title: C2

city: chengdu

first: Yixin

last: Wang

state: sichuan

address: 211 huimin street

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

data_processing:
High quality data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
High quality data were mapped to the mouse reference genome using Tophat version 2.0.11 for RNA-seq. When multiple reads from one sequencing library were mapped to same genomic location, these reads were regarded as potential clonal duplicates arising from PCR amplification biases and were identified to be a single read.
Cufflinks version 2.2.1 was used to quantify gene expression and obtain FPKM expression values.
Genome_build: Mus_musculus. GRCm38.81
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Normal mouse

growth_protocol: Three hemicastrated mice and three normal mice were fed until body maturation.

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols.
Agarose gel electrophoresis and Agilent 2100 (Agilent Technologies, CA, USA) were applied to assessed RNA integrities , while Nanodrop (IMPLEN, CA, USA) and Qubit (Life Technologies, CA, USA) were used for concentration detection. Subsequently, RNA from 4 individuals were used for cDNA library construction and Illumina deep sequencing (NEB, USA) respectively. Briefly, the poly(A) RNA enrichment by oligo(dT) magnetic beads from total RNA, then fragment as template and reverse transcription with random hexamer primers to synthesis first-strand cDNA. Following supplement with buffer, dNTPs, DNA polymerase I and RNase H to obtain second-strand cDNA. Double-stranded cDNA was purified by AMPure XP beads (Beckman Coulter, Beverly, USA). Subsequently, it would undergo end-repairment, an A tail added, ligation to paired-end Illumina sequencing adaptors, selection size of fragment by AMPure XP beads and amplification by polymerase chain reaction (PCR) for lirary preparation. The high quanlity library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

treatment_protocol: Three pretubertal mice were performed hemicastration to removed left testis. At the same time, three normal mice were operated sham surgery. Until body maturation, right testis were sampled rapidly, and immediately frozen in liquid nitrogen

tag: strain

value: KM

value: Testis


title: H2

status: Public on Jan 24 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Hemicastrated mouse

tag: tissue


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell007

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

country: USA

institute: La Jolla Institute for Allergy and Immunology

description: Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)

library_source: transcriptomic

data_processing:
Single-cell RNA–seq data were mapped against the human hg19 reference genome using TopHat (v1.4.1., --library-type fr-secondstrand -C) and Gencode version 19 (GRCh37.p13) as gene model reference for alignment.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: SC_raw_counts.txt contains raw counts of sequencing reads obtained with HTSeq-count

molecule: total RNA

organism: Homo sapiens

source_name: Subject12_DENV positive_PBMC_TEMRA

growth_protocol: CD4 memory cell types were isolated from PBMCs and directly sorted by Flow cytometry into a 96-well plate wells with lysis buffer with RNAase inhibitor (Takara) - Described in Picelli et al. Nat Protoc. 2014, PMID:24385147. No particular cell growth procedure was required.

extract_protocol:
Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification.
Single cell RNAseq was perfromed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturer's protocol.
DNA sequencing - Libraries were sequenced on the Illumina HiSeq 2500  platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

treatment_protocol: For DENV antigen specifc cells, PBMCs were stimulated with DENV peptide pool following the protocol described previously by Weiskopf et al., 2014 and IFNγ producing single cells were sorted for single-cell RNA-seq analysis

tag: subject id

tag: dengue infections history

value: DENV positive

tag: cell type

value: PBMC

tag: cell subtype surface markers

tag: cell subtype

value: TEMRA


title: C1


title: H1


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell006


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell004


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell003


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell002


title: GF01

city: Philadelphia

first: Elizabeth

middle: A

last: Grice

state: PA

address: 1007 BRB II/III, 421 Curie Blvd

department: Dermatology

institute: University of Pennsylvania

description:
Sample_6600
Processed data file: gf_vs_spf_rna_seq.txt

data_processing:
Transcripts were aligned to the mouse reference genome GRCm38.p4 v9, using STAR in conjunction with AlignerBoost, specifying a seed length of 25, 4% seed mismatch, 0% seed indels, 8% all mismatch, and 3% all indels.
Reads mapping to numbered and sex chromosomes were retained using samtools.
Read counts were generated using featureCount in the subread package in R and counts to ribosomal RNA were removed.
Reads were filtered with the NOISeq R package using method 1, which removes features with a sum of expression values less than 1 count per million multiplied by the number of samples in the condition.
Post filtering, TMM normalization was applied and technical batch effects associated with sequencing run were removed using ARSyNseq, using the NOISeq R package.
Genome_build: GRCm38.p4 v9
Supplementary_files_format_and_content: Tab-delimited text files ending in "counts.txt" include count values for each Sample generated from R subread package; tab-delimited text files ending in "filtered_normalized_counts.txt" include counts for each sample, post filtering and normalization with NOISeq package in R; gf_vs_spf_rna_seq.txt is a tab-delimited text file containing filtered normalized counts for all 16 samples.

molecule: polyA RNA

source_name: dorsum skin, GF

extract_protocol:
Skin was collected from the dorsum of mice and stored in RNAlater. Poly-A enriched RNA was isolated from harvested skin and RNA-seq libraries were constructed using the unstranded Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: gender

value: male

tag: age

tag: condition

value: germ free

value: dorsal skin


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell005


title: Stat3 ChIPseq in AtT-20 expressing ERPax7 (stable induction)

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

description: AtT-20 cells cells expressing 3x flag-ER-Pax8

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 1 --best mm10 –S
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

value: pituitary corticotroph cell

tag: passages

tag: cell line

value: AtT-20 cells

tag: treatment

value: 30 minutes of LIF and Dexamethasone; >20 days of 4-hydroxy-tamoxifen

tag: chip antibody


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (stable induction followed by stable withdrawal)

description: AtT-20 cells cells expressing 3x flag-ER-Pax10

value: >20 days of 4-hydroxy-tamoxifen followed by 18 days of Ethanol treatment

value: FlagM2 Sigma F1365


title: Stat3 ChIPseq in AtT-20 expressing ERPax7 (stable induction followed by stable withdrawal)

description: AtT-20 cells cells expressing 3x flag-ER-Pax9

value: 30 minutes of LIF and Dexamethasone; >20 days of 4-hydroxy-tamoxifen followed by 18 days of Ethanol treatment


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell015


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell001


title: Pax7 ChIPseq in AtT-20 expressing Pax7 (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax14

value: non treated


title: Single-cell_RNA-seq_Subject12_TCM_Cell048

source_name: Subject12_DENV positive_PBMC_TCM

value: TCM


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (48h) (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax16

value: 48 hours  of 4-hydroxy-tamoxifen


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (24h) (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax15

value: 24 hours  of 4-hydroxy-tamoxifen


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (1h) (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax13

value: 1 hours  of 4-hydroxy-tamoxifen


title: Single-cell_RNA-seq_Subject12_TCM_Cell046

value: DENV positive


title: Tpit ChIPseq in AtT-20

description: AtT-20 cells cells expressing 3x flag-ER-Pax7

value: Tpit Pulichino et al. 2003


title: Single-cell_RNA-seq_Subject12_TCM_Cell047

value: PBMC


title: Single-cell_RNA-seq_Subject12_TCM_Cell042


title: Single-cell_RNA-seq_Subject12_TCM_Cell043


title: ATACseq in AtT-20 expressing ER-Pax7 (24 hours)

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 1 --best mm10 –S
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

source_name: AtT-20 cells expressing 3x flag-ER-Pax7

extract_protocol:
Transposase reaction was performed on 100 000 nuclei using Nextera enzyme
Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocol.

treatment_protocol: (if applicable) Treatment was added directly in the media of the cultured cells and left for the mentioned amount of time

value: 24 hours of 4-hydroxy-Tamoxifen treatment


title: ATACseq in AtT-20 expressing ER-Pax7 (48 hours)

value: 48 hours of 4-hydroxy-Tamoxifen treatment


title: Single-cell_RNA-seq_Subject12_TCM_Cell041


title: ATACseq in AtT-20 expressing ER-Pax7 (12 hours)

value: 12 hours of 4-hydroxy-Tamoxifen treatment


title: Single-cell_RNA-seq_Subject12_TCM_Cell039


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell123

value: TEMRA


title: ATACseq in AtT-20 expressing ER-Pax7 (72 hours) 50k cells (rep1)

value: pituitary corticotroph cell

value: AtT-20 cells

value: 72 hours of 4-hydroxy-Tamoxifen treatment


title: Single-cell_RNA-seq_Subject12_TCM_Cell040


title: Single-cell_RNA-seq_Subject12_TCM_Cell038


title: Single-cell_RNA-seq_Subject12_TCM_Cell036


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (72h) (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax12

value: 72 hours  of 4-hydroxy-tamoxifen

value: FlagM2 Sigma F1365


title: Pax7 ChIPseq in AtT-20 expressing ERPax7 (30 minutes) (exo-like protocol)

description: AtT-20 cells cells expressing 3x flag-ER-Pax11

value: 30 minutes  of 4-hydroxy-tamoxifen


title: Single-cell_RNA-seq_Subject12_TCM_Cell044

value: TCM


title: RNAseq in melanotropes replicate 1

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the GRCm38 mouse genome build using TopHat
gene expression FPKM was determined using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression analysis was performed with EdgeR

source_name: FACS-purified melanotrope cells

extract_protocol:
We separated by dissection the two pituitary lobes from a POMC-EGFP mouse line, FACS-sorted the GFP-positive cells to extract purified melanotropes and corticotropes from each lobes. We extracted total RNA using the zymo quick RNA miniprep kit. Ribosomal depletion was performed on the extracted RNA.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

value: Melanotropes

tag: purification

value: FACS-sorting from POMC-EGFP mouse line

tag: mrna enrichment protocol

value: Ribosomal depletion


title: WGBS in AtT-20 expressing Neo

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 100bp reads were mapped to thebisulfite converted reference genome GRCm38 with bismarck. After alignement, we removed duplicate reads.
Genome_build: mm10
Supplementary_files_format_and_content: Differential methylation analsysis was performed using methylkit

source_name: AtT-20 cells expressing 3x flag-Neo

extract_protocol:
Genomic DNA was extracted from 1,000,000 cells and bisulfite conversion was performed with the Zymo Research EZ DNA Methylation-  Lightning Kit.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 100bp paired end reads.

value: non treated

value: Bisulfite conversion


title: WGBS in AtT-20 expressing Pax7

source_name: AtT-20 cells expressing 3x flag-Pax7


title: Single-cell_RNA-seq_Subject12_TCM_Cell034

value: DENV positive

value: PBMC


title: Single-cell_RNA-seq_Subject12_TCM_Cell045


title: RNAseq in corticotropes replicate 2

source_name: FACS-purified corticotrope cells

value: Corticotropes

tag: strain


title: Single-cell_RNA-seq_Subject12_TCM_Cell031


title: Single-cell_RNA-seq_Subject12_TCM_Cell030


title: RNAseq in corticotropes replicate 1


title: RNAseq in AtT-20 expressing ER-Pax7 (96 hours) replicate 2

extract_protocol:
We extracted total RNA using the Qiagen Rneasy kit and then performed ribosomal depletion on the extracted RNA
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

value: 96h hours of 4-hydroxy-Tamoxifen


title: RNAseq in AtT-20 expressing ER-Pax7 (96 hours) replicate 3


title: Single-cell_RNA-seq_Subject12_TCM_Cell032


title: ATACseq in AtT-20 expressing ER-Pax7 (72 hours) 100k cells (rep2)


title: Single-cell_RNA-seq_Subject12_TCM_Cell029


title: RNAseq in AtT-20 expressing ER-Pax7 (24 hours) replicate 2

value: 24 hours of 4-hydroxy-Tamoxifen


title: RNAseq in melanotropes replicate 2


title: Single-cell_RNA-seq_Subject12_TCM_Cell037


title: Single-cell_RNA-seq_Subject12_TCM_Cell028


title: Single-cell_RNA-seq_Subject12_TCM_Cell026


title: Single-cell_RNA-seq_Subject12_TCM_Cell027


title: Single-cell_RNA-seq_Subject12_TCM_Cell025


title: RNAseq in AtT-20 expressing ER-Pax7 (24 hours) replicate 3

value: pituitary corticotroph cell


title: RNAseq in AtT-20 expressing ER-Pax7 (12 hours) replicate 3

value: AtT-20 cells

value: 12 hours of 4-hydroxy-Tamoxifen


title: RNAseq in AtT-20 expressing ER-Pax7 (24 hours) replicate 1


title: RNAseq in AtT-20 expressing ER-Pax7 (12 hours) replicate 2


title: Single-cell_RNA-seq_Subject12_TCM_Cell024


title: Single-cell_RNA-seq_Subject12_TEMRA_Cell022

value: TEMRA


title: Single-cell_RNA-seq_Subject12_TCM_Cell033


title: RNAseq in AtT-20 expressing ER-Pax7 (12 hours) replicate 1


title: Single-cell_RNA-seq_Subject12_TCM_Cell023


title: RNAseq in AtT-20 expressing ER-Pax7 (no induction) replicate 2


title: Single-cell_RNA-seq_Subject12_TCM_Cell022


title: Single-cell_RNA-seq_Subject12_TCM_Cell021


title: RNAseq in AtT-20 expressing ER-Pax7 (96 hours) replicate 1


title: RNAseq in AtT-20 expressing ER-Pax7 (no induction) replicate 1


title: Single-cell_RNA-seq_Subject12_TCM_Cell019


title: RNAseq in AtT-20 expressing Pax7 replicate 2

description: diffExp_RNA_AtTNeo_vs_Pax7_ribo_EdgeR.txt


title: RNAseq in AtT-20 expressing Pax7 replicate 1


title: Single-cell_RNA-seq_Subject12_TCM_Cell018


title: Single-cell_RNA-seq_Subject12_TCM_Cell017


title: RNAseq in AtT-20 expressing Neo replicate 2


title: Single-cell_RNA-seq_Subject12_TCM_Cell016


title: RNAseq in AtT-20 expressing Neo replicate 1


title: Input of AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7


title: Single-cell_RNA-seq_Subject12_TCM_Cell015


title: Single-cell_RNA-seq_Subject12_TCM_Cell014


title: Input of AtT-20

description: AtT-20 cells

source_name: AtT-20 cells


title: RNAseq in AtT-20 expressing ER-Pax7 (no induction) replicate 3


title: IgG ChIPseq in AtT-20

description: AtT-20 cells expressing 3x flag-Pax7

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp single end reads.

value: IgG Sigma I5381


title: 3x Flag ChIPseq in AtT-20 expressing Neo

description: AtT-20 cells expressing 3x flag-Neo

value: Flag Sigma F1365


title: Pax7 ChIPseq in AtT-20 expressing ER-Pax7 (no ER-Pax7 induction)

description: AtT-20 cells expressing chimera of 3x flag-Pax7 with ERtm LBD

source_name: AtT-20 cells expressing chimera of 3x flag-ER-Pax7

value: 3 days of 0.1% ethanol

value: Pax7 3xflag Sigma F1365


title: Single-cell_RNA-seq_Subject12_TCM_Cell012

value: TCM


title: Single-cell_RNA-seq_Subject12_TCM_Cell020


title: Single-cell_RNA-seq_Subject12_TCM_Cell011


title: Single-cell_RNA-seq_Subject12_TCM_Cell010


title: Single-cell_RNA-seq_Subject12_TCM_Cell009


title: Single-cell_RNA-seq_Subject12_TCM_Cell008


title: Single-cell_RNA-seq_Subject12_TCM_Cell007


title: Stat3 ChIPseq in AtT-20 expressing Pax7 (Dex+LIF)

description: AtT-20 cells expressing 3x flag-Pax7

value: 30 minutes LIF and Dexamethasone


title: H3K27ac ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7

value: non treated


title: H3 ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7


title: Stat3 ChIPseq in AtT-20 expressing Neo (Dex+LIF)

description: AtT-20 cells expressing 3x flag-Neo


title: Single-cell_RNA-seq_Subject12_TCM_Cell006


title: Single-cell_RNA-seq_Subject12_TCM_Cell004


title: H3K27ac ChIPseq in AtT-20 expressing Neo

description: AtT-20 cells expressing 3x flag-Neo


title: p300 ChIPseq in AtT-20 expressing Neo

description: AtT-20 cells expressing 3x flag-Neo


title: Single-cell_RNA-seq_Subject12_TCM_Cell005


title: p300 ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7


title: Single-cell_RNA-seq_Subject12_TCM_Cell002


title: Single-cell_RNA-seq_Subject12_TCM_Cell003


title: Single-cell_RNA-seq_Subject12_TCM_Cell013


title: Single-cell_RNA-seq_Subject12_TCM_Cell001


title: H3K4me1 ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7


title: H3K4me1 ChIPseq in AtT-20 expressing Neo

description: AtT-20 cells expressing 3x flag-Neo


title: GR ChIPseq in AtT-20 expressing Pax7 (Dex+LIF)

description: AtT-20 cells expressing 3x flag-Pax7

value: GR Sc1004


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell048

source_name: Subject11_DENV positive_PBMC_TEMRA

value: DENV positive


title: GR ChIPseq in AtT-20 expressing Neo (Dex+LIF)

description: AtT-20 cells expressing 3x flag-Neo


title: Single-cell_RNA-seq_Subject12_TCM_Cell035

value: PBMC


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell047


title: Tpit ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7

value: Tpit Pulichino et al. 2003


title: H3 ChIPseq in AtT-20 expressing Neo

description: AtT-20 cells expressing 3x flag-Neo


title: Pax7 ChIPseq in AtT-20 expressing Pax7

description: AtT-20 cells expressing 3x flag-Pax7


title: ATACseq in melanotropes replicate 2

extract_protocol:
We separated by dissection the two pituitary lobes from a POMC-EGFP mouse line, FACS-sorted the GFP-positive cells to extract purified melanotropes and corticotropes from each lobes. Transposase reaction was performed on 100 000 nuclei.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

value: Melanotropes

value: FACS-sorting from POMC-EGFP mouse line


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell044


title: ATACseq in melanotropes replicate 1


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell043


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell045


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell042


title: ATACseq in corticotropes replicate 2

value: Corticotropes


title: ATACseq in corticotropes replicate 1


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days of treatment followed by 18 days without treatment) replicate 2

treatment_protocol: Treatment was added directly in the media of the cultured cells and left for the mentioned amount of time. Treatment was applied every day while changing the medium.

value: pituitary corticotroph cell

value: AtT-20 cells

value: more than 20 days of 4-hydroxy-Tamoxifen treatment followed by removal of Tamoxifen for more than 20 days


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell040

value: TEMRA


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell039


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days of treatment followed by 18 days without treatment) replicate 1


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell038


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell037


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days of treatment followed by 3 days without treatment) replicate 1

value: more than 20 days of 4-hydroxy-Tamoxifen treatment followed by removal of Tamoxifen for 3 days


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell036


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days) replicate 2

value: more than 20 days of 4-hydroxy-Tamoxifen treatment


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell046


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell035


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell034


title: ATACseq in AtT-20 expressing ER-Pax7 (30 minutes) replicate 2

treatment_protocol: Treatment was added directly in the media of the cultured cells and left for the mentioned amount of time

value: 30 minutes of 4-hydroxy-Tamoxifen treatment


title: ATACseq in AtT-20 expressing ER-Pax7 (30 minutes) replicate 1


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell033


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell032


title: ATACseq in AtT-20 expressing ER-Pax7 (no induction) replicate 2


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell041


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell030


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell031


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell026


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell028


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days of treatment followed by 3 days without treatment) replicate 2


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell027


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell025


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell029


title: ATACseq in AtT-20 expressing Pax7


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell021


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell019


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell023


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell018


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell022


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell016


title: ATACseq in AtT-20 expressing ER-Pax7 (more than 20 days) replicate 1


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell017


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell012


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell014


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell013


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell015


title: ATACseq in AtT-20 expressing Neo


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell010


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell006


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell011


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell009


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell008


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell024


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell007


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell020


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell048

source_name: Subject10_DENV negative_PBMC_TEMRA

value: DENV negative


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell002


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell004


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell003


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell005


title: Single-cell_RNA-seq_Subject11_TEMRA_Cell001


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell046


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell047


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell043


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell042


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell044


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell045


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell041


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell040


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell039


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell038


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell037


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell034


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell033


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell035


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell032


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell030


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell031


title: ATACseq in AtT-20 expressing ER-Pax7 (no induction) replicate 1


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell029


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell028


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell026


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell027


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell025


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell024


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell018


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell020


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell021


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell023


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell022


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell017


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell015


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell014


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell013


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell036


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell009


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell008


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell011


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell010


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell006


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell007


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell004


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell002


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell003


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell012


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell001


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell005


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell019


title: Single-cell_RNA-seq_Subject10_TEMRA_Cell016


title: 1620_4hr

city: San Diego

first: Matthew

last: Janes

state: CA

address: 3033 Science Park Rd, Suite 220

institute: Wellspring Biosciences

data_processing:
qiagen genomics biomedical workbenchv4.1.1, genome annotated with genes and transcripts from homo_sapiens_sequence_hg19; ensembl_v74genes; ensembl_v74mRNA;
mismatch cost=2, insertion.deletion cost=3, length fraction=0.8; RNA-seq Analysis 2.15 pipeline
Genome_build: hg19
Supplementary_files_format_and_content: fastq files for raw data; and tab-delimited txt files for RPKM values for each sample

growth_protocol: 0.5-1.0million cells seeded in 6well-plate (2ml media) and allowed to adhere overnight.  Indicated treatment or infection was subsequently performed

extract_protocol:
Qiagen RNAeasy mini kit
see supplemental STAR methods; standard Illumina protocols

treatment_protocol: ARS-1620 (1uM), trametinib (50nM), or viral supernatants (neat, 1ml added to 1ml culture media; spinfect for 1hr, replace with fresh growth media 1hr after)

tag: agent

value: ARS-1620 treated 1uM


title: 1620_24hr


title: 1620_48hr


title: A549_trametinib_rep2

value: trametinib treated 50nM


title: trametinib_48hr


title: A549_trametinib_rep1


title: A549_DMSO_rep1

value: DMSO treated


title: A549_DMSO_rep2


title: A549_1620_rep2


title: A549_1620_rep1


title: LU65_trametinib_rep1


title: LU65_trametinib_rep2


title: LU65_1620_rep3


title: LU65_1620_rep2


title: LU65_1620_rep1


title: trametinib_4hr


title: LU65_DMSO_rep1


title: H358_trametinib_rep1


title: LU65_DMSO_rep3


title: shKRAS_2_rep2

value: shRNA KRAS #2 hairpin


title: shKRAS_2_rep1


title: shKRAS_1_rep1

value: shRNA KRAS #1 hairpin


title: shLUC_rep2

value: shRNA Luciferase control


title: shLUC_rep1


title: 1620_rep4


title: 1620_rep3 (May)


title: 1620_rep2 (April)


title: 1620_rep1 (March)


title: DMSO_rep3 (May)


title: DMSO_rep1 (March)


title: DMSO_rep2 (April)


title: IPF1s2

city: Baltimore

first: Sergei

middle: P

last: Atamas

state: MD

address: 10 S. Pine St., MSTF 834

department: Department of Medicine

institute: University of Maryland School of Medicine

description:
IPF patient 1 scarred area 2
OtB5254

data_processing:
Transcript abundance was estimated using the htseq-count script of the Python package HTSeq 0.6.1p2
Genome_build: hg19 / GRCh37 assembly
Supplementary_files_format_and_content: Tab-delimited abundance measurements

source_name: lung tissue

extract_protocol:
Total RNA extracted with TRIzol reagent per manufacturer's recommendations
Illumina library preparation using SPRIWorks HT (Beckman Coulter, Indianapolis IN)

tag: tissue

value: lung

value: idiopathic pulmonary fibrosis

tag: macroscopic appearance

value: scarred


title: IPF1s3

description:
IPF patient 1 scarred area 3
OtB5169


title: IPF1s1

description:
IPF patient 1 scarred area 1
OtB5166


title: IPF3n3

description:
IPF patient 3 normal-appearing area 3
OtB5180

value: normal


title: IPF2s3

description:
IPF patient 2 scarred area 3
OtB5258


title: IPF3n1

description:
IPF patient 3 normal-appearing area 1
OtB5178


title: IPF2s4

description:
IPF patient 2 scarred area 4
OtB5177


title: IPF3s1

description:
IPF patient 3 scarred area 1
OtB5264


title: IPF3n2

description:
IPF patient 3 normal-appearing area 2
OtB5179


title: IPF2s2

description:
IPF patient 2 scarred area 2
OtB5175


title: IPF2n2

description:
IPF patient 2 normal-appearing area 2
OtB5172


title: LU65_DMSO_rep2


title: IPF1n4

description:
IPF patient 1 normal-appearing area 4
OtB5165


title: IPF1n2

description:
IPF patient 1 normal-appearing area 2
OtB5163


title: IPF1n1

description:
IPF patient 1 normal-appearing area 1
OtB5162


title: IPF1n3

description:
IPF patient 1 normal-appearing area 3
OtB5164


title: HC33

description:
healthy control 3 area 3
OtB5161

value: healthy control


title: IPF2n1

description:
IPF patient 2 normal-appearing area 1
OtB5170


title: HC32

description:
healthy control 3 area 2
OtB5160


title: HC21

description:
healthy control 2 area 1
OtB5156


title: HC23

description:
healthy control 2 area 3
OtB5256


title: HC22

description:
healthy control 2 area 2
OtB5157


title: HC12

description:
healthy control 1 area 2
OtB5155


title: HC11

description:
healthy control 1 area 1
OtB5154


title: IPF2s1

description:
IPF patient 2 scarred area 1
OtB5174


title: Small RNAs from ovaries of 2.4 transgenic strain

city: Moscow

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
Reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly and transgene sequencies.
Genome_build: dm3
Supplementary_files_format_and_content: smallRNA-seq: Tab-delimited file include the raw counts of clipped read occurrences.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol: smallRNA-seq: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt). Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries

value: 2.4 transgenic


title: xrn3-8_small_RNA_rep2

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Illumina HiSeq; strand specific

data_processing:
quality filtering and trimming, adapter removal
mapping with bowtie
expression estimation with HTseq-count and DESeq2
bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: 14 day old seedlings

extract_protocol:
trizol
BGI

tag: genotype

tag: media

value: grown on MS plates


title: ATAC in Pax7 KO replicate 1

source_name: neuro-lntermediate lobe

extract_protocol:
We performed the ATACseq on dissected neuro-intermediate lobe from Pax7 WT and Pax7 KO mice. Transposase reaction was performed on 50 000 nuclei.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads.

tag: strain background

tag: cell type

value: pituitary

tag: genotype/variation

value: Pax7 KO


title: Col0_small_RNA_rep3

description: Illumina HiSeq; strand specific

value: wild type


title: xrn3-8_small_RNA_rep3

description: Illumina HiSeq; strand specific


title: Beta_Subject23-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)

data_processing:
The sequencing data was mapped and analyzed using MIGEC software ( version 1.2.6) with default settings.
Sample fastq were obtained with command Checkout (parameters -cute) from MIGEC software.
Histogram, AssembleBatch, CdrBlastBatch and FilterCDRBlastResultsBatch functions from MIGEC were used to define TCR sequences.
Downstream analysis was performed using V(D)J tools with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: TCR alpha and TCR beta chain reconstruction in 14 subjects from TCR-seq analysis.

source_name: PBMC

growth_protocol: CD4 memory cell types were isolated from PBMCs and directly sorted by Flow cytometry into trizol. No particular cell growth procedure was required.

extract_protocol:
TCR-seq was performed as described previously by Shugay et al., 2014  with 1ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
TCR-seq was performed as described previously by Shugay et al., 2014  with 1ng of total RNA.
DNA sequencing - libraries were prepared using True-seq nano DNA library kit (Illumina). Libraries were pooled and sequenced on the MiSeq Illumina platform to obtain 200-bp paired end reads.

treatment_protocol: PBMCs were immuno stained and FACS sorted into Trizol for RNA isolation

tag: subject id

value: PBMC

tag: cell subtype surface markers

tag: cell subtype


title: IPF2n3

description:
IPF patient 2 normal-appearing area 3
OtB5259


title: Col0_small_RNA_rep2

description: Illumina HiSeq; strand specific


title: Col0_small_RNA_rep1

description: Illumina HiSeq; strand specific


title: xrn3-8_small_RNA_rep1

description: Illumina HiSeq; strand specific


title: ATAC in Pax7 WT replicate 1

value: Pax7 WT


title: Beta_Subject23-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: ATAC in Pax7 WT  replicate 2


title: Beta_Subject23-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)

value: TEM


title: HC31

description:
healthy control 3 area 1
OtB5159


title: Beta_Subject23-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)

value: TCM


title: Beta_Subject23-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject23-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject23-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V2-TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V2-TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V2-TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V2-TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject22-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject21-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject23-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject20-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject19_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject19_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject19_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject18_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject19_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject18_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject17_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject18_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject17_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject18_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject15_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject15_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject15_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject17_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V2-TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V2-TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V2-TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject17_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V2-TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject16-V1_TEMRA_IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Beta_Subject15_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V1_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V1_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject19_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject19_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject19_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject22-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject18_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject19_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject18_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject18_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject18_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject23-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject17_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject17_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V2_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject17_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V2_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V2_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V1_TEMRA_IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject20-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject15_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject16-V1_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject15_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject15_TEMRA-IL7Rhigh

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject17_TEMRA-IL7Rlow

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject15_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Alpha_Subject21-V1_TEM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Nanobiopsy Sample_2_30

city: Santa Cruz

first: Nader

last: Pourmand

address: 1156 High Street

department: Department of Biomolecular Engineering

institute: University of California at Santa Cruz

data_processing:
Illumina MiSeq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. RNA-seq reads were aligned to the hg38 UCSC human reference genome using STAR aligner. Genes were scored positive for expression if at least one read mapped uniquely to an annotated transcript.
Gene expression was quantified using HTSeq .
Genome_build: hg38 UCSC
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: human iPS-derived neuronal cells

growth_protocol: Cells were plated at 20,000 cells/cm2 density in 3.5 cm diameter, CELLview™ Cell Culture Dishes (Greiner Bio-One GmbH, Rainbach im Mühlkreis, Austria) pre-treated with 0.05% poly-ethylene-imine (PEI) (Sigma-Aldrich, St. Louis, MO) for 1h and coated with 5.0 µg/ml laminin (Sigma-Aldrich, St. Louis, MO) for 1h. Cells were grown in media provided by Cellular Dynamics supplemented with 1% PenStrep (Lonza, Basel, Switzerland), at 37°C, with 5% CO2/95% air.

extract_protocol:
Neuron cell bodies and neurites were sampled using the nanobiopsy platform developed by our laboratory. Each nanobiopsy sample was ~50 fL corresponding to ~1% of the cell's total volume. Aspirated RNA samples were processed to cDNA using the ultra low RNA input SMART-Seq system (Takara Bio USA, Mountain View, CA). The cDNA was prepared for each individual aspiration for library preparation.50 ul of 1:5,000 dilution ERCC RNA Spike-In Mix (Ambion) was added to each sample for quality control. cDNA was amplified by KAPA HiFi HotStart ReadyMix PCR Kit using SMART-Seq PCR primers. cDNA was purified by AmPure XP beads.
Tagmentation of cDNA for the preparation of RNA-Seq libraries was performed by Nextera XT DNA Library preparation kit (Illumina, San Diego, CA). Multiplexed sequencing adapters were ligated to tagmented cDNA by limited-cycle polymerase chain reaction (10 cycles), according to manufacturer's instructions. The final, amplified libraries were purified by AmPure XP beads (Beckman Coulter Genomics, Danvers, MA), and size-selected in the range of 200-600 bp using the Caliper LabChip XT system (PerkinElmer, Waltham, MA). The final RNA-Seq libraries were quantified using the Agilent Bioanalyzer 2100 High Sensitivity DNA Assay and KAPA Library Quantification Kit, and pooled together in equal concentration for sequencing. The pooled multiplexed libraries were sequenced for 2 × 150 bp paired-end or 2 × 80 bp paired-end reads on Illumina MiSeq (Illumina, San Diego, CA).

value: Cellular Dynamics iCell Neuron

tag: cell structure

value: neurite

tag: cell id

tag: time of aspiration


title: Nanobiopsy Sample_2_29

value: cell body


title: Sample_NC

source_name: Negative control, ERCC only

value: Negative control, ERCC only


title: Nanobiopsy Sample_2_22


title: Nanobiopsy Sample_2_27


title: Nanobiopsy Sample_2_26


title: Nanobiopsy Sample_2_23


title: Nanobiopsy Sample_2_28


title: Nanobiopsy Sample_2_21


title: Nanobiopsy Sample_2_19


title: Nanobiopsy Sample_2_25


title: Nanobiopsy Sample_2_17


title: Nanobiopsy Sample_2_18


title: Alpha_Subject16-V2_TCM

description: UMI-based TCR-seq(Shugay et. al., 2014)


title: Nanobiopsy Sample_2_16


title: Nanobiopsy Sample_2_15


title: Nanobiopsy Sample_2_13


title: Nanobiopsy Sample_2_14


title: Nanobiopsy Sample_2_11


title: Nanobiopsy Sample_2_10


title: Nanobiopsy Sample_2_12


title: Nanobiopsy Sample_2_7


title: Nanobiopsy Sample_2_9


title: Nanobiopsy Sample_2_8


title: Nanobiopsy Sample_2_20


title: LTBI_16

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

description: LTBI subject 16

data_processing:
Sequence Quality control: FastQC_v0.11.5 (default) + trimmomatic-0.36 (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Alignment: Rsubread-1.8.2 (indels = 5, unique = TRUE)
Gene Filtering: rowSums(matrix) > 20
Normalization: DEseq2 1.14.1 (RLE method)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file matrix of normalized expression counts with genes in rows and samples in columns

source_name: Whole blood

extract_protocol:
PAXgene blood RNA kit (Cat # 762164, Qiagen, Hilden, Germany)
SureSelect Strand-Specific mRNA Library Prep kit (Cat #5190-6411, Agilent, Santa Clara, USA)

tag: condition

value: latent TB infection


title: Nanobiopsy Sample_2_6


title: Nanobiopsy Sample_2_3


title: Nanobiopsy Sample_2_4


title: LTBI_15

description: LTBI subject 15


title: Nanobiopsy Sample_1_23


title: LTBI_9

description: LTBI subject 9


title: LTBI_13

description: LTBI subject 13


title: LTBI_11

description: LTBI subject 11


title: LTBI_12

description: LTBI subject 12


title: Nanobiopsy Sample_1_16


title: LTBI_10

description: LTBI subject 10


title: Nanobiopsy Sample_1_15


title: LTBI_8

description: LTBI subject 8


title: Nanobiopsy Sample_1_17


title: LTBI_14

description: LTBI subject 14


title: Nanobiopsy Sample_1_14


title: Nanobiopsy Sample_1_13


title: Nanobiopsy Sample_1_12


title: LTBI_7

description: LTBI subject 7


title: LTBI_6

description: LTBI subject 6


title: LTBI_5

description: LTBI subject 5


title: Nanobiopsy Sample_1_11


title: Nanobiopsy Sample_1_8


title: LTBI_3

description: LTBI subject 3


title: Nanobiopsy Sample_1_7


title: Nanobiopsy Sample_1_21


title: LTBI_2

description: LTBI subject 2


title: Nanobiopsy Sample_1_6


title: Nanobiopsy Sample_1_5


title: LTBI_1

description: LTBI subject 1


title: Nanobiopsy Sample_1_4


title: TB_28

description: TB subject 28

value: TB


title: TB_20

description: TB subject 20


title: TB_21

description: TB subject 21


title: TB_25

description: TB subject 25


title: TB_23

description: TB subject 23


title: TB_24

description: TB subject 24


title: TB_27

description: TB subject 27


title: TB_26

description: TB subject 26


title: TB_17

description: TB subject 17


title: Nanobiopsy Sample_2_2


title: TB_16

description: TB subject 16


title: TB_15

description: TB subject 15


title: LTBI_4

description: LTBI subject 4


title: TB_14

description: TB subject 14


title: TB_13

description: TB subject 13


title: TB_11

description: TB subject 11


title: TB_10

description: TB subject 10


title: TB_22

description: TB subject 22


title: TB_18

description: TB subject 18


title: TB_7

description: TB subject 7


title: TB_8

description: TB subject 8


title: TB_9

description: TB subject 9


title: TB_19

description: TB subject 19


title: TB_4

description: TB subject 4


title: TB_5

description: TB subject 5


title: TB_2

description: TB subject 2


title: TB_6

description: TB subject 6


title: Nanobiopsy Sample_1_2


title: Nanobiopsy Sample_1_3


title: ATAC in Pax7 KO replicate 2


title: Chou-10

first: Ian

last: Henrich

address: 803D Abramason Research Center, 3615 Civic Center Blvd

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to human genome hg19 and Refseq transcriptome, and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: hg19
Supplementary_files_format_and_content: Excel format file of transcript raw read counts of each sample

growth_protocol: USP6 was stably overexpressed in the parental RD-ES cell line under a doxycycline promoter (RD-ES/USP6(Pool))

extract_protocol:
RNA was extracted using trizol
RNA libraries were prepared for sequencing using Illumina's TruSeq® Stranded Total RNA Library Prep kit.

treatment_protocol: Cells were seeded at sub-confluent densities and allowed to attach overnight. Doxycycline was used to induce USP6 expression for 24 hours followed by treatment with 1000 U/mL interferon alpha for 24 hours

tag: cell line

tag: treatment (doxycycline)

value: Yes

tag: treatment (interferon alpha)


title: Chou-6

value: No


title: Chou-8


title: Chou-9


title: Chou-7


title: TB_1

description: TB subject 1


title: Chou-5


title: Chou-3


title: U87 cells_Myt1 rep3

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base. Filtered reads were assessed for quality using FastQC (1). 1. Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010.
Reads were splice-aware aligned to the reference genome using STAR (2), and reads overlapping gene regions were counted using featureCounts (3). 2. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; doi:10.1093/bioinformatics/bts635. 3. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923-30. doi:10.1093/bioinformatics/btt656
The DESeq2 Bioconductor package (4) in the R statistical computing environment (5) was used for normalizing count data, performing exploratory data analysis, estimating dispersion, and fitting a negative binomial model for each gene comparing the expression from Myt1 or Myt1l expressing samples versus control samples. 4. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi:10.1186/PREACCEPT-8897612761307401. 5. R Core Development Team. R: A Language and Environment for Statistical Computing. ISBN 3-900051-07-0, URL http://www.R-project.org/. Vienna, Austria; 2010.
After obtaining a list of differentially expressed genes, log fold changes, and p-values, Benjamini-Hochberg False Discovery Rate procedure was used to correct p-values for multiple testing.
Genome_build: GRCh38
Supplementary_files_format_and_content: [ctrl_Myt1_Myt1l_pairend.csv] comma separated file, including read counts for each sample

source_name: U87 cells_Myt1

extract_protocol:
RNA was isolated using an Absolutely RNA Miniprep Kit (Agilent) according to the manufacturer's instructions.
Poly-A RNA-seq libraries were generated at HudsonAlpha with Illumina barcodes and sequenced (Illumina HiSeq) to a target depth of ~ 25M paired end 50bp reads per sample
RNA-seq, poly A selection, 50bp paired end reads.

value: U87 glioblastoma cells

value: Myt1 expression


title: U87 cells_Myt1 rep2


title: U87 cells_Myt1 rep1


title: TB_12

description: TB subject 12


title: U87 cells_Myt1l rep2

source_name: U87 cells_Myt1l

value: Myt1l expression


title: U87 cells_Myt1l rep1


title: U87 cells_Myt1l rep3


title: TB_3

description: TB subject 3


title: U87 cells_ctrl rep1

source_name: U87 cells_ctrl

value: control vector


title: U87 cells_ctrl rep2


title: U87 cells_ctrl rep3


title: Chou-4


title: RNA-seq_Blau2-corrected_IFN-γ

city: Kyoto

first: Akira

last: Niwa

address: 53, Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Clinical Application

country: Japan

institute: CiRA, Kyoto University

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format as described in "library construction protocol" section
Data sets which filtered by the criterion requiring FPKM >0 in at least one sample were first performed variance-stabilizing transformation and interquartile range filtering.
Upper-quartile (UQ) normalization followed by RUV normalization regarding each three line of treated and untreated samples as a replicated group (RUVs), modeling k = 1 factors of unwanted variation was performed to remove unwanted variations*(ref.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Corrected iPSC-derived macrophage

extract_protocol:
Total RNA was extracted using the RNeasy kit, and the quality was tested with a Bioanalyzer.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent). Sequencing was performed on an Illumina HiSeq1500 using a HiSeq Rapid SBS kit v2 (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks (ver 2.2.1) software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments)

treatment_protocol:
Macrophage induction protocol: Macrophages were induced from ESC/iPSC-derived immortalized proliferating myeloid cell lines (iPS-MLs) by MCSF stimulation
When mentioned, IFN-γ alone, MDP alone or IFN-γ+MDP were added to culture

value: iPSC-derived macrophage

tag: disease state

value: wild type(Corrected)

tag: infg treatment

tag: mdp treatment


title: RNA-seq_Blau2-R334W_MDP

description: Bulk RNA-Seq data

source_name: Disease iPSC-derived macrophage

value: Blau syndrome


title: RNA-seq_201B7-WT_untreated

description: Bulk RNA-Seq data

source_name: WT ESC-derived macrophage

value: ESC-derived macrophage

value: wild type


title: RNA-seq_Blau2-corrected_MDP

description: Bulk RNA-Seq data


title: RNA-seq_Blau2-R334W_untreated

description: Bulk RNA-Seq data


title: RNA-seq_201B7-WT_IFN-γ

description: Bulk RNA-Seq data


title: RNA-seq_Blau2-corrected_IFN-γ+MDP

description: Bulk RNA-Seq data


title: RNA-seq_201B7-WT_MDP

description: Bulk RNA-Seq data


title: RNA-seq_Blau2-corrected_untreated

description: Bulk RNA-Seq data


title: RNA-seq_201B7-WT_IFN-γ+MDP

description: Bulk RNA-Seq data


title: RNA-seq_Blau2-R334W_IFN-γ+MDP

description: Bulk RNA-Seq data


title: BMDM IL13-12h-3

status: Public on Jan 23 2018

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for base calling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: treated with IL-13 (10 ng/ml) for 12 hrs

growth_protocol: Growth protocol for BMDMs: BMDMs were isolated from C57BL/6 mice. To initiate differentiation, the medium was supplemented with 25 ng/ml recombinant macrophage colony-stimulating factor (M-CSF) (R&D Systems 416-ML) for 4 days. BMDMs were grown in Dulbecco’s Modified Eagle’s Medium (DMEM; Life Technologies, Carlsbad, CA) that was supplemented with 10% foetal bovine serum (FBS) and 4 mM glutamine (Life Technologies, Carlsbad, CA). The cells were maintained in a humidified incubator with a 95% air, 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow derived macrophage (BMDM)

tag: strain


title: BMDM IL13-12h-2


title: RAW264.7-Control-2

source_name: cultured for 4 hrs

growth_protocol: Growth protocol for RAW 264.7 macrophage cell line: RAW 264.7 macrophage cell line were grown in RPMI medium supplemented with FBS, 100 IU/ml penicillin, and 10 µg/ml of streptomycin (Invitrogen, USA). The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. RAW264.7 macrophage cell line were incubated with LPS (100 ng/ml) for the specified times under normal culture conditions. The medium, containing the appropriate agents, was replaced every other day. LPS (L6529; strain 055:B5) were purchased from Sigma-Aldrich, St. Louis, MO.

value: RAW264.7 macrophage cell line


title: RAW264.7-Control-1


title: RAW264.7-LPS-4h-2

source_name: treated with LPS (100 ng/ml) for 4 hrs


title: RAW264.7-LPS-4h-1


title: BMDM IL13-12h-1


title: BMDM IL4-12h-2

source_name: treated with IL-4 (10 ng/ml) for 12 hrs


title: BMDM IL4-12h-3


title: BMDM IL4-12h-1


title: BMDM IFN-γ-LPS-24h-3

source_name: treated with IFN-γ (100 U/ml) and LPS (100 ng/ml) for 24 hrs


title: BMDM IFN-γ-LPS-12h-3

source_name: treated with IFN-γ (100 U/ml) and LPS (100 ng/ml) for 12 hrs


title: BMDM IFN-γ-LPS-12h-1


title: BMDM IFN-γ-LPS-4h-3

source_name: treated with IFN-γ (100 U/ml) and LPS (100 ng/ml) for 4 hrs


title: BMDM IFN-γ-LPS-4h-2


title: BMDM IFN-γ-LPS-24h-1


title: BMDM IFN-γ-LPS-12h-2


title: RNA-seq_Blau2-R334W_IFN-γ

description: Bulk RNA-Seq data


title: BMDM-Control-1


title: L-DKO pTαKO DP #1 (new)

city: Durham

first: Yuan

last: Zhuang

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

data_processing:
RNA-sequencing reads were trimmed for removal of adapter sequences and low quality bases with Trimmomatic (version 0.32; adapters:2:20:7:1:true, leading:5, trailing:5, slidingwindow:4:10, minlen:21).
Reads were aligned with Tophat (version 2.0.9) to the mm10 transcriptome (Ensembl GRCm38), with remaining reads aligned to the mm10 genome.
Expression quantification was done using Cufflinks (version 2.2.0).
Log2 transformed FPKM (fragments per kilobase exon-model per million reads mapped) were used for downstream analyses. An FPKM gene expression matrix was generated for the samples.
Genes with low expression (FPKM< 1) in 50% of the samples, or with mean expression < 3  were filtered out as poorly expressed/covered genes.  Samples found with expression > 1 in <10,000 genes were also filtered out as bad quality samples.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel file with log2(FPKM) values and fold change in knockout mice compared to wild type samples

source_name: sorted cells from thymus

extract_protocol:
Thymii were harvested from mice, and thymocytes were stained with appropriate antibodies for sorting. Following sorting in TRI reagent, RNA was extracted. RNA was assessed for quality using the Agilent Bioanalyzer RNA Pico chip.  After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads.
First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: LP

tag: age

value: 4-5 weeks

tag: tissue

value: thymus

value: double-positive (DP) thymocyte

tag: sorting strategy

value: TCRγδ- CD4+ CD8+


title: L-DKO pTαKO DP #2 (new)

tag: genotype/variation

tag: cell type


title: L-DKO DP #2 (new)

value: LDKO


title: BMDM IFN-γ-LPS-4h-1


title: L-DKO DP #1 (new)


title: BMDM IFN-γ-LPS-1h-3

source_name: treated with IFN-γ (100 U/ml) and LPS (100 ng/ml) for 1 hr


title: BMDM IFN-γ-LPS-1h-2


title: BMDM-Control-2


title: BMDM IFN-γ-LPS-24h-2


title: pTαKO DP #1 (new)

value: pTA


title: BMDM IFN-γ-LPS-1h-1


title: WT DP (new)

value: WT


title: BMDM-Control-3


title: pTαKO DP #2 (new)


title: Input_normal_1

city: Goettingen

first: Laura

middle: C

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University Medical Center, Goettingen

data_processing:
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and files were generated using MACS2. Narrowpeaks and Broadpeaks were called on TCF7L2 and H3K27ac bound regions respectively. RPKM normalized bigwigs were generated using bamCoverage in Galaxy deepTools platform with default settings.

source_name: cardiac ventricles

growth_protocol: 15 weeks-old adult murine cardiac ventricles; mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
For each IP, ventricles from atleast two murine hearts were pooled, washed in PBS, minced finely and fixed in 1.3% Formaldehyde for 20 min. The nuclei from tissue extracts were sonicated for 45 cycles to obtain the fragmented chromatin. Chromatin extracts containing DNA fragments with an average size of 300 bp were immunoprecipitated using 2µg/IP of different antibodies.
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions

treatment_protocol: 12 weeks-old adult mice were administered with TX 30mg/Kg/day for 3 days and were sacrificed 3 weeks-post induction

tag: genotype

value: alphaMHC Cre recombinase positive, WT for beta-catenin (normal)

tag: chip-seq antibody

value: none (input)


title: Input_normal_2


title: H3K27ac_normal_2

value: anti-H3K27ac (C15410196, Diagenode)


title: TCF7L2_normal

description: pooled 4 ventricles to obtain a single sequencing replicate. Since, Wnt is lowly active in the normal adult myocardium, it was challenging to ChIP for TCF7L2. However, we sequenced this replicate and visualized some known target gene promoters like Axin2 and found an enrichment in some known target loci. This data was NOT used for any statistical analyses and was used ONLY for visualization.

value: anti-TCF7L2 (17-10109, Millipore)


title: H3K27ac_normal_3


title: Input_normal_3


title: H3K27ac_normal_1


title: Id3KO gamma delta #2

data_processing:
RNA-sequencing reads were trimmed for removal of adapter sequences and low quality bases with Trimmomatic (version 0.32; adapters:2:20:7:1:true, leading:5, trailing:5, slidingwindow:4:10, minlen:21).
Reads were aligned with Tophat (version 2.0.9) to the mm10 transcriptome (Ensembl GRCm38), with remaining reads aligned to the mm10 genome.
Expression quantification was done using Cufflinks (version 2.2.0).
Log2 transformed FPKM (fragments per kilobase exon-model per million reads mapped) were used for downstream analyses. An FPKM gene expression matrix was generated for 12 samples.
Genes with low expression (FPKM< 1) in 50% of the samples, or with mean expression < 3  were filtered out as poorly expressed/covered genes.  Samples found with expression > 1 in <10,000 genes were also filtered out as bad quality samples.
FPKM gene expression measurements were log10 transformed after adding 1 to the expression values.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel file with FPKM values and fold change in knockout mice compared to wild type samples

extract_protocol:
Thymii were harvested from mice, and thymocytes were stained with appropriate antibodies for sorting. Following sort, total RNA was extracted using the RNAqeous kit (Ambion) according to manufacturer's protocol. RNA was assessed for quality using the Agilent Bioanalyzer RNA Pico chip.  Ribosomal RNA was depleted using the RiboErase method from Kapa Biosystems. In short, 1ug of total RNA was hybridized with 1ug of hybridization oligos tiling the 18s, 28s, 5.8s and mitochondrial rRNA sequences. Each sample was then RNaseH treated to degrade complementary rRNA sequence. The product was cleaned and purified using 2.2X AMPure beads (Agencourt). The cleaned product was DNase treated to degrade the DNA oligo mix.  The remaining rRNA depleted samples were then purified using 2.2X AMPure XP beads.
The Kapa Stranded RNA-Seq Kit was used to generate stranded Illumina sequencing libraries (Kapa Biosystems).  RNA was fragmented at 94°C for 6 minutes. Briefly, RNA was hybridized to random primers, followed by first-strand cDNA synthesis, second-strand cDNA synthesis with marking, A-tailing, ligation of Illumina paired-end adapters with 8 bp barcodes, and 9 cycles of PCR amplification.  Reactions were purified with Agencourt AMPure XP beads where necessary. Libraries were multiplexed in equimolar amounts and sequenced as paired-end 50-bp (100 bp) reads on an Illumina Hiseq 2500 V4 Sequencing System.

value: Id3KO (lacking Id3)

value: gamma delta T cells

value: TCRγδ+ CD3+


title: TCF7L2_Wntup_2

value: alphaMHC Cre recombinase positive, beta-catenin exon3 deleted-stabilized beta-catenin (transgenic)


title: H3K27ac_Wntup_1


title: Input_Wntup_2


title: Id3KO gamma delta #1


title: H3K27ac_Wntup_2


title: TCF7L2_Wntup_1


title: Input_Wntup_1


title: L-DKO NKT #2

value: L-DKO (deficient in Id2 and Id3)

value: Invariant Natural Killer T (iNKT) cells

value: CD1dTet+ TCRβ+


title: B6 gamma delta #2

value: wild type

value: 4-5 weeks

value: thymus


title: L-DKO NKT #1


title: B6 DP #2

value: double-positive (DP) thymocyte

value: TCRγδ- CD4+ CD8+


title: B6 DP #1


title: B6 NKT #1


title: mouse023_d14_M

city: Seattle

first: Ting

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

data_processing:
Quality control for raw fastq files were performed with FastQC
Low quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt.
The trimmed reads were aligned to mm10 with the RNA-seq aligner STAR v2.5.2a
Gene expressions of every sample were quantified by counting the number of unique fragments mapped to genes using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts of genes for each sample.

source_name: Pancreas

growth_protocol: Caerulein hyperstimulation was performed on C57BL/6 mouse strain from Charles River Laboratories, 6- to 8-weeks of age, weighing 20 to 25 g.

extract_protocol:
Total RNA was immediately extracted from the head of the pancreas using TRIzol (Ambion). RNA was treated with DNase I (Zymo Research) at room temperature for 20 minutes. The concentration of DNase I-treated RNA was measured using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and the integrity of the DNase I-treated RNA was analyzed on the Agilent TapeStation. All DNase I-treated RNA samples used for RNA library construction had RNA Integrity Numbers (RINs) above 6.4.
RNA libraries were prepared for sequencing using Illumina TruSeq Total Stranded RNA sample preparation kit with ribosomal depletion. Adaptor-ligated fragments were amplified by PCR for nine cycles. The quality and size of the final library preparations were analyzed on an Agilent TapeStation.
RNA-Seq using Illumina NextSeq 500 NGS platform, with approximately 40 million paired-end 75 bp reads for each sample.

treatment_protocol: Caerulein hyperstimulation was induced in both male and female mice by 8 hourly intra-peritoneal injections (50 µg/kg) for 2 consecutive days. The mice were maintained on a 12-hour light-dark cycle, and had free access to standard laboratory chow and water. All animal experiments were performed using a protocol approved by the University of Pittsburgh Institutional Animal Care and Use Committee.

tag: group

value: day 14 post-injury

tag: gender

value: Male

value: Pancreas


title: mouse024_d14_M


title: L-DKO DP #1

value: CD1dTet- CD4+ CD8+


title: L-DKO DP #2


title: mouse021_d14_M


title: mouse019_d14_F

value: Female


title: mouse018_d14_F


title: mouse017_d14_F


title: mouse013_d7_M

value: day 7 post-injury


title: mouse012_d7_F


title: mouse014_d7_M


title: mouse015_d7_M


title: B6 gamma delta #1

value: gamma delta T cells


title: mouse008_BL_M

value: baseline (non-injured)


title: mouse010_d7_F


title: mouse011_d7_F


title: hsa.poly.TUBB_heavy

first: Manolis

last: Maragkakis

address: 251 Bayview Blvd

institute: National Institute on Aging

description: RNA isolated from heavy polysome fraction

data_processing:
Adaptor trimming: The adapter sequences were trimmed from the paired-end reads using the cutadapt software in paired-end mode. The adapter GTGTCAGTCACTTCCAGCGG was trimmed from the 3’ end of read1 whereas CCGCATCGTCCTCCCT was trimmed from the 3’ end of read2. A constant adapter sequence of 16 nt was removed from the 5’ end of read1. Only reads longer than 25 nt after adapter trimming were retained.
First alignment: The reads were aligned to the human genome (hg19) using the STAR aligner (v2.5.2a). Reads were aligned in paired-end mode.
Collapsing: To exclude potential PCR artifacts, reads with the same 5’ end (defined from read1) and the same 3’ end (defined from read2) were collapsed.
Alignment: Akron5: The retained reads were re-aligned in single end mode using read1 only and the following parameters --outFilterMultimapScoreRange 0 --alignIntronMax 50000 --outFilterMatchNmin 8 --outFilterMatchNminOverLread 0.7 --sjdbOverhang 80 --alignSJDBoverhangMin 1 --seedSearchStartLmax 15. Akron3: Only read2 were aligned after they were reverse complemented to facilitate downstream analysis. The STAR parameters were selected to permit the alignment of reads with poly(A) tails. Specifically the following parameters were used --alignIntronMax 50000 --outFilterMultimapScoreRange 0 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 30 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --sjdbOverhang 100 --alignSJDBoverhangMin 1.
Aligned reads were loaded into a SQLite3 database for further processing with CLIPSeqTools (v0.1.7).
The read 5' and 3' ends for Akron5 and Akron3, respectivelly were extracted in bedgraph format. For Akron-SMRT the whole reads were extracted in bedgraph format.
Bedgraph files were converted to BigWig with UCSCtools bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to the fragments 5’ and 3’ ends for Akron5 and Akron3, respectively and to the whole reads for Akron-SMRT.

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM (Gibco) supplemented with 10% FBS (Sigma), at 37 °C, in 5% CO2. Cells were harvested at ~80% confluence.

extract_protocol:
Total RNA was extracted with Trizol (Ambion)
For Akron-SMRT, total RNA was extracted by Trizol from HeLa total cells and sucrose gradient polysome fractions. RNA was treated with 5’-phosphate specific Terminator exonuclease to remove non-capped mRNA. The 3’ ends of mRNA molecules were marked by ligation to an adapter that contains a biotin group at the 3’ end, allowing for further purification. We generated cDNA in conditions that favor full-length molecule amplification using primers designed to specifically amplify mRNAs encoded by CDK4 and TUBB genes. To avoid capturing 5’ OH mRNAs we used two PCR amplification steps for each gene using forward primers that started at the 5’ UTR and at the start codon. We then size-selected by gel purification to enrich for larger mRNAs and performed SMRT sequencing.    For Akron3,  abundant small RNAs was first substracted by dynabeads size-selection, and ribosomal RNAs and small-capped RNAs (i.e U snRNAs) were depleted using synthesized biotinylated oligonucleotides.  Capped mRNAs were then  selected by Terminator exonuclease treatment followed by biotinylated adapter ligation at the 3’ end and streptavidin capture. Similarly, for Akron5, polyadenylated mRNAs were enriched using Oligo(dT) followed by biotinylated adapter ligation at the 5’ end and streptavidin capture. While capped mRNAs are carried over, only poly(A) mRNAs with 5’ monophosphate are captured. The native ends of RNAs in Akron3 and Akron5 are marked by adapter ligation. In Akron3 and Akron5, RNA was chemically fragmented before the second adapter ligation. After fragmentation, RNA in Akron3 was size selected (>400 bp) on denaturing polyacrylamide. In Akron3 and Akron 5, a second adatpter was ligated and cDNA was generated by Superscript III with specific primers that recognize the adapter sequence. PCR amplification was performed with primers compatible with Illumina sequencer. PCR products were purified (~500-800 bp) on Metaphore agarose gels and were identified by paired-end, sequence-by-synthesis

treatment_protocol: Cells were pretreated with 100 µg/ml cycloheximide (Sigma) for 10 min at 37 °C, only for sucrose gradient fractionation.

value: HeLa

tag: protocol

value: Akron-SMRT

tag: rna fraction

value: heavy polysomes

tag: amplified mrna

value: TUBB


title: hsa.whole.TUBB

description: no fractionation of RNA

tag: cell line

value: whole cell (no fractionation)


title: mouse007_BL_M

last: Wang


title: hsa.whole.CDK4

description: no fractionation of RNA


title: mouse022_d14_M


title: mouse009_d7_F


title: hsa.poly.CDK4_heavy


title: B6 NKT #2

value: wild type

value: 4-5 weeks

value: Invariant Natural Killer T (iNKT) cells

value: CD1dTet+ TCRβ+


title: Nine hours post fertilization replicate 2013_49

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

state: Missouri

address: 1000 E 50th Street

institute: The Stowers Institute for Medical Research

description:
9hpf_2013_49
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

data_processing:
Bowtie2 with the --norc parameter was used to align reads from each developmental timepoint to the reference transcriptome.
Samtools idxstats quantified the alignments for each reference sequence.
Counts for trinity isoforms were summed to create a count 'per gene'.
RPKMs were calculated for each reference sequence.
Genome_build: Mnemiopsis leidyi transcriptome shotgun assembly (TSA): GFAT01000000
Supplementary_files_format_and_content: counts.txt: A tab-delimited text file with the first two columns being the transcript ID, and the transcript length. All subsequent columns are the names of the samples and their counts for each transcript ID.
Supplementary_files_format_and_content: rpkm.txt: A tab-delimited text file with the first two columns being the transcript ID, and the transcript length. All subsequent columns are the names of the samples and their rpkm for each transcript ID.

organism: Mnemiopsis leidyi

source_name: Mnemiopsis leidyi embryo, 9 hpf

growth_protocol: Animals were collected in the wild at various locations around Woods Hole, MA either by net or by a plastic beaker attached to a pole for gently scooping the animals from the water.

extract_protocol:
Total RNA was harvested for 100-200 embryos per stage with the Trizol reagent. Dynabeads were used to extract mRNA.
Libraries were prepared using ScriptSeq V2 (Epicenter) with some modifications. Briefly, instead of the manufacturer’s recommended 5 minute fragmentation, we performed a 90 second fragmentation at 85oC, followed by 15 rounds of PCR amplification. The quality of the resulting libraries was tested using High Sensitivity DNA Chip Kits (Agilent). After quality testing, the libraries were subjected to targeted size selection using Pippin Prep (Sage Science) to a range encompassing 350bp to 600bp. After size selection, the samples were cleaned up with PCR minElute columns from Qiagen to both concentrate the DNA and to remove the EtBr from the Pippin Prep. The samples were then run again on High Sensitivity DNA Chips to confirm quality. The resulting high quality libraries were pooled and sequenced with an Illumina High Seq sequencer (Illumina).

tag: developmental stage

value: embryo

value: whole body

tag: time point

value: 9 hours post fertilization


title: mouse003_BL_F

value: Pancreas


title: mouse006_BL_M

value: Male


title: Eight hours post fertilization replicate 2013_48

description:
8hpf_2013_48
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 8 hpf

value: 8 hours post fertilization


title: Nine hours post fertilization replicate 2012_37

description:
9hpf_2012_37
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: mouse004_BL_F

value: Female


title: Eight hours post fertilization replicate 2013_18

description:
8hpf_2013_18
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: mouse005_BL_M

value: baseline (non-injured)


title: mouse002_BL_F


title: mouse016_d7_M

value: day 7 post-injury


title: Eight hours post fertilization replicate 2012_N8B

description:
8hpf_2012_N8B
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: mouse001_BL_F


title: Seven hours post fertilization replicate 2013_47

description:
7hpf_2013_47
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 7 hpf

value: 7 hours post fertilization


title: Eight hours post fertilization replicate 2012_18

description:
8hpf_2012_18
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: hsa.Akron5.Hela.1

value: HeLa


title: hsa.Akron3.Hela.2


title: hsa.Akron3.Hela.1


title: Six hours post fertilization replicate 2013_26

description:
6hpf_2013_26
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 6 hpf

value: 6 hours post fertilization


title: Seven hours post fertilization replicate 2013_17

description:
7hpf_2013_17
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Seven hours post fertilization replicate 2012_N1

description:
7hpf_2012_N1
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Seven hours post fertilization replicate 2013_27

description:
7hpf_2013_27
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Six hours post fertilization replicate 2013_46

description:
6hpf_2013_46
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Six hours post fertilization replicate 2012_N2

description:
6hpf_2012_N2
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Eight hours post fertilization replicate 2013_28

description:
8hpf_2013_28
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: N8 A2M* 0 micromolar

city: Leipzig

first: Ronny

last: Amberg

state: Saxony

address: Talstrasse 33

department: Faculty of Life Sciences

institute: University of Leipzig

description: biological control replicate 8

data_processing:
Removal of adapter sequences with basic quality control and trimming was performed using Illumina’s BCL2FastQ v2.16.0.10, on default setting.
Firstly, reads were mapped with default parameters with the splice-aware alignment program Hisat v2.0.0b.
Secondly, reads for which no alignment position was reported by Hisat, were then mapped with Bowtie2 v.2.2.6.
The abundance of transcript isoforms (TPM – transcript per million) was estimated using the RNA-Seq assembler StringTie v1.1.0.
Expression values were extracted from the appropriate gtf files and Welch’s unequal variances t-test was performed on transcript level.
Genome_build: Ensembl Genome GRCh38.p2 Release 80
Supplementary_files_format_and_content: gtf files - containing the StringTie Output
Supplementary_files_format_and_content: xlsx - containing the tTest Results as Excel file

source_name: epithelial lung carcinoma

growth_protocol: Cells were cultured at a density of 106 /mL in RPMI 1640 medium, containing penicillin (100 U/mL), streptomycin (100 μg/mL), glutamine (2 mM) and 10% fetal calf serum (FCS). Cells were seeded 48h and the medium was replenished 24h prior adding of A2M*.

extract_protocol:
QIAamp RNA Blood Mini Kit
Library preparation was done using ScriptSeq™ Complete Gold Kit (LOT. V224-41214) with the required additional FailSafe™ PCR Enzyme Mix (LOT. 10059394) following the Epicentre® manual, November 2014. The library preparation was executed on a Caliper Life Sciences Sciclone G3, by Perkin Elmer.

treatment_protocol: Cells were treated with 30 nM A2M* for 24h.

tag: biomaterial provider

value: ATCC

tag: isolate

tag: agent


title: N8 A2M* 30 micromolar

description: biological treated replicate 8

value: 30 nM A2M


title: N7 A2M* 30 micromolar

description: biological treated replicate 7


title: N5 A2M* 0 micromolar

description: biological control replicate 5


title: Five hours post fertilization replicate 2013_25

description:
5hpf_2013_25
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 5 hpf

tag: tissue

value: 5 hours post fertilization


title: Six hours post fertilization replicate 2012_23

description:
6hpf_2012_23
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Five hours post fertilization replicate 2012_14

description:
5hpf_2012_14
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: N7 A2M* 0 micromolar

description: biological control replicate 7


title: N5 A2M* 30 micromolar

description: biological treated replicate 5


title: Five hours post fertilization replicate 2012_N3

description:
5hpf_2012_N3
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Four hours post fertilization replicate 2013_34

description:
4hpf_2013_34
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 4 hpf

value: 4 hours post fertilization


title: N4 A2M* 30 micromolar

description: biological treated replicate 4


title: Four hours post fertilization replicate 2013_24

description:
4hpf_2013_24
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: hsa.Akron5.Hela.3


title: Δwc2_constant light

city: Heidelberg

first: Michael

last: Brunner

address: Im Neuenheimer Feld 328

institute: BZH

description: Sample 7

data_processing:
Reads were mapped to the NC10 and NC12 genome using Bowtie2 (v 2.1.0 and 2.2.5) and Tophat2 (v 2.0.13 and 2.0.14) softwares.
Dataset normalisation was done by library size.
HTSeq was used for read counting over genes.
BigWig coverage files were created by custom R scripts.
Splice site analysis was done by the Tophat2 junction output.
BigWig files were used to generate the data tracks of the NEUTRA database.
Genome_build: Neurospora crassa NC10 and NC12
Supplementary_files_format_and_content: [List_of_lincRNAs.txt] tab-delimited text file, list of identified lincRNAs with read counts from pooled polysome-RNA-seq
Supplementary_files_format_and_content: [BigWig files] Coverage on plus and minus strand
Supplementary_files_format_and_content: [W*.txt and w*.txt files] Read counts over genes, strand specific in samples 1-4, non-specific in 5-7

organism: Neurospora crassa

source_name: Δwc2_constant light

growth_protocol: Samples 1,2,3 and 4  were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min. Samples 5, 6 and 7 were grown in constant light for 48 h at 25°C. Sample 8 was grown for 1 day in light at 25°C, released to constant darkness for 22 h and individual samples of the pooled data were harvested at 2 h intervals.

extract_protocol:
RNA was prepared with peqGOLD TriFAST (peqLab, Erlangen, Germany).
For 1,2, 3 and 4; NEBNext Ultra Directional RNA prep Kit for Illumina (E7420) was used. For samples 5,6,7 and 8 RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples were pulverized in liquid nitrogen and approximately 0.25 g of the ground mycelia was used for each experiment. For sample 8, cycloheximide was added to the cultures prior to harvesting. Gradients containing 10-50-60% sucrose were used.

tag: strain

tag: treatment

value: constant light

tag: growth protocol

value: Liquid culture

value: mycelia


title: hsa.Akron5.Hela.2


title: Δwc1_constant light

description: Sample 6

source_name: Δwc1_constant light

tag: genotype


title: WT_constant light

description: Sample 5

source_name: wild type, constant light

value: wildtype


title: Four hours post fertilization replicate 2012_N4

description:
4hpf_2012_N4
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

value: embryo

value: whole body


title: N4 A2M* 0 micromolar

description: biological control replicate 4


title: Three hours post fertilization replicate 2013_N5

description:
3hpf_2013_23
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 3 hpf

value: 3 hours post fertilization


title: Three hours post fertilization replicate 2013_33

description:
3hpf_2013_33
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: N6 A2M* 30 micromolar

description: biological treated replicate 6


title: N1 A2M* 30 micromolar

description: biological treated replicate 1


title: Two hours post fertilization replicate 2013_32

description:
2hpf_2013_32
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 2 hpf

value: 2 hours post fertilization


title: Two hours post fertilization replicate 2013_42

description:
2hpf_2013_42
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Two hours post fertilization replicate 2013_22

description:
2hpf_2013_22
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: Three hours post fertilization replicate 2012_N5

description:
3hpf_2012_N5
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: One hour post fertilization replicate 2013_41

description:
1hpf_2013_41
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt

source_name: Mnemiopsis leidyi embryo, 1 hpf

value: 1 hour post fertilization


title: Two hours post fertilization replicate 2012_N6

description:
2hpf_2012_N6
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: PANC1_control_rep4

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

data_processing:
Fastq raw sequencing files were preprocessed using cutadapt to remove sequencing adapters and low quality sequencing tails (options –q 10).
Trimmed files were aligned to the human genome (GRCh37/hg19) using tophat2 and using the UCSC gtf file provided by Illumina iGenomes as an annotation file (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Gene counts were calculated using htseq-count and the same gtf file. Differential expression analysis was done using the R package edgeR.
Differentially expressed genes were estimated independently for both cell lines (MIA PaCa-2 and PANC-1) and for the different time points (6 and 24 h), and were then intersected to inspect the common genes.
Genome_build: hg19

source_name: ATCC Cell Lines

growth_protocol: PANC-1 (ATCC, cat #CRL-1469) and MIA PaCa-2 (ATCC, cat # CRL-142-) were maintained in DMEM (ThermoFisher, cat #11965092) supplemented with 10% (v/v) heat inactivated FBS (ThermoFisher) in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy® Plus Mini Kit (ThermoFisher, cat #74134) as per the manufacturer’s instructions.
RNA-seq libraries were  generated using the Illumina Truseq RNA HT (stranded mRNA) kit (Illumina, cat #RS-122-2103) as per the manufacturer’s instructions and sequenced using an Illumina NextSeq 500.

treatment_protocol: PANC-1 and MIA PaCa-2  cell lines were treated with 400 nM CM03 for 6 and 24 h. For gemcitabine treatment, cells were treated for 6 and 24 h with DMSO or 30 nM, 100 nM, 300 nM, 1 μM, 3 μM and 10 μM gemcitabine-HCL for PANC-1 and 30 nM, 300 nM and 3 μM gemcitabine-HCl for MIA PaCa-2

tag: cell type

value: untreated


title: PANC1_control_rep3


title: PANC1_control_rep2


title: PANC1_control_rep1


title: 267O

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Transcript abundances were calculated with kallisto v0.43.0.
Genome_build: S. mediterranea dd_Smed_v6 transcriptome assembly
Supplementary_files_format_and_content: Tab-separated values file containing TPM expression values.

organism: Schmidtea mediterranea

source_name: whole animal

extract_protocol:
RNA was extracted with TRIzol® (Invitrogen) following the manufacturer's instructions. Quantification of RNA was assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and quality check was performed by capillary electrophoresis in an Agilent 2100 Bioanalyzer (Agilent Technologies)prior to library preparation.
cDNA libraries were prepared using the Illumina® TruSeq Stranded mRNA Library Prep Kit and sequenced as paired-end reads in an Illlumina® HiSeq 2000 sequencer. Quality check of the reads was performed with the FastQC suite.

value: asexual BCN-10 clonal line

value: whole animal

value: Smed-hippo(RNAi) 3 weeks


title: 268O

value: Smed-hippo(RNAi) 4 weeks


title: PANC1_6hr_3uM_rep3

value: gemcitabine 3uM 6h


title: PANC1_6hr_3uM_rep2


title: PANC1_6hr_3uM_rep1


title: 269O


title: 264O


title: 266O


title: 254O

value: Smed-hippo(RNAi) 1 week


title: 252O


title: 262O

value: gfp(RNAi) 4 weeks


title: 263O


title: PANC1_6hr_30nM_rep2

value: gemcitabine 30nM 6h


title: PANC1_6hr_30nM_rep3


title: One hour post fertilization replicate 2012_N7

description:
1hpf_2012_N7
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: 261O


title: One hour post fertilization replicate 2013_21

description:
1hpf_2013_21
PolyA RNA
Processed data file: counts.txt
Processed data file: rpkm.txt


title: PANC1_6hr_300nM_rep4

value: gemcitabine 300nM 6h


title: PANC1_6hr_30nM_rep1


title: PANC1_6hr_300nM_rep2


title: PANC1_6hr_300nM_rep1


title: 260O


title: PANC1_6hr_300nM_rep3


title: PANC1_6hr_1uM_rep4

value: gemcitabine 1uM 6h


title: 258O

value: gfp(RNAi) 3 weeks


title: 253O


title: PANC1_6hr_1uM_rep3


title: 251O

value: gfp(RNAi) 1 week


title: PANC1_6hr_1uM_rep2


title: PANC1_6hr_10uM_rep4

value: gemcitabine 10uM 6h


title: PANC1_6hr_1uM_rep1


title: PANC1_6hr_30nM_rep4


title: 257O


title: PANC1_6hr_10uM_rep3


title: PANC1_6hr_100nM_rep4

value: gemcitabine 100nM 6h


title: PANC1_6hr_100nM_rep3


title: PANC1_6hr_100nM_rep2


title: N1 A2M* 0 micromolar

description: biological control replicate 1

value: ATCC