title: WT-D3-0h lifetime

source_name: WT dendritic cells not treated with Actinomycotoxin D


title: LV1356_donor_RNA

status: Public on Apr 02 2019

type: SRA

city: Berkeley

first: Axel

last: Visel

state: CA

address: 1 Cyclotron Road

country: USA

institute: Lawrence Berkeley National Laboratory

description: Stranded (first-strand synthesis)

library_source: transcriptomic

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC RNA-seq pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Gene-wise counts were computed using htseq-count from the HTSeq package (PMID: 25260700; v0.9.1) with -s set to no.
Genome_build: hg38
Supplementary_files_format_and_content: *.counts.txt, HTseq quantifications

molecule: total RNA

organism: Homo sapiens

source_name: adult left ventricle, total RNA

extract_protocol:
RNA was isolated from homogenized left ventricle using the TRIzol Reagent (Thermo Fisher Scientific). RNA samples were DNase-treated with the TURBO DNA-free Kit (Thermo Fisher Scientific), and then RNA quality was assessed via 2100 Bioanalyzer (Agilent) and an RNA 6000 Nano Kit (Agilent).
RNA-seq libraries were generated via the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina), according to manufacturer protocols.
RNA-seq libraries were subjected to additional purification steps to remove remaining high molecular weight products.

tag: tissue

value: left ventricle

tag: developmental stage

value: adult

tag: disease


title: KO-D2-6h lifetime

city: Beijing, China

first: Huamin

last: Wang

address: Three N0. 5 dongdan street, Dongcheng District, Beijing

department: Department of Immunology

country: China

institute: Peking Union Medical College, Chinese Academy of Medical Sciences,

data_processing:
Basecalls performed using Illumia bcl2fastq2.17
Raw reads after quanlity analysis were aligned to the reference genome (mm10) using TopHat (v2.0.14) after removing adapter
RPKM (Reads Per Kilobase per Million mapped reads) were calculated by Cuffnorm
The degradation rate of RNA k was estimated by Log2(At/Ao)=-kt, where t is transcription inhibition time (h), At and A0 represent mRNA quantity (attomole) at time t and time 0. Two k values were calculated: time 3 h versus time 0 h, and time 6 h versus time 0 h. The final lifetime was calculated by using the average of k3h and k6h, that is t1/2=2/(k3h+k6h)
Genome_build: mm10
Supplementary_files_format_and_content: excel document containg RPKM values for each sample and the calculated lifetime

molecule: polyA RNA

organism: Mus musculus

source_name: KO dendritic cells treated with Actinomycotoxin D for 6 h

growth_protocol: Bone marrow (BM) from 6 week’s C57 BL/6 mice were cultured in RPMI-1640 medium (PAA laboratories) supplemented with 10% FBS (fetal bovine serum) (Gibco), recombinant mouse GM-CSF (granulocyte-macrophage colony-stimulating factor) (10ng/ml) (R&D) and IL-4 (1ng/ml) (R&D). After 3d, non-adherent cells were gently removed and the remaining cells were further cultured with fresh medium containing GM-CSF and IL-4. On the fifth day, loosely adherent cells were subjected to positive selection with magnetic beads coated with anti-mouse CD11c and were defined as immature DC (imDC). The CD11c+imDC were stimulated with LPS (100 ng/ml) for 24 h and were defined as mature DC (maDC).

extract_protocol:
Total RNA of BMDCs was isolated with Trizol regent (Invitrogen) and mRNA was enriched by Dynabeads mRNA Purification Kit (Invitrogen). Removal of ribosomal RNA was confirmed by 2200 Tape Station detection (Agilent). ERCC RNA spike-in control (Ambion) was added to each sample proportional to total RNA according to the instructions.
The library preparation was constructed according to NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Microbeads anti-CD11c were cocultured with BMDC from Mettl3 WT or Mettl3 KO mice at 4 ℃ for 15 min, and then the cells-microbeads mix flow through MACS column, during which the CD11c+ dendritic cells were separated . After the CD11c+ BMDC were stimulated for 24hours with LPS(100ng/ml), cells were divided in triplicate, one for Actinomycotoxin D 6h, another for 3h and the last with no treatment.

tag: cell type

value: Bone marrow derived mature dendritic cells

tag: genotype

tag: time (hours)

tag: strain


title: UBC-CreERT2;Ddx5flox/flox spermatogonia TMX-treated (Ddx5 knockout) replicate 1

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Raw sequencing reads in FASTQ format were filtered and trimmed with Trimmomatic (v0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt)
Reads mapped to the complete mouse genome (GENCODE GRCm38 primary, annotation version vM15) with STAR
Gene read counting was performed with featureCounts.
Differential gene expression was performed with Degust webtool (http://degust.erc.monash.edu) using limma-voom.
Genome_build: GENCODE GRCm38 primary, annotation version vM15
Supplementary_files_format_and_content: Raw counts file was generated by featureCounts and uploaded to Degust.

source_name: Cultured undifferentiated spermatogonia

growth_protocol: Cultured undifferentiated spermatogonia were maintained in StemPro-34 media supplemented with GDNF, bFGF, EGF, insulin and other additives.

extract_protocol:
RNA was extracted using Trizol LS (Thermo Fisher Scientific) and Direct-zol RNA Miniprep kit (Zymo Research).
Libraries were generated according to the Illumina Stranded mRNA protocol using 12 cycles of amplification. Library size (~350bp) was checked using Bioanalyzer and quantified with Qubit and qPCR.

treatment_protocol: Cells were treated with 4-hydroxytamoxifen for 4 days.

value: Testis

value: Cultured undifferentiated spermatogonia

tag: treatment

value: TMX-treated


title: KO-D2-0h lifetime

source_name: KO dendritic cells not treated with Actinomycotoxin D


title: LV1277_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1259_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1248_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1226_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1202_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1072_explant_RNA

description: Stranded (first-strand synthesis)

value: idiopathic dilated cardiomyopathy (DCM)


title: LV1183_donor_RNA

description: Stranded (first-strand synthesis)


title: LV1160_donor_RNA

description: Stranded (first-strand synthesis)


title: 1033_baseline

city: Philadelphia

first: Katherine

middle: N

last: Theken

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Systems Pharmacology and Translational Therapeutics

institute: University of Pennsylvania

data_processing:
Illumina adapter sequences were trimmed from the raw, gzipped FASTQ files using the BBDuk tool from the BBTools suite v37.99. BBDuk was supplied with Illumina universal adapter sequences, along with their reverse complements, and was run with the following command line options: -Xmx5g threads=1 ktrim=r k=23 hdist=2 mink=10 hdist2=1 tpe=f tbo=t ordered=t.
Reads from the trimmed FASTQ files were aligned to GRCh38 build of the human reference genome using STAR v2.6.0c. STAR was supplied with gene models from v92 of the Ensembl annotation, and was run with the following command line parameters: --runThreadN 4 --outSAMtype BAM Unsorted --outSAMunmapped Within KeepPairs –outFilterMismatchNmax 33 --seedSearchStartLmax 33 --alignSJoverhangMin 8 --readFilesCommand zcat. Additionally, the --outSAMattrRGline argument was used to specify read group information for each BAM file (this is required to merge BAM files).
Next, for each library, all BAM files (one for each lane of sequencing) were merged into single files using the SAMtools v1.8 merge command. The trimmed FASTQ files for each library were merged using the unix cat command.
The merged data were normalized and quantified using the Pipeline Of RNA-seq Transformations v0.8.5b-beta (PORT; https://github.com/itmat/Normalization), a resampling-based method that accounts for confounding factors like read depth, ribosomal RNA, mitochondrial RNA content, and genes with extremely high expression. PORT was run at the gene level in strand-specific mode and was provided with gene models from v92 of the Ensembl annotation. During normalization, the following 11 samples (listed by subject and timepoint) were excluded due to low read depth: 1004 post-surgery 1, 1005 post-surgery 1, 1007 baseline, 1008 baseline, 1008 post-surgery 1, 1008 post-surgery 2, 1011 post-surgery 1, 1011 post-surgery 2, 1012 post-surgery 2, 1020 baseline. The low coverage for these samples is due to the low levels of input RNA for library preparation (these samples had among the lowest input material).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

source_name: peripheral blood mononuclear cell

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a standard Ficoll-Paque density gradient centrifugation method.  Total RNA was isolated using the RNeasy Miniprep Kit (QIAGEN) per the manufacturer’s instructions.
Total RNA from each sample was converted to sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech), following the manufacturer’s protocol.

value: peripheral blood mononuclear cell

tag: subject

tag: gender

value: Male

tag: timepoint

value: baseline

tag: library barcode

value: CGCTCATT-CAGGACGT

tag: drug treatment

value: ibuprofen sodium

tag: response group

value: Full responder


title: 1033_post-surgery_2

value: post-surgery 2

value: ATTCAGAA-CAGGACGT


title: 1032_post-surgery_2

value: Female

value: TCCGGAGA-CAGGACGT

value: Placebo


title: 1032_post-surgery_1

value: post-surgery 1

value: ATTACTCG-CAGGACGT


title: 1032_baseline

value: AGCGATAG-TAATCTTA


title: 1030_post-surgery_2

value: TCTCGCGC-TAATCTTA

value: Partial responder


title: 1033_post-surgery_1

value: GAGATTCC-CAGGACGT


title: 1030_baseline

value: peripheral blood mononuclear cell

value: CGGCTATG-TAATCTTA


title: 1029_baseline

value: Male

value: baseline

value: GAATTCGT-TAATCTTA


title: 1028_post-surgery_1

value: GAGATTCC-TAATCTTA

value: ibuprofen sodium


title: 14.5dpc pregnant liver rep 1

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: pregnant mouse liver

hyb_protocol: Five and one-half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

label: biotin

source_name: liver RNA from 14.5 dpc pregnant mouse

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

extract_protocol: Trizol followed by Qiagen Rneasy isolation

treatment_protocol: virgin and 14.5dpc timed pregnant female mice

value: female

value: liver

value: pregnant


title: 1028_post-surgery_2

value: post-surgery 2

value: ATTCAGAA-TAATCTTA


title: virgin liver rep 2

description: virgin mouse liver

source_name: liver RNA from virgin mouse

value: virgin


title: virgin liver rep 3

description: virgin mouse liver


title: virgin liver rep 4

description: virgin mouse liver


title: 14.5dpc pregnant liver rep 4

description: pregnant mouse liver


title: 14.5dpc pregnant liver rep 3

description: pregnant mouse liver


title: 1028_baseline

value: CGCTCATT-TAATCTTA


title: 1027_post-surgery_1

value: Female

value: post-surgery 1

value: ATTACTCG-TAATCTTA

value: Placebo


title: 1026_post-surgery_1

value: peripheral blood mononuclear cell

value: TCCGCGAA-AGGCGAAG


title: 1024_post-surgery_1

value: CTGAAGCT-AGGCGAAG

value: Partial responder


title: 1029_post-surgery_1

value: Male

value: CTGAAGCT-TAATCTTA


title: 1027_baseline

value: baseline

value: AGCGATAG-AGGCGAAG


title: 1030_post-surgery_1

value: TCCGCGAA-TAATCTTA

value: ibuprofen sodium


title: 1029_post-surgery_2

value: post-surgery 2

value: TAATGCGC-TAATCTTA


title: 14.5dpc pregnant liver rep 2

description: pregnant mouse liver

value: female

value: liver

value: pregnant


title: virgin liver rep 1

description: virgin mouse liver

value: virgin


title: Gr_48S3

city: Anyang

first: Dong

middle: Odongo

last: Qi

state: Henan

address: HUANGHE ROAD, No 38.

department: Cotton research Institute

institute: Chinese Academy of Agricultural Sciences

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of pig was sequenced run with Illumina 4000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_raimondii/JGI_221_G.raimondii_Dgenome/assembly/G.raimondii_JGI_221_v2.0.assembly.fasta.gz
Supplementary_files_format_and_content: xls include RPKM values，time point and tissue.

organism: Gossypium raimondii

source_name: cotton plant

growth_protocol: To ensure maximum germination, a small slit was made on the seed coat, and then pre-germinated in the incubator using sterilized moist filter paper for 2-3 days until the radicle was approximately 1 cm long, the condition of the incubator was set at 28℃ and with > 90% ambient humidity. The seedlings were then transplanted into sterilized vermiculite filled in small conical pots, with dimensions of 5 cm bottom region, 7 cm top region and 8 cm in depth

extract_protocol:
Fresh tissues  were harvested at 0h, 12h and 48h of post inoculation,flash frozen into liquid nitrogen.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.Approximately 10 ug of total RNArepresenting a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: At one true leaf stage, the plants were inoculated with 8 ml suspension of V. dahliae at 1 × 107 conidia per mL. The samples were then taken at 0h, 12h and 48h for RNA sequencing.

value: Stem

value: one true leaf stage

tag: time point (hour)


title: Gr_48L1

value: Leaf


title: 1026_baseline

value: peripheral blood mononuclear cell

value: Female

value: CGGCTATG-AGGCGAAG

value: Placebo


title: 1024_baseline

value: baseline

value: GAATTCGT-AGGCGAAG

value: Partial responder


title: Gr_48L2


title: Gr_48S1


title: 1022_baseline

value: Male

value: AGCGATAG-GGCTCTGA

value: ibuprofen sodium

value: Full responder


title: 1023_post-surgery_1

value: post-surgery 1

value: GAGATTCC-AGGCGAAG


title: Gr_48S2


title: 1026_post-surgery_2

value: post-surgery 2

value: TCTCGCGC-AGGCGAAG


title: Gr_48R3

value: Root

value: one true leaf stage


title: 1023_baseline

value: peripheral blood mononuclear cell

value: CGCTCATT-AGGCGAAG


title: 1020_post-surgery_2

value: Female

value: TAATGCGC-GGCTCTGA


title: 1020_baseline

value: baseline

value: GAATTCGT-GGCTCTGA

value: Placebo


title: 1020_post-surgery_1

value: CTGAAGCT-GGCTCTGA


title: 1022_post-surgery_2

value: Male

value: TCCGGAGA-AGGCGAAG


title: 1022_post-surgery_1

value: ATTACTCG-AGGCGAAG

value: ibuprofen sodium

value: Full responder


title: Gr_48R2


title: Gr_12L3

value: Leaf


title: Gr_12S3

value: Stem


title: Gr_48R1

value: Root


title: 1019_post-surgery_1

value: post-surgery 1

value: GAGATTCC-GGCTCTGA


title: 1021_post-surgery_2

value: peripheral blood mononuclear cell

value: post-surgery 2

value: TCTCGCGC-GGCTCTGA

value: Partial responder


title: 1021_baseline

value: Female

value: baseline

value: CGGCTATG-GGCTCTGA


title: Gr_12L1

value: one true leaf stage


title: 1024_post-surgery_2

value: TAATGCGC-AGGCGAAG


title: Gr_12S2


title: 1019_post-surgery_2

value: Male

value: ATTCAGAA-GGCTCTGA


title: 1018_baseline

value: AGCGATAG-CCTATCCT

value: ibuprofen sodium

value: Full responder


title: 1021_post-surgery_1

value: TCCGCGAA-GGCTCTGA


title: 1018_post-surgery_1

value: post-surgery 1

value: ATTACTCG-GGCTCTGA


title: 1023_post-surgery_2

value: peripheral blood mononuclear cell

value: ATTCAGAA-AGGCGAAG

value: Placebo


title: Gr_12S1

value: Stem


title: Gr_12L2

value: Leaf


title: 1017_post-surgery_2

value: post-surgery 2

value: TCTCGCGC-CCTATCCT


title: 1019_baseline

value: baseline

value: CGCTCATT-GGCTCTGA


title: BT-RH probe 5

city: Salamanca

first: Javier

last: Pérez Peña

address: C/Richard Ford Nº39, 2ºB

department: Centro Regional de Investigaciones Biomédicas

country: Spain

institute: Universidad de Castilla La Mancha

description: Gene expression data from BT-RH cells under standard conditions

hyb_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix) and then hybridized to HG-U133 plus 2.0 GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The data were analysed with Transcriptome Analysis Console (TAC) Software.

source_name: BT-RH cell line

growth_protocol: BT474 and BT-RH cells were grown in DMEM with 10% of FBS and added to a final concentration of 500.000 cells/plate.

extract_protocol: Total RNA was extracted from purified cell populations using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: No treatment.

tag: cell line

value: BT-RH

value: Breast


title: Gr_12R3

value: Root

value: one true leaf stage


title: 1017_baseline

value: Male

value: CGGCTATG-CCTATCCT


title: 1018_post-surgery_2

value: Female

value: TCCGGAGA-GGCTCTGA

value: ibuprofen sodium

value: Full responder


title: 1016_post-surgery_1

value: peripheral blood mononuclear cell

value: post-surgery 1

value: CTGAAGCT-CCTATCCT


title: 1016_baseline

value: GAATTCGT-CCTATCCT


title: Gr_12R1


title: Gr_12R2


title: Gr_48L3

value: Leaf


title: 1015_post-surgery_2

value: post-surgery 2

value: ATTCAGAA-CCTATCCT


title: 1017_post-surgery_1

value: TCCGCGAA-CCTATCCT

value: Placebo


title: 1015_post-surgery_1

value: GAGATTCC-CCTATCCT


title: 1016_post-surgery_2

value: TAATGCGC-CCTATCCT


title: 1015_baseline

value: Male

value: baseline

value: CGCTCATT-CCTATCCT


title: 1014_post-surgery_2

value: TCCGGAGA-CCTATCCT


title: 1014_post-surgery_1

value: ATTACTCG-CCTATCCT


title: Gr_0L3

value: one true leaf stage


title: 1014_baseline

value: peripheral blood mononuclear cell

value: AGCGATAG-ATAGAGGC


title: 1012_post-surgery_2

value: Female

value: TCTCGCGC-ATAGAGGC

value: ibuprofen sodium

value: Partial responder


title: BT-RH probe 4

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix) and then hybridized to HG-U133 plus 2.0 GeneChip oligonucleotide arrays (Affymetrix).

value: BT-RH

value: Breast


title: BT-RH probe 1


title: Gr_0S3

value: Stem


title: RNA-seq 2cell control rep2

city: Fukuoka

first: Wan Kin

last: Au Yeung

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

country: Japan

institute: Kyushu University

data_processing:
ChIP-seq data analysis: Low quality bases in the 3’ portion and adapter sequences were removed from raw reads and trimmed reads were mapped to mouse genome mm10 by bowtie2 v2.2.9 with options ‘--end-to-end --no-1mm-upfront -N 0 -D 500 -X 1000 --no-mixed --no-discordant’. Duplicate and low quality reads (MapQ <5) were removed using Picard v2.6.0.
WGBS data analysis: Low quality bases in the 3’ portion (Q <30) and adapter sequences were removed from raw reads by Trim-Galore! v0.3.3 and trimmed reads were mapped to mouse genome mm10 by Bismark v0.14.5 with options ‘--bowtie2 --pbat -D 75’. For allelic-specific analysis, trimmed reads were mapped to N-masked mm10 genome using published SNP data of JF1 strain. Allelic reads were selected using SNPsplit v0.3.2.
RNA-seq data analysis: Low quality bases in the 3’ portion and adapter sequences were removed from raw reads and trimmed reads were mapped to mouse genome mm10 by HISAT2 v2.0.5 with options ‘--dta --pen-canintronlen G,-8,3 --pen-noncanintronlen G,-8,3 -k 50 --no-mixed --no-discordant’. Transcripts were assembled by StringTie v1.3.3. Repeat masker-annotated microRNA, rRNA, tRNA-like, snRNA and transcripts with CDS <200 bp were excluded in the downstream analyses. For allelic-specific analysis, trimmed reads were mapped to N-masked mm10 genome using published SNP data of JF1 strain. Allelic reads were selected using SNPsplit v0.3.2.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: [ChIP-seq] Normalized H3K9me2 profiles of rep1 and rep 2 are provided in 10-kb sliding windows and input-normalized.
Supplementary_files_format_and_content: [WGBS] The CG coverage files are tab-delimited, 1-based genomic coordinates for every covered CG site in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation level> <methylated cytosine> <unmethylated cytosine>.
Supplementary_files_format_and_content: [RNA-Seq] FPKM values are tab-delimited text files for each sample and are in the following format: <chromosome> <geneName> <start position> <end position> <Control rep1 FPKM> <Control rep2 FPKM> <mat-KO rep1 FPKM> <mat-KO rep2 FPKM> OR <chromosome> <geneName> <start position> <end position> <Control rep1 FPKM> <Control rep2 FPKM> <cKO rep1 FPKM> <cKO rep2 FPKM>

source_name: 2-cell embryos

growth_protocol: All animal experiments were performed under the ethical guidelines of Kyushu University, Kindai University, and The Canadian Council on Animal Care (CCAC). All mice used in this manuscript were aged 4 weeks or older and were euthanized by CO2 asphyxiation.

extract_protocol:
Total RNA was extracted from pooled FGOs and 2-cell embryos using Trizol reagent (Thermo Fisher Scientific).
ULI-NChIP-seq libraries were prepared from about 200 FGOs based on previous reports (Brind'Amour et al., 2015). ChIP was performed with 0.15 μg of anti-H3K9me2 (abcam ab1220) in 200-μl NChIP buffer. WGBS libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012). Pooled  GOs, FGOs, MII oocytes, 2-cell embryos and blastocysts were spiked with 1% unmethylated lambda phage DNA (Promega). Libraries were amplified with KAPA library amplification kit (KAPA) for 4 cycles using primers AATGATACGGCGACCACCGAGATCTACAC and CAAGCAGAAGACGGCATACGAGAT. For RNA-seq, libraries were constructed using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), NEBNext® RNA First Strand Synthesis Module, NEBNext® Ultra Directional RNA Second Strand Synthesis Module, and NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocols. Libraries were amplified by PCR for 10 cycles. WGBS libraries were sequenced on HiSeq 1500 or 2500 (Illumina) (FGOs and blastocysts: HCS v2.0.5 and RTA v1.17.20; MII oocytes and 2-cell embryos: HCS v2.2.68 and RTA v1.18.66.3) using TruSeq SBS kit v3-HS and HiSeq Rapid SBS Kit v2 (Illumina) according to manufacturer’s protocols. For ULI-ChIP-seq and RNA-seq, libraries were sequenced on NextSeq 500, HiSeq 1500, or HiSeq 2500 (Illumina) according to manufacturer’s protocols.

treatment_protocol: Growing oocytes (GOs) were harvested by sequential digestion of P10 ovaries in 1 mg/ml collagenase (Sigma-Aldrich), 0.25% trypsin-EDTA (Invitrogen), and 0.5% protease type XIV (C9891 Sigma-Aldrich). Fully grown oocytes (FGOs) were harvested from ovaries of 10 weeks or older by needle puncture. Superovulation was induced by injecting females at 10 weeks or older with 7.5 U of pregnant mare serum gonadotrophin (PMSG) and then 48 hour later with 7.5 U of human chorionic gonadotropin (hCG). Cumulus-oocyte complexes were collected from the oviducts and fertilized with C57BL/6J sperm for whole genome bisulfite sequencing (WGBS) of blastocysts; or with JF1 sperm for WGBS and RNA-seq of 2-cell embryos. MII oocytes were harvested by digestion in hyaluronidase (H4272 Sigma-Aldrich), and polar bodies were removed by sequential digestion in 0.5% protease type XIV (C9891 Sigma-Aldrich) and hypotonic treatment in 1% sodium citrate (31404-15 Nacalai Tesque). Cumulus cells were removed by capillary washing in PBS and zygotes were cultured in EmbryoMax KSOM Medium (1X) w/ 1/2 Amino Acids (Merck Millipore) at 37˚C and 5% CO2. Two-cell embryos were harvested within 2 hours after completion of the first mitotic division for WGBS and at 24 hpf for RNA-seq. Polar bodies of 2-cell embryos for WGBS were also removed. Blastocysts were harvested at 120 hpf for WGBS. For ULI-ChIP-seq, zona pellucida of FGOs was removed by acid Tyrode’s solution, followed by neutralization in M2 medium (Sigma-Aldrich) before fresh frozen in liquid nitrogen

value: C57BL/6 (maternal), JF1 (paternal)

value: 2-cell embryos

value: control


title: Gr_0S2


title: Gr_0S1


title: BT-RH probe 2


title: 1011_post-surgery_2

value: post-surgery 2

value: TAATGCGC-ATAGAGGC

value: Full responder


title: BT474 probe 8

description: Gene expression data from BT474 cells under standard conditions

source_name: BT474 cell line


title: BT474 probe 7


title: BT-RH probe 3


title: 1012_post-surgery_1

value: post-surgery 1

value: TCCGCGAA-ATAGAGGC


title: Gr_0L2

value: Leaf

value: one true leaf stage


title: Gr_0R3

value: Root


title: PBAT 2cell mat-KO rep1

description: CG_context_2cell_maternal_mat-KO.cov.txt

library_source: genomic

molecule: genomic DNA

value: G9a maternal KO


title: BT474 probe 6


title: BT474 probe 5


title: PBAT 2cell mat-KO rep2


title: 1011_post-surgery_1

value: peripheral blood mononuclear cell

value: Female

value: CTGAAGCT-ATAGAGGC

value: ibuprofen sodium


title: 1011_baseline

value: baseline

value: GAATTCGT-ATAGAGGC


title: BT474 probe 4

value: Breast


title: PBAT 2cell control rep2

description: CG_context_2cell_maternal_control.cov.txt

value: C57BL/6 (maternal), JF1 (paternal)

value: 2-cell embryos

value: control


title: 1012_baseline

value: CGGCTATG-ATAGAGGC

value: Partial responder


title: PBAT 2cell control rep1


title: BT474 probe 1


title: 1008_post-surgery_2

value: Male

value: post-surgery 2

value: ATTCAGAA-ATAGAGGC

value: Placebo


title: Gr_0R2

value: Root

value: one true leaf stage


title: BT474 probe 3


title: Gr_0R1


title: 1008_post-surgery_1

value: peripheral blood mononuclear cell

value: post-surgery 1

value: GAGATTCC-ATAGAGGC


title: 1008_baseline

value: baseline

value: CGCTCATT-ATAGAGGC


title: PBAT MII control rep2

source_name: MII oocytes

value: MII oocytes


title: 1007_post-surgery_1

value: TCCGGAGA-ATAGAGGC

value: ibuprofen sodium

value: Full responder


title: PBAT MII cKO rep2

value: G9a conditional KO


title: PBAT MII cKO rep1


title: MSC+LLC-serum-exosome

city: ChangSha

first: xina

last: zhang

state: HuNan

address: 110 XiangYa Road

department: Cancer Research Institute

institute: Central South University

description: Exosomes are isloated from MSCs+LLCs were co-injection subcutaneous tumorigenic group.

hyb_protocol: Dry sample with vacuum concentrator,approximately 2 to 3 hours,45℃ to 55℃.Assemble Hybridization Mixture+Hyb Spike-ln.Heat,ice.Hybridize 20 hours,55℃,20RPM.

scan_protocol: After the hybridization,in the first 42℃ about containing 0.2% SDS,2 x SSC lotion | in 5 min, and then in 0.2 x SSC lotion Ⅱ wash 5 min, glass can be used for scanning after dry. The cleaned chip was scanned using the Agilent chip scanner (G2565CA), and the hybridization diagram was obtained Slice.

data_processing: First,the Agilent Feature Extraction(v10.7) software was used to analyze and extract the number of hybrid images;The data was then normalized using Agilent GeneSpring software, the software was used to analyze the differences between groups, such as t-test method to analyze the differentially expressed genes of the two groups. ANOVA method was used to analyze multiple groups of differentially expressed genes.

source_name: Mesenchymal stem cells,murine lewis lung cancinoma cells

label_protocol: Agilent's miRNA Complete Labeling and Hyb kit generates fluorescent miRNA with a sample input of 100ng of total RNA.This method involves the ligation of one cyanine 3-pCP molecule to the 3' end of a RNA molecule with greater than 90% efficiency.

growth_protocol: mBMSCs were cultured in MEM medium and LLC were cultured in DMEM high glucose medium supplemented with penicillin G (100 U/mL),streptomycin (100 mg/mL)and 10% fetal calf serum.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: A total of 1 x106 of murine Lewis Lung Cancer LLC-luciferase cells with or without murine BMSCs were injected subcutaneously into mice, and when the mean tumor volume reached 200mm3,the serum was extracted after the mice were killed by the neck,and  exosomes were isolated.

value: MSCs+LLCs

value: bone marrow,lung


title: PBAT MII control rep1

value: control


title: Control1

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

country: France

institute: University Grenoble Alpes

data_processing:
Basecalling was performed using HCS HD 3.4.0.38 & RTA 2.7.7
reads were aligned using bwa 0.7.x
files were converted into bam formate using samtools 0.1.19
duplicated reads were removed using Picard-tools 1.105
bed files were generated using bedtools v2.17.0
The SICER-df-rb function of SICERV V1.1 (Zang et al., 2009) with no shifting of the reads and an effective genome size of 0.9 was employed to identify both THS and dTHS. The e-value for detection of ATAC enriched regions was set to 100, no gabs were allowed to keep the resolution of separate peaks. The window size was 100 bases for THS and 25 bases for dTHS to obtain a very precise resolution. The p-value for the discovery of differentially enriched regions was chosen as 0.001. Regions were considered as THS/dTHS when they were identified as significantly enriched/differentially enriched in all three replicates.
Genome_build: tair10
Supplementary_files_format_and_content: For each sample (excluding input controls), a bed file containing transposase hypersensitive sites (THS) for the respective sample in the formate "Chromosome, start, stop, mean normalised read count" is provided. This file corresponds to the output of SICER (scoreisland file). As a supplementary file, an excel table containing genes that overlap with THS in all three replicates and genes that overlap with differentially accessible sites (dTHS). Up denoted higher accessibility in GFP+, down denotes lower accessibility in GFP+. Genes are defined as coding regions including 1kb upstream and downstream. Pseudogenes and transposable element genes were excluded from the analysis.

organism: Arabidopsis thaliana

source_name: Control, inflorescence meristem

growth_protocol: Plants were cultivated on soil in controlled conditions (longday) for four to five weeks.

extract_protocol:
Inflorescence apices of approximately 700-900 DRNL::erGFP ap1cal plants were collected  and FACS was performed as described in Frerichs et al., 2016. After separation of GFP-positive (GFP+) and GFP-negative (GFP–) cells with a FACS Vantage SE (Becton Dickinson) sorter for a maximum period of 1 h (36,000 cells s-1 flow rate; 100 µm aperture), the protoplasts were directly collected into 10 mL FACS-medium. The number of collected GFP+ protoplasts typically varied between 95,000 to 300,000 per experiment, for comparison approximately 300,000 GFP− protoplasts were collected as control. Protoplasts treatment after FACS separation followed the protocol of (Buenrostro et al., 2013) with some adaptations. Protoplasts in FACS medium were collected by centrifugation (500 rpm, 10 min, 4 °C), washed once in 500 µL FACS-medium and pelleted by centrifugation before cells were lysed in 10 mM TrisHCl pH 7,4, 10 mM NaCl, 3 mM MgCl2, 0,1 % IGEPAL CA-630 for 30 min on ice. After centrifugation (1000 rpm, 4 °C), the nuclei were washed twice successively for 10 min or 2 min in lysis buffer before being resuspended in 15 µl nuclease-free H2O. 25 µl 2x TD Tagment DNA buffer and 10 µl TDE1 Tagment DNA Enzyme (TruSight One Kit) were added to a total reaction mix of 50 µl followed by an incubation at 37 °C for 30 min with gentle mixing every 5 min. Subsequently nuclear DNA was isolated with the MinElute PCR Purification Kit (28004, Qiagen, Hilden, Germany) and eluted in 10 µL elution buffer. For Input control samples, inflorescences (0.6 g) of DRNL::erGFP ap1cal plants were directly grinded in liquid nitrogen and the powder resuspended in 20 ml nuclei isolation buffer (NIB:10 mM NaPO4 pH 7, 100 mM NaCl, 1 M 2-methyl-2,4-pentanediol, 10 mM β-Mercaptoethanol, spplementation with SigmaFAST Protease Inhibitor (S8820)). Cell debris was removed by sieving (mesh 100 µm), the sieve was washed once with 5 ml NIB, nuclei were pelleted by centrifugation (1,000 g, 20 min, 4 °C). The pellet was resuspended and centrifuged 5-times with 5 ml NIB supplemented with 10 mM MgCl2, 0,5 % (v/v) Triton X-100 before purified nuclei were resuspended in sonification buffer (10 mM NaPO4 pH 7, 10 mM NaPO4 pH 7, 100 mM NaCl, 17 mM Sarkosyl, 10 mM EDTA, SigmaFAST Protease Inhibitor) and sonified in a Branson Sonifier II w-450 (80 % Duty Cycle, 7 Output Control) for 18 min at 4 °C to a fragment size of 200-500 bp. Chromatin was cleared twice by centrifugation at 21,000 g (4 °C) before genomic DNA was isolated using the Qiagen MinElute PCR Purification Kit (28004, Qiagen, Hilden, Germany) and eluted in 10 µl elution buffer.
Libraries for the purified control DNA were constructed using Illumina's TruSeq DNA nano kit. For the ATAC-seq samples, purified tagmented DNA was amplified via a 12 or 15-cycle PCR program using reagents from the Illumina TruSight One Library Preparation Kit. This procedure adds index 1 (i7) and index 2 (i5) information needed for multiplexing, as well as common adapters (P5 and P7) required for cluster generation and sequencing. To remove unwanted products the final Library has been purified by using Beckman Coulter Ampure XP Beads. After purification and validation (2200 TapeStation; Agilent Technologies), libraries are quantified by using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems) and subsequently sequenced on an Illumina HiSeq4000 sequencing system and a paired end 2x75nt sequencing protocol.

value: inflorescence meristem

tag: sample type

value: sheared chromatin of isolated nuclei of the inflorescence meristem

value: DRNL::erGFP ap1cal

value: sonication


title: LLC-serum-exosome

description: Exosomes are isloated from LLCs was a separate subcutaneous tumorigenic group.

source_name: murine lewis lung cancinoma cells

value: LLCs

tag: tissue

value: lung


title: shP53_Noc-2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description:
cultured cells
processed2_fpkm.txt

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg38 genome using STAR.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated by Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: Text files of gene names and FPKM values for each sample.

source_name: cultured cells

growth_protocol: Undifferentiated hESCs cultured in E8 medium without feeders.

extract_protocol:
Total RNA was extracted using TRIZOL and treated with DNase.
RNA was used for reverse-transcription followed the SMART-seq2 protocol. Then cDNA was fragmented by sonication using the Covaris sonicator. Fragmented cDNA was end-repaired, ligated with A base. After A base addition, the pre-indexed Illumina adapters were ligated. cDNA with adapters were enriched for another 11 cycles. Finally, the acquired cDNA libraries were sequenced on HiSeq X Ten platform.

treatment_protocol: hPSCs were treated with MCL1 inhibitor A1210477 0.6uM for 2 days or treated with NOC 50ng/ml for 12 hrs.

value: Embryonic stem cells

tag: passage number

value: TP53 knock down H9

value: 50ng/ml Nocodazol treatment for 12hrs


title: GFP-_rep3

source_name: GFP-, inflorescence meristem

value: FACS sorted inflorescence meristem cells depleted of LOFCs

value: transposase treatment for ATAC-seq


title: GFP-_rep2


title: shP53_Noc-1

description:
cultured cells
processed2_fpkm.txt


title: PBAT FGO cKO rep2

source_name: fully grown oocytes

tag: developmental stage

value: fully grown oocytes


title: 1006_post-surgery_1

tag: cell type

value: peripheral blood mononuclear cell

value: Male

value: post-surgery 1

value: AGCGATAG-TATAGCCT

value: ibuprofen sodium

value: Partial responder


title: shP53_A121-2

description:
cultured cells
processed2_fpkm.txt

value: 0.6uM A1210477 treatment for 2days


title: GFP-_rep1

value: inflorescence meristem

tag: genotype

value: DRNL::erGFP ap1cal


title: PBAT FGO cKO rep1

value: G9a conditional KO


title: BT474 probe 2

value: Breast


title: GFP+_rep3

source_name: GFP+, inflorescence meristem

value: FACS sorted lateral organ founder cells


title: MHCCLM3 cell Replicate 2 vs. HOXB7 depletion MHCCLM3 cell Replicate 2

city: Shanghai

first: weimin

last: wang

address: 136 Yi Xue Yuan Road

institute: Zhongshan Hospital, Fudan University

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: negative control siRNA-treated MHCCLM3 cells Replicate 2

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: MHCCLM3 cells were maintained in high-glucose DMEM  supplemented with 10% heat-inactivated FBS at 37°C in a humidified incubator under 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol  (Invitrogen) following manufacturer's instructions

treatment_protocol: HOXB7  knockdown using siRNA (Transfection of HOXB7-siRNA in MHCCLM3 cells was performed using Lipofectamine 2000 according to the manufacturer’s instructions).

source_name: HOXB7 depletion MHCCLM3 cell


title: PBAT FGO control rep2

value: control


title: shP53_A121-1

description:
cultured cells
processed2_fpkm.txt

value: Embryonic stem cells

value: TP53 knock down H9


title: MHCCLM3 cell Replicate 1 vs. HOXB7 depletion MHCCLM3 cell Replicate 1

source_name: negative control siRNA-treated MHCCLM3 cells Replicate 1


title: GFP+_rep2

value: transposase treatment for ATAC-seq


title: PBAT FGO control rep1

value: fully grown oocytes


title: 1005_baseline

source_name: peripheral blood mononuclear cell

value: peripheral blood mononuclear cell

value: baseline

value: CGGCTATG-TATAGCCT

value: Placebo


title: 1004_post-surgery_1

value: Male

value: post-surgery 1

value: TAATGCGC-TATAGCCT

value: ibuprofen sodium


title: shP53_Ctrl-2

description:
cultured cells
processed2_fpkm.txt

value: DMSO treatment


title: 1007_baseline

value: ATTACTCG-ATAGAGGC

value: Full responder


title: shP53_Ctrl-1

description:
cultured cells
processed2_fpkm.txt


title: DKO colon 2

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 2215-B Garland Ave, 1075 MRB4

institute: Vanderbilt University Medical Center

description:
DKO vs WT
16KO_DKO_gene_exp

data_processing:
TruSeq adaptors were trimmed by Trimmomatic-0.32
Trimmed paired end reads were aligned to the mouse genome (mm10, downloaded from UCSC) using TopHat (v2.0.11)
Differential gene expression was determined by Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: Adjacent normal colon

growth_protocol: Mice were aged 8-12 weeks prior to treatment

extract_protocol:
Colons were removed and placed into RNALater prior to freezing. Colon samples were homogenized in Trizol reagent and RNA extracted with Qiagen Rneasy mini kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were injected with 10 mg/kg of azoxymethane intraperitoneally. Three days post-injection, the animals were started on the first of two cycles of 2% DSS ad libitum. Each cycle lasted 5 days and was followed by a 16-day recovery period

value: AOM/DSS

value: DKO

value: adjacent normal colon


title: DKO colon 3

description:
DKO vs WT
16KO_DKO_gene_exp


title: 56d HS_d

city: Rohnert Park

first: Sean

last: Place

address: 1801 E. Cotati Ave.

department: Biology

institute: Sonoma State University

data_processing:
The data were first filtered by discarding low quality reads and reads <15 bases in length after adapter trimming using the CLC Genomics Workbench (v11.0.1) software.
The filtered reads were mapped to known mature miRNAs and miRNA precursors in miRBase (v21.0). Read mapping was restricted to miRNA precursors in other fish species and prioritized based on phylogenetic relatedness. Species included in the read mapping were Salmo salar (ssa), Ictalurus punctatus (ipu), Fugu rubripes (fru), Tetraodon nigroviridis (tni), Danio rerio (dre), and Oryzias latipes (ola)
The mapped reads were first normalized in each sample by counts per million reads. After normalization, DE of miRNAs between fish acclimated to control temperatures (-1.5 °C) or a thermal stress (+4 °C) at each time point (7d, 28d, and 56d) were calculated using a Baggerley’s test in the CLC Genomics Workbench (v11.0.1) program.

organism: Trematomus bernacchii

source_name: Gill tissue

growth_protocol: Fish were maintained at the respective acclimation temperature for a total of 7, 28, or 56 days. At each time point five fish were removed and euthanized by anesthetic overdose in MS-222. Gill tissue was removed from the gill raker and flash frozen in liquid nitrogen.

extract_protocol:
Total RNA from n=4 fish per treatment per time point was extracted in Trizol using an automated TissueLyser II (Qiagen) according to manufacturer’s recommended protocol. The quality of RNA extracts was determined by gel electrophoresis and peak analysis on an Agilent 2100 bioanalyzer. Only RNA samples with RIN scores greater than 8 were utilized for library preparation and subsequent sequencing.
The Illumina Truseq Small RNA library prep kit and size selection with the BluePippin automated gel extraction system was carried out to create small cDNA libraries. 50 bp SE sequencing libraries were then indexed and pooled prior to sequencing on 2 lanes of an Ilumina 4000 HiSeq platform housed in the UC Davis Genome Center.

value: gill

value: thermal stress (+4 °C)


title: 56d HS_c


title: 1004_baseline

value: CTGAAGCT-TATAGCCT

value: Partial responder


title: 1006_baseline

value: peripheral blood mononuclear cell

value: baseline

value: TCTCGCGC-TATAGCCT


title: 1005_post-surgery_1

value: Male

value: TCCGCGAA-TATAGCCT

value: Placebo


title: HA_BCLXL- Noc-1

description:
cultured cells
processed2_fpkm.txt

value: Embryonic stem cells

value: Inducible HA-BCLXL overexpressed H9

value: 50ng/ml Nocodazol treatment for 12hrs


title: RNA-seq 2cell mat-KO rep2

value: C57BL/6 (maternal), JF1 (paternal)

value: 2-cell embryos

value: G9a maternal KO


title: 1003_post-surgery_1

value: post-surgery 1

value: GAATTCGT-TATAGCCT

value: ibuprofen sodium

value: Full responder


title: HA_BCLXL+ dox-2

description:
cultured cells
processed2_fpkm.txt

value: DMSO treatment


title: 1003_baseline

value: peripheral blood mononuclear cell

value: ATTCAGAA-TATAGCCT


title: MTG16 null colon 3

description:
wt_16KO_gene_exp
16KO_DKO_gene_exp

value: AOM/DSS

value: MTG16 null

value: adjacent normal colon


title: 56d HS_a

value: gill

value: thermal stress (+4 °C)


title: 1027_post-surgery_2

value: Female

value: post-surgery 2

value: TCCGGAGA-TAATCTTA

value: Placebo


title: GFP+_rep1

value: inflorescence meristem

value: FACS sorted lateral organ founder cells

value: DRNL::erGFP ap1cal

value: transposase treatment for ATAC-seq


title: HA_BCLXL- Noc-2

description:
cultured cells
processed2_fpkm.txt

value: Embryonic stem cells

value: Inducible HA-BCLXL overexpressed H9

value: 50ng/ml Nocodazol treatment for 12hrs


title: 56d HS_b


title: HA_BCLXL+ dox-1

description:
cultured cells
processed2_fpkm.txt

value: DMSO treatment


title: Gr_0L1

source_name: cotton plant

value: Leaf

value: one true leaf stage


title: 28d HS_d


title: 1001_post-surgery_1

value: peripheral blood mononuclear cell

value: post-surgery 1

value: TCCGGAGA-TATAGCCT

value: ibuprofen sodium

value: Partial responder


title: 1002_baseline

value: Female

value: baseline

value: CGCTCATT-TATAGCCT


title: 28d HS_b

value: gill

value: thermal stress (+4 °C)


title: MTG16 null colon 1

description:
wt_16KO_gene_exp
16KO_DKO_gene_exp

value: AOM/DSS

value: MTG16 null

value: adjacent normal colon


title: DKO colon 1

description:
DKO vs WT
16KO_DKO_gene_exp

value: DKO


title: 1002_post-surgery_1

value: GAGATTCC-TATAGCCT

value: Placebo


title: Kaiso null colon 1

value: Kaiso null


title: 7d HS_d


title: Kaiso null colon 3


title: Kaiso null colon 2


title: WT colon 3

description:
WT_v_KaisoKO_gene_exp
wt_16KO_gene_exp
DKO vs WT

value: WT


title: HA_BCLXL- AZD-1

description:
cultured cells
processed2_fpkm.txt

value: Embryonic stem cells

value: Inducible HA-BCLXL overexpressed H9

value: 100nM AZD treatment for 24hrs


title: NOXA8----Ctrl-1

description:
cultured cells
processed_fpkm.txt

value: NOXA knock-out H9 clone8

value: DMSO treatment


title: 28d HS_c


title: 7d HS_b


title: 1001_baseline

value: peripheral blood mononuclear cell

value: Female

value: baseline

value: ATTACTCG-TATAGCCT

value: ibuprofen sodium

value: Partial responder


title: NOXA8----Noc-2

description:
cultured cells
processed_fpkm.txt

value: 50ng/ml Nocodazol treatment for 12hrs


title: 28d HS_a

value: gill

value: thermal stress (+4 °C)


title: NOXA8----Ctrl-2

description:
cultured cells
processed_fpkm.txt


title: HA_BCLXL- AZD-2

description:
cultured cells
processed2_fpkm.txt


title: WT colon 2

value: AOM/DSS

value: adjacent normal colon


title: NOXA8----Noc-1

description:
cultured cells
processed_fpkm.txt


title: NOXA8----A121-2

description:
cultured cells
processed_fpkm.txt

value: 0.6uM A1210477 treatment for 2days


title: 7d HS_a


title: 7d HS_c


title: MTG16 null colon 2

description:
wt_16KO_gene_exp
16KO_DKO_gene_exp

value: MTG16 null


title: WT colon 1

value: WT


title: UBC-CreERT2;Ddx5flox/flox spermatogonia TMX-treated (Ddx5 knockout) replicate 4

source_name: Cultured undifferentiated spermatogonia

value: Testis

value: Cultured undifferentiated spermatogonia

value: TMX-treated


title: NOXA8----A121-1

description:
cultured cells
processed_fpkm.txt

value: Embryonic stem cells

value: NOXA knock-out H9 clone8


title: 56d Control_d

value: control temperatures (-1.5 °C)


title: 56d Control_c


title: NOXA4----Ctrl-2

description:
cultured cells
processed_fpkm.txt

value: NOXA knock-out H9 clone4

value: DMSO treatment


title: s3

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
Mus musculus (host) and Homo sapiens (donor)
barcode and uniform molecular identifier in R1 read, mRNA sequence in R2 read

data_processing:
Sequencing reads were extracted into paired fastq files using Illumina software.
Cellranger (10X Genomics, v. 3.0.0) was used to align reads with a mixture of mouse (mm10) and human (hg18) genomes, using the count command.
Seurat (v. 2.3.4) was used to combine and normalize counts.  Clustering revealed one distinct group of cells that was clearly human.  These were extracted into a table of raw counts, converted to homologous mouse gene symbols, and then recombined with the raw counts from the remaining mouse cells and re-imported into a Seurat data model.
Genome_build: mm10
Supplementary_files_format_and_content: The Seurat scale.data slot from the combined mouse and human cells, converted to mouse gene symbols, containing 15,058 cells x 17,683 gene symbols, in a tab-delimited text format.

source_name: mouse brain, including cerebral cortex, hippocampus, corpus callosum, and olfactory bulb

growth_protocol: Primitive macrophage precursor (PMP) cells were prepared from human iPSC via yolk sac embryoid bodies, which were plated and stimulated with IL-3 and M-CSF to promote myeloid differentiation.  PMP emerged into the medium.

extract_protocol:
The forebrain were dissected and dissociated with Papain, centrifuged to remove debris, and approximately 20,000 cells were loaded into the 10X Genomics Chromium instrument for processing and library preparation.
The 10X Genomics single cell gene expression profiling kit was used following manufacturers recommendations.

treatment_protocol: PMPs were transplanted into P0 Rag2-/- hCSF1 mice (C; 129S4-Rag2tm1.1Flv Csf1tm1(CSF1)Flv Il2rgtm1.1Flv/J, The Jackson Laboratory). Cells were transplanted bilaterally. The precise transplantation sites were bilateral from the midline = ± 1.0 mm, posterior bregma = -2.0 mm, and dorsoventral depth = -1.5 and -1.2 mm.  0.5 μl of cells were injected into each site (total 4 sites).

tag: month posttransplant

value: 6 mo

tag: transplant

value: Human iPSC-derived primitive macrophage precursors (PMP)


title: s2


title: NOXA4----A121-2

description:
cultured cells
processed_fpkm.txt

tag: treatment


title: NOXA4----Ctrl-1

description:
cultured cells
processed_fpkm.txt


title: 28d Control_d

value: gill


title: 56d Control_b


title: 56d Control_a


title: s4


title: NOXA4----A121-1

description:
cultured cells
processed_fpkm.txt


title: NOXA4----Noc-2

description:
cultured cells
processed_fpkm.txt

value: 50ng/ml Nocodazol treatment for 12hrs


title: s1


title: 28d Control_b


title: IPS-Noc-2

description:
cultured cells
processed_fpkm.txt

value: Induced pluripotent stem cells

value: Wild Type CD34 iPSC


title: D8_KO_CD8_001

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

description: CD8+ T cells were MACS-purified and directly used for RNA preparation.

data_processing:
Bcl2fastq 2.19.0.316 was used for base calling.
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the read needing a quality phred score > 20.
Homertools 4.7 (Heinz et al., 2010) were used for PolyA-tail trimming, and reads with a length < 17 were removed
STAR 2.3 (Dobin et al., 2013) was used for mapping against mouse genome 38 (mm10) using default parameters
featureCounts (Liao et al., 2014)(parameters --minReadOverlap 3 -T 3 -M -O) was used for counting of the genes annotated in the gencode.vM16.gtf file. For comparison, DESeq2, DESeqDataSetFromMatrix was applied, followed by estimateSizeFactors, estimateDispersions, and nbinomWald testing.
Genome_build: mm10
Supplementary_files_format_and_content: Cui_RNA-Seq_ILSE9960_raw_counts.txt, tab delimited table of raw counts, annotated with gencode.vM16.annotation.gtf

source_name: CD8+ T cells,

growth_protocol: mouse T cells were cultured in complete RPMI 1640 medium (plain RPMI 1640 medium with 10% fetal bovine serum, Penicillin and Streptomycin, 2-mercaptoethanol, L-Glutamine and non-essential amino acids).

extract_protocol:
CD8+ T cells were MACS-purified from naïve or LCMV-Armstrong-infected (2×105 pfu, day 8 after infection, i.p.) Cd4Cre×Sptlc2Flox/Flox mice and wildtype littermates. The purity of CD8+ T cells was checked using FACS and it was higher than 96%. Total RNA of transfected cells was prepared using the QIAGEN RNeasy Mini Kit. DNA was removed using the QIAGEN RNase-Free DNase Set.
Illumina TruSeq Stranded RNA Kit was used

treatment_protocol: naïve or LCMV-Armstrong-infected (2×105 pfu,  i.p)

value: infected with LCMV Armstrong

tag: strain background


title: 28d Control_c


title: NOXA4----Noc-1

description:
cultured cells
processed_fpkm.txt


title: Healthy Cartilage Biopssy of Patient 4

city: ankara

first: mehmet

middle: dogan

last: asik

state: Select Your State or Province

address: kızılcaşar mah mehmetçik cad no 15, gölbaşı

department: School of Medicine

country: Turkey

institute: Ankara Yildirim Beyazit University

hyb_protocol: Streptavidin Phycoerythrin

scan_protocol: standard Illumina protocol

data_processing: Affymetrix Expression concole V1 and Transriptome Analysis console V1

source_name: Cartilage

label_protocol: Affymetrix IVT kit

extract_protocol: RNeasy Mini Kit and RNeasy Micro Kit (QIAGEN)

treatment_protocol: Cartilage Debriment from patients

tag: condition

value: healthy


title: Healthy Cartilage Biopssy of Patient 5


title: Healthy Cartilage Biopssy of Patient 9


title: Healthy Cartilage Biopssy of Patient 7


title: Healthy Cartilage Biopssy of Patient 3


title: Healthy Cartilage Biopssy of Patient 8


title: Healthy Cartilage Biopssy of Patient 6


title: D8_KO_CD8_003


title: IPS-Noc-1

description:
cultured cells
processed_fpkm.txt


title: D8_KO_CD8_002


title: D8_WT_CD8_002

value: Wild-type


title: D8_WT_CD8_003


title: 7d Control_d


title: D0_KO_CD8_003

value: no treatment


title: 7d Control_c


title: 7d Control_b


title: 28d Control_a


title: D8_WT_CD8_001


title: IPS-A121-2

description:
cultured cells
processed_fpkm.txt

value: 0.6uM A1210477 treatment for 2days


title: IPS-Ctrl-2

description:
cultured cells
processed_fpkm.txt


title: 7d Control_a


title: D0_KO_CD8_002


title: IPS-A121-1

description:
cultured cells
processed_fpkm.txt


title: D0_KO_CD8_001


title: H9-Noc-2

description:
cultured cells
processed_fpkm.txt

value: Wild Type H9


title: D0_WT_CD8_003


title: IPS-Ctrl-1

description:
cultured cells
processed_fpkm.txt


title: H9-Noc-1

description:
cultured cells
processed_fpkm.txt

value: Embryonic stem cells


title: H9-Ctrl-2

description:
cultured cells
processed_fpkm.txt


title: D0_WT_CD8_002


title: H9-Ctrl-1

description:
cultured cells
processed_fpkm.txt


title: D0_WT_CD8_001


title: HX10_Stat5 OE 4

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
HX10_GAGTGG
Stat5 OE_colon from male mouse at 8-12 weeks, VilCreER;icS5 (STAT5IEC+++)

data_processing:
Following removal of primers and barcodes, raw reads passing quality filtration were aligned to the mm10 mouse genome using TopHat aligment and Cufflinks assembly with annotations provided by UCSC.
Reads were filtered for expression >3 in 100% of at least one experimental condition.
ANOVA was performed to identify differentially regulated transcripts between the three Stat5 conditions, where p<0.05 and fc>1.5 was considered significant.
Genome_build: mm10
Supplementary_files_format_and_content: text file with transcript information and FPKM

source_name: Stat5 OE_colon

growth_protocol: Colonic crypts were isolated from 12-week-old mice, by shaking colonic tissue in PBS with 10mM EDTA at 37C for 30 minutes.

extract_protocol:
Total RNA was extracted using mirVana mRNA isolation kit using the total RNA extraction protocol.  Integrity was determined by Bioanalyzer.
Single end libraries were constructed according to standard Illumina protocols.

tag: stat5 genotype

value: VilCreER;icS5 (STAT5IEC+++)

tag: age

value: 8-12 weeks

tag: Sex

value: male

value: colon


title: patient_7_acute_rep2

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

hyb_protocol: Fragmented labeled RNA (2 ug) was hybridized at 40°C for 18-20 hours in Hyb-solution (6xSSPE, 20mM EDTA, 0,05% Tween-20, salmon sperm DNA 10 mg/ml, 0,04% SDS,  formamide 25%vol). Arrays were sequentially washed  by 3хSSPE, 0,05% Tween-20 → 0,5хSSPE, 0,05% ТTween20 → 2xPBS 0,1% Tween-20. Subsequent blocking, labeling, label wash, substrate solution treatment were fulfilled using ElectraSense Detection Kit (CustomArray Inc., WA, USA)

scan_protocol: Amperometric signal measurements were performed using ElectraSense Reader device and ElectraSense application software (CustomArray Inc., WA, USA)

data_processing: Feature data from .ecd-files was exported to csv.-files using ElectraSense Analysis 3.4.2. All calculations were performed in Python and R. Background correction was made using rma.background.correct  function from preprocessCore package [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] Samples of same type were organized in matrix 1042xN, where 1856 – number of probes and N – number of repeating measures of sample. Two matrix of samples to compare were normalized using normalize.quantiles.robust function from preprocessCore package [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] . To calculate fold-change and its significance, stats.ttest function from scipy.stats package [Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source Scientific Tools for Python, 2001-, http://www.scipy.org/ [Online; accessed 2017-11-13] was used. subColSummarizeMedianpolish [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] was used to calculate overall gene expression, using all the probes aimed to isoforms of a gene. P=0.05 was selected as threshold value. Fold-changes ≥ 1,1 and ≤ -1,1 were taken into consideration.

source_name: peripheral blood leukocytes

label_protocol: 1. Total RNA (1,5-2 ug) was converted to T7-promoter-containing cDNA by Mint cDNA synthesis kit (Evrogen, Russia, http://evrogen.ru/technologies/Mint-cDNA-synthesis.shtml), kit' 3'-oligo-T-primer was replaced by T7-promoter-containing-oligo-T-primer (DNA-synthesis, Russia); 2. cDNA was complemented to ds-cDNA by 15-cycles PCR amplification; 3. ds-cDNA (2 ug) was transcribed by T7 RNA-polimerase (Thermo Scientific, EU). Biotin-labeled RNA was obtained using biotinylated UTP (DNA-synthesis, Russia) by substitution of a half of its unlabeled counterpart in reaction mix.

extract_protocol: Total RNA was isolated by magnetic beads-containg kit (Magnosorb kit, Russia) followed by phenol-chloroform purification

tag: patient id

value: peripheral blood leukocytes

tag: Stage

value: acute HHV-6 mononucleosis

tag: gender

value: female


title: patient_7_acute_rep3


title: Control2

source_name: Control, inflorescence meristem

value: inflorescence meristem

tag: sample type

value: sheared chromatin of isolated nuclei of the inflorescence meristem

value: DRNL::erGFP ap1cal

value: sonication


title: Damaged Cartilage Biopsy of Patient 10

value: damage


title: patient_7_recovery_rep1

value: after recovery


title: patient_7_recovery_rep2


title: HX9_Stat5 control 3

description:
HX9_CGTACG
Stat5 control_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5+/+)

source_name: Stat5 control_colon

value: VilCreER;Stat5 (STAT5+/+)

tag: tissue


title: Healthy Cartilage Biopssy of Patient 1

value: healthy


title: H9-A121-1

description:
cultured cells
processed_fpkm.txt

source_name: cultured cells

tag: passage number

tag: cell line

value: Wild Type H9

value: 0.6uM A1210477 treatment for 2days


title: patient_7_recovery_rep3

tag: cell type


title: HX8_Stat5 KO 3

description:
HX8_GTCCGC
Stat5 KO_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5IEC-/-)

source_name: Stat5 KO_colon

value: VilCreER;Stat5 (STAT5IEC-/-)


title: Healthy Cartilage Biopssy of Patient 2


title: Damaged Cartilage Biopsy of Patient 5


title: Damaged Cartilage Biopsy of Patient 8


title: Damaged Cartilage Biopsy of Patient 7


title: Damaged Cartilage Biopsy of Patient 3


title: patient_6_recovery_rep3


title: Damaged Cartilage Biopsy of Patient 9


title: Damaged Cartilage Biopsy of Patient 4


title: Damaged Cartilage Biopsy of Patient 2


title: BCL-XL-Noc-2

description:
cultured cells
processed_fpkm.txt

value: Embryonic stem cells

value: Constitutive BCL-XL overexpressed H9

value: 50ng/ml Nocodazol treatment for 12hrs


title: Damaged Cartilage Biopsy of Patient 6


title: HX7_Stat5 KO 2

description:
HX7B_GTAGAG
Stat5 KO_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5IEC-/-)

value: 8-12 weeks

value: male

value: colon


title: H9-A121-2

description:
cultured cells
processed_fpkm.txt


title: LLC+BMSC3

description:
the red fluorescent protein positive LLC cells were collected from the tumor sites by flow cytometry cell sorting and subjected to RNA sequencing analysis
LLCT3_FPKM

data_processing:
Sequencing data filtering
After obtaining clean reads, we compared clean reads to reference genome sequences using HISAT
Using StringTie,Each sample is reconstructed with a transcript, which is then reconstructed with a Cuffcompare (one of the Cufflinks tools).The new transcripts were obtained by referring to the annotation information, and the coding potential of the new transcripts was predicted with the CPC software.
We use GATK to test each sample SNP and INDEL information, the final result is stored in VCF format
Detection of differential splicing genes (DSG) between samples using rMATS
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include Fpkm values for each Sample ...

source_name: lewis lung cancinoma cells and Mesenchymal stem cells

growth_protocol: water and sunlight and air and food

extract_protocol:
flow cytometry cell sorting,and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: subcutaneously injected with LLC-RFP alone or subcutaneously injected with LLC-RFP with BMSCs

tag: strain

tag: genotype

value: wild type

tag: agent

value: LLC-RFP with BMSCs

value: primary cancer sites


title: BCL-XL-Noc-1

description:
cultured cells
processed_fpkm.txt

tag: treatment


title: patient_6_recovery_rep2

value: peripheral blood leukocytes

value: female


title: HX6_Stat5 control 2

description:
HX6_CCGTCC
Stat5 control_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5+/+)


title: LLC+BMSC2

description:
the red fluorescent protein positive LLC cells were collected from the tumor sites by flow cytometry cell sorting and subjected to RNA sequencing analysis
LLCT2_FPKM


title: LLC+BMSC1

description:
the red fluorescent protein positive LLC cells were collected from the tumor sites by flow cytometry cell sorting and subjected to RNA sequencing analysis
LLCT1_FPKM


title: patient_7_acute_rep1

value: acute HHV-6 mononucleosis


title: HX5_Stat5 OE 3

description:
HX5_ATGTCA
Stat5 OE_colon from male mouse at 8-12 weeks, VilCreER;icS5 (STAT5IEC+++)

value: VilCreER;icS5 (STAT5IEC+++)


title: LLC3

description: the red fluorescent protein positive LLC cells were collected from the tumor sites by flow cytometry cell sorting and subjected to RNA sequencing analysis

source_name: lewis lung cancinoma cells

value: LLC-RFP alone


title: BCL-XL-Ctrl-1

description:
cultured cells
processed_fpkm.txt

value: DMSO treatment


title: Damaged Cartilage Biopsy of Patient 1

value: damage


title: HX4_Stat5 OE 2

description:
HX4_GGTAGC
Stat5 OE_colon from male mouse at 8-12 weeks, VilCreER;icS5 (STAT5IEC+++)


title: BCL-XL-A121-2

description:
cultured cells
processed_fpkm.txt

value: 0.6uM A1210477 treatment for 2days


title: patient_6_acute_rep3


title: patient_6_acute_rep2


title: LLC2


title: patient_6_recovery_rep1

value: after recovery


title: HX3_Stat5 OE 1

description:
HX3_GGCTAC
Stat5 OE_colon from male mouse at 8-12 weeks, VilCreER;icS5 (STAT5IEC+++)


title: HX2_Stat5 KO 1

description:
HX2_ATCACG
Stat5 KO_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5IEC-/-)

value: VilCreER;Stat5 (STAT5IEC-/-)


title: BCL-XL-A121-1

description:
cultured cells
processed_fpkm.txt

value: Embryonic stem cells

value: Constitutive BCL-XL overexpressed H9


title: BCL-XL-Ctrl-2

description:
cultured cells
processed_fpkm.txt


title: HX1_Stat5 control 1

description:
HX1_TAGCTT
Stat5 control_colon from male mouse at 8-12 weeks, VilCreER;Stat5 (STAT5+/+)

value: VilCreER;Stat5 (STAT5+/+)

value: 8-12 weeks

value: male


title: patient_6_acute_rep1


title: Gth_48L3

organism: Gossypium thurberi

value: Leaf

tag: developmental stage

value: one true leaf stage

tag: time point (hour)


title: patient_5_recovery_rep2

value: peripheral blood leukocytes


title: patient_5_recovery_rep3

value: female


title: Gth_48L2


title: Gtr_48L3

organism: Gossypium trilobum


title: Gth_48L1


title: Gth_48S3

value: Stem


title: Gtr_48L2


title: >80% FVC group replicate 6

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

description: Analysis used  normal human tissues as common reference samples for the comparison of IPF samples between different FVC groups.

hyb_protocol: Each IPF sample was hybridized to a miRNA microarray slide with the common reference for 16 - 18 h at 56°C. . After hybridization, the slides were stringency washed and dried.

scan_protocol: The hybridized slides were scanned with ScanArray Express (PerkinElmer Life and Analytical Sciences, Boston, MA)

data_processing: The images were analyzed using GenePix 5.0 pro (Axon Instruments, Inc., Union City, CA) for data extraction. The images and raw data were imported into the RealSpot software that was developed in our laboratory for quality control and Lowess normalization. The average of log2 (median-back ground) of the duplicated spots in each hybridization were calculated, and then the log2 ratio of the sample signal to the reference signal was calculated. The average of the log2 ratio from two channels hybridization was considered as the signal of that particular miRNA.

source_name: IPF patient >80% FVC group

label_protocol: Total RNAs from IPF lung tissues or the common reference were labeled with Hy3 or Hy5 using the miRCURY LNA™ microRNA power labeling kit (Exiqon, Woburn, MA)

extract_protocol: Total RNA was isolated from these lung tissues using Tri Reagents (Molecular Research Center, Cincinnati, OH)

tag: subject status

value: Idiopathic pulmonary fibrosis (IPF) patient

tag: fvc group

value: >80% FVC group

value: lung tissue

source_name: Normal human tissues

value: common reference sample

tag: tissue type

value: normal human tissues


title: >80% FVC group replicate 8


title: Gtr_48L1


title: patient_5_acute_rep2

tag: patient id

value: acute HHV-6 mononucleosis

tag: age


title: patient_5_recovery_rep1

tag: Stage

value: after recovery

tag: gender


title: >80% FVC group replicate 7

tag: tissue

tag: sample type


title: patient_5_acute_rep3


title: >80% FVC group replicate 5


title: LLC1

value: wild type

value: LLC-RFP alone

value: primary cancer sites


title: patient_5_acute_rep1


title: Gth_48R3

value: Root


title: >80% FVC group replicate 4-2


title: >80% FVC group replicate 4-1


title: Gtr_48S1


title: patient_4_recovery_rep3


title: >80% FVC group replicate 3


title: patient_4_recovery_rep2


title: Gth_48R1


title: Gtr_48R3


title: patient_4_recovery_rep1


title: Gtr_48S3


title: Gth_48S1


title: Gth_48S2


title: Gth_12L3


title: Gtr_48R2


title: >80% FVC group replicate 1


title: patient_4_acute_rep3


title: Gtr_48R1


title: Gtr_48S2


title: Gth_12L1


title: Gtr_12L3


title: Gth_12L2


title: 50%-80% FVC group replicate 10

source_name: IPF patient 50%-80% FVC group

value: 50%-80% FVC group


title: Gth_48R2


title: patient_4_acute_rep2


title: 50%-80% FVC group replicate 8


title: patient_4_acute_rep1


title: patient_3_recovery_rep3


title: Gth_12S3


title: Gtr_12L2

value: Leaf


title: Gtr_12L1

value: one true leaf stage


title: Gth_12S2


title: 50%-80% FVC group replicate 7


title: patient_3_recovery_rep2

value: peripheral blood leukocytes


title: Gtr_12S3


title: Gtr_12S2


title: Gth_12S1


title: >80% FVC group replicate 2


title: 50%-80% FVC group replicate 6


title: patient_3_recovery_rep1

value: female


title: 50%-80% FVC group replicate 5


title: Gtr_12S1

value: Stem


title: Gth_12R2


title: 50%-80% FVC group replicate 4

value: Idiopathic pulmonary fibrosis (IPF) patient


title: patient_3_acute_rep2


title: patient_3_acute_rep3


title: Gtr_12R3


title: 50%-80% FVC group replicate 9


title: Gth_12R1


title: 50%-80% FVC group replicate 3


title: patient_3_acute_rep1


title: Gtr_12R1


title: Gth_0L2


title: patient_2_recovery_rep3


title: patient_2_recovery_rep2


title: 50%-80% FVC group replicate 1


title: <50% FVC group replicate 10

source_name: IPF patient <50%FVC group

value: <50% FVC group


title: Gtr_0L3

source_name: cotton plant


title: Gth_0L1


title: patient_2_recovery_rep1


title: Gth_12R3


title: Gtr_0L2


title: Gth_0L3


title: <50% FVC group replicate 9

value: lung tissue


title: patient_2_acute_rep3


title: Gtr_0L1


title: Gth_0S2


title: <50% FVC group replicate 8

value: common reference sample


title: Gtr_12R2


title: Gtr_0S3


title: 50%-80% FVC group replicate 2

value: normal human tissues


title: Gtr_0S2


title: Gth_0R3


title: Gth_0S1


title: patient_2_acute_rep1

value: acute HHV-6 mononucleosis


title: <50% FVC group replicate 6


title: <50% FVC group replicate 7


title: Gtr_0S1


title: patient_1_recovery_rep2

value: after recovery


title: <50% FVC group replicate 5


title: patient_1_recovery_rep1


title: Gth_0R2


title: Gtr_0R3


title: Gth_0R1


title: patient_1_acute_rep3


title: Gtr_0R2


title: Gth_0S3


title: patient_1_acute_rep2


title: <50% FVC group replicate 4


title: Gtr_0R1


title: patient_2_acute_rep2


title: LCL_E

status: Public on Apr 01 2019

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

institute: University of Sydney

description: Whole blood samples were collected from healthy controls. For LCL generation, fresh or frozen PBMCs were infected with supernatant from B95.8 producer cell line for 1 hour at 37°C. Cells were then suspended in complete medium, consisting of RPMI-1640 (Lonza) supplemented with 10% fetal bovine serum (FBS, Sigma Aldrich), 2 mM L-glutamine (Life Technologies), 50 units per ml penicillin/50 g per ml streptomycin (Life Technologies) plus 2 μg/ml of cyclosporin A (Sigma Aldrich) and plated at 2.5×106 or 5×106 cells/well in 48-well plates. Cells were fed weekly, expanded into 25 cm2 flask. LCLs were cryopreserved in 10% DMSO (MP Biomedical) 50% FBS and RPMI.

data_processing:
Fastq files were aligned to hg19 using Tophat2 v2.0.9
Counts and RPKM per gene was calculated using the RAEM algorithm in SAMmate v2.6.1
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing counts and RPKM summarised at gene level using the RAEM algorithm in SAMmate v 2.6.1. Length of gene (sum of exons) in bp is also listed for each gene.

source_name: Lymphoblastoid cell line

extract_protocol:
Qiagen Rneasy Mini Kit
Illumina TruSeq V2 library preparation Kit

value: LCL

tag: individual id

value: E


title: 163A: HEK293T-P2A-EGFP-rep1

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). HepG2 cells (HB80-65, obtained from ATCC) were grown in EMEM (ATCC) supplemented with 10% FBS and 0.5% penicillin-streptomycin (Gibco).  Both cell lines were used for experiments until passage 20 for HEK293T and passage 12 for HepG2. Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells  were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s  NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep) encoding desired P2A-EGFP, variants thereof o. 6x10E6 HEK293T or 15x10E6 HepG2 were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) or 150uL transfeX (HepG2, ATCC) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). Cells were sorted 36-40h after transfection, for either top 5% or all-GFP after doublet-exlusion and gating for the cell population on a BD FACSARIA II.

tag: cell type

tag: guide

value: No gRNA

tag: gfp

value: Top 5%

tag: figure


title: <50% FVC group replicate 2


title: 149A: HepG2-P2A-EGFP-rep1

tag: treatment


title: <50% FVC group replicate 1


title: LCL_C

value: C


title: CD19+B_E

description: Whole blood samples were collected from healthy controls. B lymphocytes were purified by immunomagnetic human B cell enrichment Kit (Stem Cell Technologies) according to manufacturer's instructions.

source_name: CD19+ B cells


title: LCL_D

value: D


title: CD19+B_D


title: LCL_B

value: B


title: CD19+B_C


title: CD19+B_B


title: High vitamin D primary prostate epithelial cells

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

data_processing:
Fastq files were generated with the bclfastq v1.88.4 Conversion Software (Illumina).
Adaptor sequences were removed using cutadapt, and 3’ end trimming of bases with a Phred quality score <20. After processing, reads less than 17bp were discarded
Reads were aligned using SHRIMP 2.2.3 aligner (ungapped local alignment mode, seed size=14, 2 mismatched allowed) to miRNA stem-loop sequences from miRBase (release 21), piRNA sequences from piRNABank, and rRNA, snRNA, snoRNA and tRNA sequences were retrieved from Ensembl (version 90)
Only the highest scoring match strata were reported. Counts were generated using a custom script so that if one read sequence mapped to multiple small RNA species the final designation would be given in hierarchical order: miRNA, rRNA, snoRNA, snRNA, tRNA or piRNA. If one read sequence mapped to multiple of one species of small RNA, the read was split proportionally.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing counts data for miRNA, rRNA, snoRNA, snRNA, tRNA and piRNA for each sample

source_name: cells

growth_protocol: Isolated from benign prostatectomy tissue sample and grown for 1 passage in PrEGM media on collagen-coated dish.

extract_protocol:
RNAqueous-Micro kit (Ambion)
1000 ng of total RNA input into TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were multiplexed and sequenced on 1 lane (with other PrE sample, separate from tissue) for 51 cycles on a HiSeq2500 (Illumina).

treatment_protocol: 50nM of 1,25D (calcitriol) for 24hr

value: de-identified primary prostate epithelial cells

tag: vitamin d

value: high


title: High vitamin D prostate epithelium 3

source_name: tissue

extract_protocol:
Laser-capture microdissection of frozen tissue followed by RNAqueous-Micro kit (Ambion)
500 ng of total RNA input into TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were multiplexed and sequenced on 1 lane (with other prostate tissue samples) for 51 cycles on a HiSeq2500 (Illumina).

treatment_protocol: 40,000IU of vitamin D3 supplement daily for 3-8 weeks prior to prostatectomy

value: de-identified benign prostate epithelium


title: CD19+B_A

value: A


title: Control primary prostate epithelial cells

treatment_protocol: Ethanol (vehicle) for 24hr

value: control


title: High vitamin D prostate epithelium 4


title: Control prostate epithelium 3

treatment_protocol: 400IU of vitamin D3 supplement daily for 3-8 weeks prior to prostatectomy


title: <50% FVC group replicate 3

value: Idiopathic pulmonary fibrosis (IPF) patient

value: <50% FVC group

value: lung tissue


title: Control prostate epithelium 4


title: Control prostate epithelium 1

extract_protocol:
Laser-capture microdissection of frozen tissue followed by RNAqueous-Micro kit (Ambion)
500 ng of total RNA input into TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were multiplexed and sequenced on 1 lane (with other tissue samples) for 51 cycles on a HiSeq2500 (Illumina).


title: High vitamin D prostate epithelium 1


title: patient_1_acute_rep1

value: peripheral blood leukocytes

value: acute HHV-6 mononucleosis

value: female


title: MSC-exosome-hypoxia

description: Exosomes are isloated after MSCs were cultured in hypoxia

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: GeneSpring13.0(Agilent) was used for background subtraction and  normalization use in 90 percentile shift.

source_name: Mesenchymal stem cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: mBMSCs were cultured in MEM medium supplemented with penicillin G (100 U/mL),streptomycin (100 mg/mL)and 10% fetal calf serum.For hypoxia induction, cells were incubated in 0.2% oxygen concentration, 37 °C temperature, 5% CO2 concentration and 90% humidity in Hypoxic Workstation.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: After 72 h, cell culture medium were collected, and exosomes were isolated.

tag: cell line

value: MSCs

value: bone marrow


title: Vitamin D VDR-ChIP

description: Treated with 50nM of 1,25D (calcitriol) for 2 hr

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina).
Peak calling was performed using MACS2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing VDR binding peak locations

source_name: Primary prostate epithelial cells

growth_protocol: Primary prostate epithelial cells (PrE) were isolated from de-identified benign prostatectomy tissue and grown in PrEGM media (Lonza) for 1 passage.

extract_protocol:
Cross-linked using 1% formaldehyde for 10 min at RT, then 125 mM glycine for 5 min. Plates were washed 2X with ice-cold PBS, incubated in TrypLE at 37˚C for 3 min, and washed 2X with ice-cold PBS. Cells were lysed in Nuclear Isolation Buffer from Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore) on ice for 20 min with vortexing for 10 s every 5 min. Nuclei were pelleted at 800xg 5 min, then re-suspended in 1 ml RIPA buffer with Protease Inhibitor Cocktail III (Millipore). Cells were sonicated on ice for 15 s 9X setting 2 on a Sonic Dismembrator model 100 (Thermo Fisher). 10 µl of sonicated DNA (~10 ng) was saved as input control. 1ml of sonicated DNA (~1 µg) was used for VDR and normal IgG ChIPs. 300 µl Dynabeads (Thermo Fisher) were washed twice with 1.5 mL 1 mg/ml BSA/PBS 2 mM EDTA solution and once with 1.5 ml 5 mg/ml BSA/PBS. Beads were re-suspended in 1000 µl with 1 mg/ml BSA/PBS 2 mM EDTA solution and incubated with 24 µg of anti-VDR C-20x sc-1008x rabbit polyclonal (Santa Cruz) for 5 hrs, then washed again as above. Antibody-conjugated beads were incubated with sonicated DNA overnight rotating at 4˚C. Beads were washed 1x with 5:1 RIPA:PBS containing 5mg/mL BSA (fraction V) and Protease Inhibitor Cocktail III (Millipore), then 5x in LiCl IP wash buffer (100 mM Tris-HCl pH 7.5/ 500 mM LiCl/1% NP-40 /1% Sodium deoxycholate) and 1x in TE buffer. Bound DNA was eluted off the beads twice, with 100 µl ChIP Elution Buffer (Millipore) containing 283 mM NaCl and 1 µl proteinase K and heated at 65˚C for 1 hr with vortexing every 15 min. Eluted samples were combined and incubated at 65˚C overnight. Input 10 µl sample was combined with 90 µl ChIP Elution Buffer (Millipore) and 283 mM NaCl and 1 µl proteinase K and incubated at 65˚C along with the other samples. DNA was purified using the Clontech NucleoSpin kit (Clontech) and eluted twice using 20 µl of 70˚C elution buffer.
Libraries were prepared from 10 ng of ChIP DNA with the Library Construction Kit Kapa Biosystems (Wilmington, MA) with two modifications: adaptors were diluted 1:20 and adaptor-modifed DNA were amplified for 10 cycles. The pooled libraries were sequenced on one lane each for 101 cycles on a HiSeq2500 in High Output mode using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Six 100 mm dishes of PrE per condition were treated for 2 hr with 50 nM 1,25-VitaminD3 or EtOH (vehicle)

value: Primary prostate epithelial cells

tag: treatment group

value: vitamin D

tag: chip antibody

value: VDR


title: Vitamin D input


title: LCL_A

value: LCL


title: Ethanol input

description: Treated with ethanol (vehicle) for 2 hr


title: MSC-exosome-normoxia

description: Exosomes are isloated after MSCs were cultured in normoxia


title: 22Rv1_Oct1_DHT

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: ChIP by OCT1 antibody (Abcam ab15112)

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-5)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files that summarized significant peak regions (P-value < 10xE-5)

source_name: prostate cancer cells

growth_protocol: 22Rv1 cells were cultures in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.  Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN).  The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: 22Rv1 cells were treated with vehicle or DHT 10 nM for 24 h.

value: 22Rv1 cells

value: DHT10 nM

tag: antibody


title: 22Rv1_Oct1_Vehicle

description: ChIP by OCT1 antibody (Abcam ab15112)

value: ethanol (Vehicle) treatment


title: High vitamin D prostate epithelium 2

value: de-identified benign prostate epithelium

value: high


title: 22Rv1_Input_1

description: Input for FOXA1, K4me1

value: Input


title: 22Rv1_FOXA1_Vehicle

description: ChIP by FOXA1 antibody (abcam 23738)


title: 22Rv1_AcH3_Vehicle

description: ChIP by AcH3 antibody (Millipore #06-599)


title: 22Rv1_FOXA1_DHT

description: ChIP by FOXA1 antibody (abcam 23738)


title: 22Rv1_AcH3_DHT


title: C4-2R sample 3

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Tophat2 wass used to aligne the data with mismatches set at 1 and library type set to "fr-firststrand"
HTSeq Count v. 0.6.1  was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
EdgeR v. 3.12.1 (using Bioconductor v 3.2) were used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes (false discovery raye of 1%)
GSEA v. 3 was used in performing the GSEA analysis
Genome_build: GRCh38.p12 Ensembl reference genome
Supplementary_files_format_and_content: raw abundance measurements

source_name: whole cell

growth_protocol: prostate adenocarcinoma cells

extract_protocol:
TruSeq stranded kit
2x100 on a HiSeq2500

treatment_protocol: cell type

value: resistant


title: Control prostate epithelium 2

value: control


title: C4-2R sample 1


title: C4-2 sample 3

value: sensitive


title: 22Rv1_Input_2

description: Input for OCT1, AcH3


title: 22Rv1_K4me1_Vehicle

description: ChIP by K4me1 (Abcam ab8895)


title: LNCaP sample 2

value: LNCaP


title: MR49F sample 3


title: LNCaP sample 1


title: C4-2 sample 1


title: LNCaP sample 3


title: MR49F sample 2


title: MR49F sample 1


title: 22Rv1_K4me1_DHT

description: ChIP by K4me1 (Abcam ab8895)


title: Ethanol VDR-ChIP

description: Treated with ethanol (vehicle) for 2 hr


title: 153_GS1149_3_Bulk_TEM_93

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts of sequencing reads of genes for each sample

source_name: Cryopreserved PBMC_Bulk_TEM

growth_protocol: Human PBMCs were rested overnight at 37 °C and subsequently stimulated with DENV CD8 T cell peptide pool (1 μg/ml for individual peptides) for 3 h (Weiskopf et al., 2015b). IFN-gamma-producing cells were labeled using IFN-γ Secretion Assay – Detection Kit (catalog# 130-054-202, Miltenyi Biotech) according to the manufacturer’s instructions. Subsequently, PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD45RA, and CCR7 (see Supplementary Table 2 for antibody details). CD8 IFN-gamma- and IFN-gamma+ naïve (CD14-CD19-CD3+CD4-CD8+CD45RA+CCR7+), TCM (CD14-CD19-CD3+CD4-CD8+CD45RA-CCR7+), TEM (CD14-CD19-CD3+CD4-CD8+CD45RA-CCR7-), and TEMRA (CD14-CD19-CD3+CD4-CD8+CD45RA+CCR7-) cells were sorted into 8 μL of lysis buffer consisting of Triton X-100 (Sigma-Aldrich), recombinant ribonuclease inhibitor (Takara), and dNTP mix (Thermo Fisher Scientific).

extract_protocol:
For each condition, 200 cells were collected at 4 ˚C in 8 μL of lysis buffer composed by 0.2% Triton X-100, 2 U/ul of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in 0.2 ml PCR tube (Maxymum recovery, Axygen). Right after sort, tubes were vortexed at medium speed, spun for 5 minutes at >2000 g and stored at -80˚C until the completion of the whole set of samples. Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al., 2014; Rosales et al., 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo (Picelli et al., 2014; Rosales et al., 2018). cDNA was amplified by PCR for 18 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).
For each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina). Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size. Samples that failed quality controls were eliminated from downstream steps. Library that passed strict quality controls were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference, generating a total of about 204.3 million mapped reads (median of about 8.6 million filtered mapped reads per sample).
RNA-Seq (Microscaled (SmartSeq2) cDNA amplification; HISeq 2500 illumina, Single-end 50bp)

tag: disease group

value: Sri Lanka secondary

tag: donor id

tag: cell subset


title: C4-2 sample 2


description: X081_GS1188_12_MHCI_IFNgamma_pos_TEMRA_90_N712S503


title: 144_GS1188_11_MHCI_IFNgamma_pos_TEM_69

description: X144_GS1188_11_MHCI_IFNgamma_pos_TEM_69_N726S518


title: C4-2R sample 2


title: 078_GS1188_4_Bulk_TEMRA_87

source_name: Cryopreserved PBMC_Bulk_TEMRA


title: 077_GS1188_3_Bulk_TEM_86


title: 070_GS1178_11_MHCI_IFNgamma_pos_TEM_79

description: X070_GS1178_11_MHCI_IFNgamma_pos_TEM_79_N710S508


title: 043_GS1169_4_Bulk_TEMRA_51


title: 064_GS1178_4_Bulk_TEMRA_73


title: 042_GS1169_3_Bulk_TEM_50


description: X048_GS1169_12_MHCI_IFNgamma_pos_TEMRA_57_N708S502


title: 034_GS1168_11_MHCI_IFNgamma_pos_TEM_42

description: X034_GS1168_11_MHCI_IFNgamma_pos_TEM_42_N706S503


description: X035_GS1168_12_MHCI_IFNgamma_pos_TEMRA_43_N706S504


description: X016_GS1149_12_MHCI_IFNgamma_pos_TEMRA_17_N703S502


title: 026_GS1168_3_Bulk_TEM_34


title: 027_GS1168_4_Bulk_TEMRA_35


title: 002_GS1180_3_Bulk_TEM_2


title: 008_GS1180_12_MHCI_IFNgamma_pos_TEMRA_9

description: X008_GS1180_12_MHCI_IFNgamma_pos_TEMRA_9_N702S502


title: 007_GS1180_11_MHCI_IFNgamma_pos_TEM_8

description: X007_GS1180_11_MHCI_IFNgamma_pos_TEM_8_N701S517


title: 003_GS1180_4_Bulk_TEMRA_3


title: 012_GS1149_4_Bulk_TEMRA_13