title: 19-VAT-Treg-F1_S3: VAT-Treg-Female-Rep1

source_name: Treg cells were Flow cytometry sorted from 25 week old female Foxp3RFP mice (RFP+) n=4 mice, pooled

value: Treg cells


title: 34-VAT-CD4-F1_S11: VAT-CD4-Female-Rep1

status: Public on Feb 28 2020

type: SRA

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

library_source: transcriptomic

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Subread-1.6.2; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.10 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

molecule: total RNA

organism: Mus musculus

source_name: CD4+ T cells were Flow cytometry sorted from 25 week old female Foxp3RFP mice (RFP-) n=4 mice, pooled

extract_protocol:
RNA purification was performed following the manufacturer's protocol using the RNAeasy Plus Mini or Micro Kit (Qiagen). For VAT and adipocyte samples RNA was extracted using Qiagen Rneasy lipid tissue mini kit as per the manufacterurs protocol.  tissue RNA kit was used
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA). Library for Stroma-GP38+ Male/female, Stroma-GP38- Male/Female and VAT ILC2 Male/Female RNA libraries were made using Clontech kit as per the manufacterurs protocol.

tag: strain

tag: tissue

value: visceral adipose tissue

tag: cell type

value: CD4 T cells

tag: Sex

value: Female


title: 25-VAT-CD4-M1_S9: VAT-CD4-Male-Rep1

source_name: CD4+ T cells were Flow cytometry sorted from 25 week old male Foxp3RFP mice (RFP-) n=4 mice, pooled

value: Male


title: MDA-MB-231_rep3_hydroseq

city: Barcelona

first: Luis

last: Serrano

address: C/ Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

description: Size-fractionated RNA (~60-100 nt)

data_processing:
Sequencing adapters were trimmed using BBDuk from the BBMap toolkit [v38.22] (https://sourceforge.net/projects/bbmap): k-mer=10 (allowing 8 at the end of the read), Hamming distance=1, length=10-50bp, Phred>25.
A total of 856 nuclear tRNAs and 21 mitochondrial tRNAs were annotated with tRNAscan-SE [v2.0]
Trimmed fastq files were then mapped using a specific pipeline for tRNAs (Hoffmann et al., Bioinformatics, 2018). Summarizing, an artificial genome is first generated by masking all annotated tRNA genes and adding pre-tRNAs (i.e. tRNA genes with 3' and 5' genomic flanking regions) as extra chromosomes. Upon mapping to this artificial genome with Segemehl [v0.3.1], reads that map to the tRNA-masked chromosomes or to the tRNA flanking regions are filtered out in order to remove non-tRNA reads and unmature-tRNA reads respectively. After this first mapping step, a second library is generated by adding 3' CCA tails and removing introns from tRNA genes. All 100% identical sequences of this so-called mature tRNAs are clustered to avoid redundancy. Next, the subset of filtered reads from the first mapping is aligned against the clustered mature tRNAs using Segemehl [v0.3.1]. Mapped reads are then realigned with GATK IndelRealigner [v3.8] to reduce the number of mismatching bases across all reads.
For quantification, isoacceptors were quantified as reads per million (RPM). In order to increase the coverage for anticodon-level quantification, we consider all reads that map unambiguously to a certain isoacceptor, even though they ambiguously map to different isodecoders (i.e. tRNA genes that differ in their sequence but share the same anticodon). Ambiguous reads mapping to genes of different isoacceptors were discarded.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-separated file that, for each sample, includes the RPM values for each isoacceptor, as well as the total number of mature tRNA mapped reads.

organism: Homo sapiens

growth_protocol: Cells were maintained at 37 °C in a humidified atmosphere at 5% CO2 in DMEM 4.5g/L Glucose with UltraGlutamine media supplemented with 10% of FBS and 1% penicillin/streptomycin.

extract_protocol:
Hydro-tRNAseq: Total RNA was resolved on 15% Novex TBE urea gels and size-selected for 60-100 nt fragments. The recovered material was then alkaline hydrolyzed (10mM sodium carbonate and 10mM sodium bicarbonate) for 10 minutes at 60ºC. The resulting RNA was de-phosphorylated with Antarctic Phosphatase (New England Biolabs) at 37ºC for 1 hour. De-phosphorylated RNA was purified with an RNeasy MinElute spin column and re-phosphorylated with Polynucleotide Kinase (NEB). PNK-treated tRNAs were purified with an RNeasy MinElute spin column and, similar to small RNA-seq library preparation, adaptor-ligated, reverse-transcribed and PCR-amplified for 14 cycles.
Cells were grown in 60mm dishes for 48h. Total RNA from HeLa, HEK293, HCT116, MDA-MB-231 and fibroblast BJ/hTERT was extracted using the miRNeasy Mini kit. Independent replicates where grown and RNA was extracted on different days.
Upon applying either the hydro-tRNAseq or small RNA-seq protocol, the resulting cDNA was purified using a QIAQuick PCR Purification Kit. The adaptor ligated to the 3' end of the RNA is the standard TruSeq adaptor: 5’-AGATCGGAAGAGCACACGTCT-3’. The adaptor ligated to the 5' end is the TruSeq smallRNA adaptor: 5’-GTTCAGAGTTCTACAGTCCGACGATC-3’.

tag: cell line

value: breast

tag: fraction

value: Size-fractionated RNA (~60-100 nt)


title: PHH_day0_rep3

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

country: Japan

institute: Takeda pharmaceuticals

description: Sample 12

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer ( Torrent suite ver.5.10.1 ) .
Sequenced reads were trimmed for adaptor sequence low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using a combination of using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.10.1  )
RPM were calculated using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.0.4.0  )
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: Tab-delimited text file includes gene symbol and gene expression (RPM) for each sample.

source_name: PHH at day0 #3

extract_protocol:
RNAs were extracted using RNAeasy mini Kit (Qiagen) following manufacturer's instructions.
Libraries were prepared according to the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). Briefly, cDNA was generated from 10ng of total RNA. The resulted cDNA was amplified and barcoded using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Barcoded cDNA Libraries were quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific). Libraries were then diluted to 45 pM and pooled  by combining an equal volume of each.

tag: genotype

value: wild type

value: primary hepatocytes

tag: age

value: day 0


title: PHH_day0_rep1

description: Sample 10

source_name: PHH at day0 #1


title: PXB_cells_day8_rep3

description: Sample 9

source_name: PXB cells at day8 #3

value: hepatocytes from liver humanized mice

value: day8 in culture


title: HEK293_rep3_smallRNAseq

description: No fractionation

extract_protocol:
Small RNA-seq: Total RNA was directly adaptor-ligated, reverse-transcribed and PCR-amplified for 12 cycles.
Cells were grown in 60mm dishes for 48h. Total RNA from HeLa, HEK293, HCT116, MDA-MB-231 and fibroblast BJ/hTERT was extracted using the miRNeasy Mini kit. Independent replicates where grown and RNA was extracted on different days.
Upon applying either the hydro-tRNAseq or small RNA-seq protocol, the resulting cDNA was purified using a QIAQuick PCR Purification Kit. The adaptor ligated to the 3' end of the RNA is the standard TruSeq adaptor: 5’-AGATCGGAAGAGCACACGTCT-3’. The adaptor ligated to the 5' end is the TruSeq smallRNA adaptor: 5’-GTTCAGAGTTCTACAGTCCGACGATC-3’.

value: kidney

value: No fractionation


title: PHH_day0_rep2

description: Sample 11

source_name: PHH at day0 #2


title: 6-VAT-adipocytes-M2_S6: VAT-adipocytes-Male-Rep2

source_name: Stromal vascular fraction removed adipocytes from 25 week old male mice (n=4, pooled)

value: Adipocytes


title: 5-VAT-adipocytes-M1_S5: VAT-adipocytes-Male-Rep1


title: BJ_rep3_hydroseq

description: Size-fractionated RNA (~60-100 nt)

value: BJ fibroblasts

value: fibroblasts


title: MDA-MB-231_rep1_hydroseq

description: Size-fractionated RNA (~60-100 nt)


title: PXB_cells_day8_rep2

description: Sample 8

source_name: PXB cells at day8 #2


title: MDA-MB-231_rep2_hydroseq

description: Size-fractionated RNA (~60-100 nt)


title: 7-VAT-adipocytes-F1_S7: VAT-adipocytes-Female-Rep1

source_name: Stromal vascular fraction removed adipocytes from 25 week old female mice (n=4, pooled)


title: PHH_day1_rep2

description: Sample 14

source_name: PHH at day1 #2

value: day 1 in culture


title: PXB_cells_day8_rep1

description: Sample 7

source_name: PXB cells at day8 #1


title: PXB_cells_day4_rep3

description: Sample 6

source_name: PXB cells at day4 #3

value: day 4 in culture


title: 2-Subcutaneous-adipose-tissue-M2_S2: Subcutaneous-adipose-tissue-Male-Rep2

source_name: Inguinal adiose tissue from 25 wek old male mice (n=4, pooled)

value: Subcutaneous adipose tissue

value: adipose tissue


title: 1-Subcutaneous-adipose-tissue-M1_S1: Subcutaneous-adipose-tissue-Male-Rep1

value: Male


title: BJ_rep1_hydroseq

description: Size-fractionated RNA (~60-100 nt)


title: 4-Subcutaneous-adipose-tissue-F2_S4: Subcutaneous-adipose-tissue-Female-Rep2

source_name: Inguinal adiose tissue from 25 wek old female mice (n=4, pooled)

value: Female


title: HCT116_rep3_hydroseq

description: Size-fractionated RNA (~60-100 nt)

value: colon

value: Size-fractionated RNA (~60-100 nt)


title: pbNK; #2

type: RNA

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: microRNA expression data of pbNK isolated from peripheral blood of healthy pregnant woman in the first trimester of gestation

hyb_protocol: The Biotin labelled RNA was subsequently hybridized to a GeneChip™ miRNA 4.1 array plate (Thermo Fisher Scientific). The hybridization, wash and staining procedures were done in according to the manufacturer’s protocol (Thermo Fisher Scientific).

scan_protocol: The scanning procedure was done in a GeneTitan™ Instrument (Thermo Fisher Scientific).

data_processing: The .cel file output were used as input in the Transcriptome Analysis Console Software v 4.0.1 (TAC; Thermo Fisher Scientific) for generation of RMA normalized data using default settings for Affymetrix miRNA 4.1 library configuration. eBayes Anova method was used for limma differential expression analysis

label: biotin

source_name: pbNK cells

label_protocol: Total RNA (140 ng per sample) was used as start material for the microarray. Biotin labelled RNA was generated using the FlashTag Biotin HSR Labelling Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.

extract_protocol: Total RNA extraction was performed with miRNeasy micro kit following the manufacturer’s protocol (Qiagen)

treatment_protocol: pbNK isolated from peripheral blood of pregnant woman with RosetteSep human  NK enrichment cocktail (StemCell Technologies)

tag: gender

value: female

tag: developmental stage

value: pregnant

value: peripheral blood

value: pbNK cells


title: 8-VAT-adipocytes-F2_S8: VAT-adipocytes-Female-Rep2

value: visceral adipose tissue

value: adipocytes


title: pbNK; #4


title: pbNK; #3


title: HCT116_rep2_hydroseq

description: Size-fractionated RNA (~60-100 nt)


title: PXB_cells_day4_rep1

description: Sample 4

source_name: PXB cells at day4 #1

value: wild type

value: hepatocytes from liver humanized mice


title: 3-Subcutaneous-adipose-tissue-F1_S3: Subcutaneous-adipose-tissue-Female-Rep1

value: Adipose tissue


title: PXB_cells_day1_rep3

description: Sample 3

source_name: PXB cells at day１ #3

value: day 1 in culture


title: HELA_rep3_hydroseq

description: This sample has also been deposited in ArrayExpress under accession number E-MTAB-8144.

value: HELA

value: cervix


title: PXB_cells_day1_rep2

description: Sample 2

source_name: PXB cells at day１ #2


title: 14-Stroma-GP38-neg-M2_S2: Stroma-GP38-neg-Male-Rep2

source_name: CD45-Ter119-GP38 stromal cells were flow cytometry sorted from 25 week old male mice (n=4, pooled)

value: stromal cells


title: dILC3; pool #3

description: microRNA expression data of dNK sorted from decidua of healthy pregnant woman in the first trimester of gestation

source_name: NCR+ dILC3 cells

treatment_protocol: Sorted cells from cell suspensions of decidual tissue obtained with GentleMacs dissociator (Miltenyi Biotech)

value: decidua basalis

value: NCR+ dILC3 cells


title: 13-Stroma-GP38-neg-M1_S1: Stroma-GP38-neg-Male-Rep1

value: Male


title: BJ_rep2_hydroseq

description: Size-fractionated RNA (~60-100 nt)

value: BJ fibroblasts

value: fibroblasts

value: Size-fractionated RNA (~60-100 nt)


title: PXB_cells_day4_rep2

description: Sample 5

source_name: PXB cells at day4 #2

value: day 4 in culture


title: 16-Stroma-GP38-neg-F2_S4: Stroma-GP38-neg-Female-Rep2

source_name: CD45-Ter119-GP38 stromal cells were flow cytometry sorted from 25 week old female mice (n=4, pooled)

value: Female


title: PXB_cells_day1_rep1

description: Sample 1

source_name: PXB cells at day１ #1


title: dILC3; pool #2

value: female

value: pregnant


title: dILC3; pool #1

description: microRNA expression data of dNK sorted from decidua of healthy pregnant women in the first trimester of gestation


title: HELA_rep2_hydroseq


title: HELA_rep1_hydroseq


title: 15-Stroma-GP38-neg-F1_S3: Stroma-GP38-neg-Female-Rep1

value: visceral adipose tissue


title: pbNK; #1

value: peripheral blood

value: pbNK cells


title: HCT116_rep1_hydroseq

description: Size-fractionated RNA (~60-100 nt)

value: colon


title: LLO118 D7-biological replicate 3

city: St. Louis

first: Paul

middle: M

last: Allen

state: MO

address: 660 S. Euclid, Box 8118

department: Pathology and Immunology

country: USA

institute: Washington University

description:
Gene expression data from D7 activated T cells
sample name:
24673

hyb_protocol: 5.5 µg cDNA were hybridized to Affymetrix Mouse Gene 1.0 ST arrays using standard Affymetric protocols (GPL6246).

scan_protocol: scan protocol not provided

data_processing: The naive and D7 data were normalized separately using RMA in Arraystar 12.

source_name: CD4+ T cells

label_protocol: RNA was purified from 1.5 – 2 x 106 T cells using an RNeasy Mini Kit (Qiagen #74104) and a cDNA library generated using a NuGen Pico SL kit.

extract_protocol: Naive LLO118 and LLO56 T cells were purified from the spleens of individual mice from each of the TCRtg lines using a Miltenyi CD4+ isolation selection kit (#130-104-454). For the D7 in vivo activated T cell isolation, 10e4 of naive either LLO118 or LLO56 T cells were injected into a wildtype C57BL/6J mouse on Day-1.  On D0, they were infected with Listeria monocytogenes and the spleens from individual mice were harvested on D7. The T cells were purified by FACS on a BD FACSAria by sorting on CD4+ and the appropriate congenic marker (Thy1.1 for LLO118 and Ly5.1 for LLO56).  A dump gate of CD8, CD11b, CD11c, CD19, NK1.1, and MHC class II was used to exclude non-CD4+ cells.

tag: background strain

tag: tcr transgenic line

value: spleen

value: CD4+ T cells

tag: activation state

value: D7 in vivo activated


title: LLO118 D7-biological replicate 2

description:
Gene expression data from D7 activated T cells
sample name:
24672


title: HEK293_rep3_hydroseq

value: kidney


title: dNK; #5

source_name: dNK cells

value: decidua basalis

value: dNK cells


title: dNK; #4


title: LLO118 D7-biological replicate 1

description:
Gene expression data from D7 activated T cells
sample name:
24671


title: 9-Stroma-GP38-M1_S9: Stroma-GP38-Male-Rep2

source_name: CD45-Ter119-GP38+ stromal cells were flow cytometry sorted from 25 week old male mice (n=4, pooled)

value: stromal cells

value: Male


title: 10-Stroma-GP38-M2_S10: Stroma-GP38-Male-Rep1


title: HEK293_rep1_hydroseq

value: Size-fractionated RNA (~60-100 nt)


title: HEK293_rep2_hydroseq


title: dNK; pool #3


title: 12-Stroma-GP38-F2_S12: Stroma-GP38-Female-Rep2

source_name: CD45-Ter119-GP38+ stromal cells were flow cytometry sorted from 25 week old Female mice (n=4, pooled)

value: Stromal cells


title: LLO56 D7-biological replicate 4

description:
Gene expression data from D7 activated T cells
sample name:
24669


title: dNK; pool #2


title: RPE3

city: Dresden

first: Seba

last: Almedawar

address: Fetscherstrasse 105

country: Germany

institute: CRTD- TU Dresden

data_processing:
basecalling: Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
mapping: Reads were aligned to the human genome assembly (hg38) using GSNAP (2014-12-17; parameters: gsnap  -d hg38 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-81.ss.hg38.iit  -n 1 -A sam) with known splice sites from Ensembl (v81) as support.
gene counting: Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.4.6-p5; parameters: -a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx582.featureCounts.hg38.e81.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

growth_protocol: stem cells were maintained with mTESR1 on human qualified matrigel and passaged with dispase. RPE were differentiated on traswells, which were coated with growth factor reduced matrigel. The RPE was maintained with RPE media containing serum knock out as decribed in Zhu et al. PlosOne. 2013. RPE were passaged twice on transwells before RNA was isolated

extract_protocol:
RNA was extracted from one well from each of the three preps using Qiagen RNeasy Mini kit by lysing the cells inside the well.
mRNA enrichment and  reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

treatment_protocol: no treatment

value: hESC derived RPE

tag: passage

tag: genotype/variation

value: wild-type


title: 11-Stroma-GP38-F1_S11: Stroma-GP38-Female-Rep1

value: Female


title: RPE2


title: LLO56 D7-biological replicate 3

description:
Gene expression data from D7 activated T cells
sample name:
24668


title: LLO118 D7-biological replicate 4

description:
Gene expression data from D7 activated T cells
sample name:
24674


title: RPE1


title: 21-Spl-Treg-M1_S5: Spl-Treg-Male-Rep1

source_name: Treg cells were sorted from the spleen of male Foxp3RFP mice (n=3, pooled)

value: Spleen

value: Treg cells


title: 22-Spl-Treg-M2_S6: Spl-Treg-Male-Rep2


title: LLO56 D7-biological replicate 2

description:
Gene expression data from D7 activated T cells
sample name:
24667


title: LLO56 D7-biological replicate 1

description:
Gene expression data from D7 activated T cells
sample name:
24666


title: ESC2

value: human embryonic stem cells (hESC)


title: ESC3


title: LLO118 naive-biological replicate 4

description:
Gene expression data from naive T cells
sample name:
24338

value: naive


title: ESC1


title: 24-Spl-Treg-F2_S8: Spl-Treg-Female-Rep2

source_name: Treg cells were sorted from the spleen of female Foxp3RFP mice (n=3, pooled)


title: MaleVATILC2-2_S2: MaleVATILC2-Rep2

source_name: ILC2s were flow cytometry sorted (Lin-CD25+ST2+KLRG1+) from VAT of 25 week old male mice (n=5, pooled)

value: Visceral adipose tissue


title: 23-Spl-Treg-F1_S7: Spl-Treg-Female-Rep1


title: LLO56 D7-biological replicate 5

description:
Gene expression data from D7 activated T cells
sample name:
24670

value: spleen

value: CD4+ T cells


title: LLO118 naive-biological replicate 2

description:
Gene expression data from naive T cells
sample name:
24329


title: MaleVATILC2-1_S1: MaleVATILC2-Rep1


title: LLO118 naive-biological replicate 3

description:
Gene expression data from naive T cells
sample name:
24335


title: 19484 RNA-Seq

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
RNA-Seq data: Cutadapt (version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Bowtie2 (version 2.3.1) was used to align the trimmed reads to the GENCODE comprehensive gene annotation (release 23, hg38) and RSEM (version 1.2.30) was used to quantify gene expression in a strand-specific manner by setting parameter “--forward-prob 0”. DESeq2 (version 1.12.4) was used to perform differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content:  [RNA-Seq data]  gene id, transcript id, length, effective_length, expected count, TPM, FPKM

source_name: blood

extract_protocol:
Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit.
Illumina’s TruSeq Stranded RNA with Ribo-Zero (Human) for ribo-depletion kit was used to construct strand specific libraries for each sample.

tag: individual

tag: chromosomes

value: XO

value: blood

value: primary lymphocytes


title: LLO118 naive-biological replicate 1

description:
Gene expression data from naive T cells
sample name:
24328


title: dNK; pool #1

value: female

value: pregnant

value: decidua basalis

value: dNK cells


title: M2-ND_S2: Male-ND-Rep2

source_name: Epididymal adipose tissue from 3 25 week old male mice pooled

tag: strain

value: Adipose tissue

value: Male


title: M3-ND_S3: Male-ND-Rep3

tag: tissue


title: LLO56 naive-biological replicate 4

description:
Gene expression data from naive T cells
sample name:
24327

tag: cell type


title: 19630 RNA-Seq

value: XX


title: 19426 RNA-Seq


title: LLO56 naive-biological replicate 3

description:
Gene expression data from naive T cells
sample name:
24326


title: M1-ND_S1: Male-ND-Rep1

tag: Sex


title: 29-Foxp3Cre-VAT-Treg-1_S7: Foxp3Cre-VAT-Treg

source_name: Treg cells  (YFP+) were Flow cytometry sorted from spleens of 25 week old lFoxp3cre mice. Spleens from 4 mice pooled


title: 33-Foxp3Cre-Spl-Treg-2_S11: Foxp3Cre-Spl-Treg-Rep2

value: Spleen


title: 19360 RNA-Seq

value: XXY


title: 19361 RNA-Seq

value: XY


title: 19406 RNA-Seq


title: LLO56 naive-biological replicate 1

description:
Gene expression data from naive T cells
sample name:
24324

value: naive


title: 19355 RNA-Seq


title: 32-Foxp3Cre-Spl-Treg-1_S10: Foxp3Cre-Spl-Treg-Rep1

source_name: Treg cells (YFP+) were Flow cytometry sorted from spleens of 25 week old lFoxp3cre mice. Spleens from 4 mice pooled

value: Treg cells


title: 19293 RNA-Seq


title: LM5-M

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
The total  number of usable reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST, onto the mature miRNA sequence
The abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: UCSC mm10

growth_protocol: 4 week old mice were shaved and euthanized as untreated mice or included in the UVB treatment protocol

extract_protocol: Total RNA from frozen (-80C) skin and tumors were extracted using the Ambion miRVANA RNA extraction kit

treatment_protocol: Dorsal skin from control mice was collected and flash frozen in liquid nitrogen and stored at -80C, while SCC tissues were harvested from euthanized mice chronically treated with UVR (2.5 kJ/m2, 3x a week) and flash frozen in liquid nitrogen and stored at -80C

value: >35 weeks

tag: treatment

value: Chronic UVR (2.5 kJ/m2, 3x a week)

value: cutaneous squamous cell carcinoma


title: LM6-M


title: LLO56 naive-biological replicate 2

description:
Gene expression data from naive T cells
sample name:
24325

value: spleen

value: CD4+ T cells


title: 19198 RNA-Seq

value: blood

value: primary lymphocytes


title: LM4-M


title: FemaleVATILC2-1_S3: FemaleVATILC2-Rep1

source_name: ILC2s were flow cytometry sorted (Lin-CD25+ST2+KLRG1+) from VAT of 25 week old female mice (n=5, pooled)

value: Visceral adipose tissue

value: Female


title: 19197 RNA-Seq


title: FemaleVATILC2-2_S4: FemaleVATILC2-Rep2


title: 19171 RNA-Seq


title: F3-ND_S6: Female-ND-Rep3

source_name: periovarian adipose tissue from 3 female 25 week old mice pooled

value: adipose tissue


title: F2-ND_S5: Female-ND-Rep2


title: LM2-M

value: Wild-type


title: 19170 RNA-Seq


title: 28-Blimp1Foxp3Cre-VAT-Treg-2_S6: Blimp1Foxp3Cre-VAT-Treg-Rep2

source_name: Treg cells were Flow cytometry sorted from visceral adipose tissue (VAT) of 25 week old male Blimp1fl/flFoxp3cre mice. VAT from 5 mice pooled

value: Male


title: 19150 RNA-Seq


title: 27-Blimp1Foxp3Cre-VAT-Treg-1_S5: Blimp1Foxp3Cre-VAT-Treg-Rep1

source_name: Treg cells  (YFP+) were Flow cytometry sorted from visceral adipose tissue (VAT) of 25 week old male Blimp1fl/flFoxp3cre mice. VAT from 5 mice pooled


title: 19169 RNA-Seq


title: F1-ND_S4: Female-ND-Rep1

value: Adipose tissue


title: LM1-M


title: Su-M6

value: 4 weeks

value: Untreated

value: skin


title: Su-M5


title: 19018 RNA-Seq

value: XY


title: Su-M4


title: 30-Blimp1Foxp3Cre-Spl-Treg-1_S8: Blimp1Foxp3Cre-Spl-Treg-Rep1

source_name: Treg cells  (YFP+) were Flow cytometry sorted from spleens of 25 week old Blimp1fl/flFoxp3cre mice. Spleens from 4 mice pooled

value: Treg cells


title: 19117 RNA-Seq

value: XX


title: 31-Blimp1Foxp3Cre-Spl-Treg-2_S9: Blimp1Foxp3Cre-Spl-Treg-Rep2


title: Su-M3


title: 18968 RNA-Seq

value: XO


title: Su-M2


title: Su-M1


title: LM3-M

value: >35 weeks

value: Chronic UVR (2.5 kJ/m2, 3x a week)

value: cutaneous squamous cell carcinoma


title: 18833 RNA-Seq

value: XXY

value: blood

value: primary lymphocytes


title: 18825 RNA-Seq


title: SAG2

city: Madrid

first: Ignacio

last: Benedicto

state: Madrid

address: Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description:
SAG2_S46_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt

data_processing:
Single cell RNAseq: primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA). 10X Genomics Cell Ranger Single Cell Software suite v2.1.0 was used to perform sample de-multiplexing, alignment (mm10), filtering, UMI counting, single-cell 3’end gene counting and performing quality control using the manufacturer parameters. Unsupervised cell clustering analysis was carried out using the Seurat 2.1 R package. Cells with <1700 UMIs, <600 genes or >10% mitochondrial genes were excluded from the analysis, as well as genes detected in <3 cells. Gene expression raw counts were normalized following a global-scaling normalization method with a scale factor of 10,000 and a log transformation, using the Seurat NormalizeData function. The top 2000 highly variable genes from C57BL/6J and B6129PF1/J datasets were selected, followed by a canonical correlation analysis (CCA) to identify common sources of variation between the two datasets and minimize batch effect. The first 11 aligned CCA results were used to generate 2-dimensional t-Distributed Stochastic Neighbor Embedding (RunTSNE in Seurat, perplexity = 30) and unsupervised cell clustering by a shared nearest neighbor (FindClusters in Seurat, k.param = 30 and resolution = 0.8).
Bulk RNAseq: Illumina Casava 1.8.2 software used for basecalling. Upon quality control using FastQC, raw reads were aligned to the mouse genome (mm10) using STAR_2.4.0f1 and SAMTOOLS v0.1.19 for sorting and indexing reads. Cufflinks (2.0.2) was used to get the expression values (FPKM; Fragments Per Kilobase of transcripts per Million reads). To determine the genes differentially expressed between choroidal ECs and ECs from neural retina, lung, liver and heart, statistical significance was calculated using DEseq2 bioconductor package in R, which uses read counts (htseq-count).
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNAseq of RPE/choroid tissue: tab-delimited text files include gene ID, AdjP_val (P-value calculated using likelihood-ratio test and adjusted by the Benjamini-Hochberg method), avg_diff, (log e fold change between the average expression in a given cluster and the average expression of all cells in the rest of clusters) and avg_UMI (average normalized UMIs). Bulk RNAseq of tissue-specific ECs: tab-delimited text file includes gene ID, average FPKMs, fold change versus choroid ECs and adjusted P value versus choroid ECs. Bulk RNAseq of RPE/choroid tissue from Ihh+/+ and IhhiΔEC/ΔiEC mice and from cultured choroidal GLI1+ cells: tab-delimited text files include gene ID, log2 fold change, adjusted P value and average FPKMs.

source_name: Cultured choroidal GLI1+ cells

extract_protocol:
Single cell RNAseq: after eye enucleation, neural retina was removed and RPE/choroid was mechanically dissected from the sclera and digested in the presence of 1mM Hoechst to label nuclei during digestion. The cell suspension was pelleted, resuspended in sorting buffer (PBS plus 5% FBS and 2mM EDTA), filtered through a 70 µm cell strainer, stained with 1 µg/ml TO-PRO-3 and purified by fluorescence-activated cell sorting with gates set to include Hoechst+ nucleated particles and to exclude TO-PRO-3+ dead cells. Collected cells were pelleted, resuspended in sorting buffer at a concentration between 250-500 cells/µl and loaded onto the 10x Genomics Chromium platform. Bulk RNAseq of tissue-specific endothelial cells: after tissue digestion, ECs were isolated by fluorescence-activated cell sorting and RNA was extracted immediately with TRI Reagent (Molecular Research Center, Inc.) and purified with RNeasy Mini Kit (Qiagen). Bulk RNAseq of RPE/choroid tissue from Ihh+/+ and IhhiΔEC/ΔiEC mice: after eye enucleation, neural retina was removed and RPE/choroid was mechanically dissected and used for RNA extraction using the RNeasy Mini Kit (Qiagen). Bulk RNAseq of cultured choroidal GLI1+ cells: RNA was extracted with RNeasy Mini Kit (Qiagen). All cDNA libraries for bulk RNAseq assays were prepared with the TruSeq RNA Sample Preparation Kit (Illumina).
Single cell RNAseq: the 10x Genomics Chromium platform was used to generate barcoded single-cell GEMs, targeting about 5000 single cells per sample. GEM-reverse transcription (53 °C for 45 min, 85 °C for 5 min) was performed in a C1000 Touch thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules, CA). Next, GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified (98 °C for 3 min; 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min x 12 cycles) using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Quality of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1170 bp. Amplified cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min). Indexed libraries were subjected to a second double-sided size selection, and libraries were then quantified using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA). The quality was assessed on an Agilent Bioanalyzer 2100, obtaining an average library size of 455bp. Bulk RNAseq: RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: SWR/J

value: 100nM SAG for 24h

value: Cultured choroidal GLI1+ cells


title: 18665 RNA-Seq


title: 18707 RNA-Seq


title: SAG1

description:
SAG1_S45_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt


title: C3

description:
C3_S44_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt

value: DMSO (24h)


title: SAG3

description:
SAG3_S47_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt


title: 18632 RNA-Seq


title: 18576 RNA-Seq


title: C1

description:
C1_S42_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt


title: C2

description:
C2_S43_L005
processed data file: Bulk RNAseq_cultured GLI1+ cells.txt


title: TPC-1-Input

city: Baltimore

first: Bonita

middle: H

last: Powell

state: MD

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

data_processing:
FASTQC run before and after adapter trimming. The reads were aligned to the reference transcriptomes in a sequential manner.   First, all reads were mapped to RNA species with low sequence complexity and/or high number of repeats: rRNA, tRNA, RN7S, snRNA, snoRNA, scaRNA, VT-RNA, Y-RNA as well as mitochondrial chromosome (mtRNA). All reads that did not map to the above RNAs were aligned to premiRNA reference, then to protein coding mRNA transcripts (pc) and long non-coding RNAs (lncRNAs). Please note that some % of reads always overlaps between pc and lncRNAs. The reads which did not map to premiRNA, protein coding (pc) transcripts and lncRNAs were aligned to the remaining transcriptome [other ncRNAs containing mostly pseudogenes and non-protein coding parts of mRNAs]. Finally, all reads which did not map to human transcriptome were aligned to the hg38 genome reference (rest_hg38).
The mapping was performed with bowtie2 default settings for all references except premiRNA. For premiRNA alignment I used sequential mapping with bowtie using settings with: 0 mismatch tolerance, then 1 mismatch tolerance and finally 2 mismatches tolerance.
Genome_build: Hg38
Supplementary_files_format_and_content: Mature_miRNA_mapped_reads

source_name: Thyroid

extract_protocol:
Pre-cleared cell lysates were fractionated through a superose 6 size-exclusion chromatography column to separate active HMW-RISCs and inactive LMW-RISCs by molecular weight. Total RNA was extracted pooled Input, HMW-RISC, MMW-RISC, LMW-RISC, and RISC-poor fractions by miRNeasy serum/plasma kit according to manufacturer's instructions.
Small RNA libraries were constructed using the CATS ligation-independent method for 3'OH only ends following the protocol by Diagenode.

tag: cell line

tag: cancer type

value: Papillary Thyroid Cancer


title: TPC-1-HMWR


title: TPC-1-MMWR


title: SW1736-HMWR

value: Anaplastic Thyroid Cancer


title: TPC-1-LMWR


title: SW1736-LMWR


title: SW1736-R-Poor


title: TPC-1-R-Poor


title: SW1736-Input


title: 18525 RNA-Seq


title: 18886 RNA-Seq


title: KO_734

description:
KO_734_S38_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt

source_name: RPE/choroid tissue

value: Ihhi{delta}EC/{delta}iEC

tag: age

value: 6 month-old

value: Tamoxifen (12 weeks before sacrifice)

value: RPE/choroid tissue


title: 18501 RNA-Seq

value: XX


title: 18499 RNA-Seq


title: 18805 RNA-Seq

value: XY


title: 18467 RNA-Seq


title: T7_Naive_brain

city: Wuhan

first: Zhaochen

last: Luo

state: Hubei

address: No.1 Shi-zi-shan Street

country: China

institute: Huazhong Agricultural University

data_processing:
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were  generated
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain

extract_protocol:
Brains were removed, and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain

value: post natal day 49

tag: genotype

tag: infected with

value: not infected


title: 18466 RNA-Seq

value: XXY

value: blood


title: T7_B2c_brain

value: rabies virus strain Bc2


title: 18465 RNA-Seq

value: primary lymphocytes


title: Wt_Naive_brain

value: wild type


title: 19293 Methylation

library_source: genomic

data_processing:
Methylation data: Cutadapt (Version 1.8.1) was used to trim Illumina adapters and low-quality ends from the raw reads. The trimmed reads were mapped to human RefSeq genome (GRCh38.p10) using Bismark (Version 0.16.3). Duplicates were removed by the deduplicate_bismark script in Bismark. Only one copy of the overlapping parts in the middle of paired-end reads was retained after clipping the read with the lower average quality in the overlap region by the “clipOverlap” tool in bamUtil (Version 1.0.14). Methylation ratio for each CpG was extracted by the bismark_methylation_extractor script in Bismark. Differentially methylated regions (DMRs) were identified between cell types as well as between patients and controls within each cell type by metilene (Version 0.2-6) with >= 3 CpGs and a mean methylation difference between the two compared groups of >= 0.2. DMRs with FDR corrected p-value < 0.05 were considered significant.
Genome_build: hg38
Supplementary_files_format_and_content:  [Methylation data]  chromosome, CpG position, CpG methylation ratio

molecule: genomic DNA

extract_protocol:
Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit.
Library preparation was performed using Roche’s SeqCap Epi CpGiant Probes kit.


title: KO_618

description:
KO_618_S37_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt


title: 18463 RNA-Seq

value: XO


title: 19197 Methylation


title: Wt_B2c_brain


title: 19169 Methylation


title: WT-125ug-calp-treated-rep-1_S4_R1_001

city: HOUSTON

first: Muthiah

last: Kumaraswami

state: TEXAS

address: 6670 BERTNER AVE

department: Infectious Diseases

institute: Houston Methodist Research Institute

data_processing:
multiplexed SE libraries were sequenced on an Illumina HiSeq 2500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-Seq reads from strain MGAS10870 were mapped to reference strain MGAS315 (GenBank accession number AE014074.1) using Edge-pro v1.3.1(Estimated Degree of Gene Expression for Prokaryotes).
mapping reads from each strain to respective refrence using Edge-pro v1.3.1 yields raw and normalized (RPKM) expression values for each gene.
varible gene content and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
differential expression analysis was perfomed using DESeq2 v1.6.3 runing in R version 3.1.3. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approcah was used to generate fold change values for each gene. Multiple testing correction was performed using Benjamini-Hochberg method.

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: cells were grown in 38% (v/v) of Todd-Hewitt broth supplemented with yeast extract (THY media) and 62% (v/v) calprotectin medium (20mM Tris HCL Ph 7.5, 100mM NaCl, 10mM β-mercaptoethanol, 3mM CaCl2) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Epicentre)
resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre)

treatment_protocol: at the desired growth stage, late-exponential OD 600nm 1.0, the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

value: calprotectin

tag: serotype

tag: isolate

value: invasive infection isolate

tag: growth phase

value: Late-exponential (LE, OD600nm=1.0)


title: 18452 RNA-Seq


title: 19150 Methylation


title: 18426 RNA-Seq


title: 18447 RNA-Seq


title: WT-125ug-calp-treated-rep-2_S2_R1_001


title: 19117 Methylation


title: WT-untreated-rep-2_S1_R1_001

value: untreated


title: 18419 RNA-Seq


title: KO_603

description:
KO_603_S36_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt

tag: genotype/variation

value: Ihhi{delta}EC/{delta}iEC

value: 6 month-old

value: Tamoxifen (12 weeks before sacrifice)


title: WT_799

description:
WT_799_S41_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt

value: RPE/choroid tissue


title: WT_738

description:
WT_738_S39_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt


title: WT_749

description:
WT_749_S40_L005
processed data file: Bulk RNAseq_Ihh idECKO.txt


title: LIVER3

description:
LIVER3_AGTCAA_L003
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

source_name: Liver endothelial cells

value: 1 month-old

value: Liver endothelial cells


title: HEART2

description:
HEART2_CGATGT_L003
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

source_name: Heart endothelial cells

value: Heart endothelial cells


title: HEART

description:
HEART_GTGGCC_L007
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: HEART3

description:
HEART3_GTGAAA_L003
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: LIVER2

description:
LIVER2_ATTCCT_L002
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: WT-untreated-rep-1_S3_R1_001


title: 18411 RNA-Seq

tag: individual

value: XXY


title: 18886 Methylation

tag: chromosomes

value: blood


title: 18665 Methylation

value: XY


title: LIVER

description:
LIVER_GAGTGG_L007
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: 18226 RNA-Seq

value: XX

value: primary lymphocytes


title: LUNG3

description:
LUNG3_CAGATC_L003
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

source_name: Lung endothelial cells

value: Lung endothelial cells


title: 18467 Methylation

source_name: blood


title: LUNG2

description:
LUNG2_GAGTGG_L002
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: 18102 RNA-Seq


title: 15938 Methylation

value: XO


title: NR3

description:
NR3_GTGGCC_L002
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

source_name: Neural retina endothelial cells

value: Neural retina endothelial cells


title: LUNG

description:
LUNG_ATTCCT_L007
processed data file: Bulk RNAseq_choroid EC enriched genes.txt


title: 17972 RNA-Seq


title: 18076 Methylation


title: 18076 RNA-Seq


title: G47∆-mIL12 treated 935 T1

city: Abilene

first: Dipongkor

last: Saha

state: Texas

address: 1718 Pine Street

institute: Texas Tech University Health Sciences Center

description: 100 ng of total RNA per sample was mixed with a 3′-biotinylated capture probe and a 5′-reporter probe tagged with a fluorescent barcode from the custom gene expression code set. Probes and target transcripts were hybridized at 65°C for 16h. Hybridized samples were run on the prep station platform as recommended by the manufacturer’s protocol. The samples were scanned at maximum scan resolution on the nCounter Digital Analyzer. Data were processed using nSolver Analysis Software and the nCounter Advanced Analysis module. For gene expression analysis, data were normalized using the geometric mean of housekeeping genes selected by the GeNorm algorithm. Gene expression signatures were analyzed using Nsolver advanced analysis software (4.0) according to the manufacturer’s guidelines. For heatmap generation, normalized data were scaled, and average linkage performed using cluster 3.0, and heat maps were generated using JavaTree.

hyb_protocol: RNA is hybridized according to Nano string protocol. 100 ug of RNA is hybridized at 65℃ for 16 hr

scan_protocol: Nano string scan system is used to scan the slides

data_processing: Data is analysed suing Nsolver advanced analysis software version 4.0

source_name: primary mouse 4T1 breast tumor

label_protocol: Samples are labelled according to the treatment

extract_protocol: RNA extracted from mouse tumors

treatment_protocol: Mice are treated with either mock (PBS) or G47△-mIL12

value: primary mouse 4T1 breast tumor


title: G47∆-mIL12 treated 933 T1

label: 3′-biotinylated capture probe and a 5′-reporter probe tagged with a fluorescent barcode from the custom gene expression code set


title: G47∆-mIL12 treated 932 T1


title: 15190 Methylation


title: PBS treated 929 T1


title: pigeon_muff_HL_HH29_rep4

city: SLC

first: Elena

last: Boer

state: UT

department: School of Biological Sciences

institute: University of Utah

data_processing:
Sequencing read quality was assessed with FastQC.
Illumina adapters were trimmed with STAR.
Reads were aligned to the pigeon Cliv_2.1 reference assembly or chicken Gallus_gallus-5.0 genome assembly with STAR using the 2-pass mode.
Mapped reads were assigned to genes using FeatureCounts.
Principal component and differential expression analyses were performed with the R package DESeq2.
Genome_build: Cliv_2.1
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited text (.txt) files include read count files (FeatureCounts output) for each sample.
Supplementary_files_format_and_content: Comma-separated value (.csv) files include differential expression results (DESeq2 output) for each phenotypic comparison at each developmental stage.

organism: Columba livia

source_name: limb bud

extract_protocol:
Pairs of forelimb (FL) and hindlimb (HL) buds were dissected from scaled, grouse and muff pigeon embryos or chicken embryos at HH21 (embryonic day E3.5), HH25 (E4.5), and HH29 (E6) and stored in RNAlater (ThermoFisher Scientific) at -80°C. Total RNA was extracted from FL and HL bud samples using the RNeasy Mini Kit with RNase-Free DNAse Set and a TissueLyser LT (Qiagen).
RNA-sequencing libraries were prepared and sequenced by the High-Throughput Genomics and Bioinformatic Analysis Shared Resource at the University of Utah. RNA sample quality was assessed using the RNA ScreenTape Assay (Agilent) and a sequencing library was prepared using the TruSeq Stranded mRNA Sample Prep Kit with oligo(dT) selection (Illumina). 125-cycle paired-end sequencing was performed on an Illumina HiSeq 2500 instrument (12 libraries/lane).

tag: developmental stage

tag: limb type

value: HL

tag: phenotype

value: muff


title: LeCre_rep3

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

description: lens

data_processing:
RNA seq datafiles were trimmed using the Trimmomatic tool
Reads were aligned against Mus musculus reference genome (mm10) using Tophat v2.0.9  and gene-, cds-, and transcripts-level expression were computed through Cufflinks
The transcript expression counts generated using “classic-FPKM” normalization method Cuffnorm
Genome_build: Mus musculus reference genome (mm10)
Supplementary_files_format_and_content: matrix table with counts-per-million from all samples in a tab-delimited text file

source_name: Lens

extract_protocol:
Total RNA was isolated from each replicate using the mirVana isolation kit (Ambion, Life Technologies, Grand Island, NY). Total RNA samples with the RNA integrity number (RIN, Agilent 2100 Bioanalyzer) ≥8.0 were used to prepare a library of template molecules suitable for subsequent sequencing on an Illumina (St. Louis, MO) HiSeq platform. Polyadenylated RNA was purified from the total RNA samples using Oligo dT conjugated magnetic beads and prepared for single-end sequencing according to the Illumina TruSeq RNA Sample Preparation Kit v3. All the libraries were sequenced using the TruSeq SBS kit on an Illumina HiSeq 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LeCre


title: 14465 Methylation

tag: tissue

tag: cell type


title: PBS treated 928 T1


title: NR1

description:
NR1_ATGTCA_L005
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

tag: strain background


title: pigeon_muff_FL_HH29_rep4

value: FL


title: PBS treated 927 T1


title: pigeon_muff_HL_HH29_rep3


title: LeCre_rep2

description: lens


title: 15915 RNA-Seq


title: NP_115 (pwbc)

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
Reads were aligned to the bovine genome (ARS-UCD1.2 obtained from Ensembl) using HISAT2 (version 2.1.0)
The sequences were then marked for duplicates, and non-duplicated pairs of reads (mRNA) or single reads (miRNA) were used for transcript quantification at the gene level. The fragments were counted against the Ensembl gene annotation (version 1.87) using featureCounts (version 1.6.0)
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Bos taurus

source_name: peripheral white blood cells

extract_protocol:
Total RNA was isolated from PWBCs of 18 heifers (AI-pregnant (n=6), NB-pregnant (n=6), and not pregnant (n=6)) using TRIzol reagent following the manufacturer’s protocol. Total RNA (circulating extracellular RNA) was isolated from 1ml of plasma by adding 9 ml of TRIzol reagent and following manufacturer’s protocols through organic phase separation. The aqueous phase containing the RNA was then collected and purified with the RNA Clean & Concentrator-5 kit, according to manufacturer’s instructions.
Aproximatly 500 mg of total RNA was used as input for the TruSeq Stranded mRNA Library Prep kit. Total RNA obtained from plasma was desiccated to a volume of 2.5ul for library preparation with the TruSeq Small RNA Library Prep kit.

tag: heifer id

value: peripheral white blood cells

tag: classification

value: not-pregnant


title: NP_113 (pwbc)


title: LeCre_rep1

description: lens


title: 15830 RNA-Seq


title: pigeon_muff_FL_HH29_rep3


title: Fgfr2Pten_rep3

description: lens


title: 15622 RNA-Seq


title: NP_101 (pwbc)


title: NR2

description:
NR2_GTCCGC_L005
processed data file: Bulk RNAseq_choroid EC enriched genes.txt

tag: age

value: 1 month-old


title: NP_94 (pwbc)


title: 15190 RNA-Seq


title: 16053 RNA-Seq


title: pigeon_grouse_HL_HH29_rep4

value: grouse


title: pigeon_grouse_FL_HH29_rep4


title: NB_121 (pwbc)

value: NB-pregnant


title: 15938 RNA-Seq

value: blood


title: pigeon_grouse_HL_HH29_rep3


title: 14782 RNA-Seq


title: NP_107 (pwbc)


title: NB_116 (pwbc)


title: Fgfr2Pten_rep1

description: lens

tag: genotype


title: Pten_rep3

description: lens

value: Pten


title: 14552 RNA-Seq


title: NB_108 (pwbc)


title: Pten_rep2

description: lens


title: 14465 RNA-Seq


title: 14356 RNA-Seq

value: XX


title: pigeon_grouse_FL_HH29_rep3


title: Fgfr2Pten_rep2

description: lens


title: pigeon_scale_FL_HH29_rep4

value: scale


title: NB_103 (pwbc)


title: Fgfr2_rep3

description: lens


title: pigeon_scale_HL_HH29_rep3


title: 14307 RNA-Seq

value: primary lymphocytes


title: NB_93 (pwbc)


title: Fgfr2_rep2

description: lens


title: pigeon_scale_FL_HH29_rep3


title: 13880 RNA-Seq

value: XO


title: metastasis pt003

city: Montreal

first: Gerald

last: Batist

state: Québec

address: 3755 Cote Ste-Catherine

country: Canada

institute: Jewish General Hospital

description:
sample name:
05-2-003-2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR v2.3.0e
Raw count for each samples were obtained using featureCount using UCSC hg19 gtf file annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file containing the raw count for all the samples

source_name: liver

extract_protocol:
Tissues were parafin embedded, and RNA was harvested using AllPrep extraction kit from Qiagen. Illumina TruSeq HT Kit was used with 150 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: crizotinib

value: liver

tag: disease state

value: ALK+ NSCLC

tag: treatment

value: after crizotinib treatment

tag: patient id


title: Fgfr2_rep1

description: lens


title: AI_120 (pwbc)

value: AI-pregnant


title: NB_111 (pwbc)


title: pigeon_scale_HL_HH29_rep4

value: HL


title: AI_119 (pwbc)


title: AN5 [Lmb2]

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
Basecalling- CASAVA 1.8.2
trimReads.py (https://github.com/safisher/ngs/blob/master/trimReads.py) - adaptor trimming, low quality base masking, polyA/T trimming
alignment to reference genome - STAR 2.4.0j  (--outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMismatchNmax 100 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.4)
Quantification- Uniquely mapped reads quantifed with HTSeq v0.6.1p1 (--mode=intersection-strict --stranded=no --type=exon --idattr=gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq gene counts

source_name: Freshly isolated heart cell

extract_protocol:
Ventricular cardiac cells were dissociated by enzymatic digestion from Azami green geminin (mAG-Geminin) transgenic mice and sorted by FACS. Following cell lysis, mRNA was reverse transcribed into 1st strand cDNA. Single cell cDNA was subjected to quality control using PCR for the cardiomyocytespecific marker, troponin T2 (Tnnt2). Potential contamination from non-cardiomyocytes (i.e. cardiac fibroblasts and endothelial cells) was detected by PCR for platelet derived growth factor receptor ß (Pdgfrb).Single cells showing Tnnt2 positive and Pdgfrb negative were considered as confirmed cardiomyocytes.
library preparation using the Illumina TruSeq RNA sample preparation kit according to the manufacturer's protocol

value: Postnatal days 19

value: single cardiomyocytes

tag: group

value: mAG-hGem negative


title: pigeon_muff_HL_HH29_rep2

value: muff


title: pigeon_muff_FL_HH29_rep2

value: FL


title: AI_117 (pwbc)

value: peripheral white blood cells


title: Pten_rep1

description: lens


title: AN4 [Lmb2]


title: primary pt011

description:
sample name:
05-1-011-1

source_name: lung

value: lung

value: before crizotinib treatment


title: pigeon_muff_HL_HH29_rep1


title: AI_114 (pwbc)


title: AN3 [Lmb2]


title: metastasis pt004

description:
sample name:
05-2-004-1


title: pigeon_muff_FL_HH29_rep1


title: pigeon_grouse_HL_HH29_rep2

value: grouse


title: pigeon_grouse_FL_HH29_rep2


title: pigeon_grouse_HL_HH29_rep1


title: AP7 [Lmb2]

value: mAG-hGem positive


title: AP6 [Lmb2]


title: metastasis pt011

description:
sample name:
05-2-011-1


title: pigeon_grouse_FL_HH29_rep1


title: AP4 [Lmb2]


title: pigeon_scale_HL_HH29_rep2

value: scale


title: AP5 [Lmb2]


title: pigeon_scale_FL_HH29_rep2


title: AP2 [Lmb2]


title: AP3 [Lmb2]


title: AP1 [Lmb2]


title: AN1 [Lmb2]


title: pigeon_muff_HL_HH25_rep4


title: primary pt004

description:
sample name:
05-1-004-1


title: AI_99 (pwbc)


title: N28 [Lmb2]

value: embryonic days 14.5


title: AI_92 (pwbc)


title: N30 [Lmb2]


title: N25 [Lmb2]


title: AP8 [Lmb2]


title: pigeon_grouse_HL_HH25_rep4


title: pigeon_muff_FL_HH25_rep3


title: pigeon_muff_HL_HH25_rep3


title: N24 [Lmb2]


title: pigeon_grouse_FL_HH25_rep4


title: pigeon_scale_HL_HH29_rep1


title: SW1736-MMWR

tag: cell line

tag: cancer type

value: Anaplastic Thyroid Cancer


title: pigeon_scale_FL_HH29_rep1


title: pigeon_grouse_HL_HH25_rep3


title: pigeon_scale_HL_HH25_rep4


title: pigeon_grouse_FL_HH25_rep3


title: pigeon_muff_FL_HH25_rep4


title: pigeon_scale_HL_HH25_rep3


title: pigeon_scale_FL_HH25_rep4


title: N10 [Lmb2]


title: N7 [Lmb2]


title: N8 [Lmb2]


title: N5 [Lmb2]


title: N23 [Lmb2]


title: N3 [Lmb2]


title: pigeon_muff_HL_HH25_rep2


title: G28 [Lmb2]


title: G29 [Lmb2]


title: pigeon_muff_FL_HH25_rep2


title: G27 [Lmb2]


title: pigeon_muff_HL_HH25_rep1


title: G25 [Lmb2]


title: G10 [Lmb2]


title: pigeon_grouse_HL_HH25_rep2


title: G8 [Lmb2]


title: G6 [Lmb2]


title: pigeon_grouse_FL_HH25_rep1


title: G5 [Lmb2]


title: G2 [Lmb2]


title: pigeon_scale_FL_HH25_rep3


title: pigeon_scale_HL_HH25_rep2


title: pigeon_scale_FL_HH25_rep2


title: Uncleaved_substrate_sequencing_replicate3

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description:
processed data file: arti1_raw_count_replicate3.txt
processed data file: arti1_variant_sequence.txt

data_processing:
The base calling was done by Illumina CASAVA.
The 3' and 5'-adapters in raw reads were trimmed using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC). Paired-end reads were then joined together using fastq-join (default parameters), after which fastq_quality_filter (-q 20 -p 90) was used to filter low-quality reads.
We then used fastx_collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html , version 0.0.13) to remove the duplicated reads containing the same 6-nt random barcode at the 5' end. After discarding the barcode sequences, the processed reads were mapped to the reference sequences using BWA42. The reference sequence library contains 42,496 possible variants of the 11 groups. The perfectly mapped reads were selected for further analysis. The read cutoff of 30 and 15 were used for the original substrate and cleaved product samples, respectively. In each sample, the raw read counts were normalized as the counts per million.
Genome_build: n/a
Supplementary_files_format_and_content: arti1_variant_sequence.txt: Tab-delimited text file contains sequence of variants.
Supplementary_files_format_and_content: arti1_raw_count_replicate*.txt: Tab-delimited text files contain raw read counts.
Supplementary_files_format_and_content: Count_JC_cleaved_product_replicate1.txt: Count number of products at different cleavage sites in replicate 1
Supplementary_files_format_and_content: Count_JC_cleaved_product_replicate2.txt: Count number of products at different cleavage sites in replicate 2
Supplementary_files_format_and_content: Count_JC_cleaved_product_replicate3.txt: Count number of products at different cleavage sites in replicate 3

molecule: other

organism: synthetic construct

source_name: synthetic

extract_protocol: The ssDNAs were used as PCR templates to synthesize dsDNAs that were subsequently transcribed in vitro to generate an RNA pool with different variants. The synthesized RNAs were run in 10% Urea-PAGE and purified by gel elution followed by Isopropanol precipitation. A minimal human Microprocessor complex that contains the DROSHA fragment and DGCR8 fragment were co-expressed and purified in HEK293 cells using tandem chromatography. Purified Microprocessor complex then was used in processing assays for the artificial pri-miRNA pool. The reaction mixtures were separated in 10% Urea-PAGE. The original substrates, uncleaved substrates, and cleaved products were gel-eluted and cloned to construct a DNA library for sequencing.

tag: barcode

value: CTGATC


title: Cleaved_product_sequencing_replicate2

description:
processed data file: arti1_raw_count_replicate2.txt
processed data file: arti1_variant_sequence.txt

value: GATCTG


title: G1 [Lmb2]

tag: developmental stage


title: pigeon_scale_HL_HH25_rep1

tag: limb type


title: control_Il1b_rep8.4155

first: Gregory

middle: Robert

last: Grant

address: 3400 Civic Center Blvd.

department: Genetics

data_processing:
CASAVA (v1.8.1 and v1.8.2) was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-2.5.1b.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.1-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: aorta thoracica

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
Aorta were homogenized using magnetic beads and a TissueLyzer. RNA was extracted using Trizol and Qiagen Rneasy Mini kit.
Library construction was carried out using TruSeq RNA Sample Prep kit Set B. In line controls were not used, and samples were barcoded using kit adapters. Library construction was carried out over three days. Selection strategy: polyA; PCR cycles: 13

treatment_protocol:
Mice were fed regular chow for 3 weeks containing celecoxib (100 mg/kg/day), rofecoxib (50 mg/kg/day) or with no added NSAID.
IL-1B stimulus protocol: Mice were injected (IP injection) with IL-1beta (10ug/kg) 4 hrs before sacrifice.

tag: strain

value: adult

tag: Sex

value: male

value: 10 to 12 week

tag: genetic alteration

value: wildtype

tag: nsaid

tag: nsaid dose

tag: duration of dosing

value: 3 weeks

tag: collection time

value: aorta thoracica


title: Cleaved_product_sequencing_replicate3

value: AAGCTA


title: Uncleaved_substrate_sequencing_replicate2

value: ATTGGC


title: Cleaved_product_sequencing_replicate1

description:
processed data file: arti1_raw_count_replicate1.txt
processed data file: arti1_variant_sequence.txt

value: GCCTAA


title: pigeon_muff_HL_HH21_rep4

value: HL

tag: phenotype

value: muff


title: control_Il1b_rep7.4154

tag: age

tag: tissue


title: control_Il1b_rep6.4153


title: pigeon_scale_FL_HH25_rep1

value: FL


title: pigeon_muff_FL_HH25_rep1


title: N21 [Lmb2]

tag: cell type

value: single cardiomyocytes

value: mAG-hGem negative


title: pigeon_grouse_FL_HH25_rep2

value: grouse


title: pigeon_grouse_HL_HH25_rep1


title: control_Il1b_rep5.4151


title: 16054 RNA-Seq

tag: individual

tag: chromosomes

value: XX

value: blood

value: primary lymphocytes


title: Original_substrate_sequencing_replicate3

value: TCAAGT

tag: group


title: pigeon_muff_FL_HH21_rep4


title: pigeon_muff_HL_HH21_rep3


title: control_Il1b_rep4.4149

value: adult

value: male

value: 10 to 12 week


title: Original_substrate_sequencing_replicate2

tag: barcode

value: TGGTCA


title: control_Il1b_rep3.4148

tag: developmental stage

value: wildtype

value: 3 weeks

value: aorta thoracica


title: pigeon_muff_FL_HH21_rep3

tag: limb type


title: Original_substrate_sequencing_replicate1

value: CGTGAT


title: pigeon_grouse_HL_HH21_rep4

value: HL


title: Uncleaved_substrate_sequencing_replicate1

value: ACATCG


title: control_Il1b_rep1.4146

tag: strain


title: TR_WD_2

city: Brookings

first: Sharon

last: Clay

state: SD

address: Box 2140C, 1390 College Ave

department: Agronomy, Horticulture and Plant Science

institute: South Dakota State University

data_processing:
Raw sequence reads were checked for quality using FastQC
Reads were trimmed from 5 prime and 3 prime ends to have Phred quality score of >= 20 and length of at least 20 nucleotides using prinseq
De novo transcriptome was constructed with cleaned sequence reads using Trinity
Gene expression levels were quantified using RSEM and normalized in Transcripts Per Million (TPM) to account for gene length and sequencing depth
Differential gene expression analysis was performed using R bioconductor package edgeR
Genome_build: De novo transcriptome
Supplementary_files_format_and_content: Read Count and Abundance measurements in tab-delimited text files

organism: Tamarix ramosissima

source_name: T. ramosissima_water deficit

growth_protocol: T. chinensis and T. ramosissima seeds were planted and after 14 weeks, plants were placed in growth chamber at 25 degree C

extract_protocol:
RNA was isolated using Sigma Spectrum Plant Total RNA isolation kit
NEBNext Ultra RNA Library Prep kits were used for CDNA library construction and sequenced using paired end protocol on Illumina HiSeq 2000

treatment_protocol: Tamarix plants were subjected to well-watered control and water deficit by withholding water and plants reached wilting point at 10 and 17 days respectively. Leaf tissue was collected from 3 replicates for RNA extraction

tag: treatment

value: water deficit by withholding water

value: leaf tissue


title: control_Il1b_rep2.4147

tag: Sex

tag: genetic alteration


title: TR_WD_3


title: rofecoxib_IL1b_rep8.4145

tag: nsaid

value: rofecoxib

tag: nsaid dose

value: 50 mg/kg/day


title: TR_C_3

source_name: T. ramosissima_control

value: well-watered control


title: pigeon_grouse_FL_HH21_rep4

value: FL

value: grouse


title: pigeon_grouse_HL_HH21_rep3


title: TR_C_2


title: rofecoxib_IL1b_rep5.4142

value: adult

tag: duration of dosing

tag: collection time


title: rofecoxib_IL1b_rep7.4144

value: male

tag: age


title: rofecoxib_IL1b_rep6.4143

value: 10 to 12 week

tag: tissue


title: pigeon_scale_FL_HH21_rep4

tag: phenotype

value: scale


title: TR_C_1


title: TC_WD_3

organism: Tamarix chinensis

source_name: T. chinensis_water deficit


title: pigeon_scale_HL_HH21_rep4


title: rofecoxib_IL1b_rep4.4141

value: wildtype


title: pigeon_scale_HL_HH21_rep3


title: NP_107 (plasma)

source_name: plasma

tag: heifer id

value: plasma

tag: classification

value: not-pregnant


title: rofecoxib_IL1b_rep3.4140

value: 3 weeks

value: aorta thoracica


title: NP_115 (plasma)


title: NP_101 (plasma)


title: NP_113 (plasma)


title: pigeon_scale_FL_HH21_rep3


title: TC_WD_2


title: rofecoxib_IL1b_rep2.4139


title: TC_WD_1


title: pigeon_grouse_FL_HH21_rep3


title: TR_WD_1


title: rofecoxib_IL1b_rep1.4138


title: celecoxib_IL1b_rep8.4134

value: celecoxib

value: 100 mg/kg/day


title: celecoxib_IL1b_rep7.4133


title: NP_94 (plasma)


title: pigeon_muff_HL_HH21_rep2

value: HL

value: muff


title: NB_111 (plasma)

value: NB-pregnant


title: NB_121 (plasma)


title: L3

city: Rongchang

first: Jie

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

institute: Southwest University

data_processing:
Use Seqtk (https://github.com/lh3/seqtk) to filter out reads with low overall quality, sequencing primers, and low end quality to obtain clean reads for downstream analysis.
The clean reads are compared with the goose reference genome (Anser cygnoides, AnsCyg_PRJNA183603_v1.0, NCBI) using the Hisat2 (version: 2.0.4) spliced mapping algorithm, which allows comparison of reads that cannot be fully matched.
The number of Fragments per gene after Hisat2 alignment was counted by Stringtie (version: 1.3.0), then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM (fragments per kilobase of exon model per million mapped reads) of each gene was calculated using perl script, that is, the amount of gene expression after reads normalization.
Genome_build: AnsCyg_PRJNA183603_v1.0
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values for each Sample.

organism: Anser cygnoides

source_name: Liver

growth_protocol: 200 1-day-old healthy white geese with similar body weight were selected and raised under the same natural environment. Use the ground level raising, routine immunization procedures, free access to drinking water until 70-days-old to slaughter.

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using RNAiso Plus Total RNA extraction reagent (Cat#9109). VAHTS Stranded mRNA-seq Library Prep Kit (NR602-02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Sichuan white goose

value: Liver

value: Postnatal day 70

value: Low weight


title: TC_C_1

source_name: T. chinensis_control

value: well-watered control

value: leaf tissue


title: NB_93 (plasma)


title: NB_116 (plasma)


title: TC_C_2


title: L1


title: NB_103 (plasma)


title: pigeon_grouse_HL_HH21_rep2

value: grouse


title: pigeon_muff_FL_HH21_rep1

value: FL


title: celecoxib_IL1b_rep5.4131

value: adult

value: male

value: 10 to 12 week

value: wildtype


title: M3

value: Middle weight


title: celecoxib_IL1b_rep4.4130

value: celecoxib

value: 100 mg/kg/day

value: 3 weeks

value: aorta thoracica


title: pigeon_muff_HL_HH21_rep1

value: HL

value: muff


title: pigeon_muff_FL_HH21_rep2


title: celecoxib_IL1b_rep6.4132


title: celecoxib_IL1b_rep3.4129


title: NB_108 (plasma)

value: plasma

value: NB-pregnant


title: pigeon_grouse_HL_HH21_rep1


title: M2

value: Sichuan white goose

value: Liver

value: Postnatal day 70


title: AI_119 (plasma)

value: AI-pregnant


title: celecoxib_IL1b_rep2.4128

value: adult


title: AI_117 (plasma)


title: pigeon_grouse_FL_HH21_rep2

value: FL

value: grouse


title: pigeon_grouse_FL_HH21_rep1


title: celecoxib_IL1b_rep1.4126

value: male

value: 10 to 12 week

value: wildtype


title: M1

value: Middle weight


title: pigeon_scale_FL_HH21_rep2

value: scale


title: AI_120 (plasma)


title: pigeon_scale_HL_HH21_rep1


title: L2

value: Low weight


title: AI_114 (plasma)


title: AI_92 (plasma)


title: AI_99 (plasma)


title: H1

value: High weight


title: H3


title: pigeon_scale_HL_HH21_rep2

value: HL


title: pigeon_scale_FL_HH21_rep1


title: H2


title: +NH4_Rep3

status: Public on Feb 27 2020

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adapter clipping and quality filtering with Trimmomatic 0.33
mapping with tophat-2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis usign Cufflinks version 2.2.1 --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: tab-delimited matrix with normalized RPKM values for all the samples

molecule: polyA RNA

organism: Zea mays

source_name: primary root apexes

growth_protocol: Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, seedlings were moved to a controlled environmental chamber in 500 ml tanks containing a nutrient medium (Quaggiotti et al. 2003).

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by DNAse treatment
TruSeq RNA Library Prep Kit

treatment_protocol: 24h of growth in nutrient solution supplemented with 1mM KNO3 or 1mM NH4Cl

tag: inbred


title: +NH4_Rep1


title: +NH4_Rep2


title: PorcineAdipocyte_Without_stimulation_rep1

city: Sendai

first: Haruki

last: Kitazawa

state: Miyagi

address: 468-1 Aramaki Aza Aoba, Aoba-ku,, Sendai

institute: Tohoku University

hyb_protocol: The Gene Expression Hybridization kit (Agilent Technologies) was used for hybridization. In brief, 1650 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Porcine (V2) Gene Expression Microarray, 4x44K  (G2519F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sus scrofa

source_name: Adipocyte without stimulation, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The porcine intramuscular pre-adipocyte (PIP) cell lines (between the 26th and 35th passages) were maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco, Paisley, Scotland, UK) supplemented with 10% fetal calf serum (FCS), 100 mg/ml penicillin, and 100 U/ml streptomycin as a growth medium. PIP cells were plated at density of 2.5×104/cm2 in 6-well cell culture plates (BD Falcon, Tokyo, Japan) and incubated at 37°C in a humidified atmosphere of 5% CO2. The 4-day post-confluent PIP cells were fed with differentiation medium for another 4 more days to yield the differentiated adipocyte. The differentiation medium was DMEM containing 10% FBS, 50 ng/ml insulin (swine, Sigma-Aldrich), 0.25 μM dexamethasone (Sigma-Aldrich), 2 mM octanoate (Wako, Osaka, Japan), 200 μM oleate (Ardorich, Milwaukee, WI, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from the ligand-treated and control PMA cells using PureLink RNA Mini Kit (Life Technology Inc., USA) along with on-column DNase treatment. RNA integrity, quality and quantity were evaluated with microcapillary electrophoresis (2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano kit.

treatment_protocol: The 4-day post-confluent Porcine intramuscular preadipocyte (PIP) cells were fed with differentiation medium for another 4 more days to yield the differentiated adipocyte. The differentiation medium was prepared by DMEM with 10% FBS, 50 ng/ml insulin (swine, Sigma), 0.25 μM dexamethasone (Sigma), 2 mM octanoate (Wako), 200 μM oleate (Ardorich, Milwaukee, WI, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin. The differentiated pMA cells were cultured at density of 2.5×104/cm2 in 6 well or 12 well plates (BD Falcon, Tokyo, Japan). The 4-day post-confluent pMA cells were stimulated with 5-HT @100 μM/ml for 12 hours and TNF-α @ 2.5 µg/ml for 12 hours.

value: adipogenic differetiation


title: PorcineAdipocyte_12hr_Serotonin(5-HT)_stimulation_rep1

source_name: Adipocyte, 12hr with Sertonon (5-HT) stimulation, replicate 1

value: Serotonin stimulation


title: order2_P2_A6.single.cell

city: Shanghai

first: Bo O.

last: Zhou

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Reads were aligned to the GRCm38 genome using HISAT (version 2-2.1.0)
gene counts were generated using HTseq (version 0.6.0) with default parameters.
All mapped reads were processed by StringTie (version 1.3.3b) to evaluate the gene expression levels (measured by FPKM, Fragment Per Kilobase per Million) with default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: expression count of all single cells

source_name: Skeletal Stem Cells

extract_protocol:
cells were lysed in single-cell RNA lysis buffer containing 0.45% NP-40, then subjected to reverse transcription with SuperScript Ⅱ reverse transcriptase (Invitrogen) and whole transcription amplification with KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: sources

value: Tomato+

tag: genotype

value: KitMerCreMer; R26tdTomato mice


title: order2_P2_A3.single.cell


title: order2_P2_A22.single.cell


title: order2_P2_A7.single.cell


title: order2_P2_A24.single.cell


title: order2_P2_A2.single.cell


title: order2_P2_A18.single.cell


title: order2_P2_A23.single.cell


title: order2_P2_A10.single.cell


title: order2_P2_A4.single.cell


title: order2_P2_A12.single.cell


title: order2_P2_A20.single.cell


title: order2_P2_A17.single.cell


title: order2_P2_A15.single.cell


title: order2_P2_A14.single.cell


title: order2_P2_A16.single.cell


title: order2_P2_A8.single.cell


title: order2_P2_A5.single.cell


title: order2_P2_A19.single.cell


title: order2_P2_A11.single.cell


title: PorcinePreAdipocyte_Without_stimulation_rep1

source_name: Preadipocyte without stimulation, replicate 1

value: Control


title: order2_P2_A9.single.cell


title: order2_P2_A13.single.cell


title: PorcineAdipocyte_12hr_TNFa_stimulation_rep1

source_name: Adipocyte, 12hr with TNFa stimulation, replicate 1

value: TNF-a stimulation


title: order2_P2_A21.single.cell


title: ipsilateral_cerebellar_cortex

city: Okayama

first: Naoya

last: Kidani

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Neurological Surgery

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Right cerebellar cortex, 2days after MCAO

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the NucleoSpin RNA kit (Macherey-Nagel GmbH & Co. KG, Duren, Germany) following the manufacturer's recommendations.

tag: tissure

value: Cerebellar cortex

value: Wistar

tag: gender


title: control

source_name: Left cerebellar cortex, 2days after sham operation

tag: strain

value: male


title: contralateral_cerebellar_cortex

source_name: Left cerebellar cortex, 2days after MCAO


title: order2_P2_A1.single.cell


title: order2_P1_A23.single.cell


title: order2_P1_A18.single.cell


title: order2_P1_A20.single.cell


title: order2_P1_A22.single.cell


title: order2_P1_A3.single.cell


title: order2_P1_A2.single.cell


title: order2_N2_A66.single.cell

value: Tomato-


title: order2_N2_A67.single.cell


title: order2_P1_A12.single.cell


title: order2_N2_A69.single.cell


title: order2_P1_A13.single.cell


title: order2_P1_A8.single.cell


title: order2_P1_A10.single.cell


title: order2_P1_A7.single.cell


title: order2_P1_A14.single.cell


title: order2_P1_A4.single.cell


title: order2_P1_A21.single.cell


title: order2_P1_A16.single.cell


title: order2_P1_A15.single.cell


title: order2_P1_A11.single.cell


title: order2_P1_A1.single.cell


title: order2_P1_A17.single.cell


title: order2_P1_A19.single.cell


title: order2_N2_A70.single.cell


title: order2_P1_A24.single.cell


title: order2_N2_A68.single.cell


title: order2_N2_A65.single.cell


title: order2_N2_A64.single.cell


title: order2_P1_A9.single.cell


title: order2_N2_A63.single.cell


title: order2_N2_A60.single.cell


title: order2_N2_A61.single.cell


title: order2_N2_A50.single.cell


title: order2_N2_A55.single.cell


title: order2_N2_A49.single.cell


title: order2_N2_A51.single.cell


title: order2_N2_A56.single.cell


title: order2_N2_A44.single.cell


title: order2_N2_A46.single.cell


title: order2_N2_A58.single.cell


title: order2_N2_A48.single.cell


title: order2_N2_A53.single.cell


title: order2_N2_A45.single.cell


title: order2_N2_A57.single.cell


title: order2_N2_A42.single.cell


title: order2_N2_A41.single.cell


title: order2_N2_A52.single.cell


title: order2_N2_A59.single.cell


title: order2_N2_A62.single.cell


title: order2_N2_A40.single.cell


title: order2_N2_A54.single.cell


title: order2_N2_A39.single.cell


title: order2_N2_A37.single.cell


title: order2_P1_A5.single.cell


title: order2_P1_A6.single.cell


title: order2_N2_A35.single.cell


title: order2_N2_A33.single.cell


title: order2_N2_A34.single.cell


title: order2_N2_A36.single.cell


title: order2_N2_A31.single.cell


title: order2_N2_A30.single.cell


title: order2_N2_A32.single.cell


title: order2_N2_A29.single.cell


title: order2_N2_A25.single.cell


title: order2_N2_A24.single.cell


title: order2_N2_A28.single.cell


title: order2_N2_A20.single.cell


title: order2_N2_A23.single.cell


title: order2_N2_A22.single.cell


title: order2_N2_A21.single.cell


title: order2_N2_A19.single.cell


title: order2_N2_A27.single.cell


title: order2_N2_A17.single.cell


title: order2_N2_A16.single.cell


title: order2_N2_A38.single.cell


title: order2_N2_A14.single.cell


title: order2_N2_A15.single.cell


title: order2_N2_A12.single.cell


title: order2_N2_A13.single.cell


title: order2_N2_A11.single.cell


title: order2_N2_A10.single.cell


title: order2_N2_A26.single.cell


title: order2_N2_A7.single.cell


title: order2_N2_A6.single.cell


title: order2_N2_A8.single.cell


title: order2_N2_A3.single.cell


title: order2_N2_A18.single.cell


title: order2_N2_A5.single.cell


title: order2_N2_A4.single.cell


title: order2_N1_A71.single.cell


title: order2_N2_A2.single.cell


title: order2_N1_A70.single.cell


title: order2_N2_A1.single.cell


title: order2_N1_A67.single.cell


title: order2_N1_A68.single.cell


title: order2_N1_A64.single.cell


title: order2_N1_A61.single.cell


title: order2_N1_A66.single.cell


title: order2_N1_A60.single.cell


title: order2_N1_A63.single.cell


title: order2_N1_A69.single.cell


title: order2_N1_A59.single.cell


title: order2_N1_A57.single.cell


title: order2_N2_A9.single.cell


title: order2_N1_A56.single.cell


title: order2_N1_A54.single.cell


title: order2_N1_A52.single.cell


title: order2_N1_A65.single.cell


title: order2_N1_A62.single.cell


title: order2_N1_A51.single.cell


title: ChIP-seq_H3K27me3_CR3flp_P4-rep2

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Reads were filtered based on a mean base quality score >20.
Quality-filtered reads were mapped against the hg19 reference assembly (excluding haplotype chromosomes) via Bowtie v1.2 with parameters "-m 1 -X 1000 --chunkmbs 1024".
Multiple sequencing runs of the same library were merged via MergeSamFiles.jar (Picard tools v1.110).
Duplicate reads per sample were removed via MarkDuplicates.jar (Picard tools v1.110).
For visualization purposes, paired-end reads were converted to a single fragment spanning the two mapped ends and replicate samples per condition were combined.
Alignments were converted to bedGraph format via genomeCoverageBed (Bedtools v2.24.0) then depth normalized to 50M fragments, followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: normalized depth tracks; format = bigWig

growth_protocol: Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS.

extract_protocol: Libraries were prepared according to BIOO SCIENTIFIC instruction.

treatment_protocol: The cells were treated with 150 nM progesterone for 3 h. Cells were then fixed with 1% formaldehyde at room temperature for 10 min and quenched with glycine. Fixed cells were treated with a hypotonic buffer, and lysed with Tris-HCl pH 8.0 based buffer with 0.1% SDS. Chromatin fragmentation was performed by sonication with Covaris. DNA was precipitated with antibody against each target protein.

tag: cell line

tag: genotype/variation

value: wt/R330fsl cells

tag: passages

tag: antibody

value: anti-H3K27me3 (abcam, ab192985)


title: order2_N1_A49.single.cell


title: ChIP-seq_H3K27ac_T47Dflp_P4-rep2

value: Flp control cells

value: anti-H3K27ac (abcam, ab4729)


title: order2_N1_A48.single.cell


title: ChIP-seq_H3K27ac_T47Dflp_P4-rep1


title: ChIP-seq_H3K27me3_T47Dflp_P4-rep2


title: order2_N1_A47.single.cell


title: ChIP-seq_H3K27me3_CR3flp_P4-rep1


title: order2_N1_A46.single.cell


title: order2_N1_A45.single.cell


title: order2_N1_A58.single.cell


title: order2_N1_A44.single.cell


title: ChIP-seq_H3K27me3_T47Dflp_P4-rep1


title: order2_N1_A55.single.cell


title: ChIP-seq_H3K4me1_CR3flp_P4-rep1

value: anti-H3K4me1 (abcam, ab8895)


title: order2_N1_A43.single.cell


title: ChIP-seq_H3K4me1_T47Dflp_P4-rep2


title: order2_N1_A53.single.cell


title: order2_N1_A50.single.cell


title: ChIP-seq_H3K27ac_CR3flp_P4-rep2


title: ChIP-seq_H3K4me1_T47Dflp_P4-rep1


title: order2_N1_A42.single.cell


title: ChIP-seq_H3K27ac_CR3flp_P4-rep1


title: order2_N1_A41.single.cell


title: order2_N1_A40.single.cell


title: order2_N1_A39.single.cell


title: ChIP-seq_H3K4me1_CR3flp_P4-rep2


title: order2_N1_A38.single.cell


title: H2A.Z2 ChIP-seq in U2OS Flag-Z2 cells - Replicate #2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

data_processing:
ChIP-sequencing in U2OS cells were performed single-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (Heidelberg) with at least 400 millions reads for the 4 samples in multiplex. Drosophila Spike-in (Active Motif) was added in each ChIP-seq experiment. Alignment on a combined Drosophila dm6 and human hg38 genome was performed with BWA version 2.5.2b. Aligned data were processed with samtools: reads were selected, counted and PCR duplicates were removed. The coverage was then computed with the GenomicAlignments Bioconductor R package. For each sample, normalization was performed on BigWig file by multiplying the coverage for each base by the factor (100,000/ number of Drosophila aligned reads).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: BigWig

source_name: ChIP using anti-Flag M2 antibody (Sigma) in U2OS Flag-Z2 cells

growth_protocol: U2OS cells expressing Flag-H2A.Z.1 or Flag-H2A.Z.2.

extract_protocol:
Nuclei were isolated and chromatin was sonicated and precleared. The H2A.Z histone-DNA complexes were isolated using anti-Flag M2 antibody (Sigma). Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiment. After purification, 10 ng of immunoprecipitated DNA was sent to EMBL Genecore (Heidelberg, Germany) for library construction and sequencing.
Library construction (NEBNext® Ultra™ II DNA Library Prep Kit for Illumina) was performed by EMBL GeneCore. The 4 samples were barcoded and sequenced in one lane by NextSeq 500 Illumina device.

treatment_protocol: Before harvesting, cells were crosslinked for 15 min using 1% formaldehyde.

value: U2OS Flag-Z2 cells

tag: chip antibody

value: anti-Flag M2 antibody (Sigma)


title: H2A.Z1 ChIP-seq in U2OS Flag-Z1 cells - Replicate #2

source_name: ChIP using anti-Flag M2 antibody (Sigma) in U2OS Flag-Z1 cells

value: U2OS Flag-Z1 cells


title: order2_N1_A36.single.cell

value: bone marrow


title: H2A.Z2 ChIP-seq in U2OS Flag-Z2 cells - Replicate #1


title: order2_N1_A37.single.cell


title: order2_N1_A35.single.cell


title: order2_N1_A34.single.cell


title: order2_N1_A33.single.cell


title: order2_N1_A31.single.cell


title: order2_N1_A32.single.cell


title: Strand-specific RNA-seq in siPHF14 treated cells- Replicate #2 [WI38]

description:
si-PHF14-n3
Transfected with siRNA against PHF14 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_PHF14vsCtrl.csv

data_processing:
Strand-specific RNA-sequencing in proliferative cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 6 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2b, datasets were processed (sorting and indexing) with samtools.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv).
Differential analysis (siPHF14 vs. siCtrl, siSIRT1 vs. siCtrl) was done with DESeq2 Bioconductor R package, Version 1.22.1 with default parameters.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .csv files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq.

source_name: Total RNA (ribosomal RNA depleted) from siPHF14-treated proliferative WI38 hTERT RAF1-ER cells

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 6 samples were barcoded, sequenced paired-end in one lane by NextSeq 500 Illumina device and demultiplexed.

treatment_protocol: Proliferative WI38 hTERT RAF1-ER cells were transfected by siRNAs for 3 days.

value: WI38 hTERT RAF1-ER

tag: sirna


title: Strand-specific RNA-seq in siCtrl treated cells- Replicate #2 [WI38]

description:
si-Ctrl-n3
Transfected with control siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_PHF14vsCtrl.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_SIRT1vsCtrl.csv

source_name: Total RNA (ribosomal RNA depleted) from siCtrl-treated proliferative WI38 hTERT RAF1-ER cells

value: siCtrl


title: Strand-specific RNA-seq in siPHF14 treated cells- Replicate #1 [WI38]

description:
si-PHF14-n2
Transfected with siRNA against PHF14 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_PHF14vsCtrl.csv


title: Strand-specific RNA-seq in siSIRT1 treated cells- Replicate #2 [WI38]

description:
si-SIRT1-n3
Transfected with siRNA against SIRT1 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_SIRT1vsCtrl.csv

source_name: Total RNA (ribosomal RNA depleted) from siSIRT1-treated proliferative WI38 hTERT RAF1-ER cells


title: order2_N1_A29.single.cell

value: KitMerCreMer; R26tdTomato mice


title: order2_N1_A30.single.cell


title: Strand-specific RNA-seq in siH2A.Z1 and siH2A.Z2 treated cells- Replicate #2 [WI38]

description:
si-Z1_2-n2
Transfected with siRNAs against H2A.Z1 and H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1_2vsCtrl.csv

data_processing:
Strand-specific RNA-sequencing in proliferative cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 7 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2b, datasets were processed (sorting and indexing) with samtools.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv).
Differential analysis (siH2A.Z1 vs. siCtrl, siH2A.Z2 vs. siCtrl, siH2A.Z1 and siH2A.Z2 vs. Ctrl) was done with DESeq2 Bioconductor R package, Version 1.22.1 with default parameters. For the DE analysis in siH2A.Z1 versus siCtrl-treated WI38 cells, the GEO Sample GSM2781958 (Series GSE85083) was used as the second replicate for the siH2A.Z1 RNA-seq datasets.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .csv files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq.

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z1 and siH2A.Z2-treated proliferative WI38 hTERT RAF1-ER cells

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 7 samples were barcoded, sequenced paired-end in one lane by NextSeq 500 Illumina device and demultiplexed.

value: siH2A.Z1 and siH2A.Z2


title: Strand-specific RNA-seq in siH2A.Z1 and siH2A.Z2 treated cells- Replicate #1 [WI38]

description:
si-Z1_2-n1
Transfected with siRNAs against H2A.Z1 and H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1_2vsCtrl.csv


title: order2_N1_A28.single.cell