio by agarose gel electrophoresis.
Library construction was performed by Eurofins Genomics under their NGSelect RNA on Illumina. The library construction involved purification of poly-A containing mRNA molecules, mRNA fragmentation, random pried cDNA synthesis, adaptor ligation and adapter specific PCR amplification.

treatment_protocol: Neuro differentiation - cells were grown to near confluence under normal maintenance conditions prior to the start of differentiation. 1X105 cells/well were seeded in a 6 well plate. After 24 hours media was changed to DMEM containing 2% Fetal Bovine Serum (FBS: Gibco, #A3840001) and10 µM of all-trans retinoic acid (ATRA: Sigma, #R2625). At day 4 cells were passaged and resuspended in neurobasal media (Gibco, #21103049) supplemented with B27 (Gibco, #17504044) 50 ng/ml Brain-Derived Neurotrophic Factor (BDNF: Sigma, #B3795), and 10 µM RA. At day 12 media was supplemented with 2 mM dibutyryl cyclic AMP (dc-AMP: Santa Cruz, sc-201567A). Media was changed every other day with fresh aliquots of RA, BDNF and dcAMP. Cells were harvested at day 15.

value: Neuroblastoma

value: neuronal differentiation


title: SH-SY5Y KO 2


title: SH-SY5Y KO 1


title: SH-SY5Y WT 1


title: SH-SY5Y WT 2


title: ETP Inf 4

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

data_processing:
Fastq files resulting from RNA-Seq were quality controlled using FastQC (version 0.11.7) and MultiQC (version 1.0.dev0)
Samples were aligned to the Ensembl human reference genome using STAR aligner (version 2.5.4b)
HTSeq (version 0.8.0) was used to generate read count files
Genome_build: Ensembl GRCh38 v91
Supplementary_files_format_and_content: Processed files are tab-delimited counts produced by HT-Seq’s “count” function.

molecule: polyA RNA

source_name: Monocyte-derived macrophages

growth_protocol: Blood samples were obtained from donors, and PBMCs were isolated with Lymphoprep. PBMCs were plated into 24-well plates at 2 x 10^6 cells/mL in serum-free RPMI media plus 2mM L-Glutamine and 1mM sodium pyruvate and incubated at 37°C, 5% CO2 for 1 hr. After this, media was replaced with RPMI containing 10% heat-inactivated FBS, 2mM L-glutamine, 1mM sodium pyruvate (cRPMI), and 10ng/mL M-CSF. The resulting monocytes were matured for 7 days in this media, changing media on days 3 and 5.

extract_protocol:
Cells were immediately treated with 300µL RNAProtect (Qiagen), collected into sterile RNAse-free tubes, and pelleted by centrifugation at 400 x g for 5 minutes using a MicroCL 21R microcentrifuge. Cells were lysed using 350µL of lysis buffer from an RNAeasy Plus Mini kit (Qiagen), with added β-mercaptoethanol, and lysate was stored at -80°C
RNA was isolated from MDM lysates stored at -80°C using an RNAeasy Plus Mini kit (Qiagen) with DNAse treatment (RNAfree DNAse kit, Qiagen). RNA quality met sequencing standards upon analysis on an RNA 6000 Nano Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). From total RNA, mRNA was isolated using polyA enrichment with d(T) beads (New England Biolabs), and strand-specific cDNA libraries were created using a KAPA RNA HyperPrep kit (Roche cat. no.: 07277253001). Library quality was assessed with an Agilent 2100 Bioanalyzer using a High Sensitivity DNA chip (Agilent). Libraries were sequences on an Illumina HiSeq2500.

treatment_protocol:
MDMs were polarized on day 7 by removing the media, washing in PBS, and replacing with cRPMI containing the indicated Polarization compound (50ng/mL IFNγ for M1, 50ng/mL IL-4 for M2, or 10ng/mL LPS for MEP), or no stimuli for control samples. LPS used was extracted from Pseudomonas aeruginosa PAO1 strain H103.
Polarized MDMs were washed with PBS, and media was replaced with cRPMI. Salmonella that had been cultured overnight under static conditions were diluted and added with a calculated multiplicity of infection (MOI) of 20:1, based on OD600 values. For the uninfected condition, an equal volume of cRPMI media was instead added to wells. Following Salmonella addition, plates were swirled and centrifuged at 1,500 rpm for 5 min to distribute and sediment bacteria. Plates were returned to the incubator for 30 min to allow association of the bacteria with MDMs. The medium was then removed and replaced with cRPMI + 50µg/mL gentamicin, and intracellular infection was allowed to proceed for 4 hours in the incubator before collecting samples for RNA-Seq.

tag: polarization

value: LPS

tag: donor


title: Ler PI rep2

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR_2.7.0b with parameters --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate
Count reads  were calculated using with featureCounts v1.6.0 with parameters  -t exon -g gene_id -T 20 -O -s 0  -M
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Samples are listed in sequential order. i.e,. rep1, rep2, rep3

organism: Arabidopsis thaliana

source_name: Pistil

growth_protocol: Arabidopsis plants were grown on rockwool blocks watered with 1.3g/l hyponex in a growth chamber at 21C and long days (16h/8h)

extract_protocol:
The RNA was extracted with a CTAB/LiCL protocol. The samples contained each about 20 pistils/siliques or 20 dissected inflorescence meristems. RNA was extracted using CTAB/LiCL.
RNA libraries were prepared for sequencing using standard Illumina protocols. The total RNA was enriched for mRNA and processed into cDNA libraries using the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). After quality control (Qubit and Fragment Analyzer), samples were sequenced using Illumina NovaSeq 2x150 nt Paired End sequencing.

treatment_protocol: No treatment

tag: tissue

value: Pistil/silique stages 12-16 (Smyth et al., 1990)

value: wild type

tag: ecotype

value: Ler


title: M0 Inf 4

value: ctrl


title: M1 Inf 4

value: IFNy


title: SH-SY5Y KO 3


title: M0 Un 4

value: untreated


title: M2 Un 4


title: M1 Un 4


title: ETP Inf 3


title: M1 Inf 3


title: M2 Inf 3


title: M0 Inf 3


title: ETP Un 3


title: M2 Un 3


title: M1 Un 3


title: M2 Inf 2


title: M0 Un 3


title: M1 Inf 2


title: M0 Inf 2


title: ETP Inf 2


title: ETP Un 2


title: M1 Un 1


title: M1 Inf 1


title: M2 Un 2


title: M2 Inf 4


title: M1 Un 2


title: M0 Un 2


title: M0 Un 1


title: 508N

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Adaptor sequences and poor quality bases were removed using Trim Galore (v0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters. bwa-meth (v0.10) was used to align reads to hg19 using default parameters. PCR duplicates were removed using Picard (v1.91, http://broadinstitute.github.io/picard). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using the ‘tabulate’ module of bwa-meth and BisSNP (v0.82.2) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file containing counts of C (methylated) and T (unmethylated) and coverage at each CpG site assayed

source_name: Normal prostate tissue adjacent to tumour

extract_protocol:
For each patient, five 1 mm tumour tissue cores from within the histologically verified tumour region (or tumour adjacent region) were taken for genomic DNA extraction. DNA was extracted using the AllPrep FFPE DNA/RNA Kit (Qiagen, Cat. No. 80234), quantified with the Qubit dsDNA HS Assay Kit (Life Technologies, USA), and stored at -80 °C until use.
For library preparation of patient specimens extracted DNA were bisulphite treated using the EZ DNA Methylation-Lightning Kit (Zymo Research, USA, Cat. No. D5030 & D5033) according to the manufacturer’s instructions. DNA methylation profiling was performed using WGBS). WGBS libraries were prepared using the EpiGnome Methyl-Seq kit (Epicentre, EGMK81312), according to the manufacturer’s protocol. Library quality was assessed with the Agilent 2100 Bioanalyzer using the High-sensitivity DNA kit (Agilent, CA, USA). DNA was quantified using the KAPA Library Quantification kit by quantitative PCR (KAPA 6 Biosystems). Libraries from patient specimens were analysed with 70 bp paired end sequencing on the Illumina HiSeq 2500 platform using TruSeq® Rapid SBS Kit – HS (50 cycle) and TruSeq® Rapid PE Cluster Kit – HS. 6 samples were multiplexed across 2 lanes. Sequencing was performed multiple times to gain sufficient coverage.

value: prostate

tag: Sex

value: Male

tag: tissue type

value: Adjacent normal

tag: patient outcome


title: M2 Un 1


title: ETP Un 4


title: 564N


title: 1601N


title: 5237C

source_name: Prostate tumour tissue

value: Tumour

value: non-lethal


title: 448N


title: 34C


title: 506C


title: 202C


title: 361C


title: 174C


title: 1579C


title: 120C


title: 564C

value: lethal


title: 514C


title: 46C


title: 379C


title: 349C


title: 1601C


title: 139C


title: Med16/Taf13-AID, +DMSO, rep-1

city: Bloomington

first: Moustafa

last: Saleh

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

description: newly synthesized RNA

data_processing:
Alignment with STAR v2.6.1a
Quantification of reads per gene with STAR --quant mode
Differential expression analysis was performed with DESeq2. Size factors were determined by estimateSizeFactors on the count matrix of S.pombe reads for all of the samples. These size factors were then used for the S. cerevisiae libraries using "sizeFactors="
Assembly: sacCer3
Supplementary files format and content: raw counts per gene

organism: Saccharomyces cerevisiae

growth_protocol: Grown at 30C in YPD

extract_protocol:
nsRNA-seq was done as prevously described in Saleh et al, 2021 [PMID: 34383744]. Briefly, Cells were labelled with 4tU for 6 minutes. Total RNA was extracted using the Masterpure Yeast RNA extraction kit (Lucigen MPY03100) as per the manufacturer’s protocol. Total RNA was biotinylated using MTSEA-biotin for 30 mins in the dark at room temperature. Then, the biotinylated RNA was purified using Dynabeads MyOne Streptavidin C1 (ThermoFisher) and then purified using Qiagen RNeasy MinElute Cleanup Kit (#74204). rRNA was depleted from the purified nascent RNA fraction using Terminator™ 5′-Phosphate-Dependent Exonuclease (Lucigen TER51020) as per the manufacturer’s protocol. rRNA-depleted nascent RNA was purified and concentrated using RNAClean XP clean beads (1.8:1 beads:sample ratio).
TruSeq Stranded Total RNA kit for Illumina

treatment_protocol: 3-IAA-treated samples were treated with 3-IAA in DMSO at a final concentration of 0.5mM for 30 minutes. DMSO-treated samples were treated with DMSO (1:2000 by culture volume) for 30 minutes.

tag: auxin-inducible degron (aid) tag

value: Med16-3V5-IAA7, Taf13-3xHA-IAA7

tag: background


title: Med16/Taf13-AID, +DMSO, rep-3

description: newly synthesized RNA


title: Med16/Taf13-AID, +IAA, rep-2

description: newly synthesized RNA


title: Med16/Taf13-AID, +IAA, rep-3

description: newly synthesized RNA


title: Med16/Taf13-AID, +DMSO, rep-2

description: newly synthesized RNA


title: Med16/Taf13-AID, +IAA, rep-1

description: newly synthesized RNA


title: Med16/Spt20-AID, +DMSO, rep-1

description: newly synthesized RNA

value: Med16-3V5-IAA7, Spt20-3xHA-IAA7


title: Med16/Spt20-AID, +DMSO, rep-3

description: newly synthesized RNA


title: Med16/Spt20-AID, +DMSO, rep-2

description: newly synthesized RNA


title: Spt20-AID, +IAA, rep-2

description: newly synthesized RNA


title: Spt20-AID, +IAA, rep-3

description: newly synthesized RNA


title: Spt20-AID, +DMSO, rep-1

description: newly synthesized RNA


title: Med16/Spt20-AID, +IAA, rep-2

description: newly synthesized RNA


title: Spt20-AID, +DMSO, rep-3

description: newly synthesized RNA


title: Spt20-AID, +DMSO, rep-2

description: newly synthesized RNA


title: Spt20-AID, +IAA, rep-1

description: newly synthesized RNA


title: Spt3-ChEC in Spt20-AID, +IAA, rep-1

data_processing:
Alignment with Bowtie2 (default settings plus "--no-unal --dovetail –no-discordant --no-mixed")
HOMER makeTagDirectory
HOMER makeUCSCfile ("-bigWig -norm 1e6")
Assembly: sacCer3
Supplementary files format and content: bigWig

growth_protocol: Cells were grown at 30℃ in YPD to an OD600 of 0.7-1.0

extract_protocol:
ChEC performed as described in Tourigny et al. 2018, PMID: 30275344
NEB Next Ultra II DNA Library Prep Kit for Illumina
ChEC-seq

treatment_protocol: For the AID strains, 3-IAA treated samples were treated with 3-IAA in DMSO at a final concentration of 0.5mM for 30 minutes. DMSO-treated samples were treated with DMSO (1:2000 by culture volume) for 30 minutes

tag: chec tag


title: Med16/Spt20-AID, +IAA, rep-3

description: newly synthesized RNA


title: Med16/Spt20-AID, +IAA, rep-1

description: newly synthesized RNA


title: Taf1-ChEC in Med16-AID, +IAA, rep-2


title: Taf1-ChEC in Med16-AID, +IAA, rep-1


title: Spt3-ChEC in Spt20-AID, +IAA, rep-2


title: Taf1-ChEC in Med16-AID, +DMSO, rep-2


title: D3_2DomLib_2_CARseq

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH

library_source: transcriptomic single cell

data_processing:
Allignment to CAR library and 10X barcode identification using Biostrings R package
.csv file containing Pooled CAR library identity

source_name: TCR negative T cells

growth_protocol: Primary human T cells were isolated from PMCS derived from healthy donors and activated with anti-CD3/CD28 Dynabeads in X-VIVO15 medium supplemented with IL-2 (200 IU/mL). After 3 days, Dynabeads were magnetically removed and cells were engineered to incorporate a single CAR gene into the TRAC locus using CRISPR-Cas9 genome editing. CAR+/TCR- (and CAR-/TCR-) cells were sorted 5-7 days later and rested for 3 additional days.

extract_protocol:
Single cell gene expression library preparation was done following the the Chromium Next GEM Single Cell 3' Reagent Kits v3 User Guide (CG000183 Rev C; 10x Genomics). Resulting cDNA was used to do a target amplification of the CAR cDNA barcoded transcripts. Such transcripts were then sequenced using PacBio Sequel II
T cells were extracted from the co-culture using Fluorescence Activated Cell Sorting (FACS).

treatment_protocol: With the exception of the unstimulated control sample, cells were co-cultured for 36h with SKBR3 cells.

tag: car

value: Pooled CAR library

value: TCR negative T cells

value: Donor 3

value: 36h co-culture with SKBR3

tag: genome build

value: Synthetic (CAR library)


title: D3_2DomLib_WT_CARseq

value: Pooled CAR library + 28z and BBz

tag: cell type

tag: genotype


title: V. cholerae Δtgt + ciprofloxacin_replicate 2 [tgtcip2_S59]

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

country: France

institute: Institut Pasteur

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: number of reads and differencial expression values

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: bacterial culture

growth_protocol: growth in liquid MH supplemented or not up to OD 0,3

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: no treatment or supplemented with tobramycin 0.4 µg/ml or ciprofloxacin 0.0005 µg/ml

tag: growth phase

value: exponential phase OD 0.3

tag: treatment

value: ciprofloxacin 0.0005 µg/ml


title: V. cholerae Δtgt + ciprofloxacin_replicate 3 [tgtcip3_S60]


title: V. cholerae Δtgt + ciprofloxacin_replicate 1 [tgtcip1_S58]


title: Taf13-ChEC in Med16-AID, +IAA, rep-2


title: Taf1-ChEC in Med16-AID, +DMSO, rep-1


title: V. cholerae Δtgt + tobramycin_replicate 2 [tgttob2_S50]

value: tobramycin 0.4 µg/ml


title: V. cholerae Δtgt + tobramycin_replicate 3 [tgttob3_S51]


title: Taf13-ChEC in Med16-AID, +IAA, rep-1


title: V. cholerae Δtgt_replicate 3 [tgtMH3_S42]

value: untreated


title: Taf13-ChEC in Med16-AID, +DMSO, rep-2


title: Spt3-ChEC in Spt20-AID, +DMSO, rep-2


title: V. cholerae Δtgt_replicate 1 [tgtMH1_S40]


title: V. cholerae WT + ciprofloxacin_replicate 3 [J085cip3_S54]


title: V. cholerae Δtgt + tobramycin_replicate 1 [tgttob1_S49]


title: Spt8 in WT, rep-1


title: Taf13-ChEC in Med16-AID, +DMSO, rep-1


title: D3_2DomLib_1_CARseq


title: V. cholerae WT + ciprofloxacin_replicate 2 [J085cip2_S53]


title: Spt3-ChEC in Spt20-AID, +DMSO, rep-1


title: V. cholerae WT + ciprofloxacin_replicate 1 [J085cip1_S52]


title: Spt8 in  med16-deletion, rep-1


title: Spt3 in WT, rep-3


title: Spt3 in WT, rep-2


title: V. cholerae WT + tob_replicate 2 [J085tob2_S44]


title: Spt3 in WT, rep-1


title: V. cholerae WT + tob_replicate 1 [J085tob1_S43]


title: Spt3 in  med16-deletion, rep-3


title: V. cholerae WT_replicate 3 [J085MH3_S36]


title: Spt3 in  med16-deletion, rep-1


title: V. cholerae WT_replicate 1 [J085MH1_S34]


title: V. cholerae WT_replicate 2 [J085MH2_S35]


title: 6D_48H_High Dose [A9-44]

city: Cincinnati

first: Gregory

middle: Peter

last: Toth

state: OH

address: 26 W ML King Jr. Dr.

department: CCTE

institute: USEPA/ORD

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads in the RNA-Seq fastq(.gz) file for each sample were mapped to indexed transcripts from each of the 47,578 gene models (which include isoforms) from the newly updated FHM genome (WIOS00000000; BioSample SAMN12875914
Differential expression analysis was performed using the R limma package (version 3.40.6. Between sample normalization was conducted using the trimmed mean of M-values method implemented by the calcNormFactors function from the R edgeR package (version 3.26.8). Precision weights were calculated using the voom function from the limma package. The limma lmFit function was used to fit a generalized linear model with a term for chemical treatment effects. Moderated t-statistics were calculated for chemical treatment effects using the limma eBayes function, and the limma topTable function was used to sort features (i.e. genes) based on their nominal p-values.
Count data were filtered for features which had at least 3 samples with at least 10 counts
Genome_build: EPA_FHM_2.0.b
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Pimephales promelas

source_name: 6d post-fertilization larva

extract_protocol:
Larvae were removed from exposure vessels, placed into Eppendorf tubes together with a steel bead and frozen in liquid nitrogen.  MagMax lysing/binding buffer (100 μl) was added to each tube.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: 48h post-hatch fathead minnow larvae were statically exposed to 0, 0.12, 1.2, 2.5, 5 or 10 ng ethinyl estradiol /l for 48 hours

tag: age

tag: duration

tag: dose

value: H


title: Spt8 in WT, rep-2


title: Spt3 in  med16-deletion, rep-2


title: V. cholerae Δtgt_replicate 2 [tgtMH2_S41]


title: 6D_48H_High Dose [A9-41]


title: Spt8 in  med16-deletion, rep-2


title: 6D_48H_High Dose [A9-43]


title: Skeletal muscle Sample 3 pre exercise

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  (Cell Ranger 3.1.0).
Assembly: GRCh38-3.0.0
Supplementary files format and content: (Filtered) matrix.mtx.gz - matrix is stored in Market Exchange Format (MEX) where each element is the number of UMIs associated with a feature (row) and barcode (column)
Supplementary files format and content: (Filtered) feature.tsv.gz - tab separated file. Features correspond to row indices with given ID, name and type
Supplementary files format and content: (Filtered) barcode.tsv.gz - tab separated file. Barcode sequence correspond to column indices where each sequence includes suffix with a dash separator followed by a number

source_name: Vastus lateralis

extract_protocol:
Vastus lateralis biopsy was performed via percutaneous needle, following removal of adipose and connective tissue. Muscle biopsy was minced in DMEM-F12 GlutaMAX basal medium. In order to remove myofibre debris cell suspension was passed through pluriStainers (pluri Select), for removal of cell debris Debris Removal Soultion (Miltenyi Biotech) was used, and Red Blood Cell Lysis solution (Miltenyi Biotech) was used for removal of red blood cells. Samples were stored on ice prior single-cell RNA seq.
In accordance with 10X standard procedure, a single-cell RNA library was generated using the GemCode Single-Cell Instrument (10x Genomics) and Single Cell 3’ Library & Gel Bead Kit and Chip Kit (10x Genomics). The sequencing ready library was purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin Elmer) and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824).

value: Mononuclear cells

tag: tissue

value: Vastus lateralis

value: 3x30-s all-out sprint exercise on a mechanically braked cycle ergometer

tag: condition

value: Pre exercise

value: Male


title: Skeletal muscle Sample 3 post exercise

description: 10x Genomics

value: Post exercise

tag: Sex


title: Skeletal muscle Sample 3 pre exercise (deep-seq)

description: 10x Genomics


title: 6D_48H_High Dose [A9-40]


title: Skeletal muscle Sample 2 post exercise

description: 10x Genomics


title: Skeletal muscle Sample 3 post exercise (deep-seq)

description: 10x Genomics


title: V. cholerae WT + tob_replicate 3 [J085tob3_S45]


title: 6D_48H_High Dose [A9-38]


title: 6D_48H_High Dose [A9-37]


title: 6D_48H_High Dose [A9-35]


title: Skeletal muscle Sample 1 post exercise

description: 10x Genomics

value: Female


title: 6D_48H_High Dose [A9-32]


title: 6D_48H_High Dose [A9-34]


title: Skeletal muscle Sample 1 pre exercise

description: 10x Genomics


title: 6D_48H_Low Dose [A9-29]

value: L


title: 6D_48H_High Dose [A9-31]


title: Smooth muscle cell - D99_Quiescent

city: Charlottesville

first: Mete

last: Civelek

state: VA

address: 21 Hospital Drive, Old Medical School Room 3836

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
ATAC-seq Read 2 reads were trimmed 30 bp using FastX-Toolkit
Reads were mapped to the hg38 version of the human reference genomce using Bowtie2 -x hg38 and converted to .sam file
Only uniquely mapped reads with MAPQ > 10 were kept and coverted to .BAM file (samtools)
BAM files were merged for each treatment group using Samtools merge
MACS2 -f BAMPE -g hs -p 0.001 -q 0.1 was used to call peaks
Assembly: grch38
Supplementary files format and content: narrowPeaks files containing called peaks

source_name: Smooth Muscle Cell

growth_protocol: SMCs were grown till 80% confluence

extract_protocol:
ATAC-seq Kit (APEXBIO) and ZYMO DNA Clean and Concentrator-5 Kit
Index Kit 1 for Illumina (APEXBIO)

treatment_protocol: proliferative SMCs were grown in the presence of 5% FBS while quiescent SMCs were cultered without FBS for 24 hours

value: ascending aorta

value: Quiescent


title: Smooth muscle cell - D80_Proliferative

value: Proliferative


title: 6D_48H_Low Dose [A9-28]


title: 6D_48H_Low Dose [A9-26]


title: Smooth muscle cell - D80_Quiescent


title: Smooth muscle cell - D77_Proliferative


title: 6D_48H_Low Dose [A9-25]


title: Smooth muscle cell - D77_Quiescent


title: 6D_48H_Low Dose [A9-23]


title: 6D_48H_Low Dose [A9-22]


title: Smooth muscle cell - D76_Proliferative


title: Skeletal muscle Sample 2 pre exercise

description: 10x Genomics


title: Smooth muscle cell - D76_Quiescent


title: Smooth muscle cell - D73_Quiescent


title: Smooth muscle cell - D73_Proliferative


title: 6D_48H_Low Dose [A9-19]


title: 6D_48H_Low Dose [A9-20]


title: 6D_48H_Low Dose [A9-16]


title: 6D_48H_Control [A9-13]

value: C


title: 6D_48H_Low Dose [A9-17]


title: 6D_48H_Control [A9-14]


title: Smooth muscle cell - D99_Proliferative


title: Null + Mock(Nm) AC1050227

city: Johnston

first: Shawn

last: Thatcher

state: Iowa

address: South Drive

institute: Corteva Agriscience

description:
Null + Mock(Nm)
Counts from running Salmon

data_processing:
Illumina NovaSeq 6000
Low-quality reads and adapter sequences were trimmed using custom scripts
High-quality reads were quantified against Maize B73 v4 transcriptome using Salmon
DESeq2 was used for differential expression analysis
Assembly: Maize B73 v4 transcriptome
Supplementary files format and content: Counts from running Salmon

organism: Zea mays

source_name: plant

extract_protocol: RNA-seq was done on Illumina NovaSeq 6000

value: plant

value: Null maize + inoculated with mock inoculum

tag: time

value: 168 hours after inoculation


title: 6D_48H_Control [A9-11]


title: Transgenic + Mock(Tm) AC1050231

description:
Transgenic + Mock(Tm)
Counts from running Salmon

value: Transgenic Ht1 + inoculated with mock inoculum


title: Null + Mock(Nm) AC1050228


title: Transgenic + Mock(Tm) AC1050229


title: Transgenic + Mock(Tm) AC1050230


title: Null + Mock(Nm) AC1050226


title: 6D_48H_Control [A9-10]


title: 6D_48H_Control [A9-8]


title: 6D_48H_Control [A9-7]


title: 6D_48H_Control [A9-5]


title: Transgenic + Inoculated(Ti) AC1050214

description:
Transgenic + Inoculated(Ti)
Counts from running Salmon

value: Transgenic Ht1 + inoculated with NLB inoculum


title: Transgenic + Inoculated(Ti) AC1050215


title: 6D_48H_Control [A9-2]


title: 6D_48H_Control [A9-4]


title: 6D_48H_Control [A9-1]


title: Null + Inoculated(Ni) AC1050212

description:
Null + Inoculated(Ni)
Counts from running Salmon

value: Inoculated with NLB inoculum


title: Null + Inoculated(Ni) AC1050213


title: Transgenic + Mock(Tm) AC1050200

value: 72 hours after inoculation


title: 6D_24H_High Dose [A8-43]

value: H


title: Null + Inoculated(Ni) AC1050211

value: Null maize +Inoculated with NLB inoculum


title: 6D_24H_High Dose [A8-40]


title: Null + Mock(Nm) AC1050198


title: Transgenic + Mock(Tm) AC1050199


title: Null + Mock(Nm) AC1050197


title: 6D_24H_High Dose [A8-38]


title: 6D_24H_High Dose [A8-37]


title: Transgenic + Inoculated(Ti) AC1050216


title: Transgenic + Inoculated(Ti) AC1050186


title: Transgenic + Inoculated(Ti) AC1050185


title: 6D_24H_High Dose [A8-35]


title: 6D_24H_High Dose [A8-34]


title: 6D_24H_High Dose [A8-32]


title: 6D_24H_High Dose [A8-31]


title: 6D_24H_High Dose [A8-44]


title: 6D_24H_Low Dose [A8-28]


title: Null + Inoculated(Ni) AC1050181


title: 6D_24H_Low Dose [A8-26]


title: 6D_24H_High Dose [A8-41]


title: Transgenic + Mock(Tm) AC1050201


title: Transgenic + Mock(Tm) AC1050171

value: 48 hours after inoculation


title: 6D_24H_Low Dose [A8-23]


title: Null + Inoculated(Ni) AC1050182


title: 6D_24H_Low Dose [A8-22]


title: Transgenic + Mock(Tm) AC1050169


title: 6D_24H_Low Dose [A8-25]


title: Null + Mock(Nm) AC1050168


title: Null + Mock(Nm) AC1050167


title: Null + Mock(Nm) AC1050166


title: 6D_24H_Low Dose [A8-17]


title: Null + Mock(Nm) AC1050196


title: 6D_24H_Low Dose [A8-19]


title: 6D_24H_Low Dose [A8-20]


title: Transgenic + Inoculated(Ti) AC1050184


title: 6D_24H_Low Dose [A8-16]


title: Transgenic + Inoculated(Ti) AC1050156


title: 6D_24H_Control [A8-14]


title: Transgenic + Inoculated(Ti) AC1050155


title: Null + Inoculated(Ni) AC1050183


title: Transgenic + Inoculated(Ti) AC1050154


title: 6D_24H_Control [A8-13]


title: 6D_24H_Low Dose [A8-29]


title: 6D_24H_Control [A8-11]


title: Transgenic + Mock(Tm) AC1050170


title: Null + Inoculated(Ni) AC1050152


title: Null + Inoculated(Ni) AC1050151


title: Transgenic + Mock(Tm) AC1050141

value: 24 hours after inoculation


title: 6D_24H_Control [A8-10]


title: Transgenic + Mock(Tm) AC1050140


title: 6D_24H_Control [A8-7]


title: 6D_24H_Control [A8-8]


title: 6D_24H_Control [A8-5]


title: Transgenic + Mock(Tm) AC1050139


title: 6D_24H_Control [A8-4]


title: Null + Mock(Nm) AC1050138


title: 6D_24H_Control [A8-1]


title: 6D_24H_Control [A8-2]


title: Null + Mock(Nm) AC1050137


title: Transgenic + Inoculated(Ti) AC1050125


title: Null + Inoculated(Ni) AC1050153


title: Transgenic + Inoculated(Ti) AC1050126


title: 6D_6H_High Dose [A7-44]


title: Transgenic + Inoculated(Ti) AC1050124


title: Null + Inoculated(Ni) AC1050123


title: 6D_6H_High Dose [A7-40]


title: 6D_6H_High Dose [A7-41]


title: Null + Mock(Nm) AC1050136


title: 6D_6H_High Dose [A7-38]


title: Null + Inoculated(Ni) AC1050122


title: 6D_6H_High Dose [A7-37]


title: 6D_6H_High Dose [A7-34]


title: 6D_6H_High Dose [A7-35]


title: Null + Inoculated(Ni) AC1050121


title: Transgenic + Mock(Tm) AC1050111

value: 12 hours after inoculation


title: Transgenic + Mock(Tm) AC1050110


title: 6D_6H_High Dose [A7-31]


title: Transgenic + Mock(Tm) AC1050109


title: 6D_6H_High Dose [A7-32]


title: 6D_6H_Low Dose [A7-29]

value: L


title: Null + Mock(Nm) AC1050108


title: Null + Mock(Nm) AC1050107


title: Transgenic + Inoculated(Ti) AC1050096


title: 6D_6H_High Dose [A7-43]


title: 6D_6H_Low Dose [A7-28]


title: 6D_6H_Low Dose [A7-26]


title: Transgenic + Inoculated(Ti) AC1050095


title: 6D_6H_Low Dose [A7-25]


title: Transgenic + Inoculated(Ti) AC1050094


title: Null + Inoculated(Ni) AC1050093


title: Null + Inoculated(Ni) AC1050092


title: 6D_6H_Low Dose [A7-19]


title: 6D_6H_Low Dose [A7-23]


title: 6D_6H_Low Dose [A7-22]


title: 6D_6H_Low Dose [A7-20]


title: 6D_6H_Low Dose [A7-16]


title: Transgenic + Mock(Tm) AC1050081

value: 6 hours after inoculation


title: Transgenic + Mock(Tm) AC1050079


title: 6D_6H_Control [A7-13]


title: Null + Mock(Nm) AC1050078


title: 6D_6H_Control [A7-11]


title: 6D_6H_Control [A7-10]


title: Null + Mock(Nm) AC1050077


title: Null + Mock(Nm) AC1050076


title: Null + Mock(Nm) AC1050106


title: 6D_6H_Control [A7-8]


title: 6D_6H_Control [A7-7]


title: Transgenic + Inoculated(Ti) AC1050065


title: 6D_6H_Control [A7-5]


title: Transgenic + Inoculated(Ti) AC1050064


title: Null + Inoculated(Ni) AC1050063


title: 6D_6H_Control [A7-4]


title: Null + Inoculated(Ni) AC1050062


title: Null + Inoculated(Ni) AC1050091


title: 6D_6H_Low Dose [A7-17]


title: 6D_6H_Control [A7-2]


title: Null + Inoculated(Ni) AC1050061


title: Transgenic + Mock(Tm) AC1050051

value: 3 hours after inoculation


title: Transgenic + Mock(Tm) AC1050049


title: Transgenic + Mock(Tm) AC1050050


title: Transgenic + Mock(Tm) AC1050080


title: 5D_48H_High Dose [A6-43]

source_name: 5d post-fertilization larva


title: 5D_48H_High Dose [A6-44]


title: 6D_6H_Control [A7-14]


title: 5D_48H_High Dose [A6-41]


title: 5D_48H_High Dose [A6-40]


title: Null + Mock(Nm) AC1050047


title: 5D_48H_High Dose [A6-38]


title: 6D_6H_Control [A7-1]


title: 5D_48H_High Dose [A6-37]


title: Null + Mock(Nm) AC1050046


title: Null + Mock(Nm) AC1050048


title: 5D_48H_High Dose [A6-35]


title: 5D_48H_High Dose [A6-34]


title: Transgenic + Inoculated(Ti) AC1050035


title: 5D_48H_High Dose [A6-32]


title: 5D_48H_High Dose [A6-31]


title: Null + Inoculated(Ni) AC1050032


title: Null + Inoculated(Ni) AC1050033


title: 5D_48H_Low Dose [A6-29]


title: Null + Inoculated(Ni) AC1050031


title: 5D_48H_Low Dose [A6-28]


title: Transgenic + Mock(Tm) AC1050021

value: 0.5 hours after inoculation


title: 5D_48H_Low Dose [A6-26]


title: Transgenic + Mock(Tm) AC1050019


title: 5D_48H_Low Dose [A6-23]


title: Transgenic + Mock(Tm) AC1050020


title: Null + Mock(Nm) AC1050018


title: Null + Mock(Nm) AC1050017


title: 5D_48H_Low Dose [A6-22]


title: 5D_48H_Low Dose [A6-20]


title: Null + Mock(Nm) AC1050016


title: 5D_48H_Low Dose [A6-17]


title: Transgenic + Inoculated(Ti) AC1050036


title: Transgenic + Inoculated(Ti) AC1050006


title: 5D_48H_Low Dose [A6-19]


title: Transgenic + Inoculated(Ti) AC1050034


title: Transgenic + Inoculated(Ti) AC1050005


title: 5D_48H_Low Dose [A6-16]


title: 5D_48H_Control [A6-14]

value: C


title: 5D_48H_Control [A6-13]


title: 5D_48H_Control [A6-11]


title: Null + Inoculated(Ni) AC1050003

value: plant


title: Transgenic + Inoculated(Ti) AC1050004


title: Null + Inoculated(Ni) AC1050002


title: Null + Inoculated(Ni) AC1050001


title: 5D_48H_Control [A6-10]


title: 5D_48H_Control [A6-7]


title: 5D_48H_Low Dose [A6-25]


title: 5D_48H_Control [A6-8]


title: 5D_48H_Control [A6-4]


title: 5D_48H_Control [A6-2]


title: D2_2DomLib_WT_CARseq

value: Pooled CAR library + 28z

value: TCR negative T cells

value: Donor 2

value: 36h co-culture with SKBR3

value: Synthetic (CAR library)


title: 5D_24H_High Dose [A5-44]


title: 5D_48H_Control [A6-1]


title: 4T1 cells, LINC01133 #1

city: Boston

first: Antoine

middle: Elias

last: Karnoub

state: MA

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0)
Sequence reads were trimmed and mapped to mm10 using CLC Genomics Workbench using standard parameters
CLC Genomics Workbench was also used for read count extraction and data normalization
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Expression Table LINC01133 versus WT.txt is tab-delimited text file that contains gene annotations (Uniprot, Ensembl), expression values in logFC (fold change of LINC01133 over WT Control), logCPM, P-value, and FDR corrected p-value. p-values<1E-16 are represented as 0.000.

organism: Mus musculus

growth_protocol: 4T1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in a humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina RNA TruSeq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: malignant cells

value: LINC01133 overexpression


title: 4T1 cells, LINC01133 #3


title: 4T1 cells, LINC01133 #2


title: D1_2DomLib_CARseq

value: Pooled CAR library

value: Donor 1


title: 4T1 cells, control #2

value: WT


title: D1_2DomLib_WT_CARseq


title: 5D_24H_High Dose [A5-40]

value: H


title: 4T1 cells, control #3


title: 5D_24H_High Dose [A5-43]


title: 5D_24H_High Dose [A5-38]


title: 5D_24H_High Dose [A5-37]


title: 5D_24H_High Dose [A5-41]


title: R5_2

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Quality control was checked using FastQC
high quality reads were mapped on Medicago truncatula (Mtv5) reference transcriptome using quasi-mapping alignment and quantification methods of Salmon algorithm v.1.2 (Patro et al., 2017)
Assembly: Medicago truncatula (Mtv5) from https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/ (file MtrunA17r5.0-ANR-EGN-r1.6.mrna.fasta)
Supplementary files format and content: tab-delimited text files  corresponding to the Count table of all samples (columns) and all transcripts annotated in Mtv5 gff r1.6 (rows) (= count.txt)

organism: Medicago truncatula

source_name: radicle (5mm radicle seed)

growth_protocol: The seed germination was accessed by germinating triplicates of 50 dried seeds on Whatman paper No1 imbibed with 1ml of autoclaved water in 3 cm diameter Petri dishes at 20°C under a 16h/8h photoperiod for eight days. Then, seeds exhibiting a 1 mm (called 1mmD sample) and 5 mm (5mmD sample) radicles were sampled and used to perform a DT assay (Buitink et al., 2003), which consisted in slowly desiccating germinating seeds using a saturated solution of K2CO3 at 20°C for 72 hours.

extract_protocol:
For Medicago early post-germination seeds, samples of radicles and cotyledons were used separately for RNA extractions. Samples were named accordingly: desiccated radicles of 1mm germinating seeds were called R1 and R1P (when subjected to PEG treatment), desiccated radicles of 5 mm germinating seeds were called R5 and R5P (when subjected to PEG treatment). About 100 freshly harvested seeds in two biological replicates were used to extract RNA for each sample. All samples were ground using micropestles and liquid nitrogen and RNA was extracted using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany) with lysis buffer containing 1% of polyvinylpyrrolidone (PVP-40) followed by incubation at room temperature for 10 minutes.
All samples with good qualities (260/280 and 260/230 absorbance ratio >1.8; RNA Integrity Number, RIN>7; 28S/18S>1.7) were sent to Beijing Genomics Institute (https://www.bgi.com) (Hong Kong) for library preparation and sequencing on BGISEQ-500 platform, generating an average of 24M reads of 50bp per sample (20M SE50).

treatment_protocol: For the PEG treatment, 1mm and 5mm radicle seeds were subjected to a mild osmotic stress  (-1.7 MPa) using a polyethylene glycol (PEG8000) solution for 3 days at 10°C dark (called 1mmPD and 5mmPD samples), then were washed and underwent desiccation as previously described .

value: radicle (5mm radicle seed)

tag: developmental stage

value: 5mm germinating seed

tag: cultivar

value: PEG-untreated


title: 5D_24H_High Dose [A5-35]


title: R1_2

source_name: radicle (1mm radicle seed)

value: radicle (1mm radicle seed)

value: 1mm germinating seed


title: R5P_2

value: PEG-treated


title: 5D_24H_High Dose [A5-34]


title: R5_1


title: R5P_1


title: 5D_24H_High Dose [A5-32]


title: 5D_48H_Control [A6-5]

value: C


title: R1_1


title: 5D_24H_High Dose [A5-31]


title: R1P_2


title: 4T1 cells, control #1


title: R1P_1


title: 5D_24H_Low Dose [A5-29]

value: L


title: 5D_24H_Low Dose [A5-28]


title: 5D_24H_Low Dose [A5-25]


title: 5D_24H_Low Dose [A5-26]


title: C5_2

source_name: cotyledons (5mm radicle seed)

value: cotyledons (5mm radicle seed)


title: C5_1


title: C5P_2


title: C1_2

source_name: cotyledons (1mm radicle seed)

value: cotyledons (1mm radicle seed)


title: 5D_24H_Low Dose [A5-23]


title: 5D_24H_Low Dose [A5-20]


title: 5D_24H_Low Dose [A5-22]


title: C1P_2


title: C1_1


title: 5D_24H_Low Dose [A5-17]


title: C5P_1


title: 5D_24H_Low Dose [A5-16]


title: UC_1803_2

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to GRCh38 human genome using the STAR alingment software and HTSeq was used to generate the raw read counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: hUC-MSC

growth_protocol: cells were grown in serum-free and xenofree Mesencult media until 70-80% confluent

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: umbilical cord

value: wharton jelly


title: UC_1803_3


title: C1P_1


title: UC_1802_3


title: 5D_24H_Control [A5-11]


title: 5D_24H_Control [A5-13]


title: 5D_24H_Control [A5-10]


title: UC_1803_1


title: UC_1802_2


title: 5D_24H_Control [A5-8]


title: UC_1802_1


title: UC_1801_3


title: 5D_24H_Control [A5-7]


title: 5D_24H_Control [A5-5]


title: UC_1801_1


title: 5D_24H_Low Dose [A5-19]


title: 5D_24H_Control [A5-2]


title: 5D_24H_Control [A5-4]


title: BM_1902_1

source_name: hBM-MSC

value: adult

value: bone marrow


title: BM_1902_2


title: 5D_24H_Control [A5-14]


title: BM_1902_3


title: BM_1901_2


title: BM_1901_3


title: 5D_24H_Control [A5-1]


title: 5D_6H_High Dose [A4-43]


title: 5D_6H_High Dose [A4-40]


title: BM_1901_1


title: 5D_6H_High Dose [A4-44]


title: 5D_6H_High Dose [A4-37]


title: 5D_6H_High Dose [A4-41]


title: BM_1702_2


title: BM_1702_1


title: 5D_6H_High Dose [A4-38]


title: 5D_6H_High Dose [A4-34]


title: 5D_6H_High Dose [A4-32]


title: AD_1902_2

source_name: hAD-MSC

value: adipose


title: AD_1902_1


title: UC_1801_2


title: 5D_6H_High Dose [A4-31]


title: 5D_6H_Low Dose [A4-29]


title: 5D_6H_Low Dose [A4-28]


title: AD_1804_2


title: 5D_6H_Low Dose [A4-26]


title: BM_1702_3


title: AD_1804_1


title: AD_1802_2


title: AD_1802_3


title: AD_1802_1


title: 5D_6H_Low Dose [A4-23]


title: 5D_6H_Low Dose [A4-25]


title: AD_1902_3


title: 5D_6H_Low Dose [A4-22]


title: 5D_6H_Low Dose [A4-19]


title: 5D_6H_High Dose [A4-35]


title: M1 Activated ex vivo-purified bulk  [NK-110]

city: Iowa City

first: Nitin

last: Karandikar

address: C673 General Hospital

institute: University of Iowa

data_processing:
Single-end 50 bp sequencing was performed on the Illumina HiSeq 2000. Basecalls were converted into FASTQs using the Illumina bcl2fastq and alignment was performed using kallisto  with the GRCh38 human genome build.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files including lengths, counts and transcripts per million (TPM) for mRNA transcripts

source_name: CD4+CD25- CD45RO+ Memory T-cells

growth_protocol: Ex vivo bulk CD4+CD25-CD45RO+ T-cells were thawed in RPMI 1640 (Corning 10-040-CV) with DNase at 10KU/ml (Sigma D4513-1vl) and then resuspended at 1x10e6 cells/ml in X-VIVO 15 serum-free media (Lonza, 04-418Q)

extract_protocol: Samples were submitted to the University of Chicago Genomics facility for RNA extraction, quality assessment and sequencing

treatment_protocol: Cells were incubated 60 minutes in vitro in the presence of media alone (controls), or 10 ng/ml of recombinant human cytokine IL17A (eBioscience, 34-8179-82), IL17F (R&DSystems, 1335-IL-025/CF) or IL17A + IL17F.  Conditions were activated with 1 ug/ml each of fixed anti-CD3 (eBioscience, 16-0037-85) and anti-CD28 (eBioscience, 16-0289-85) and incubated for 48 or 168 hours. Cultured cells were pelletized, snap frozen in liquid nitrogen, and stored at -80 C for shipment to Chicago for RNA extraction and sequencing

value: ILL17A 10 ng/ml +IL17F 10 ng/ml

tag: incubation time


title: M1 Activated ex vivo-purified bulk  [NK-108]

value: IL17A 10 ng/ml


title: 5D_6H_Low Dose [A4-20]


title: 5D_6H_Low Dose [A4-17]


title: M1 Activated ex vivo-purified bulk  [NK-106]


title: M1 Activated ex vivo-purified bulk  [NK-109]

value: IL17F 10 ng/ml


title: M1 Activated ex vivo-purified bulk  [NK-107]

value: No cytokine added control


title: 5D_6H_Control [A4-13]


title: 5D_6H_Low Dose [A4-16]


title: M1 Activated ex vivo-purified bulk  [NK-104]


title: 5D_6H_Control [A4-11]


title: M1 Activated ex vivo-purified bulk  [NK-105]


title: AD_1804_3


title: M1 Activated ex vivo-purified bulk  [NK-103]


title: 5D_6H_Control [A4-10]


title: M1 Activated ex vivo-purified bulk  [NK-48]


title: 5D_6H_Control [A4-8]


title: M1 Activated ex vivo-purified bulk  [NK-47]


title: 5D_6H_Control [A4-7]


title: M1 Activated ex vivo-purified bulk  [NK-46]


title: M1 Activated ex vivo-purified bulk  [NK-45]


title: M1 Activated ex vivo-purified bulk  [NK-44]


title: 5D_6H_Control [A4-4]


title: 5D_6H_Control [A4-2]


title: 4D_48H_High Dose [A3-44]

source_name: 4d post-fertilization larva

value: H


title: 5D_6H_Control [A4-1]


title: 4D_48H_High Dose [A3-43]


title: 5D_6H_Control [A4-14]


title: 4D_48H_High Dose [A3-41]


title: M1 Activated ex vivo-purified bulk  [NK-42]


title: M1 Activated ex vivo-purified bulk  [NK-43]


title: M1 Activated ex vivo-purified bulk  [NK-38]


title: M1 Activated ex vivo-purified bulk  [NK-37]


title: 4D_48H_High Dose [A3-40]


title: M1 Activated ex vivo-purified bulk  [NK-36]


title: M1 Activated ex vivo-purified bulk  [NK-41]


title: 4D_48H_High Dose [A3-38]


title: M1 Activated ex vivo-purified bulk  [NK-35]


title: 4D_48H_High Dose [A3-37]


title: M1 Activated ex vivo-purified bulk  [NK-34]


title: 4D_48H_High Dose [A3-35]


title: M1 Activated ex vivo-purified bulk  [NK-33]


title: 4D_48H_High Dose [A3-34]


title: M1 Activated ex vivo-purified bulk  [NK-32]


title: 5D_6H_Control [A4-5]


title: M1 Activated ex vivo-purified bulk  [NK-31]


title: 4D_48H_High Dose [A3-31]


title: 4D_48H_High Dose [A3-32]


title: 4D_48H_Low Dose [A3-29]


title: MCF-7_DKO_miR-874_#3

first: Masanori

last: Fujimoto

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description: DKO miR-874

data_processing:
Sequencing was performed on the Illumina NextSeq 500 platform using the TruSeq Rapid SBS Kit (Illumina, FC-402-4002) in the 50-base single-end mode.
The HISAT2 was used to align reads to a human reference genome (hg19).
Then, gene expression values were calculated as reads per kilobase of exon unit per million mapped reads using the Cufflinks program.
Assembly: hg19

source_name: DKO miR-874

growth_protocol: MCF-7 cells were obtained from the American Type Tissue Culture Collection (ATCC, Manassas, VA, USA). MCF-7 cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Sigma‒Aldrich, St Louis, MO, USA) supplemented with 10% (v/v) foetal bovine serum (FBS) and penicillin and streptomycin (Sigma‒Aldrich).

extract_protocol:
Total RNA were extracted using the the FastGene RNA Premium kit (Nippon Gene, Tokyo, Japan).
Libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol.

treatment_protocol: described in growth protocol

value: Breast cancer cell line


title: MCF-7_DKO_miR-874_#2

description: DKO miR-874


title: 4D_48H_Low Dose [A3-26]


title: MCF-7_DKO_miR-874_#1

description: DKO miR-874


title: MCF-7_DKO_NC_#3

description: DKO cont miR

source_name: DKO cont miR

value: control miRNA


title: 4D_48H_Low Dose [A3-22]


title: 4D_48H_Low Dose [A3-23]


title: MCF-7_DKO_NC_#2

description: DKO cont miR


title: 4D_48H_Low Dose [A3-28]


title: 4D_48H_Low Dose [A3-25]


title: 4D_48H_Low Dose [A3-19]


title: MCF-7_DKO_NC_#1

description: DKO cont miR


title: MCF-7_p53KO_miR-874_#1

description: p53KO miR-874

source_name: p53KO miR-874


title: MCF-7_p53KO_miR-874_#3

description: p53KO miR-874


title: 4D_48H_Control [A3-14]


title: MCF-7_p53KO_NC_#3

description: p53KO cont miR

source_name: p53KO cont miR


title: MCF-7_p53KO_NC_#1

description: p53KO cont miR


title: 4D_48H_Control [A3-13]


title: MCF-7_WT_miR-874_#3

description: WT miR-874

source_name: WT miR-874

value: wild type


title: 4D_48H_Control [A3-11]

value: C


title: 4D_48H_Control [A3-10]


title: MCF-7_WT_miR-874_#2

description: WT miR-874


title: MCF-7_WT_miR-874_#1

description: WT miR-874


title: 4D_48H_Control [A3-8]


title: MCF-7_WT_NC_#3

description: WT cont miR

source_name: WT cont miR


title: MCF-7_p53KO_miR-874_#2

description: p53KO miR-874


title: 4D_48H_Control [A3-5]


title: 4D_48H_Control [A3-7]


title: 4D_48H_Control [A3-4]


title: 4D_48H_Low Dose [A3-20]

value: L


title: 4D_24H_High Dose [A2-44]


title: 4D_48H_Control [A3-2]


title: 4D_48H_Low Dose [A3-17]


title: 4D_24H_High Dose [A2-43]


title: 4D_48H_Control [A3-1]


title: 4D_48H_Low Dose [A3-16]


title: shAKR1B1#09 Fructose_2

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality control analysis of Fastq files were done using FastQC package.
Reads were then aligned to human reference genome with GRCh38 build (release 102) with the respective Ensembl GTF annotation file using STAR v2.7.7a aligner in a two-pass mode.
Read counts were measured with featureCounts function in Rsubread package using R 3.5.0
Differential gene expression analysis was performed using DESeq2 pipeline.
Assembly: hg38; GRCh38 (release 102)
Supplementary files format and content: tab-delimited text file includes Raw count values from featureCounts for each sample

growth_protocol: A549 NSCLC cancer cells were maintaned in glucose-free DMEM, supplemented with 10% fetal bovine serum (FBS), 5% penicillin/streptomycin and either 5mM glucose or fructose, in a humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using miRNeasy Kit (Qiagen), including a prior DNA digestion step. 1-2 ug of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using TruSeq sample Prep kit V2 (Illumina) as per the manufacturer's protocol.

treatment_protocol:
lentiviral transduction was performed to induce stable shRNA-mediated knockdown of ARK1B1. As controls, non-targeting shRNAs were delivered.
samples were collected 5 days after lentiviral transduction

value: NSCLC cell line

value: AKR1B1 knockdown

value: 5 mM fructose

value: 5days post transduction


title: MCF-7_p53KO_NC_#2

description: p53KO cont miR


title: 4D_24H_High Dose [A2-41]


title: shAKR1B1#09 Fructose_1


title: shCtrl (plko) Fructose_1

value: WT


title: shCtrl (plko) Fructose_2


title: 4D_24H_High Dose [A2-40]


title: 4D_24H_High Dose [A2-38]


title: shAKR1B1#09 Glucose_3

value: 5 mM glucose


title: shAKR1B1#09 Glucose_2


title: shAKR1B1#09 Glucose_1


title: 4D_24H_High Dose [A2-37]


title: 4D_24H_High Dose [A2-35]


title: shCtrl (plko) Glucose_3


title: 4D_24H_High Dose [A2-34]


title: shAKR1B1#09 Fructose_3


title: MCF-7_WT_NC_#2

description: WT cont miR


title: MCF-7_WT_NC_#1

description: WT cont miR


title: shCtrl (plko) Glucose_1


title: 4D_24H_High Dose [A2-32]


title: shCtrl (plko) Fructose_3


title: shCtrl (plko) Glucose_2


title: 4D_24H_High Dose [A2-31]


title: 4D_24H_Low Dose [A2-28]


title: shDNMT3B_1_rep_4

city: Philadelphia

first: T. S.

middle: Karin

last: Eisinger-Mathason

state: PA

address: 421 Curie Blvd, Rooom 414

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
Illumina .bcl files were converted to FASTQ files using the Illumina bcl2fastq command line program. Salmon was used to count raw expression data against the human transcriptome as defined in Gencode v32.
The following 3 samples were excluded from further analyses due to low mapping rates and/or total sequencing reads: shSCR_rep_1, shDNMT3B_2_rep_2, and shDNMT3A_2_rep_3
Transcript-level data normalization and differential expression analysis (sh:DNMT3A vs. sh:SCR; sh:DNMT3B vs. sh:SCR for each individual shRNA) were performed with DESeq2.
Assembly: GRCh38/Gencode 32

source_name: STS-109 undifferentiated pleomorphic sarcoma

growth_protocol: STS-109 cells were cultured in DMEM with 20% FBS, 1% L-glutamine, and 1% P/S. Routine passage was performed when cells reached approximately 50% confluence.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit with on-column DNase (Qiagen) and further purified with the RNA Clean and Concentrator Kit (Zymo Research). Samples were quality-checked using the Agilent RNA 6000 Nano Kit and Agilent 2100 BioAnalyzer (Santa Clara, CA); all samples had RNA integrity values of >8.5.
Poly(A) mRNA enrichment and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNext Ultra II RNA Library Prep Kit (New England BioLabs) with SPRIselect Beads (Beckman Coulter), and NEBNext Multiplex Oligos for Illumina (index primers sets 1 and 2) according to the manufacturer’s instructions. Library sizes were checked with the Agilent DNA 1000 Kit, and library concentrations were determined with Qubit dsDNA assays (Thermo Fisher Scientific). Equimolar amounts of each library were pooled, and pools were diluted to a final concentration of 1.8 pM in HT1 Hybridization Buffer (Illumina) and sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 75-cycle High-Output Kit v2.5.

treatment_protocol: STS-109 cells recently derived from a human UPS tumor were infected with one of two independent shRNAs targeting either DNMT3A (shDNMT3A) or DNMT3B (shDNMT3B), or a scrambled control shRNA (shSCR). Cells were selected with 3 µg/mL of puromycin 48 hours after infection, and harvested for RNA isolation 96 hours after infection. All cells were harvested at 50% confluency. shRNAs used: TRCN0000035755 (sh:DNMT3A #1), TRCN0000035757 (sh:DNMT3A #2), TRCN0000035685 (sh:DNMT3B #1), and TRCN0000035686 (sh:DNMT3B #2).

value: DNMT3B shRNA #1


title: shDNMT3B_2_rep_4

value: DNMT3B shRNA #2


title: 4D_24H_Low Dose [A2-29]


title: CGS15-3

city: Tianjin

first: Xi

last: Sun

address: Yaguan road 135

institute: Tianjin university

data_processing:
Prokaryote mRNA sequencing by Illumina HiSeq
Sequencing was carried out using a 2x150 paired-end (PE) configuration
image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
technical sequences were removed by Cutadapt (version 1.9.1) and clean data were aligned to reference genome via software Bowtie2 (v2.2.6).
Genome_build: GCA_000011325.1

organism: Corynebacterium glutamicum ATCC 13032

source_name: Bacteria

extract_protocol:
Total RNA of each sample was extracted using the RNeasy Mini Kit (Qiagen, Beijing, China) using cells grown to the mid-exponential phase at 30 ℃ and 220 rpm.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: CGS15-1


title: CGS15-2


title: shDNMT3A_1_rep_4

value: DNMT3A shRNA #1


title: shSCR_rep_4

value: scrambled shRNA


title: 4D_24H_Low Dose [A2-26]


title: CGS11-3


title: shDNMT3A_2_rep_4

value: DNMT3A shRNA #2


title: 4D_24H_Low Dose [A2-23]


title: CGS11-2


title: shDNMT3B_2_rep_3


title: CGS11-1


title: 4D_24H_Low Dose [A2-22]


title: CGS7-3


title: CGS7-2


title: CGS7-1


title: 4D_24H_Low Dose [A2-20]


title: Muscle GPR174-KO rep3

city: Shanghai

first: Jin

last: Liu

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GRCm39
Supplementary files format and content: Excel file include FPKM values for each Sample.

source_name: Muscle

extract_protocol:
Muscle 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 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Muscle

value: post HLI day 7


title: Muscle GPR174-KO rep2


title: Muscle GPR174-KO rep1


title: 4D_24H_Low Dose [A2-19]


title: Muscle WT rep3


title: shDNMT3A_1_rep_3


title: shDNMT3A_2_rep_3_excluded


title: 4D_24H_Low Dose [A2-17]


title: 4D_24H_Low Dose [A2-25]


title: Muscle WT rep2


title: shSCR_rep_3


title: 4D_24H_Low Dose [A2-16]


title: 4D_24H_Control [A2-14]


title: shDNMT3B_2_rep_2_excluded


title: shDNMT3B_1_rep_2


title: OE2

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

description: Illumina HiSeq 2500

data_processing:
RNA-seq
illuma casava 1.7 software  used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low complexity or low-quality sequence then mapped to mm10 whole genome using bowtie V0.12.2 with parameters
Trimmed sequence reads were mapped using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read per kilobase of exon per magabase of library size (FPKM) were caculated using a protocol
http://ftp.ensemblgenomes.org/pub/protists/release-51/fasta/phaeodactylum_tricornutum/cdna/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Phaeodactylum tricornutum

source_name: whole organism

growth_protocol: 24h light

extract_protocol: RNA was harvested using Trizol reagent illumina truseq RNA sample kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction

value: whole organism

value: overexpress


title: shDNMT3B_1_rep_3


title: KO1

description: Illumina HiSeq 2500

value: knockout


title: KO2

description: Illumina HiSeq 2500


title: OE1

description: Illumina HiSeq 2500


title: KO3

description: Illumina HiSeq 2500


title: WT3

description: Illumina HiSeq 2500


title: shDNMT3A_1_rep_2


title: 4D_24H_Control [A2-11]

value: C


title: WT1

description: Illumina HiSeq 2500


title: 4D_24H_Control [A2-10]


title: shSCR_rep_2


title: shDNMT3B_2_rep_1


title: 4D_24H_Control [A2-8]


title: OE3

description: Illumina HiSeq 2500


title: shDNMT3B_1_rep_1


title: Muscle WT rep1

value: wild type


title: 4D_24H_Control [A2-13]


title: 4D_24H_Control [A2-7]


title: 4D_24H_Control [A2-5]


title: shDNMT3A_2_rep_1


title: shDNMT3A_1_rep_1


title: 4D_24H_Control [A2-4]


title: shDNMT3A_2_rep_2


title: WT2

description: Illumina HiSeq 2500


title: 4D_24H_Control [A2-2]


title: shSCR_rep_1_excluded


title: 4D_24H_Control [A2-1]


title: 4D_6H_High Dose [A1-44]

value: H


title: 4D_6H_High Dose [A1-43]


title: 4D_6H_High Dose [A1-40]


title: M14-MBZ #3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
M14-MBZ #3
Transcriptome profile of M14 treated with MBZ (2uM), biological rep3

data_processing:
The reads were trimmed to remove adapter sequences and low-quality ends and reads mapping to contaminating sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Assembly: hg38
Supplementary files format and content: rawcounts.txt: Tab-delimited text file includes raw counts for each Sample.

source_name: Melanoma cell line M14

growth_protocol: RPMI 10% FBS, splitting every 48-72h at confluency.

extract_protocol:
RNA was quantified and mixed at 10ng/µl.
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 250ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp.

treatment_protocol: Cells have been treated with QNC and/or MBZ at concentration of 2uM for 48h and with DMSO (0.1%).

tag: cell type

value: Melanoma cell line

value: MBZ


title: M14-MBZ #2

description:
M14-MBZ #2
Transcriptome profile of M14 treated with MBZ (2uM), biological rep2


title: AAB_CD4_Th0_96h_RNAseq_rep2 (set7)

city: Bethesda

first: Hong-wei

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
RNAseq FASTQ alignment with Tophat 2, ChIPseq FASTQ alignment with FASTQ alignment with Bowtie 2
Gene expression read count data were generated using htseq-count
ChIPseq peak calling with MACS2 (default p-value threshold of 1E-5)
ChIPseq BigWig tracks genarted with bedtools and UCSC tools (bedGraphToBigWig)
Assembly: mm9
Supplementary files format and content: BigWig (ChIPseq), peak.bed (ChIPseq)
Supplementary files format and content: Excel file for RNA-seq gene expression count data

source_name: in vitro cultured CD4+ T cells

growth_protocol: CD4+ T cells were enriched by negative selection (Miltenyi), purified to naïve population by high speed cell sorting  (CD4+CD44-CD25-), then stimulated with with plate-bound anti-CD3 and soluble anti-CD28 under the indicated conditions

extract_protocol:
Total RNA  isolated with TRIzol and  phenol/chloroform, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Library Prep Kit for Illumina (E7530L, NEB)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

tag: genotype

value: Stat5a-/- Stat5b+/-

tag: growth protocol

value: 4 day in vitro culture


title: BBA_CD4_Th0_96h_RNAseq_rep2 (set7)

tag: treatment

value: Stat5a+/- Stat5b-/-


title: WT_CD4_Th0_96h_RNAseq_rep2 (set7)

value: Wild type


title: M14-QNC #3

description:
M14-QNC #3
Transcriptome profile of M14 treated with QNC (2uM), biological rep3

value: QNC


title: BBA_CD4_Th0_96h_RNAseq_rep1 (set7)


title: AAB_CD4_Th0_96h_RNAseq_rep1 (set7)


title: 4D_6H_High Dose [A1-38]

tag: age


title: 4D_6H_High Dose [A1-41]

tag: duration


title: WT_CD4_Th0_96h_RNAseq_rep1 (set7)


title: M14-MBZ #1

description:
M14-MBZ #1
Transcriptome profile of M14 treated with MBZ (2uM), biological rep1


title: M14-QNC #2

description:
M14-QNC #2
Transcriptome profile of M14 treated with QNC (2uM), biological rep2


title: M14-QNC #1

description:
M14-QNC #1
Transcriptome profile of M14 treated with QNC (2uM), biological rep1


title: WT_CD4_Treg_IL2_RNAseq_rep2 (set6)

value: FoxP3+ 'natural' Treg

value: Overnight in vitro culture (16-18 hours)


title: 4D_6H_High Dose [A1-35]

tag: dose


title: 4D_6H_High Dose [A1-37]


title: M14-CTR #3

description:
M14-CTR #3
Transcriptome profile of M14 treated with DMSO (0.1%), biological rep3

value: DMSO


title: WT_CD4_Treg_IL2_RNAseq_rep1 (set6)

tag: tissue


title: 4D_6H_High Dose [A1-34]


title: M14-CTR #2

description:
M14-CTR #2
Transcriptome profile of M14 treated with DMSO (0.1%), biological rep2


title: WT_CD4_Treg_NC_RNAseq_rep1 (set6)

value: Ex vivo


title: WT_CD4_Treg_NC_RNAseq_rep2 (set6)


title: 23B_DZ_Control

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.16.1) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). Sites with a detection p-value above 0.01 (n=6390) and a bead count <3 in at least 5% of samples (n=273) were removed. Moreover, also non-GpG probes (n=2929), potentially SNP affected probes (n=57525) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9673) were filtered out. As a final outcome of the filtering procedures, a total of 408711 CpG sites were retained.

source_name: Control

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

value: Whole Blood

value: F

tag: zygosity

value: Dizygotic


title: 23A_DZ_CH

source_name: Case

tag: Sex

tag: affected gene

value: TPO


title: 22A_DZ_CH

value: M


title: 4D_6H_High Dose [A1-32]

first: Gregory

address: 26 W ML King Jr. Dr.

institute: USEPA/ORD

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads in the RNA-Seq fastq(.gz) file for each sample were mapped to indexed transcripts from each of the 47,578 gene models (which include isoforms) from the newly updated FHM genome (WIOS00000000; BioSample SAMN12875914
Differential expression analysis was performed using the R limma package (version 3.40.6. Between sample normalization was conducted using the trimmed mean of M-values method implemented by the calcNormFactors function from the R edgeR package (version 3.26.8). Precision weights were calculated using the voom function from the limma package. The limma lmFit function was used to fit a generalized linear model with a term for chemical treatment effects. Moderated t-statistics were calculated for chemical treatment effects using the limma eBayes function, and the limma topTable function was used to sort features (i.e. genes) based on their nominal p-values.
Count data were filtered for features which had at least 3 samples with at least 10 counts
Genome_build: EPA_FHM_2.0.b
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Larvae were removed from exposure vessels, placed into Eppendorf tubes together with a steel bead and frozen in liquid nitrogen.  MagMax lysing/binding buffer (100 μl) was added to each tube.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

value: H


title: M14-CTR #1

description:
M14-CTR #1
Transcriptome profile of M14 treated with DMSO (0.1%), biological rep1

tag: cell line

value: Melanoma cell line


title: 21B_DZ_Control


title: 4D_6H_High Dose [A1-31]


title: 19A_DZ_CH


title: 20B_DZ_Control


title: A375_MBZ #3

description:
A375_MBZ #3
Transcriptome profile of A375 treated with MBZ (2uM), biological rep3

source_name: Melanoma cell line A375

value: MBZ


title: 4D_6H_Low Dose [A1-29]

value: L


title: 17A_DZ_CH


title: S5KO_STAT5_MYC_coRV_RNAseq_rep2 (set5)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)

value: Stat5a/b flox/flox Cd4-Cre+/-

value: 4 day in vitro culture


title: S5KO_STAT5_MYC_coRV_RNAseq_rep1 (set5)


title: A375_MBZ #2

description:
A375_MBZ #2
Transcriptome profile of A375 treated with MBZ (2uM), biological rep2


title: 21A_DZ_CH


title: 4D_6H_Low Dose [A1-28]


title: 22B_DZ_Control


title: 15B_DZ_Control


title: 16A_DZ_CH


title: 19B_DZ_Control


title: 18B_DZ_Control


title: 4D_6H_Low Dose [A1-26]


title: S5KO_STAT5_AKT_coRV_RNAseq_rep2 (set5)


title: A375_MBZ #1

description:
A375_MBZ #1
Transcriptome profile of A375 treated with MBZ (2uM), biological rep1


title: S5KO_STAT5_AKT_coRV_RNAseq_rep1 (set5)


title: A375_QNC #3

description:
A375_QNC #3
Transcriptome profile of A375 treated with QNC (2uM), biological rep3

value: QNC


title: 4D_6H_Low Dose [A1-25]


title: 4D_6H_Low Dose [A1-23]


title: 20A_DZ_CH


title: 17B_DZ_Control


title: S5KO_CTL_MYC_coRV_RNAseq_rep1 (set5)


title: S5KO_CTL_MYC_coRV_RNAseq_rep2 (set5)


title: 16B_DZ_Control


title: A375_QNC #2

description:
A375_QNC #2
Transcriptome profile of A375 treated with QNC (2uM), biological rep2


title: 15A_DZ_CH


title: 18A_DZ_CH


title: A375_QNC #1

description:
A375_QNC #1
Transcriptome profile of A375 treated with QNC (2uM), biological rep1


title: S5KO_CTL_AKT_coRV_RNAseq_rep2 (set5)


title: A375-Ctr_3

description:
A375_DMSO #3
Transcriptome profile of A375 treated with DMSO (0.1%), biological rep3

value: DMSO


title: 4D_6H_Low Dose [A1-20]


title: S5KO_CTL_AKT_coRV_RNAseq_rep1 (set5)


title: S5KO_CTL_STAT5_coRV_RNAseq_rep2 (set5)


title: 4D_6H_Low Dose [A1-19]


title: 4D_6H_Low Dose [A1-22]


title: 14B_DZ_Control


title: 14A_DZ_CH


title: 4D_6H_Low Dose [A1-17]


title: 13B_DZ_Control


title: A375-Ctr_2

description:
A375_DMSO #2
Transcriptome profile of A375 treated with DMSO (0.1%), biological rep2


title: S5KO_CTL_STAT5_coRV_RNAseq_rep1 (set5)


title: 13A_DZ_CH


title: MCF7_mir874

data_processing:
Sequencing was performed using the Illumina Novaseq6000 on a paired-end read flow cell, and sequenced on R1 (10× barcode and the UMIs), followed by eight cycles of the I7 index (sample index) and 89 based on R2 (transcript).
The 10× Genomics Cell Ranger Single Cell Software was used for sample demultiplexing, alignment to the human reference genome (hg38), filtering, UMI counting, single-cell 3ʹ-end gene counting, and quality control, according to the manufacturer’s parameters.
Assembly: hg38

source_name: Breast cancer cell line

growth_protocol: Single-cell suspensions of MCF-7 cells were transfected with control miRNA or miR-874 for 36 h or control siRNA or siPMVK for 48 h. Cells were washed twice with phosphate-buffered saline, trypsinized, and collected in DMEM.

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x Genomics) according to manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v3.1 according to the manufacturer's protocol.

value: Breast cancer cell line

value: wild type


title: MCF7_PMVK

value: siPMVK


title: 12B_DZ_CH

value: Whole Blood

value: Dizygotic


title: S5KO_CTL_CTL_coRV_RNAseq_rep2 (set5)


title: A375-Ctr_1

description:
A375_DMSO #1
Transcriptome profile of A375 treated with DMSO (0.1%), biological rep1


title: 4D_6H_Control [A1-14]

source_name: 4d post-fertilization larva

value: C


title: S5KO_CTL_CTL_coRV_RNAseq_rep1 (set5)


title: 4D_6H_Control [A1-13]


title: MCF7_control_siRNA

value: control siRNA


title: 4D_6H_Low Dose [A1-16]


title: WT_STAT5_MYC_coRV_RNAseq_rep2 (set5)

value: Wild type


title: 4D_6H_Control [A1-11]


title: MCF7_control_mir1

value: control mir1


title: WT_STAT5_MYC_coRV_RNAseq_rep1 (set5)


title: D3_hT

city: Basel

first: Rocio

last: Castellanos Rueda

address: Mattenstrasse 26

institute: ETH

data_processing:
Allignment and transcript counting: cellranger v3.1.0
10x format single cell gene expression matrices

source_name: TCR negative T cells

extract_protocol:
Single cell gene expression library preparation was done following the the Chromium Next GEM Single Cell 3' Reagent Kits v3 User Guide (CG000183 Rev C; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
T cells were extracted from the co-culture using Fluorescence Activated Cell Sorting (FACS).

tag: car

value: No CAR

value: TCR negative T cells

value: Donor 3

value: 36h co-culture with SKBR3

tag: genome build


title: 4D_6H_Control [A1-10]

city: Cincinnati

last: Toth


title: 11B_DZ_CH

value: M


title: 12A_DZ_CH


title: 11A_DZ_CH


title: WT_STAT5_AKT_coRV_RNAseq_rep2 (set5)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)

value: 4 day in vitro culture


title: D3_2DomLib_WT

value: Pooled CAR library + 28z and BBz


title: 4D_6H_Control [A1-8]


title: WT_STAT5_AKT_coRV_RNAseq_rep1 (set5)


title: 10B_MZ_Control

value: F

value: Monozygotic


title: D3_2DomLib_2

value: Pooled CAR library


title: WT_CTL_MYC_coRV_RNAseq_rep2 (set5)


title: 4D_6H_Control [A1-7]

value: C


title: D3_2DomLib_1


title: 10A_MZ_CH

value: Whole Blood


title: 09B_MZ_Control


title: D2_Unstim_28z

value: Donor 2

value: no co-culture


title: WT_CTL_MYC_coRV_RNAseq_rep1 (set5)

value: Wild type


title: 4D_6H_Control [A1-5]


title: 4D_6H_Control [A1-4]


title: WT_CTL_AKT_coRV_RNAseq_rep2 (set5)


title: D2_2DomLib_WT

value: Pooled CAR library + 28z

value: TCR negative T cells


title: WT_CTL_AKT_coRV_RNAseq_rep1 (set5)


title: 08A_MZ_CH


title: 4D_6H_Control [A1-2]


title: 4D_6H_Control [A1-1]


title: D1_2DomLib_WT

value: Donor 1

value: 36h co-culture with SKBR3


title: WT_CTL_STAT5_coRV_RNAseq_rep2 (set5)

value: pooled spleen and peripheral lymph nodes


title: D1_2DomLib


title: WT_CTL_STAT5_coRV_RNAseq_rep1 (set5)

value: Effector CD4+ T cell


title: 07B_MZ_Control


title: Patient C6, ascending aorta, aneurysm

city: Cambridge

first: Mark

last: Chaffin

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

description:
10X Genomics 3' v3.1
AorticAneurysm_scportal_06.29.2022.h5ad

data_processing:
Libraries were demultiplexed using cellranger mkfastq (CellRanger v4.0.0) with default settings. FASTQ files were trimmed to remove the template switch oligo (TSO) and homopolymer repeats using cutadapt. Trimmed reads were aligned to GRCh38 pre-mRNA human reference (v2020-A) using cellranger count (CellRanger v4.0.0). CellBender v0.2 (https://github.com/broadinstitute/CellBender) was used to identify non-empty droplets and remove ambient counts from droplets. scR-Invex (https://github.com/broadinstitute/scrinvex) was used to calculate the proportion of reads in droplet mapping exclusively to exonic regions as a measure of how much cytoplasmic material is captured in each droplet. Low quality nuclei were removed on the basis of total UMI, number of unique genes (nGenes), entropy, log(nGenes) * entropy, percent of reads mapping to mitochondrial genes, fraction of reads mapping exclusively to exons, and doublet scores as inferred from Scrublet. The aligned UMAP representation was created using Harmony, with individual samples serving as a batch covariate.
Please note that processed file is an h5ad file containing output from all samples
Assembly: GRCh38
Supplementary files format and content: h5ad file containing processed, unnormalized counts across nuclei from all samples

source_name: Ascending Aorta

extract_protocol:
All tissues were collected within 4 hours of death for Rapid Autopsy participants and during transplant or aortic replacement for all other participants. Tissues were transported to the laboratory on ice and immediately frozen with liquid nitrogen. Single nucleus suspensions were generated by taking approximately 30 x 100 um thick cryosections of aorta were placed into 1 mL of ice-cold digestion buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCL, 5 mM MGCl2, 0.01% IGELPAL, 0.05% BSA, 1:100 Rnase inhibitor, 1 ug/ul elastase) mixed gently, and left on ice for 10 min, with gentle mixing at 5 min. Samples were then transferred into a 7 mL dounce containing 3 mL of Lysis buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCL, 5 mM MGCl2, 0.01% IGELPAL, 0.05% BSA, 1:100 Rnase inhibitor, 1uM DTT) and were homogenized on ice 10 x with the loose pestle, then left for 5 min on ice. Samples were homogenized on ice 10 x with the tight pestle, left to sit for 5 min on ice then transferred into a 15 mL tube. Large debris was pelleted by centrifugation at 40 x g at 4 degrees for 1 min. The supernatant was filtered through stacked 40 um and 10 um filters. Filters were washed with 6 mL of PBS wash buffer (0.05% BSA, 5 mM MgCl2, PBS, 1:1000 RNase inhibitor) and the nuclei pelleted by centrifugation at 550 x g at 4 degrees for 5 min. The nuclei pellet was washed by removal of the supernatant, and addition of 6 mL of PBS wash buffer, followed by centrifugation at 550 x g at 4 degrees for 5 min. The supernatant was removed and nuclei resuspended in 100 uL of nuclei resuspension buffer (0.05% BSA, 5 mM MgCl2, 0.4 U/uL RNase inhibitor), and then counted using a hemocytometer.
Approximately 6000 nuclei per sample were loaded onto a 10x genomics microfluidic chip and samples were processed according to the 10x genomics protocol (Single cell 3’ solution, v3.1) with the following changes. First, nuclei were incubated at 4C for 15 minutes after emulsion generation to promote nuclear lysis. Second, the reverse transcription protocol was modified for one of the two replicates to be 42C for 20 minutes then 53C for 120 minutes.

value: Ascending Aorta

tag: disease

value: Aneurysm

value: Female


title: 08B_MZ_Control

value: F


title: ful IM rep3

city: Berlin

first: Jose

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR_2.7.0b with parameters --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate
Count reads  were calculated using with featureCounts v1.6.0 with parameters  -t exon -g gene_id -T 20 -O -s 0  -M
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Samples are listed in sequential order. i.e,. rep1, rep2, rep3

source_name: Inflorescence meristem

growth_protocol: Arabidopsis plants were grown on rockwool blocks watered with 1.3g/l hyponex in a growth chamber at 21C and long days (16h/8h)

extract_protocol:
The RNA was extracted with a CTAB/LiCL protocol. The samples contained each about 20 pistils/siliques or 20 dissected inflorescence meristems. RNA was extracted using CTAB/LiCL.
RNA libraries were prepared for sequencing using standard Illumina protocols. The total RNA was enriched for mRNA and processed into cDNA libraries using the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). After quality control (Qubit and Fragment Analyzer), samples were sequenced using Illumina NovaSeq 2x150 nt Paired End sequencing.

value: Dissected Inflorescence meristem, with buds until stage 3-4 (Smyth et al., 1990)

tag: ecotype


title: ful IM rep2


title: ful IM rep1


title: WT_CTL_CTL_coRV_RNAseq_rep2 (set5)

tag: strain

value: Retroviral transduction > hIL-2 (18h)

value: 4 day in vitro culture


title: 09A_MZ_CH

value: Whole Blood

value: Monozygotic


title: WT_CTL_CTL_coRV_RNAseq_rep1 (set5)

tag: cell type


title: Patient C3, ascending aorta, aneurysm

value: Male


title: Patient C2, ascending aorta, aneurysm


title: 07A_MZ_CH


title: 06B_MZ_Control


title: S5KO_iTreg_RNAseq_rep2 (set4)

value: iTreg

value: TGF-b + anti-IL-4 + anti-IFNg

tag: genotype

value: Stat5a/b flox/flox Cd4-Cre+/-

value: 3 day in vitro culture


title: Col IM rep3

value: wild type


title: Patient Ao6, ascending aorta, control

value: Control


title: 05B_MZ_Control


title: 06A_MZ_CH


title: S5KO_iTreg_RNAseq_rep1 (set4)

value: pooled spleen and peripheral lymph nodes

tag: growth protocol


title: Col IM rep2


title: Patient Ao13, ascending aorta, control

value: Ascending Aorta


title: Patient Ao12, ascending aorta, control


title: S5KO_Th17_RNAseq_rep1 (set4)

tag: treatment

value: TGF-b + IL-6 + anti-IL-4 + anti-IFNg


title: Patient 774, ascending aorta, aneurysm

value: Aneurysm

tag: age

value: Female


title: OB_5dpi_3

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
After sequencing, perl script was used to filter the original data (Raw Data) to clean reads by removing contaminated reads for adapters and low-quality reads.
Clean reads were aligned to the cavia_porcellus genome using Hisat2 v2.1.0. The number of reads mapped to each gene in each sample was counted by HTSeq v0.6.0 and TPM was then calculated  to estimate the expression level of genes in each sample.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Olfactory Bulb

extract_protocol:
Total RNA  were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)  and DNase I (NEB, USA) treated, respectively.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

value: Olfactory Bulb

value: ZIKV infected

tag: time


title: 05A_MZ_CH

value: F


title: S5KO_Th2_RNAseq_rep2 (set4)

value: IL-4 + anti-IFNg


title: Col IM rep1

value: Dissected Inflorescence meristem, with buds until stage 3-4 (Smyth et al., 1990)


title: Patient 718, ascending aorta, aneurysm

value: Male


title: S5KO_Th17_RNAseq_rep2 (set4)


title: OB_5dpi_1


title: Patient 608, ascending aorta, aneurysm


title: S5KO_Th2_RNAseq_rep1 (set4)


title: OB_5dpi_2


title: 04A_MZ_CH

value: Whole Blood

value: M

value: Monozygotic


title: OB_3dpi_3


title: 03A_MZ_CH


title: Patient 1827, ascending aorta, control


title: S5KO_Th1_RNAseq_rep2 (set4)

value: IL-12 + anti-IL-4

value: Stat5a/b flox/flox Cd4-Cre+/-

value: 3 day in vitro culture


title: OB_3dpi_2


title: S5KO_Th1_RNAseq_rep1 (set4)

value: pooled spleen and peripheral lymph nodes


title: Patient 1825, ascending aorta, control

value: Ascending Aorta

value: Control


title: S5KO_Th0_RNAseq_rep2 (set4)

value: No exogenous cytokines or blocking antibodies


title: 03B_MZ_Control


title: OB_3dpi_1


title: 04B_MZ_Control


title: OB_mock_3

value: mock


title: Patient 1820, ascending aorta, control


title: S5KO_Th0_RNAseq_rep1 (set4)


title: Patient 1817, ascending aorta, control


title: OB_mock_2

value: Olfactory Bulb


title: 02B_MZ_CH


title: WT_iTreg_RNAseq_rep2 (set4)

value: iTreg

value: TGF-b + anti-IL-4 + anti-IFNg

value: Wild type


title: OB_mock_1


title: WT_iTreg_RNAseq_rep1 (set4)


title: SK-UT-1 treated with 2C for 12h, rep 3

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

institute: university of Udine

description: 2C, 12h, round 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were clipped from their adapter sequences using the Trimmomatic software (v0.35). Reads with an average Phred quality lower than 28 were discarded.
Transcripts were quantified from raw reads with STAR (v2.5.0) on the human transcriptome GRCh38 (Ensembl 104). Quantifications were summarized to gene level with StringTie (v2.1.5).
Differential expression analysis was performed with DESeq2 package (v1.32.0)). Genes were considered differentially expressed if FDR <0.05 and abs(log2(FoldChange)) >1.
Assembly: GRCh38 (Ensembl 104)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample and quantified gene
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

extract_protocol:
Cells were lysed using Tri-Reagent (Molecular Research Center). RNA was extracted with Quick-RNA MagBead kit (Zymo Research) following the manufacturer’s instructions in the presence of DNAse I.
cDNA libraries were prepared from poly(A) selected RNA following Illumina specifications

value: leiomyosarcomas cell lines

tag: replicate

value: round 3


title: 02A_MZ_CH

tag: tissue

value: Whole Blood


title: SK-UT-1 treated with 2C for 3h, rep 3

description: 2C, 3h, round 3

value: 3 h


title: OE_5dpi_2

source_name: Olfactory Mucosa

value: Olfactory Mucosa

value: ZIKV infected


title: OM_5dpi_1


title: hutsmc treated with 2C for 12h, rep 3

description: 2C, 12h, round 3

source_name: HUtSMC

value: HUtSMC

value: human uterine smooth muscle cells


title: 01B_MZ_CH

value: F

tag: zygosity

value: Monozygotic


title: WT_Th2_RNAseq_rep2 (set4)

value: pooled spleen and peripheral lymph nodes

value: IL-4 + anti-IFNg

value: 3 day in vitro culture


title: 01A_MZ_CH

tag: Sex


title: hutsmc treated with 2C for 3h, rep 3

description: 2C, 3h, round 3


title: WT_Th17_RNAseq_rep2 (set4)

value: TGF-b + IL-6 + anti-IL-4 + anti-IFNg


title: SK-UT-1 treated with 2C for 12h, rep 2

description: 2C, 12h, round 2

value: round 2


title: WT_Th17_RNAseq_rep1 (set4)


title: OM_3dpi_1


title: OM_3dpi_2


title: SK-UT-1 treated with 2C for 3h, rep 2

description: 2C, 3h, round 2


title: OM_mock_3

value: mock


title: WT_Th2_RNAseq_rep1 (set4)

value: Wild type


title: WT_Th1_RNAseq_rep1 (set4)

value: IL-12 + anti-IL-4


title: SK-UT-1 UNTREATED, rep 3

description: UNTREATED, round 3

value: leiomyosarcomas cell lines

value: UNTREATED

value: 0 h

value: round 3


title: WT_Th0_RNAseq_rep2 (set4)

value: No exogenous cytokines or blocking antibodies


title: OE_5dpi_3

value: Olfactory Mucosa

value: ZIKV infected


title: WT_Th1_RNAseq_rep2 (set4)


title: OM_mock_2


title: OM_3dpi_3


title: WT_Th0_RNAseq_rep1 (set4)


title: hutsmc treated with 2C for 12h, rep 2

description: 2C, 12h, round 2

value: HUtSMC

value: human uterine smooth muscle cells


title: S5KO_CD25_RV_RNAseq_set1_rep2 (set3)

value: pooled spleen and peripheral lymph nodes

value: Effector CD4+ T cell

value: Retroviral transduction > hIL-2 (18h)

value: Stat5a/b flox/flox Cd4-Cre+/-

value: 4 day in vitro culture


title: hutsmc treated with 2C for 3h, rep 2

description: 2C, 3h, round 2

value: 3 h

value: round 2


title: hutsmc UNTREATED, rep 3

description: UNTREATED, round 3


title: GFP-7

city: beijing

first: Yuejiao

last: Ma

address: No. 10.wai xi tou tiao, you an men street.

description: control KD

data_processing:
Image processing and base recognition were performed using Solexa pipeline version 1.8.
The RNA sequencing reads were aligned to the mice reference genome mm10 using HISAT2 (version 2.1.0) with default parameters.
The normalized expression value, fragments per kilobase of transcript per million mapped reads (FPKM), was calculated for each gene using StringTie (version 1.3.1c).
FPKM at the gene level and transcript level were calculated using Ballgown (version 2.8.4). Differentially expressed genes with a fold change≥1.5, p-value ≤ 0.05 and FPKM≤0.5 were screened and retained in groups.
Genome_build: mm10
Supplementary_files_format_and_content: The Express file format is xlsx, which analyses the expression of gene and transcript; the Diff_express file format is xlsx, which analyses all differentially expressed genes /transcripts and differentially expressed genes /transcripts.

source_name: Liver tissues

extract_protocol:
RNA was harvested using Trizol reagent and the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
Approximately 1-2 µg of total RNA isolated from each independent biological sample was processed with a Ribo-Zero Magnetic Gold kit (Epicentre Biotechnologies) to reduce ribosomal RNA abundance. Sequencing libraries were then constructed using the KAPA Stranded RNA-Seq Library Prep kit (Illumina). The quality of the constructed sequencing libraries was analysed using an Agilent 2100 Bioanalyzer. Quantitative real-time PCR was performed to quantify the sequencing libraries, and the mixed different sample libraries were sequenced using an Illumina HiSeq 4000 platform.

treatment_protocol: The Itgα5 KD groups (n=3) were obtained by the injection of AAV8 vectors packaged with crisp-case9 target liver-specific Itgα5 sgRNA plasmids with LP1 promotor. Control KD groups (n=3) were obtained by the injection of equal dose of control AAV8 vectors. Mice were sacrificed at 4 weeks after tail vein injection.

value: BALB/c

value: liver

tag: group

value: Control


title: hutsmc UNTREATED, rep 2

description: UNTREATED, round 2

tag: cell line

value: UNTREATED

value: 0 h


title: GFP-5

description: control KD


title: S5KO_CD25_RV_RNAseq_set1_rep1 (set3)


title: S5KO_AKT_RV_RNAseq_set1_rep2 (set3)


title: GFP-3

description: control KD


title: SK-UT-1 treated with 2C for 3h, rep 1

description: 2C, 3h, round 1

value: leiomyosarcomas cell lines

value: round 1