title: Young timecourse E9.5 rep1

description: Sample 17


title: mNPC_shCont_1

status: Public on Sep 14 2017

type: SRA

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases

description: mNPC_shCont_1_TT-701-8-ATTACT_ATTACT_L008

library_source: transcriptomic

data_processing:
ChIP/Atac-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using bowtie2 version 4.8.4 --end-to-end --very-sensitive
RNA-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using RSEM rsem-calculate-expression ( v.1.2.18) with bowtie2 version 4.8.4 expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
peaks were called with Homer v4.8.3 using either --style histone, or --style factor or size=300/minDist=75 o size=150/minDist=75 or size=500/minDist=500. IgG files or input file were used as controls where appropriate
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited regions files have the peaks called from homer using histone settings, peak files have the peaks called using transcription factor settings, the counts file is the raw RNA-seq file, and the tpm file is the normalized RNA-seq data.

molecule: polyA RNA

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol:
The mouse NeuPC cell line from adult mouse hippocampus was cultured in DMEM/F-12 supplemented with N2 and B27 (Invitrogen) in the presence of FGF2 (20 ng/ml), EGF (20 ng/ml), and heparin (5 µg/ml).
The mouse NeuPC cell line from adult mouse hippocampus was cultured in DMEM/F-12 supplemented with N2 and B27 (Invitrogen) in the presence of FGF2 (20 ng/ml), EGF (20 ng/ml), and heparin (5 µg/ml).

extract_protocol: Three days after electroporation of plasmids encoding shRNA-EGFP using mouse NeuPCs, GFP-positive cells were sorted directly into Trizol-LS (Invitrogen). RNA was isolated according to the manufacturer’s instructions and digested with TURBO DNase (Life Technologies). RNA integrity numbers (RIN) were assessed using the Agilent Tape Station before library preparation. Poly(A)+ RNA was selected and fragmented to prepare sequencing libraries using the Illumina TruSeq Stranded RNA sample preparation kit. Libraries were sequenced single-end 50 bp (SE50) using an Illumina HiSeq 2500 sequencer at the Next Generation Sequencing (NGS) core at the Salk Institute according to manufacturer’s instructions (Illumina).

tag: strain

tag: cell type

value: Neural progenitor cell

tag: passage

tag: shRNA

value: shControl


title: NPC_RbH3K4Me3_1

description:
NPC_RbH3K4Me3--6-ACAGTG_ACAGTG_L006
Histone peaks called: NPC_RbH3K4Me3--6-ACAGTG_ACAGTG_regions.txt

library_source: genomic

molecule: genomic DNA

extract_protocol: Approximately 3 x106 cells were cross-linked with 2.5 mM DSG and 1% formaldehyde at room temperature for 15 min. After quenching with 125 mM glycine, samples were briefly sheared by sonication and the concentration of DNA was measured by Nanodrop. Twenty µg of chromatin were treated with Micrococcal Nuclease (1 U/µl, Worthington), and chromatin was incubated with antibodies at 4℃ overnight. Immunoprecipitated complexes were collected using Dynabeads conjugated with anti-rabbit IgG (Life Technologies). Subsequently, beads were washed and DNA was extracted and purified by Ampure XP beads (Beckman). A DNA library was generated using NEBNext Ultra DNA library prep kit for Illumina and Bioo Illumina barcodes followed by deep sequencing with the Illumina’s Hiseq2500 at SE50.

tag: chip antibody


title: Aged uterus rep3

city: Cambridge

first: Laura

last: Woods

address: Babraham Hall

country: United Kingdom

institute: The Babraham Institute

description: Sample 34

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the Mus musculus GRCm38 genome assembly using TopHat v2.0.12. Raw counts for DESeq2 analysis were generated at mRNA level using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are tab-delimited and contain the following  columns: (1) Gene ID; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description; (7-40) Raw Counts for each sample

source_name: Uterus

growth_protocol: C57BL/6Babr mice were used throughout this study. Virgin females were caged in groups up to 5 until they had reached the desired age as indicated. All animal experiments were conducted in full compliance with UK Home Office regulations and with approval of the local animal welfare committee at The Babraham Institute, and with the relevant project and personal licences in place. Timed matings were set up with standard C57BL/6Babr stud males of 8-16 weeks of age, counting the morning of the vaginal plug as E0.5.

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA Mini kit (Qiagen 80204) followed by DNase treatment using the TURBO DNA-free kit (Life Technologies AM1907)
mRNA was isolated from total DNA-free RNA (350ng) using the Dynabeads mRNA purification kit (Life Technologies 61006). Indexed, strand specific libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation kit (Epicentre SSV21106) according to the manufacturer's instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol on an Illumina HiSeq2500 sequencer.

tag: age (weeks)

tag: developmental stage

tag: tissue

value: Uterus


title: Aged abnormal rep5

description: Sample 16

source_name: Decidua

value: Decidua


title: Aged abnormal rep4

description: Sample 15


title: Young timecourse E11.5 rep2

description: Sample 24


title: Aged abnormal rep1

description: Sample 12


title: Aged abnormal rep2

description: Sample 13


title: Aged normal rep5

description: Sample 11


title: Aged normal rep2

description: Sample 8


title: Young rep5

description: Sample 5


title: Aged normal rep1

description: Sample 7


title: Young rep6

description: Sample 6


title: Young rep3

description: Sample 3


title: Young timecourse E10.5 rep3

description: Sample 22


title: Young rep2

description: Sample 2


title: Young rep1

description: Sample 1


title: B 16D - k18_ B 16 D 3

city: Antwerp

first: Kris

last: Vissenberg

state: Antwerp

address: Groenenborgerlaan 171 U636

department: Biology

country: Belgium

institute: University of Antwerp

description:
replicate 3  P21 16DAS
raw data file: k18_AGCGATAG-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k18_AGCGATAG-CCTATCCT_L002_R1_001.fastq.gz

data_processing:
Trim sequences  CLC Genomics Server 6.5.2
RNA-seq analyis References = Arabidopsis thaliana (Col-0 TAIR10) sequence-1 Default settings   CLC Genomics Server 6.5.2
Set Up experiment,  CLC Genomics Server 6.5.2
Normalized experiment Normalization method = ScalingScaling method = Mean, Trimming = 5%  Normalized data = Original expression values
Count based statistics Test = Baggerley's test  All pairs = yes Data used = Normalized expression values Calculate Bonferroni corrected p-values = Yes   Calculate FDR corrected p-values = Yes
Genome_build: Arabidopsis thaliana (Col-0 TAIR10) sequence
Supplementary_files_format_and_content: CLC data files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: first pair of leaf

growth_protocol: Seedlings were grown in 1/2 MS medium including vitamins (Duchefa, The Netherlands), containing 1% sugar, 0.5g/L MES buffer and 0.7% agar. Plants were kept at 21°C temperature with 16/8hr light period with 70-90 μmol m-2s-1 light intensity.

extract_protocol:
Total RNA was expracted using Purelink plnat RNA reagent (Ambion life technologies)
illumina protocol- TruSeq Stranded mRNA sample preparation

treatment_protocol: Plants were grown under similar control conditions without any treatments.

tag: cultivar

tag: growth stage

value: expansion

value: whole leaf tissue

tag: genotype

value: Mutant2 PID overexpression line P21


title: Young timecourse E9.5 rep3

description: Sample 19


title: J_177

city: San Diego

first: Xuejun

last: Liu

state: CA

address: 3210 Merryfield Row

department: Immunology

country: USA

institute: Janssen Research & Development, LLC

data_processing:
Raw reads were mapped to the human reference genome (Reference Human.B37.3) and the expression of individual gene was quantified as the count of the mapped reads using RefGene20121217 as the gene model. The read alignment and gene expression quantification were conducted using Array Studio (www.omicsoft.com).
Genome_build: Reference Human.B37.3
Supplementary_files_format_and_content: tab-delimited text file represents the counts of mapped reads, using RefGene20121217 as the gene model, in all 178 samples (one sample per column).

organism: Homo sapiens

source_name: CD4 T cell_RORgt_Inhibitor_A_0.1uM_48h

growth_protocol: T cells after compound or siRNA treatments were stimulated with anti-CD3/anti-CD28 coated beads (Miltenyi Biotech) at 2:1 bead to cell ratio in culture medium containing 10 ng/ml IL1β (R&D), 10 ng/ml IL23 (R&D), 30 ng/ml TGFβ1 (R&D), 10 μg/ml of anti-IL4 and anti-IFNγ (eBioscience).

extract_protocol:
Total RNA was extracted from CD4 T cells using the RNeasy mini kit (Qiagen) following the manufacture’s instruction. CD4 T cells were lysed in RLT solution supplemented with β-mercaptoethanol and cell lysates were loaded in RNeasy mini spin column. DNA was removed by on-column DNase digestion and RNA was eluted from column with 50 μl nuclease-free water and stored at –80°C until analysis. RNA integrity was assessed with LabChip GX (PerkinElmer, USA).
After extracting the total RNA from samples, mRNA was enriched by using the oligo (dT) magnetic beads, and was fragmented into short fragments (200∼500 bp) with the fragment buffer treatment. The first-strand cDNA was synthesized by random hexamer-primer with the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were used to synthesize the second strand. The double strand cDNAs, purified with QiaQuick PCR extraction kit, were used for end repair and base A addition. Finally, sequencing adaptors were ligated to the fragments. The fragments were purified by Agarose gel electrophoresis and PCR-amplified to produce the sequencing library.

treatment_protocol: For compound treatment, CD4 T cells were pre-treated with compounds or DMSO vehicle control at 37°C for 1 hour before T cell activation. For siRNA treatment, three RORγt siRNAs, two RORα siRNAs, two control siRNAs were tested at 1 μM, and mock transfected samples were included as controls

tag: donor

value: CD4 T cell

tag: treatment

tag: time


title: B 16D - k17_ B 16D 1

description:
replicate 1 P21 16DAS
raw data file: k16_TCCGCGAA-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k16_TCCGCGAA-CCTATCCT_L002_R1_001.fastq.gz


title: A 16d - k15_A 16 D 3

description:
replicate 3  P10 16DAS
raw data file: k15_CGGCTATG-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k15_CGGCTATG-CCTATCCT_L002_R1_001.fastq.gz

value: Mutant1 PID overexpression line P10


title: A 16d - k14_ A 16D 2

description:
replicate 2  P10 16DAS
raw data file: k14_TAATGCGC-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k14_TAATGCGC-CCTATCCT_L002_R1_001.fastq.gz


title: J_175

source_name: CD4 T cell_RORgt_Inhibitor_A_0.3uM_48h


title: J_174


title: A 16d - k13_ A 16d 1

description:
replicate 1 P10 16DAS
raw data file: k13_CTGAAGCT-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k13_CTGAAGCT-CCTATCCT_L002_R1_001.fastq.gz


title: WT 16d - k12_WT 16d 3

description:
replicate 3 WT 16 DAS
raw data file: k12_GAATTCGT-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k12_GAATTCGT-CCTATCCT_L002_R1_001.fastq.gz

value: WT


title: J_173


title: Aged normal rep3

description: Sample 9


title: WT 16d - k11_ WT 16d 2

description:
replicate 2 WT 16DAS
raw data file: k11_ATTCAGAA-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k11_ATTCAGAA-CCTATCCT_L002_R1_001.fastq.gz


title: Aged normal rep4

description: Sample 10


title: Young rep4

description: Sample 4


title: B 9d - k9_ B 9d 3

description:
replicate 3  P21 9DAS
raw data file: k9_CGCTCATT-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k9_CGCTCATT-CCTATCCT_L002_R1_001.fastq.gz

value: proliferation


title: J_169

source_name: CD4 T cell_RORgt_Inhibitor_B_1uM_48h


title: J_172

source_name: CD4 T cell_RORgt_Inhibitor_B_0.3uM_48h


title: B 9d - k8_ B 9d 2

description:
replicate 2  P21 9DAS
raw data file: k8_TCCGGAGA-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k8_TCCGGAGA-CCTATCCT_L002_R1_001.fastq.gz


title: J_171


title: J_170


title: WT 16d - k10_ WT 16d 1

description:
replicate 1   WT 16DAS
raw data file: k10_GAGATTCC-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k10_GAGATTCC-CCTATCCT_L002_R1_001.fastq.gz


title: J_178


title: B 16D - k17_ B 16D 2

description:
replicate 2  P21 16DAS
raw data file: k17_TCTCGCGC-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k17_TCTCGCGC-CCTATCCT_L002_R1_001.fastq.gz


title: J_176


title: J_166

source_name: CD4 T cell_RORgt_Inhibitor_C_0.3uM_48h


title: J_167


title: B 9d - k8_ B 9d 1

description:
replicate 1  P21 9DAS
raw data file: k7_ATTACTCG-CCTATCCT_L001_R1_001.fastq.gz
raw data file: k7_ATTACTCG-CCTATCCT_L002_R1_001.fastq.gz


title: A 9d - k6_ A 9d 3

description:
replicate 3 P10 9DAS
raw data file: k6_AGCGATAG-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k6_AGCGATAG-ATAGAGGC_L002_R1_001.fastq.gz


title: A 9d - k5_ A 9d 2

description:
replicate 2 P10 9DAS
raw data file: k5_TCTCGCGC-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k5_TCTCGCGC-ATAGAGGC_L002_R1_001.fastq.gz


title: J_165


title: A 9d - k4_ A 9d 1

description:
replicate 1  P10 9DAS
raw data file: k4_TCCGCGAA-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k4_TCCGCGAA-ATAGAGGC_L002_R1_001.fastq.gz


title: WT 9d - k3_ WT 9d 3

description:
replicate 3   WT 9 DAS
raw data file: k3_CGGCTATG-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k3_CGGCTATG-ATAGAGGC_L002_R1_001.fastq.gz


title: WT 9d - k2_ WT 9d 2

description:
replicate 2   WT 9 DAS
raw data file: k2_TAATGCGC-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k2_TAATGCGC-ATAGAGGC_L002_R1_001.fastq.gz


title: J_168


title: J_164


title: J_162

source_name: CD4 T cell_RORgt_Inhibitor_C_1uM_48h


title: WT 9d - k1_WT 9d 1

description:
replicate 1  WT 9 DAS
raw data file: k1_CTGAAGCT-ATAGAGGC_L001_R1_001.fastq.gz
raw data file: k1_CTGAAGCT-ATAGAGGC_L002_R1_001.fastq.gz


title: J_161


title: J_158

source_name: CD4 T cell_DMSO_48h

value: DMSO


title: d220

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.35.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Normalization was performed using TMM and converted to fragments per kilobase of exon model per million (FPKM) via edgeR.
Genome_build: GRCm38.p3 using Ensembl v82 annotation

source_name: GFP positive neural retina cells

growth_protocol: H9 hESCs were passaged every 4-5 days at 1:6 ratio by incubating with 2 mg/ml dispase (Invitrogen) at 37°C for 10 min. Colonies were washed, broken into small clumps of cells by pipetting and cultured at 37°C, 5% CO2.

extract_protocol:
Flow sorted cells were collected and total RNA was extracted by RNA purification kit (Norgen Biotek).
Directional RNA-seq library construction was performed from 100 ng of high quality RNA (RIN > 8.0) using the Illumina Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: The differentiation was performed according previous report with some modification (Nakano, Cell Stem Cell 2012). Human ESCs were dissociated by Accumax™ (Stem cell technologies) containing 10 µM Y-27632. Basal differentiation medium contained GMEM, 20 % (v/v) KSR, 0.1 mM nonessential amino acids, 1mM pyruvate 100 U/ml penicillin and 100 mg/ml streptomycin (Sigma-Aldrich). Cells on day 0 were quickly aggregated in low attachment 96 well-plates with V-bottom shape (NOF corporation) (9,000 cells/well in 100 µl) containing basal differentiation medium plus 3 µM IWR-1-endo (Wnt inhibitor, Calbiochem) and 20 µM Y-27632. Ten microliter of 1.8 µg/µl of Matrigel (growth factor reduced, BD Biosciences) solution was added in day-2 cultures. Aggregates were maintained for further 4 days when half medium was changed with medium containing 3 µM IWR-1-endo and 180 µg/ml and cultured for 6 days. Day-12 aggregates were transferred to low attachment 90 mm Dishes (NOF corporation) containing basal differentiation medium, 10% (v/v) FBS (Atlanta) and 100 nM Smoothened Agonist (SAG) (hedgehog agonist, Enzo Life Sciences) and maintained for 6 days. On day 18 medium was switched to maintenance medium which was DMEM/F12 containing 1% N2 supplement (Invitrogen), 10% (v/v) FBS, 0.5 µM retinoic acid (Sigma-Aldrich), 0.25 mg/ml Fungizone (GIBCO), 100 U/ml penicillin, and 100 mg/ml streptomycin. Human ESC-NR were grown in maintenance medium in bacterial-grade Dishes from day 18 at 40% O2 and 5% CO2 with medium changed every three day until sample collection.

tag: age

value: GFP positive neural retina cells

value: flow sorted CRXp-GFP positive cells at 220 days post neural retina induction


title: J_159


title: J_160


title: TC32_YK_RNAseq

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
Sequencing was performed on the Illumina HiSeq 2500 (Rapid run, Illumina, CA USA) with chemistry v1.0 and using the 2×106bp paired-end read mode and original chemistry from Illumina according to the manufacturer's instructions.
The initial data analysis was HiSeq 2500. The HiSeq Control Software 2.0.5 in combination with RTA 1.17.20.0 (real time analysis) performed the initial image analysis and base calling.
CASAVA-1.8.2 generated and reported run statistics and the final FASTQ files. Sequences were de-multiplexed according to the 6bp index code with 1 mismatch allowed.
FASTQ output was aligned with TopHat and quantified/normalized to the RefSeq GRCh37/hg19 transcriptome using the Cufflinks (v2.2.1) pipeline (with frag bias correction)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Gene-level FPKM

growth_protocol: TC32 cells were grown in RPMI supplemented with 10% FBS at 37C in 5% CO2

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini Kit (Qiagen), and submitted to Otogenetics Corporation (Norcross, GA USA) for RNA-Seq assays.  Briefly, the integrity and purity of total RNA were assessed using Agilent Bioanalyzer or Tapestation and OD260/280. cDNA was generated from high quality total RNA using SMARTer PCR cDNA Synthesis kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634926).
The resulting cDNA was fragmented using Bioruptor (Diagenode, Inc., Denville, NJ USA), profiled using Agilent Tapestation, and subjected to Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automatic workstation and a Beckman HT library kit (SPRIworks HT, Beckman Coulter, Inc. CA USA; PN B09855AA) to generate fragment libraries. The instructions were strictly followed to perform library construction. Briefly, after fragmentation the ends were repaired and 'A' bases were added to the 3' end of the fragments. Adapters were then ligated to both ends. The adaptor-ligated templates were further purified using Agencourt AMPure SPRI beads (Beckman Coulter, Inc. CA USA). The adaptor-ligated library was amplified by ligation-mediated PCR which consisted of 11 cycles of amplification, and the PCR product was purified using Agencourt AMPure SPRI beads again. After the library construction procedure was completed, QC was performed using Nanodrop 2000 (Thermo Scientific, USA) and an Agilent TapeStation (Agilent, USA) to ensure the library quality and quantity.

treatment_protocol: In treatment conditions, cells were treated with 3uM YK-4-279 (DMSO vehicle) for 15h

tag: cell line

value: TC32 Ewing sarcoma cell line

tag: genotype/variation

value: treatment with YK-4-279


title: d134

value: flow sorted CRXp-GFP positive cells at 134 days post neural retina induction


title: d67

value: flow sorted CRXp-GFP positive cells at 67 days post neural retina induction


title: d90

value: flow sorted CRXp-GFP positive cells at 90 days post neural retina induction


title: J_156

source_name: CD4 T cell_RORA siRNA_2_48h

value: RORA siRNA_2


title: d48

value: flow sorted CRXp-GFP positive cells at 48 days post neural retina induction


title: J_155


title: J_157


title: TC32_WT_RNAseq

value: WT Control


title: J_154

source_name: CD4 T cell_RORA siRNA_1_48h

value: RORA siRNA_1


title: d37

value: flow sorted CRXp-GFP positive cells at 37 days post neural retina induction


title: TC32_shEF_RNAseq

value: knockdown of EWS-FLI1


title: MAB-Mips #3 PMC

city: Leuven

first: Giorgia

last: Giacomazzi

address: Herestraat 49

institute: KUleuven

data_processing:
Illumina Casava2.18 software used for basecalling and demultiplexing
Sequenced reads were mapped to the hg19 genome using tophat v2.0.13 with parameters --keep-fasta-order --read-realign-edit-dist 0 --mate-inner-dist 200 --mate-std-dev 50 –no-novel-juncs
Expression quantification was performed with htseq-countv0.5.3p3 and parameters -s reverse -a 10 -i gene_name
Differential Expression analysis was performed with Deseq.
Genome_build: hg19
Supplementary_files_format_and_content: text file provide count information

source_name: Skeletal muscle Mesoangioblasts

extract_protocol:
RNA was harvest using Total RNA isolation kit and post isolation DNAase (Thermo Fisher Scientific)- 2µg were processed
Library were constructed using TruSeq RNA Library Prep Kit v2

tag: origin

value: fetal

value: Mesodermal progenitors


title: J_152

tag: cell type

value: CD4 T cell


title: J_163


title: J_151

source_name: CD4 T cell_RORC siRNA_3_48h

value: RORC siRNA_3


title: J_150


title: MAB-Mips #1 PMC

tag: passage


title: MAB-Mips #2 PMC


title: J_149


title: MAB-Mips #3 AMC


title: J_148

source_name: CD4 T cell_RORC siRNA_2_48h

value: RORC siRNA_2


title: MAB-Mips #2 AMC


title: J_147


title: Aged abnormal rep3

description: Sample 14

tag: strain

value: Decidua


title: MAB-Mips #1 AMC


title: J_146


title: J_153


title: MAB-MiPS #3 scr


title: J_144

source_name: CD4 T cell_RORC siRNA_1_48h

value: RORC siRNA_1


title: J_142

source_name: CD4 T cell_silencer_SC_48h


title: J_140


title: J_143


title: J_139

source_name: CD4 T cell_Inv_SC_48h


title: f-Mips #3 PMC

source_name: Skin fibroblasts


title: MAB-MiPS #2 scr


title: MAB-MiPS #1 scr


title: J_138


title: J_137


title: f-Mips #2 AMC


title: f-Mips #2 PMC


title: f-Mips #3 AMC


title: f-Mips #1 PMC


title: f-Mips #1 AMC


title: J_135

source_name: CD4 T cell_Mock_48h

value: Mock


title: J_136


title: f-MiPS #1 scr


title: f-MiPS #3 scr


title: J_134


title: J_145


title: J_133

source_name: CD4 T cell_RORgt_Inhibitor_A_0.1uM_24h


title: MAB-MiPs #2 miRNA

description: microRNA

extract_protocol:
miRNA was harvest using miRNA isolation kit (Thermo Fisher Scientific)- 1µg was processed
Library were constructed using TruSeq Small RNA Library Preparation Kit


title: J_131


title: f-MiPS #3 miRNA

description: microRNA


title: J_141


title: MAB-MiPs #3 miRNA

description: microRNA


title: MAB-MiPs #1 miRNA

description: microRNA


title: J_130

source_name: CD4 T cell_RORgt_Inhibitor_A_0.3uM_24h


title: J_129


title: f-MiPS #2 miRNA

description: microRNA


title: J_127

source_name: CD4 T cell_RORgt_Inhibitor_B_0.3uM_24h


title: MAB-iPSCs #3 miRNA

description: microRNA

value: iPSCs retroviral derived


title: f-MiPS #1 miRNA

description: microRNA


title: f-MiPS #2 scr


title: MAB-iPSCs #2 miRNA

description: microRNA


title: J_126


title: J_124

source_name: CD4 T cell_RORgt_Inhibitor_B_1uM_24h


title: J_123


title: J_122


title: MAB-iPSCs #1 miRNA

description: microRNA


title: MAB-MiPs #3 RNA


title: J_121

source_name: CD4 T cell_RORgt_Inhibitor_C_0.3uM_24h


title: J_125


title: J_128


title: f-iPSCs#1 miRNA

description: microRNA


title: f-IPSC#2 miRNA

description: microRNA


title: f-IPSC#3 miRNA

description: microRNA


title: J_132


title: MAB-MiPs #2 RNA


title: MAB-MiPs #1 RNA


title: J_120


title: J_119


title: f-MiPS #3 RNA


title: J_118

source_name: CD4 T cell_RORgt_Inhibitor_C_1uM_24h


title: f-MiPS #2 RNA


title: f-MiPS #1 RNA


title: J_117


title: J_116


title: J_115

source_name: CD4 T cell_DMSO_24h

value: DMSO


title: MAB-iPSCs #3 RNA


title: f-IPSC#3 RNA


title: J_113


title: J_114


title: J_112

source_name: CD4 T cell_DMSO_0h


title: J_111


title: f-IPSC#2 RNA


title: MAB-iPSCs #2 RNA


title: J_110


title: UM-UC9

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

description: Processed data file: GEO_bladder_cell_lines_normalized_counts.txt

data_processing:
Raw paired-end (PE) reads in FASTQ format were first aligned to human reference genome (GRCh37/hg19) for human RNA-Seq, using MOSAIK.
Once the standard bam files were generated by MOSAIK, we then counted the mapped reads in genomic features such as genes (mRNAs) annotated in GENCODE to generate the raw counts for each gene using the HTSeq-count script.
We used the scaling factor normalization method to perform between sample normalization as it preserves the count nature of the data and has been shown to be an effective means of improving differential expression (DE) detection by the Bioconductor package DESeq.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: GEO_bladder_cell_lines_normalized_counts.txt

source_name: urothelial cancer cell line

growth_protocol: Cell lines were cultured in MEM supplemented with 10% fetal bovine serum, vitamins, sodium pyruvate, L-glutamine, penicillin, streptomycin, and nonessential amino acids at 37°C in 5% CO2 incubator.

extract_protocol:
Total RNA from cell lines were isolated using mirVana™miRNA isolation kit (Ambion, Inc).
TruSeq Stranded Total RNA Library Prep Kit.

value: bladder cancer cell line


title: f-iPSCs#1 RNA


title: UM-UC6


title: J_107

source_name: CD4 T cell_RORA siRNA_2_24h

value: RORA siRNA_2


title: J_109


title: UM-UC7


title: J_108


title: J_105

source_name: CD4 T cell_RORA siRNA_1_24h


title: J_106


title: UM-UC5


title: J_104


title: UM-UC3


title: UM-UC1


title: UM-UC4


title: J_103

source_name: CD4 T cell_RORC siRNA_3_24h


title: J_102


title: MAB-iPSCs #1 RNA

source_name: Skeletal muscle Mesoangioblasts


title: J_101


title: UM-UC17


title: UM-UC18


title: UM-UC16


title: J_100

source_name: CD4 T cell_RORC siRNA_2_24h


title: J_099


title: UM-UC15


title: UM-UC14


title: J_098


title: UM-UC13


title: UM-UC12


title: J_097

source_name: CD4 T cell_RORC siRNA_1_24h


title: UM-UC11


title: J_095


title: TCCSUPB

value: TCCSUPB


title: T24


title: J_093

source_name: CD4 T cell_silencer_SC_24h


title: UM-UC10


title: J_094


title: SW780


title: J_091

source_name: CD4 T cell_Inv_SC_24h


title: J_089


title: RT4V6


title: J_090


title: J_088

source_name: CD4 T cell_Mock_24h


title: RT4


title: RT112


title: J82


title: HT1376


title: J_085

source_name: CD4 T cell_Mock_0h


title: J_086


title: J_084


title: BV

value: BV


title: HT1197


title: 5637


title: J_096


title: J_082

source_name: CD4 T cell_RORgt_Inhibitor_A_0.1uM_48h


title: J_081


title: J_092


title: J_080

source_name: CD4 T cell_RORgt_Inhibitor_A_0.3uM_48h


title: JD_hmc_chipseq

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Basecalls from Illumina HiSeq 2500 Sequencing System
Reads were mapped to hg19 reference with bowtie(0.12.7) with the following parameters:  –phred33-quals -k 1 --sam --tryhard -p 8 --chunkmbs=1024
Peaking calling was performed with MACS using the hmc as target and input as control.  The following parameters were used:
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing MACS software parameter settings and peak information

source_name: Pancreatic cancer cells

growth_protocol: Growth media

extract_protocol: Standard Illumina library protocols were used for sequencing library preparation as per in Song et al, Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011 Jan;29(1):68-72.  Used KAPA LT DNA prep kit and generated PCR Free libraries using 500 ng gDNA

value: Adenocarcinoma

tag: chip antibody

value: chemical conjugation with hmC-SEAL


title: J_079


title: 1A6


title: 253JP


title: J_078

source_name: CD4 T cell_RORgt_Inhibitor_B_0.3uM_48h


title: SCABER

value: SCABER


title: J_077


title: HPNE_atac-seq

data_processing:
Basecalls from Illumina HiSeq 2500 Sequencing System
Reads were mapped to hg19 reference with tophat (v2.0.13) with parameters: --no-coverage-search -p 3 -g 1
Peaking calling was performed with MACS(v 2.1.1.20160309) using the sample as target and default parameters
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing MACS2 software parameter settings and peak information

source_name: Pancreatic control cells

growth_protocol: growth media

extract_protocol:
dna extraction by qiagen
ATAC-seq was performed as per protocol established by Buenrostro JD et al, ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109: 21 29 21-29.   Used KAPA LT DNA prep kit and generated PCR Free libraries using 500 ng gDNA.

tag: sample type

value: Control


title: JRN_rna

data_processing:
Basecalls from Illumina HiSeq 2500 Sequencing System
Reads were mapped to hg19 reference with tophat (v2.0.13) with parameters: --no-coverage-search -p 3 -g 1
gene counts were generated with htseq (v0.6.1p1) using parameters: --strand=no
Genome_build: hg19
Supplementary_files_format_and_content: count files are tab delimited txt containing the number of reads mapped to each gene.

source_name: Pancreatic Cancer

growth_protocol: Regular growth media as described in the publication

extract_protocol:
Qiagen RNA Easy
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols

value: Pancreatic ductal adenocarcinoma


title: HP_hmc_chipseq


title: J_087

value: CD4 T cell


title: J_076

source_name: CD4 T cell_RORgt_Inhibitor_B_1uM_48h


title: J_083


title: BXPC3_rna


title: J_072

source_name: CD4 T cell_RORgt_Inhibitor_C_1uM_48h


title: HPNE_rna

source_name: Pancreatic Cell Control

value: Pancreatic Cell Control


title: ASPC1_rna


title: JD_atac-seq

source_name: Pancreatic Cancer Cells

value: adenocarcinoma


title: HPDE_rna


title: A6L_rna


title: J_070

source_name: CD4 T cell_DMSO_48h


title: J_069


title: A_2.1_rna


title: J_068

source_name: CD4 T cell_RORgt_Inhibitor_A_0.1uM_24h


title: J_074

source_name: CD4 T cell_RORgt_Inhibitor_C_0.3uM_48h


title: J_066

source_name: CD4 T cell_RORgt_Inhibitor_A_0.3uM_24h


title: 32.1_rna


title: 10.05_rna


title: 10RN_rna


title: J_067


title: J_064

source_name: CD4 T cell_RORgt_Inhibitor_B_0.3uM_24h


title: HN137-LN, rep2

city: Singapore

first: Ankur

last: Sharma

state: Singapore

address: 60 Biopolis St, #02-01,

department: CTSO

country: Singapore

institute: Genome Institute Singapore

description: HN137 is a patient with oral squamous cell carcinoma (OSCC).

data_processing:
Raw data was mapped to hg19.
Bam files were used to call peaks.
D-Filter was used for peak calling.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *wig and *bed files include peak calls.

source_name: HN137, lymph node metastatic cells

growth_protocol: HN137 primary and lymph node metastatic cells were grown in RPMI-1640+10%FBS media at 37 degrees Celsius in 5% carbon dioxide incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei followed by phenol/chloroform extraction of naked (open) DNA.
FAIRE-seq libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® as per manufacturer's guidelines.

tag: source

value: Patient-derived primary culture

tag: disease status

value: HNSCC (OSCC)

value: Lymph node metastatic cells

tag: passages


title: HN137-LN, rep1


title: J_063


title: J_075


title: HN137-Pri, rep2

source_name: HN137, primary cells

value: Primary cells


title: J_062

source_name: CD4 T cell_RORgt_Inhibitor_B_1uM_24h


title: J_073


title: J_071


title: HN137-Pri, rep1


title: J_061


title: J_060

source_name: CD4 T cell_RORgt_Inhibitor_C_0.3uM_24h


title: J_059


title: 38.5_rna


title: J_057

source_name: CD4 T cell_RORgt_Inhibitor_C_1uM_24h


title: J_065


title: J_055

source_name: CD4 T cell_DMSO_24h

value: DMSO


title: J_056


title: Doxorubicin-treated, rep1

city: New York

first: Andrew

last: Koff

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan Kettering Institute

data_processing:
Short reads were aligned with STAR v2.4.0c
Gencode v18 genes were quantified with featureCounts (subhead package, v1.4.3-p1)
Differential gene expression was determined using DESeq2
Genome_build: hg19, Gencode v18
Supplementary_files_format_and_content: RNA-seq

source_name: Dedifferentiated liposarcoma cells

growth_protocol: LS8817 cells were grown in DME-HG supplemented with 10% FBS (unless otherwise indicated) and split as necssary, usually 1:3 every 3 days

extract_protocol:
Qiagen RNEasy
Illumina TruSeq mRNA Library Prep Kit V2

treatment_protocol: Cells were treated 1μM PD0332991, 100nM doxorubicin or cultured in DME-HG media containing only 0.5% serum for 7 days. Media was changed and drugs were replenished after 3 days.

tag: drug treatment

value: Doxorubicin


title: CDK4-inhibitor-treated, rep3

value: CDK4 inhibitor PD0332991


title: CDK4-inhibitor-treated, rep1


title: Doxorubicin-treated, rep2


title: Doxorubicin-treated, rep3


title: CDK4-inhibitor-treated, rep2


title: J_054

source_name: CD4 T cell_DMSO_0h


title: Untreated, rep2

value: Untreated


title: J_052


title: J_053


title: 0-5% serum starvation, rep3

value: Serum-starved


title: Untreated, rep3


title: J_051

source_name: CD4 T cell_RORA siRNA_2_48h

value: RORA siRNA_2


title: Untreated, rep1


title: J_050


title: 0-5% serum starvation, rep1


title: 0-5% serum starvation, rep2


title: J_049


title: U2OS input

data_processing:
FASTQ files were adapter and quality trimmed using Trim Galore! v0.3.3
Reads were aligned to hg19 using BWA (mem) v0.7..8
Aligned reads were indel realigned and base quality recalibrated using GATK v3.1.1
Peaks were called using MACS v2.0.10
False positive peaks were reduced using IDR in phantompeakqualtools v1.1
Genome_build: hg19
Supplementary_files_format_and_content: bigWig signal files normalized by total reads, broadPeak calls, and IDR optimal peak calls

source_name: Osteosarcoma cells

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with ATRX antibody using magnetic beads.


title: Serum-starved ATRX ChIP rep2


title: J_048

source_name: CD4 T cell_RORA siRNA_1_48h

value: RORA siRNA_1


title: Serum-starved input rep2


title: J_047


title: J_058


title: J_046


title: CDK4i-treated input rep2


title: J_045

source_name: CD4 T cell_RORC siRNA_3_48h

value: RORC siRNA_3


title: CDK4i-treated ATRX ChIP rep2


title: Doxorubicin-treated input rep2


title: J_043


title: J_044


title: Untreated ATRX ChIP rep2


title: J_042

source_name: CD4 T cell_RORC siRNA_2_48h

value: RORC siRNA_2


title: Untreated input rep2


title: J_041


title: Serum-starved input rep1


title: J_038

source_name: CD4 T cell_RORC siRNA_1_48h

value: RORC siRNA_1


title: J_039

value: CD4 T cell


title: Doxorubicin-treated ATRX ChIP rep2


title: Doxorubicin-treated input rep1


title: CDK4i-treated ATRX ChIP rep1


title: Serum-starved ATRX ChIP rep1


title: Doxorubicin-treated ATRX ChIP rep1


title: J_035

source_name: CD4 T cell_silencer_SC_48h


title: J_036


title: J_034


title: J_033

source_name: CD4 T cell_Inv_SC_48h


title: Untreated input rep1


title: J_031


title: J_029

source_name: CD4 T cell_Mock_48h

value: Mock


title: J_030


title: Untreated ATRX ChIP rep1


title: J_032


title: J_027

source_name: CD4 T cell_RORA siRNA_2_24h


title: J_028


title: J_026


title: J_040


title: CDK4i-treated input rep1


title: J_037


title: J_024

source_name: CD4 T cell_RORA siRNA_1_24h


title: J_023


title: J_022


title: J_018

source_name: CD4 T cell_RORC siRNA_2_24h


title: J_017


title: J_020

source_name: CD4 T cell_RORC siRNA_3_24h


title: J_021


title: J_016


title: J_015

source_name: CD4 T cell_RORC siRNA_1_24h


title: J_014


title: J_012

source_name: CD4 T cell_silencer_SC_24h


title: J_011


title: J_009

source_name: CD4 T cell_Inv_SC_24h


title: Candida and LGGs_6h_br3 (part 2)

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 6h in KGM-Gold without antibiotics (replicate 3).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).

data_processing:
Basecalls were performed using standard software supplied by Illumina for HiSeq2000 sequencing.
Reads generated with HiSeq2000 were first quality- and adpater trimmed with BBduk and then mapped with NextGenMap (v 0.4.12) using default settings.
Gene quantification was performed based on the annotation from Grumaz et al. (BMC Genomics, 2013) and calculated with a python script `rpkmforgenes.py´ from the Sandberg laboratory (http://sandberg.cmb.ki.se/rnaseq) at readcount and RPKM +1 level (=reads per kilobase of exon model per million mapped reads) according to Mortazavi et al. (Nature, 2008).
Genome_build: Candida albicans: A21 build February 2012 (http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/)
Supplementary_files_format_and_content: Tab-delimited text files include raw readcounts (rc) or RPKM values for all samples.

organism: Candida albicans

source_name: infection with Candida and preincubated with LGGs

growth_protocol: Samples "Candida_2h/6h_br1/2/3" were grown on TR146 monolayer for 2h in KGM-Gold without antibiotics and "Candida and LGGs_2h/6h_br1/2/3" were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 2h in KGM-Gold without antibiotics

extract_protocol:
Samples of TR146 monolayers for RNA-Seq analysis were collected 2 h and 6 h after infection with Candida. Cells were scrapped into 1 ml chilled PBS and frozen as beads by dropping this suspension into liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH, Germany) with a shaking frequency of 30/s under cryo conditions. The resulting powder was resuspended in lysis buffer RLTplus (QIAGEN, Germany), supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Mechanical Disruption Protocol for the isolation of total RNA from yeast, using the RNeasy Plus Mini Kit. The experiments were performed in triplicates. RNA quality and quantity was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips, following the manufacturer’s protocol.
cDNA libraries were prepared using an initial amount of 500 ng of total RNA and Illumina’s TruSeqTM RNA Sample Preparation v2 protocol.

tag: tissue

value: hyphae


title: Treated root1

first: Prakash

middle: P

last: Kumar

address: 14 Science Drive 4,

department: Department of Biological Sciences

institute: National University of Singapore

data_processing:
Image data obtained from the sequencing machine was transformed by base calling into raw reads and stored in fastq format
Sequenced reads were trimmed for adaptor sequence and low quality reads were removed using filter_fq software.
Transcriptome de novo assembly was performed using the short read program Trinity (version release-20121005)
Gene expression analysis was carried out using reads per kilobase per million reads (RPKM) method using SOAP software (version 2.21)
A rigorous algorithm was used to identify differentially expressed genes (DEGs) in salt-treated roots compared to untreated roots. False discovery rate (FDR) ≤ 0.001 and the absolute value of log2Ratio ≥ 2 was used as the threshold to judge the significance of differential gene expression
Supplementary_files_format_and_content: all_gene_counts_and_rpkm.txt file contains RPKM and raw reads for all the unigenes identified in A.officinalis
Supplementary_files_format_and_content: The .xlsx file contains the details of differentially expressed genes. RPKM and p-values are included for each sample.
Supplementary_files_format_and_content: The .fa file contains the all unigene sequences with annotations in fasta format

organism: Avicennia officinalis

source_name: Roots

growth_protocol: The propagules of Avicennia officinalis L. (A.officinalis) were collected during fruiting seasons from the mangrove swamps in Singapore (Berlayer Creek and Sungei Buloh Wetland Reserves, Singapore). The seedlings were maintained in NaCl-free conditions by growing in potting mixture (Far East flora, Singapore) in a greenhouse (25–35 0C, 60–90% relative humidity; 12 h photoperiod).

extract_protocol:
Total RNA was extracted from roots of control and treated (500mM NaCl for 24h) greenhouse-grown mangrove plants using Qiagen RNeasy kit (QIAGEN) and DNase treated (RNase-free DNase set, QIAGEN) according to the manufacturer’s instructions. The quality of RNA samples was determined using a 2100 Bioanalyzer (Agilent Technologies). For each sample, at least 20 µg of total RNA was sent to Beijing Genomics Institute for Illumina sequencing (commercial service). From each condition, two biological replicates were used for RNA sequencing. Each biological replicate was obtained by isolating RNA from the roots of three plants.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once the plants reached four node stage (~2 months)  they were carefully transferred to pots containing sand and were allowed to adapt for two days by watering with half-strength Hoagland’s solution. The plants were then treated with half-strength Hoagland’s solution containing 500 mM NaCl for 24 hours.

value: root

value: Two-month-old

value: 500 mM NaCl


title: Control root2

value: control


title: Treated root2


title: Control root1


title: J_010

tag: donor


title: Candida and LGGs_6h_br2 (part 1)

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 6h in KGM-Gold without antibiotics (replicate 2).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: Candida and LGGs_6h_br2 (part 2)


title: J_008

tag: treatment


title: J_007

tag: time


title: Candida and LGGs_6h_br1 (part 2)

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 6h in KGM-Gold without antibiotics (replicate 1).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: Candida and LGGs_6h_br1 (part 1)


title: J_019


title: Candida_6h_br3 (part 2)

description:
Cells were grown on TR146 monolayer for 6h in KGM-Gold without antibiotics (replicate 3).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).

source_name: infection only with Candida


title: Candida_6h_br2 (part 2)

description:
Cells were grown on TR146 monolayer for 6h in KGM-Gold without antibiotics (replicate 2).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: J_013


title: Candida_6h_br3 (part 1)


title: Candida_6h_br1 (part 2)

description:
Cells were grown on TR146 monolayer for 6h in KGM-Gold without antibiotics (replicate 1).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: Candida_6h_br2 (part 1)


title: J_003

source_name: CD4 T cell_Mock_0h


title: Candida and LGGs_6h_br3 (part 1)


title: Candida and LGGs_2h_br2 (part 2)

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 2h in KGM-Gold without antibiotics (replicate 2).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: Candida and LGGs_2h_br2 (part 1)


title: Candida and LGGs_2h_br1 (part 1)

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 2h in KGM-Gold without antibiotics (replicate 1).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: J_002


title: Candida and LGGs_2h_br1 (part 2)


title: J_001


title: Candida_2h_br3 (part 2)

description:
Cells were grown on TR146 monolayer for 2h in KGM-Gold without antibiotics (replicate 3).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: Candida_2h_br3 (part 1)


title: Candida_2h_br2 (part 2)

description:
Cells were grown on TR146 monolayer for 2h in KGM-Gold without antibiotics (replicate 2).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: J_006

source_name: CD4 T cell_Mock_24h


title: M2_BCG.24h_Donor.33

city: Torrance

first: Delphine

last: Lee

address: 1124 W Carson St

department: Dermatology/Immunology

institute: Los Angeles Biomedical Institute

data_processing:
FastQC
Trimmomatic-0.32 (default)
rsem-1.2.19 (default)
bowtie2-2.2.4 (default)
Genome_build: hg19
Supplementary_files_format_and_content: RSEM isoform output

source_name: PBMC culture supernatent

extract_protocol:
After removing cell culture supernatants, uninfected and BCG-infected macrophages were harvested in trizol. Chloroform (0.2 parts) was added; total RNA in upper phase of partition was precipitated with Isopropanol and washed with 80% Ethanol.
cDNA libraries were prepared using TruSeq RNA Library Preparation Kit v2 (RS-122-2001) according to the “TruSeq RNA Sample Preparation v2 Guide”. Briefly, purification of poly-A containing mRNA molecules from 300 ng of total RNA was performed using poly-T oligo attached magnetic beads. After fragmentation into small pieces using divalent cations under elevated temperature, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was achieved using DNA Polymerase I and RNase H. These cDNA fragments went through further end repair process, single “A” base addition, and adapters ligation. The products were then purified and enriched with PCR to create the final cDNA library. Libraries were sequenced on Illumina HiSeq2000 at 50 million reads per sample and 1X50 read length. These procedures were performed by the UCLA Clinical Microarray Core facility (http://www.pathology.ucla.edu/cmc).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood of healthy adult volunteers using Ficoll-Hypaque gradient centrifugation. CD14+ monocytes were enriched from PBMCs using negative selection (EasySep Human Monocyte Enrichment Kit, Stem Cell Technologies, Vancouver, Canada). Monocytes (7.5x10^5 cells/ml) were cultured in media (10% fetal calf serum (FCS) in RPMI 1640) supplemented with either rh-GM-CSF (50U/ml) or rh-M-CSF (50ng/ml), to induce differentiation into M1- or M2-MΦ, respectively. On day 6 of culture, cells were infected with BCG at 0.18 MOI. Cells were harvested 20h after infection using warmed PBS-1mM EDTA.

value: M2 macrophage

value: BCG

tag: polarization


title: J_005


title: M2_Media.24h_Donor.33

value: Media


title: Candida_2h_br1 (part 1)

description:
Cells were grown on TR146 monolayer for 2h in KGM-Gold without antibiotics (replicate 1).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: J_025


title: J_004


title: Candida_6h_br1 (part 1)


title: Candida and LGGs_2h_br3 (part 1)

description:
Cells were grown on TR146 monolayer preincubated with Lactobacillus rhamnosus GG (LGG) for 2h in KGM-Gold without antibiotics (replicate 3).
The terms 'part 1' and 'part 2' in the sample titles represent a single library that was sequenced on two different lanes to putatively minimize risks of lane effects/defects.  They were mapped separately, but during quantification step and for gene expression analyses then fused (because there were no detected lane effects/defects).


title: M1_Media.24h_Donor.33

value: M1 macrophage


title: M2_BCG.24h_Donor.20


title: Candida and LGGs_2h_br3 (part 2)


title: Candida_2h_br1 (part 2)


title: Pool1&8_A

city: Oxford

first: Jelena

middle: M

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

institute: Oxford University

description: WGA DNA from CRISPR/Cas9 modified HSC, enriched for specific loci

data_processing:
(MAP1) Data were first mapped using in-house pipeline that automatically assesses the quality of data, trims adaptors,maps reads to the reference genome :
- Mapping : bowtie2 (2.1.0) -m 2 --maxIns 700
- For un-mapping reads : trim_galore -- length 10
- Combining trimmed+originally mapped reads, mapping again with  bowtie -m 2 --maxIns 700
(MAP2) STAR 2.5.1b mapping for reads not mapped in (MAP1) : STAR --outFilterMismatchNmax 100 --outFilterMatchNmin 50 --outFilterMatchNminOverLread 0 --outFilterMismatchNoverLmax 1.0 --outFilterMismatchNoverReadLmax 1.0 --outFilterScoreMinOverLread 0 --outFilterScoreMin 0 --outFilterMultimapNmax 20 --outMultimapperOrder Random  --outSAMmultNmax 1 --outSAMorder PairedKeepInputOrder --outReadsUnmapped Fastx --alignIntronMin 1000000 --alignIntronMax 1000000  --alignEndsType EndToEnd
(MAP3) STAR mapping for reads not mapped in (MAP2) : Like above STAR(MAP2), but --alignEndsType Local instead of  --alignEndsType EndToEnd , and adding --scoreInsBase 0
(MAP4) STAR mapping for un-mapping reads : Like above STAR(MAP3), but running 2 separate single end runs , R1 and R2 separate (to allow single end mapping)
Combine the MAP1-MAP4 bam files : samtools merge -f -r  (samtools/0.1.19)
Base counts : samtools (0.1.19) mpileup -B -d 200000 --ff 4
Quality-filtering base counts :  varscan (2.3.6) readcounts --min-base-qual 20 --min-coverage 1
Genome_build: hg38
Supplementary_files_format_and_content: Quality-filtered base counts, from  varscan (2.3.6)

source_name: Haematopoietic Stem Cells

growth_protocol: CD34+ cells were differentiated using a serum-free liquid culture system which used StemSpan SFEM II (Stemcell technologies), supplemented with stem cell factor, interleukin-3, human recombinant erythropoietin (EPO) (0.5 U/ml) and cholesterol rich lipids. Single cells were sorted into the wells in Terasaki multiwell plates and were cultured in 20 μl culture medium. Clonal colonies were expanded to 10days with no change in medium.

extract_protocol:
Whole genome amplified (WGA) DNA from clonal cells was prepared using Illustra single cell GenomiPhi DNA amplification kit (GE Healthcare)
WGA material from a total of 30 clones was combined in equimolar amounts into pools of five clones and sonicated to 200bp, then indexed using NEB UltraII (New England Biolabs). Target loci were enriched by two successive rounds of hybridization with biotinylated oligonucleotides and incubation with streptavadin beads

treatment_protocol: Cells were edited with two combinations of guide RNA (gRNAs 2/12 or 1/8) and CRISPR/Cas9 and sorted into single wells and screened for on target changes

value: CD34+ HSC


title: Pool2&12_C


title: Pool1&8_B


title: M2_Media.24h_Donor.20


title: Pool2&12_D


title: Pool2&12_B


title: Pool2&12_A


title: M1_Media.24h_Donor.20


title: M2_BCG.24h_Donor.31


title: M1_Media.24h_Donor.35


title: M2_Media.24h_Donor.35


title: M1_Media.24h_Donor.31


title: M2_Media.24h_Donor.31


title: Candida_2h_br2 (part 1)


title: M2_Media.24h_Donor.28


title: M1_Media.24h_Donor.28


title: M2_BCG.24h_Donor.28


title: M2_BCG.24h_Donor.35


title: mg95

city: Stanford

first: Michael

middle: Warren

last: Guernsey

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
Adapter sequences and low quality bases were trimmed using trim_galore v 0.3.3
The resulting sequences were aligned to the wallaby genome (m.eug_v1.0) using STAR (version 2.5.1b).
Raw counts were assigned to significantly transcribed regions using UniPeak v1.0.
Regions were then associated with the nearest gene using HOMER (version 4.7)
Multiple regions mapping to the same gene were summed to give a final read count for each gene.
Genome_build: m.eug_v1.0
Supplementary_files_format_and_content: Tab-delimited file containing summed read counts for each transcript

organism: Notamacropus eugenii

source_name: mammary gland

extract_protocol:
Fixed samples were initially subjected to a brief protease digestion to remove nucleic acid cross-linking. Total RNA was then extracted using the ambion RecoverAll Total Nucleic Acid Isolation kit and mRNA was subsequently isolated using Dynabeads Oligo (dT)25.
the samples were given a short heat-shearing treatment immediately followed by cDNA synthesis. The resulting cDNA was repaired using 3’A-tailing and ligated to linkers containing unique illumina barcodes for sequencing. An agarose gel was used for size selection and the samples were then PCR amplified for 15(fresh)-17(fixed) cycles and purified using AMPure XP beads. Quality of the libraries was assessed using both Qubit and Bioanlyzer technology and then sequenced

tag: age

value: day 95 of lactation

value: mammary gland

tag: tissue state

value: fixed, 4% paraformaldehyde


title: 21_LS

city: Moscow

first: Evgeny

last: Chekalin

address: Gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics

description: 4 mm punch biopsy specimens were taken from lesion skin (LS)

data_processing:
Raw pair-end reads (50+25 bp) were obtained from SOLID4 System (Applied Biosystems) in color space format (*.csfasta)
*.csfasta were filtered for quality, the adaptor sequences were trimmed and the reads were aligned to the UCSC human reference genome (hg19) using the Applied Biosystems’s Bioscope software  to obtain reads in the BAM format.
Mapping to multiple locations was permitted. The aligned read BAM files were assembled into transcripts, their abundance was estimated and tests for differential expression were processed by Bioconductor DESeq package
FDR correction for multiple testing was performed according to Benjamini et al.
Using the cutoffs of fold change (FC) > 1.5 and false discovery rate of (FDR) <0.05, only genes that had read counts at all samples were listed
Genome_build: UCSC human reference genome (hg19)
Supplementary_files_format_and_content: tab-delimited text file includes ensembl_gene_id, hgnc_symbol, baseMean, foldChange, log FoldChange, p-values and normalized counts produced by DESeq for each sample

source_name: Skin

extract_protocol:
TissueLyser LT homogenizer (Qiagen, USA) was used to homogenize biopsy specimens. Total RNA was extracted with ExtractRNA reagent (Evrogen, Russia) according to the manufacturer’s protocol. Isolated RNA was dissolved in RNase free water, rRNA was depleted using RiboMinus™ Eukaryote Kit for RNA-Seq (Life Technologies, USA), and the samples were stored at -80C°. The quality of total RNA was evaluated with RNA 6000 Pico Chip Kit and Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA) and with Quant-iT™ RNA Assay Kit and Qubit Fluorometer (Life Technologies, USA). The average RNA integrity number (RIN) of samples was ≥7.
Library preparation and sequencing were performed using SOLiD 4 System platform and sequencing chemistry according to the manufacturer’s instructions (Life Technologies, USA).

tag: skin phenotype

value: Lesional psoriatic skin


title: 25_NL

description: 4 mm punch biopsy specimens were taken from nonlesional (NL sample) skin 3-4 cm apart from the lesion, so as the area doesn’t have any visual signs of psoriasis

value: Non-lesional psoriatic skin


title: 26_LS


title: 19_NL


title: 25_LS


title: 26_NL


title: 21_NL


title: 20_NL


title: 22_LS


title: 27_NL


title: 22_NL


title: 23_NL


title: 20_LS


title: 28_NL


title: 24_LS


title: 27_LS


title: 23_LS


title: 19_LS


title: 24_NL


title: 28_LS


title: mg36

value: day 36 of lactation


title: mg60

value: day 60 of lactation


title: 16_NL


title: 15_LS


title: 16_LS


title: 15_NL


title: 11_NL


title: 11_LS


title: 18_NL


title: Salt-water rice in fresh water 3

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

description:
Salt-water rice in fresh water 3
G6

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble MSU6 transcript set using bowtie2. RSEM was used to estimated the gene expression and DCC was used for circRNA prediction and circRNA expression calculation.
Genome_build: Ensemble MSU6 transcript set
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples

organism: Oryza sativa

source_name: root tissue

extract_protocol:
RNA was extracted from the tissue using RNeasy Plant Mini Kit (Qiagen).
Libraries for RNA-Seq were prepared with Kapa Stranded mRNA-seq kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

tag: culture condition

value: fresh water

tag: phenotype

value: Salt-water rice

tag: cultivar

value: Oryza sativa japonica Sea_Rice_86


title: Salt-water rice in salt water 3

description:
Salt-water rice in salt water 3
G9

value: root

value: salt water


title: Salt-water rice in fresh water 2

description:
Salt-water rice in fresh water 2
G5


title: Salt-water rice in salt water 1

description:
Salt-water rice in salt water 1
G7


title: 18_LS


title: Salt-water rice in salt water 2

description:
Salt-water rice in salt water 2
G8


title: 2_3_Input_PABP_PNG

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
Total RNA
rnaseq_20170210.csv

data_processing:
Basecalling was performed using Illumina Real-Time Analysis v1.18.54 or later, and bcl2fastq2 v2.17 was used to convert to fastq format (by The Center for Applied Genetics (SickKids)).
FastQC v0.11.5 was used to analyze library quality.
TrimmomaticSE version 0.36 were used to trim and clip the reads for Illumina adaptors.
Reads were then mapped to the D. melanogaster or combined D. melanogaster (dm6) and C. elegans (ce10) genomes as according to UCSC August 7, 2016, using STAR 2.5.2a
Genes were quantified using Cufflinks 2.2.1
The data was imported as FPKM values into R version 3.1.2, where analysis was performed using in-house scripts.
In order to normalize for global changes in mRNA abundance, the embryonic input samples were normalized to the total number of reads mapping to the C. elegans genome.
To calculate binding values for each gene, the IP FPKM was divided by the unnormalized input FPKM.
Genome_build: dm6, ce10
Supplementary_files_format_and_content: comma separated values files contain FPKMs for each gene in each sample.

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Fly stocks were maintained in a 25°C room with 65% humidity according to standard protocols. S2 cells were obtained from ThermoFisher (Cat#R69007), and were maintained in ExpressFive SFM media (ThermoFisher), supplemented with 10% FBS (heat-inactivated) and 20mM L-Glutamine, at 28°C.

extract_protocol:
At collection, embryos were dechorionated with bleach, then selected through filtration. They were then washed with water and 0.1% Triton 100. Embryos were homogenized in Lysis Buffer B (150 mM KCl, 20 mM HEPES-KOH pH 7.4, 1 mM MgCl2, 1mM DTT, complete mini EDTA-free protease inhibitors), and were clarified at 15,000 rpm, at 4°C for 15 minutes. The supernatant was stored at –80°C. S2 cells were lysed using Buffer A (100 mM KCl, 0.1 mM EDTA, 20 mM HEPES-KOH pH 7.6, 0.4% NP-40, 10% glycerol, 1 mM DTT, complete mini EDTA-free protease inhibitors, SUPERase-In RNase inhibitors) 48 hours post transfection, clarified at 14000 rpm for 5 minutes at 4°C. For P3D12 (PABP) pull downs, anti-FLAG beads were washed twice with 1xPBS and blocked overnight with anti-P3D12 antibody (purified according to Na et al, 2016) and ssDNA, at a ratio of 12.5 ul beads to 2.5 ug antibody. The next day, the beads were washed 3x with buffer (Buffer A for S2 cells, Buffer B for embryo lysate) and incubated with lysate (450 ul lysate to 12.5 ul beads). After incubation for 3 hours, the beads were washed 6x with the appropriate buffer, and RNA extraction was performed. For ME31B pull downs, protein G beads were used, blocked overnight in the same way as anti-FLAG beads were, but incubated with GFP antibody [Anti-GFP (clone 7.1 and 13.1), monoclonal mouse, from Roche, Cat#11814460001, RRID:AB_390913, Lot#14442000], pulling down GFP-tagged ME31B in eGFP-ME31B flies. The next day, the beads were washed 2x with buffer, lysate was added and incubated for 2 hours. After incubation, the beads were washed 6x with the approriate buffer, and RNA extraction was performed. During RNA extraction, 600 ng worm RNA was spiked in.
After RNA extraction, the RNA underwent rRNA depletion using the Ribo-Zero Gold Kit (Illumina). Libraries for RNA sequencing were generated using Illumina’s TruSeq stranded mRNA library preparation kit.

treatment_protocol: Flies were maintained at growth conditions. To probe for ME31B, 2x106 S2 cells were seeded per well in a 6-well plate and transfected with either 1 μg of eGFP-Me31B or FLAG-eGFP plasmid after 24 hours.

tag: strain

tag: developmental stage

value: 2-3 hr embryo

value: whole embryo

tag: rip antibody


title: WT short and long footprints+DTT

first: Nicholas

middle: R

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
Ribosome-protected RNA 15-34 nt
Reads split into 15-18 nt and 25-34 nt bins for downstream analysis

data_processing:
Library strategy: Ribo-seq
Base calling was performed at Johns Hopkins sequencing facilities.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of noncoding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of transcripts by using Bowtie (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Wig files beginning with "end3" are aligned by 3' ends, all others by 5' ends. 0 mismatches were tolerated for footprint libraries, 2 mismatches for RNA-Seq libraries.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: PomBase ASM294 v2.22
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Schizosaccharomyces pombe

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Illumina Ribo-Zero kits were used to remove rRNA (from total RNA for mRNA-Seq, from size-selected footprints for 51F-56F, and from linker-ligated footprints for 63F and 64F).

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

value: WT

tag: cell culture treatment

value: DTT


title: Common rice  in fresh water 3

description:
Common rice  in fresh water 3
G3

value: common rice

value: Oryza sativa japonica Normal_Rice_R1


title: ski2KO short and long footprints+DTT


title: skiKO KO mRNA-Seq+DTT

data_processing:
Base calling was performed at Johns Hopkins sequencing facilities.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of noncoding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of transcripts by using Bowtie (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Wig files beginning with "end3" are aligned by 3' ends, all others by 5' ends. 0 mismatches were tolerated for footprint libraries, 2 mismatches for RNA-Seq libraries.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: PomBase ASM294 v2.22
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).


title: dom34KO mRNA-Seq


title: ski2KO short and long footprints


title: WT mRNA-Seq


title: ski2KO dom34KO short and long footprints

description:
Ribosome-protected RNA 15-34 nt
Contains two raw files that represent two sequencing runs of the same sample. Reads split into 15-18 nt and 25-34 nt bins for downstream analysis.

value: ski2KO dom34KO


title: skiKO KO mRNA-Seq


title: WT short and long footprints


title: Common rice  in fresh water 2

description:
Common rice  in fresh water 2
G2


title: ski2KO dom34KO mRNA-Seq


title: dom34KO mRNA-Seq+DTT


title: Salt-water rice in fresh water 1

description:
Salt-water rice in fresh water 1
G4


title: ski2KO dom34KO mRNA-Seq+DTT


title: dom34KO short and long footprints+DTT


title: dom34KO short and long footprints


title: WT mRNA-Seq+DTT


title: ski2KO dom34KO short and long footprints+DTT


title: 0_1_Input_PABP_PNG

description:
Total RNA
rnaseq_20170210.csv

value: 0-1 hr embryo


title: Common rice  in fresh water 1

description:
Common rice  in fresh water 1
G1


title: 0_1_ME31B_PNG

description:
Pulldown RNA
rnaseq_20170210.csv

value: Anti-GFP (clone 7.1 and 13.1), monoclonal mouse, from Roche, Cat#11814460001, RRID:AB_390913, Lot#14442000]


title: 0_1_Input_ME31B_PNG

description:
Total RNA
rnaseq_20170210.csv


title: Kif3a f/f ; Wnt1-Cre MNP

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
BAM files were loaded into GeneSpring Version 12.5-GX-NGS for NGS, Whole Genome RNA-seq analysis
The mouse reference genome mm9 was selected
Data Interpretation was set to program defaults
Quality inspection was performed and data proved of good quality
For qunatification, reads were considered and the detection of novel genes and exons was allowed for. Counts were normalized to one, with the baseline median to all samples. All entities were filtered on expression (3.0-8607.81) in the NRPKM with at least one out of six samples having a value within the defined range
The Audic Claverie test (no correction) was used to identify differentially expressed genes in between control and ta2 facial prominences with a p-value ≤ 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file, as exported from Genespring, all available parameters for export were included

source_name: Manidbular Promience

growth_protocol: Timed matings were recorded and embryonic day 0.5 was counted to be noon of the day on which a copulation plug was discovered.

extract_protocol:
Facial promiences were manually harvested and pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: a mixed (CD1) background

tag: genotype/variation

value: Kif3a f/f ; Wnt1-Cre

value: mutant embryo

tag: tissue subtype

value: Manidbular Promience


title: 4_5_ME31B

description:
pulldown RNA
rnaseq_20160421.csv

data_processing:
Basecalling was performed using Illumina Real-Time Analysis v1.18.54 or later, and bcl2fastq2 v2.17 was used to convert to fastq format (by The Center for Applied Genetics (SickKids)).
FastQC v0.11.5 was used to analyze library quality.
TrimmomaticSE version 0.36 were used to trim and clip the reads for Illumina adaptors.
Reads were then mapped to the D. melanogaster or combined D. melanogaster (dm6) and C. elegans (ce10) genomes as according to UCSC August 7, 2016, using STAR 2.5.2a
Genes were quantified using Cufflinks 2.2.1
The data was imported as FPKM values into R version 3.1.2, where analysis was performed using in-house scripts.
In order to normalize for global changes in mRNA abundance, the embryonic input samples were normalized to the total number of reads mapping to the C. elegans genome.
To calculate occupancy values for each gene, the IP FPKM was divided by the unnormalized input FPKM.
Genome_build: dm6, ce10
Supplementary_files_format_and_content: comma separated values files contain FPKMs for each gene in each sample.

extract_protocol:
At collection, embryos were dechorionated with bleach, then selected through filtration. They were then washed with water and 0.1% Triton 100. Embryos were homogenized in Lysis Buffer B (150 mM KCl, 20 mM HEPES-KOH pH 7.4, 1 mM MgCl2, 1mM DTT, complete mini EDTA-free protease inhibitors), and were clarified at 15,000 rpm, at 4°C for 15 minutes. The supernatant was stored at –80°C. S2 cells were lysed using Buffer A (100 mM KCl, 0.1 mM EDTA, 20 mM HEPES-KOH pH 7.6, 0.4% NP-40, 10% glycerol, 1 mM DTT, complete mini EDTA-free protease inhibitors, SUPERase-In RNase inhibitors) 48 hours post transfection, clarified at 14000 rpm for 5 minutes at 4°C.
After RNA extraction, the RNA underwent rRNA depletion using the Ribo-Zero Gold Kit (Illumina). Libraries for RNA sequencing were generated using Illumina’s TruSeq stranded mRNA library preparation kit.

treatment_protocol: Flies were maintained at growth conditions. To probe for ME31B, 2x10^6 S2 cells were seeded per well in a 6-well plate and transfected with either 1 μg of eGFP-Me31B or FLAG-eGFP plasmid after 24 hours.

value: 4-5 hr embryo

value: anti-GFP (clone 7.1 and 13.1), monoclonal mouse, Roche, Cat#11814460001, RRID:AB_390913, Lot#14442000]


title: S2_Input_ME31B

source_name: S2 Cells

tag: transfection

value: eGFP-ME31B transfected S2 cells

tag: cell line

value: S2 Cells


title: S2_ME31B

description:
pulldown RNA
rnaseq_20161020.csv


title: 4_5_Input_ME31B


title: 3_4_ME31B

description:
pulldown RNA
rnaseq_20160421.csv

value: 3-4 hr embryo


title: Control MNP

value: control

tag: tissue

value: control embryo


title: 3_4_Input_ME31B


title: 2_3_Input_ME31B

value: 2-3 hr embryo


title: 1_2_ME31B

description:
pulldown RNA
rnaseq_20160421.csv

value: 1-2 hr embryo


title: 2_3_ME31B

description:
pulldown RNA
rnaseq_20160421.csv


title: 1_2_Input_ME31B


title: S2_Input_PABP


title: 0_1_Input_ME31B


title: S2_PABP

description:
pulldown RNA
rnaseq_20161020.csv

value: anti-PABP (a synthetically generated antibody, purified according to Na et al, 2016)


title: 4_5_PABP

description:
pulldown RNA
rnaseq_20161020.csv


title: 4_5_Input_PABP


title: 3_4_Input_PABP


title: 0_1_ME31B

description:
pulldown RNA
rnaseq_20160421.csv


title: R03_miRNA

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

country: China

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

data_processing:
[miRNA] The small RNA tags were mapped to reference sequence (Amel_4.5) by Bowtie. The characteristics of hairpin structure of miRNA precursor can be used to predict new miRNA. The available software miREvo60 and mirdeep261 were integrated to predict new miRNA. Predicting the target gene of miRNA was performed by miRanda.
[mRNA and lncRNA] Index of reference genome (Amel_4.5) was built using Bowtie V2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (FPKM, expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Readcount_TPM_miRNA.txt, mRNA_FPKM_mRNA.txt

organism: Apis mellifera

source_name: ovaries

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA, according to the manufacturer’s instructions. miRNA sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA and lncRNA sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
For miRNA library preparation, a total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. A total of twelve small libraries were constructed using ovaries of virgin queens, normal queens, caged queens and released queens.
A total amout of 3 μg total RNA per sample was used as input material for the mRNA and lncRNA library. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The libraries were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of twelve libraries were constructed using ovaries of virgin queens, normal queens, caged queens and released queens.

value: ovaries

value: egg-laying recovered queen

tag: treatment

value: the queen was released after caged for seven days. And on the eighth day, the queen recovered to normal condition and laid eggs. Then, samples were collected.


title: 1_2_PABP

description:
pulldown RNA
rnaseq_20161020.csv


title: 2_3_PABP

description:
pulldown RNA
rnaseq_20161020.csv


title: 2_3_Input_PABP


title: 1_2_Input_PABP


title: R01_miRNA

tag: age


title: R02_miRNA


title: Newborn_10day_Chuong216

city: Los Angeles

first: Mingxing

last: Lei

state: California

address: 2011 Zonal Ave HMR 304A

institute: University of Southern California

data_processing:
The RNA-Seq alignment was performed by STAR 2.4.1d.  Mouse mm9 downloaded from the UCSC Genome Browser.
The quantification was performed by htseq-count 0.6.0 using the union mode
Genome_build: mm9
Supplementary_files_format_and_content: txt files including raw counts of sequencing reads for refGene produced by htseq-count

source_name: Newborn, 10 days

growth_protocol: 37℃ with 5% CO2 in incubator

extract_protocol:
Total RNA of dissociated culture cells were extracted using Trizol reagent
Illumina TruSeq RNA Sample Preparation V2

treatment_protocol: Reconstitution and in vitro culture

value: Balb/C

value: Newborn

tag: cell type

value: cultured dorsal skin dissociated cells

tag: culture time

value: 10 days


title: 0_1_PABP

description:
pulldown RNA
rnaseq_20161020.csv

value: 0-1 hr embryo


title: C03_miRNA

value: egg-laying inhibited queen

value: Caged for 7 days


title: Newborn_10day_Chuong210


title: 3_4_PABP

description:
pulldown RNA
rnaseq_20161020.csv


title: C01_miRNA


title: 0_1_Input_PABP


title: C02_miRNA


title: Newborn_7day_Chuong215

source_name: Newborn, 7 days

value: 7 days


title: Newborn_7day_Chuong209


title: Q03_miRNA

value: normal egg-laying queen


title: lraC replicate1

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the genome sequence of Aspergillus niger NRLL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1) using Bowtie to map clean reads to reference gene and BWA to reference genome. No more than 2 mismatches allowed in the alignment.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using RSEM (Li et al, 2011,BMC Bioinformatics)
Genome_build: Aspergillus niger NRLL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: File includes gene_id, transcript_id(s), length, expected_count and FPKM values for each sample.

organism: Aspergillus niger

source_name: Liquid culture

growth_protocol: Liquids cultures of two biological duplicate were inoculated with 10*6 spores/ml and incubated in a rotary shaker at 250 rpm and 30°C. Pre-cultures for RNA isolation were grown for 16 hours in 1L Erlenmeyer flasks containing 250 ml CM with 2% D-fructose. Mycelium was washed with MM and transferred for 2h in 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 25 mM L-rhamnose for RNA-seq.

extract_protocol:
Total RNA was extracted from mycelium ground in a Tissue Lyser (QIAGEN) using TRIzol reagent (Invitrogen) according to the instructions of the manufacturer. RNA integrity and quantity were analyzed on a 1% gel agarose gel using gel electrophoresis and with the RNA6000  Nano  Assay  using  the  Agilent  2100  Bioanalyzer  (Agilent  Technologies, Santa Clara, CA, USA). cDNA library preparation and sequencing reactions were performed by  BGI  Tech  Solutions  Co.,  Ltd.  (Hong Kong).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mycelium was harvested from the liquid culture by vacuum filtration after 2 hours of incubation. The mycelium samples were dried between tissue paper, frozen in liquid nitrogen and processed according to the extraction protocol.

tag: genotype

value: cspA1, pyrG-, kusA::amdS, lraC::AOpyrG

tag: substrate

value: MM + L-rhamnose

tag: sampling time

value: 2 hours

value: Mycelium


title: lraB replicate 2

tag: strain

value: cspA1, pyrG-, kusA::amdS, lraB::AOpyrG


title: Q01_miRNA

value: ovaries


title: PG0162-1660 H2O2-3

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed and filtered by Trimmomatic 0.35, and then mapped to Porphyromonas gingivalis W83 genome by Tophat v2.1.1
Reads Per Kilobase per Megabase of library size (RPKM)  was calculated by Cufflinks v2.2.1and differential expression analyses was performed by Cuffdiff v2.2.1
Genome_build: ASM758v1
Supplementary_files_format_and_content: RPKMs

organism: Porphyromonas gingivalis W83

growth_protocol: Porphyromonas gingivalis cultures were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media (Dou et al. FEMS Micro Lett. 312(1):24-32).

extract_protocol:
RNA was extracted by using SV Total RNA Isolation system (Promega)Dou et al., Journal of Bacteriology, 196(23):4057-70. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The library construction, the first- and the second- strand cDNA synthesis, and the RNA-seq barcode ligation were performed by using Nextflex RNA-Seq kit (Bioo Scientific, Austin, TX)

treatment_protocol: Porphyromonas gingivalis were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media. The culture was stressed by 0.25 mM of hydrogen peroxide for 15 min . McKenzie et al., Microbiology, 158(Pt 10):2465-79.

value: PG0162-PG1660 mutant


title: Q02_miRNA


title: V02_miRNA

value: virgin queen


title: PG0162-1660 H2O2-1


title: V01_miRNA


title: lraC replicate 2


title: W83 H2O2-3

value: wild-type


title: rhaR replicate 1


title: W83 H2O2-2


title: lraA replicate 2

value: cspA1, pyrG-, kusA::amdS, lraA::AOpyrG


title: W83 H2O2-1


title: goIFNλ_rep 3

city: Chengdu

first: Wei

last: Zhang

state: WenJiang

address: Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, 611130, China.

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step,clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: Genebank：AOGC00000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Anser anser

source_name: Peripheral blood mononuclear cells

growth_protocol: Blood from geese was collected aseptically with heparin sodium (25 IU/ml). Immediately, PBMCs were isolated with the Goose Lymphocyte Separation Medium Kit (GLSMK) (TBD Sciences, Tianjing, China) according to the manufacturer’s protocol. Subsequently, cells (1 x 108 cells/ml) were maintained in Gibco® RPMI 1640 (Gibco Life Technologies, Shanghai, China) supplemented with 10 % foetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMCs were stimulated with recombinant goIFN-α, γ and λ for 3 h, and those treated with cell lysates from pcDNA3.1 (+)-transfected BHK-21 cells were considered as control group. Cells were harvested with 1 mL RNAiso Plus reagent (Takara Bio, Otsu, Japan) for RNA extraction.

value: blood

value: Two month old

value: Peripheral blood mononuclear cells


title: PG0162-1660 H2O2-2


title: lraA replicate 1


title: rhaR replicate 2


title: lraB replicate 1


title: R03_mRNA

value: egg-laying recovered queen

value: the queen was released after caged for seven days. And on the eighth day, the queen recovered to normal condition and laid eggs. Then, samples were collected.


title: goIFNλ_rep 2

department: Institute of Preventive Veterinary Medicine


title: goIFNλ_rep 1


title: V03_miRNA


title: goIFNγ_rep 3


title: R01_mRNA


title: tpl25_4417

source_name: trilaminar omphalopleure

extract_protocol:
For fresh tissue, total RNA was isolated from placenta using a phenol–chloroform purification with Trizol (Invitrogen) and mRNA was subsequently isolated using Dynabeads Oligo (dT)25.
the samples were given a short heat-shearing treatment immediately followed by cDNA synthesis. The resulting cDNA was repaired using 3’A-tailing and ligated to linkers containing unique illumina barcodes for sequencing. An agarose gel was used for size selection and the samples were then PCR amplified for 15(fresh)-17(fixed) cycles and purified using AMPure XP beads. Quality of the libraries was assessed using both Qubit and Bioanlyzer technology and then sequenced

value: day 25 of gestation

value: placenta (trilaminar omphalopleure)

tag: tissue state

value: fresh, snap frozen


title: R02_mRNA


title: Reference strain replicate 1

value: cspA1, pyrG-::AOpyrG, kusA::amdS

value: MM + L-rhamnose


title: Reference strain replicate 2

value: 2 hours

value: Mycelium


title: C03_mRNA

value: ovaries

value: egg-laying inhibited queen

value: Caged for 7 days


title: tpl25_4060


title: goIFNα _rep 3


title: IMP2 KO Total RNA

city: Boston

first: Ning

last: Dai

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using STAR
Transcript abundance was calculated using HTseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mus

source_name: mouse embryonic fiboblast

growth_protocol: Mouse embryonic fiboblast (MEF) cells  were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
QIAGEN RNase kit
libraries were constructed according to Illumina TruSeq high throughput kit

value: IMP2 null

value: mouse embryonic fiboblast

tag: antibody


title: IMP2 WT immuno-precipitating  RNA

description: IMP2 antibody (PubMed ID: 21576258) used for immunoprecipitation

value: IMP2 WT


title: IMP2 KO immuno-precipitating  RNA


title: goIFNα _rep 2

value: blood

value: Two month old


title: C01_mRNA


title: C02_mRNA


title: Q03_mRNA

value: normal egg-laying queen


title: IMP2 WT Total RNA


title: Sample_ye-12h

city: Hangzhou

last: Zhou

state: Zhejiang

address: 548 Binwen Road, Binjiang district

department: college of pharmacy

institute: zhejiang chinese medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Raw reads after quality control testing were then assembled using trinity software
count counting
Genome_build: de novo
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Salvia miltiorrhiza

source_name: Hairy roots

growth_protocol: The hairy root clones were routinely subcultured every 30 days on solid 1/2 MS medium. Rapidly growing hairy roots with normal growth status were used to establish hairy root lines, and the liquid 1/2 MS medium were changed every 20 days.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Forty-day-old shake-flask cultured hairy roots were treated with elicitors, and the hairy roots were harvested from the culture medium at selected times after treatment by MeJA (0 h, 1h and 6h) or YE (1h and 12h) separately.

tag: treatment type

value: Induced by yeast extract

tag: induced time


title: tpl21

value: day 21 of gestation


title: tpl23

value: day 23 of gestation

value: placenta (trilaminar omphalopleure)


title: tpl25_4419

value: day 25 of gestation

value: fresh, snap frozen


title: bpl25_4419

source_name: bilaminar omphalopleure

value: placenta (bilaminar omphalopleure)


title: Q02_mRNA


title: goIFNα _rep 1

value: Peripheral blood mononuclear cells


title: Q01_mRNA

value: ovaries


title: Sample_mj-6h

value: Induced by methyl jasmonate

value: 6 h

value: Forty-day-old shake-flask cultured hairy roots


title: goIFNγ_rep 2


title: tpl25_4385


title: goIFNγ_rep 1


title: Mock_rep 3


title: bpl23


title: bpl25_4385


title: Mock_rep 2


title: Sample_mj-1h

value: 1 h


title: V02_mRNA

value: virgin queen


title: V01_mRNA


title: Sample_mj-0h

value: control

value: 0 h


title: H1_Hsv

status: Public on Sep 13 2017

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

description:
circRNAs of human 6 samples _rRNA_HSV1_CIRCexplorer.fa
Candidate_lncRNAs of human 6 samples_rRNA_HSV1.fa
isoforms.fpkm_expression
circRNA.fpkm_expression
Genes.fpkm_expression
lncRNA_Prediction.fpkm_expression

data_processing:
Raw reads of FASTQ files were obtained and assessed for quality using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The reads containing adapter, ploy-N and low quality reads were removed using Cutadapt (https://pypi.python.org/pypi/cutadapt/1.4.2) [2] to obtain clean reads with high quality.
For circRNA analysis, clean paired-end RNA-seq reads with 150 bp in length of were aligned to the human reference genome hg38 (GRCh38.p7) using Tophat (v2.1.0) (Tophat2, -N 2 -r 50 --library-type fr-firststrand --mate-std-dev20 -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 ) for linear transcripts. For the mapped reads, they were assembled into know and novel linear transcripts using Cufflinks (v2.1.1) (Cufflinks2, -I 40000 --max-bundle-frags 1000000 -p 26 -u -L CUFF). All transcripts were pooled and merged to generate final transcriptome using Cuffmerge (v 2.1.1) (Cuffmerge2, -p 26). In contrast, the unmapped reads were aligned to the AGM reference genome for fusion transcripts using Tophat-Fusion (v2.1.0) (Tophat-Fusion2, -N 2 --library-type fr-firststrand -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 --fusion-search --no-coverage-search --bowtie1). Fusion transcripts from TopHat-Fusion and the transcripts from the assembled linear RNAs were analyzed with circExplorer to identify candidate circRNAs.
For mRNA analysis, the human reference genome hg38 (GRCh38.p7) was served as mRNA annotation reference.
For lncRNA analysis, transcripts that met the following criteria were further analyzed: (1) RNA length ≥200 bp; (2) transcript reads ≥3; (3) exon number ≥1. Subsequently, transcripts were subjected to protein coding potential evaluation by CNCI (v2) [7] and CPC (0.9-r2) [8] with default parameters. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts predicted without coding potential were considered as lncRNAs.
Genome_build: human reference genome hg38 (GRCh38.p7)
Supplementary_files_format_and_content: fasta files and fpkm expression value of circRNAs, lncRNAs and genes

source_name: HSV1-infected human fibroblast KMB17 cells

growth_protocol: Human fibroblast KMB17 strain (Institute of Medical Biology, CAMS), a normal diploid cell line that was originated from fetal lung tissue, was cultured in Minimum Essential Medium (MEM) supplemented with 10% bovine serum (Minhai Biotech, Beijing, China) at 37°C in 5% CO2.

extract_protocol:
At 48 h postinfection, total RNA from HSV-1 infected and uninfected KMB17 cells was isolated with Trizol regeant (Invitrogen) followed by digestion with DNase I (Epicentre) for 15 min at 37°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KMB17 cells were mock- infected or infected with HSV-1 at a multiplicity of infection (m.o.i) of 1.

value: Human fetal lung tissue-derived fibroblast cells

tag: passages

tag: infection

value: HSV-1 strain 17 (GenBank:NC_001806.2)


title: H3_Hsv


title: C3_Ctr

source_name: human fibroblast KMB17 cells


title: C1_Ctr


title: H2_Hsv


title: Mock_rep 1

value: blood

value: Two month old


title: p65 IP in Treg, unstim, rep1

city: New York

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description:
p65_Treg_US_1
processed data file:
p65_Treg_US.pooled_peaks.noBlacklist.idr_conservative.narrowPeak

data_processing:
Raw FASTQs were adapter and quality trimmed with Trim Galore! v0.4.1
Trimmed reads were aligned to mm10 with BWA mem v0.7.15-r1140
Conservative peaks were called per group using MACS v2.1.1.20160309 within the Irreproducible Discovery Rate framework outlined by ENCODE (https://sites.google.com/site/anshulkundaje/projects/idr)
Blacklisted sites were excluced (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated representing coverage of estimated fragment length extended alinged reads, normalized by library size over autosomal chromosomes and scaled to the equivalent of 1X coverage

source_name: Treg unstimulated

growth_protocol: Isolated Tconv and Treg cells were cultured on a plate coated with anti-CD3 antibody in the presence of soluble anti-CD28 antibodies for 3 hours. 2 ng/ml IL-2 was added to Tconv culture and 10 ng/ml IL-2 was added to Treg culture.

extract_protocol:
After nuclear isolation, nuclear lysates were sonicated by using bioruptor followed by immunoprecipitating with anti-p65 antibody+ Dynabeads protein A
Library was constructed on immunoprecipitated DNA according to manufacturer's recommendations (KAPA Hyper Prep Kit). Samples were enriched with PCR with 12 cycles.Afterward, double size selection was performed with AMPure XP beads

tag: mouse strain

tag: tissues

value: Spleens+Lymph nodes

value: Regulatory T cells

tag: cell subtype

value: Treg unstimulated

tag: chip antibody

value: anti-mouse p65 (Santa Cruz, sc-372, #K-0615)


title: Sample_ye-1h

value: Induced by yeast extract

tag: tissue


title: p65 IP in Treg, anti-CD3/CD28 stim, rep2

description:
p65_Treg_S_2
processed data file:
p65_Treg_S.pooled_peaks.noBlacklist.idr_conservative.narrowPeak

source_name: Treg + anti-CD3/CD28 stim

tag: cell type

value: Treg + anti-CD3/CD28 stim


title: p65 IP in Treg, unstim, rep2

description:
p65_Treg_US_2
processed data file:
p65_Treg_US.pooled_peaks.noBlacklist.idr_conservative.narrowPeak


title: p65 IP in Treg, anti-CD3/CD28 stim, rep1

description:
p65_Treg_S_1
processed data file:
p65_Treg_S.pooled_peaks.noBlacklist.idr_conservative.narrowPeak