title: d134.Ctr.0 [103362-001-086]

description:
103362-001-086
title format: donor.allergen.dose


title: d134.Pea.50 [103362-001-073]

status: Public on Mar 17 2021

type: SRA

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

country: Netherlands

institute: TNO

description:
103362-001-073
title format: donor.allergen.dose

library_source: transcriptomic

data_processing:
Quality filtering and adapter-trimming of the Illumina Nextseq 500 V2 fastq files was performed by Trimmomatic software.
Reads (Single-end, 75bp) of the fastq files were aligned to the reference sequence (Homo_sapiens.GRCh38.primary_assembly.GENCODE) using Tophat 2.0.14 combined with Bowtie 2.1.0. The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package (88-92% of input reads were mapped to the genome).
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count files.
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample).
Supplementary_files_format_and_content: merged.counts.140samp.tsv.txt includes the mapped read counts per gene for all samples; *.counts.tsv files include the mapped read counts per gene for individual samples.

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: PBMCs were isolated from buffy coats from non-atopic donors from Sanquin (Sanquin Blood Bank, The Netherlands). The PBMCs were washed with PBS/FCS and after centrifugation, the cell pellet was reconstituted in culture medium. Cells were counted and freezing medium was added to prepare a cell suspension of 50 – 150 x 10^6 cells/mL. Cells were stored in a liquid nitrogen tank until further usage.

extract_protocol:
The RNA isolation was performed according to the manufacturer’s protocol. RNA quality was assessed using fragment analysis using the DNF-471-500 standard sensitivity RNA kit from Agilent™. RNA quality number was determined with Prosize 2.0 (Data Analysis software 2.0.0.51).
Strand-specific mRNA-seq libraries for the Illumina platform were generated using Illumina protocols and sequenced at BaseClear BV (Leiden, The Netherlands). Briefly: The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
RNA-seq. Briefly: Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used. Primary data analysis and results: Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.20. The sequencing experiments were performed at the following site(s): GenomeScan B.V., Plesmanlaan 1d, 2333 BZ, Leiden.

treatment_protocol: Frozen PBMCs were thawed in a water bath (37°C), washed in culture medium and plated into sterile 96-well plates (1 x 10^5 cells per well). Allergenic proteins and LPS controls diluted in culture medium were added to the wells and incubated (37°C, 5% CO2) for four hours. The stimulated PBMCs were harvested and RNA isolated.

tag: diagnosis

value: Healthy

tag: cell type

value: PBMCs

tag: allergen

value: 2S albumin Peanut


title: d134.Soy.50 [103362-001-051]

description:
103362-001-051
title format: donor.allergen.dose

value: Soybean 7S globulin


title: d133.Ctr.0 [103362-001-041]

description:
103362-001-041
title format: donor.allergen.dose

value: Control (no exposure)


title: d133.Lup.10 [103362-001-035]

description:
103362-001-035
title format: donor.allergen.dose

value: 2S albumin Lupine


title: d133.Lup.50 [103362-001-037]

description:
103362-001-037
title format: donor.allergen.dose


title: d133.Lup.50 [103362-001-038]

description:
103362-001-038
title format: donor.allergen.dose


title: d133.Lup.50 [103362-001-039]

description:
103362-001-039
title format: donor.allergen.dose


title: d133.Lup.50 [103362-001-040]

description:
103362-001-040
title format: donor.allergen.dose


title: d133.Pea.50 [103362-001-032]

description:
103362-001-032
title format: donor.allergen.dose


title: d133.Pea.50 [103362-001-029]

description:
103362-001-029
title format: donor.allergen.dose


title: d133.Pea.50 [103362-001-031]

description:
103362-001-031
title format: donor.allergen.dose


title: d133.Pea.50 [103362-001-030]

description:
103362-001-030
title format: donor.allergen.dose


title: d133.Lup.10 [103362-001-033]

description:
103362-001-033
title format: donor.allergen.dose


title: d133.Pea.10 [103362-001-026]

description:
103362-001-026
title format: donor.allergen.dose


title: d133.Lup.10 [103362-001-036]

description:
103362-001-036
title format: donor.allergen.dose


title: d133.Pea.10 [103362-001-025]

description:
103362-001-025
title format: donor.allergen.dose


title: d133.Pea.10 [103362-001-027]

description:
103362-001-027
title format: donor.allergen.dose


title: d133.Soy.50 [103362-001-008]

description:
103362-001-008
title format: donor.allergen.dose


title: d133.WB.50 [103362-001-004]

description:
103362-001-004
title format: donor.allergen.dose

value: White Bean 7S globulin


title: d133.WB.50 [103362-001-001]

description:
103362-001-001
title format: donor.allergen.dose


title: d133.Soy.50 [103362-001-006]

description:
103362-001-006
title format: donor.allergen.dose


title: d133.Lup.10 [103362-001-034]

description:
103362-001-034
title format: donor.allergen.dose


title: d133.WB.50 [103362-001-003]

description:
103362-001-003
title format: donor.allergen.dose


title: d133.WB.50 [103362-001-002]

description:
103362-001-002
title format: donor.allergen.dose


title: d133.Soy.50 [103362-001-005]

description:
103362-001-005
title format: donor.allergen.dose


title: d133.Soy.50 [103362-001-007]

description:
103362-001-007
title format: donor.allergen.dose


title: d150.Ctr.0 [103265-001-121]

description:
103265-001-121
title format: donor.allergen.dose

data_processing:
Quality filtering and adapter-trimming of the Illumina Nextseq 500 V2 fastq files was performed by Trimmomatic software.
Reads (Single-end, 75bp) of the fastq files were aligned to the reference sequence (Homo_sapiens.GRCh38.primary_assembly.GENCODE) using Tophat 2.0.14 combined with Bowtie 2.1.0. The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package (88-92% of input reads were mapped to the genome).
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count files.
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). JoinedCounts_123samp.txt includes the mapped read counts per gene for all samples; *.fastq.count files include the mapped read counts per gene for individual samples.

extract_protocol:
The RNA isolation was performed according to the manufacturer’s protocol. RNA quality was assessed using fragment analysis using the DNF-471-500 standard sensitivity RNA kit from Agilent™. RNA quality number was determined with Prosize 2.0 (Data Analysis software 2.0.0.51).
Strand-specific mRNA-seq libraries for the Illumina platform were generated using Illumina protocols and sequenced at BaseClear BV (Leiden, The Netherlands). Briefly: The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
RNA-seq. Briefly: Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used. Primary data analysis and results: Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17. The sequencing experiments were performed at the following site(s): GenomeScan B.V., Plesmanlaan 1d, 2333 BZ, Leiden.

value: Control


title: d150.Ctr.0 [103265-001-122]

description:
103265-001-122
title format: donor.allergen.dose


title: d150.Ctr.0 [103265-001-125]

description:
103265-001-125
title format: donor.allergen.dose


title: d150.Ctr.0 [103265-001-124]

description:
103265-001-124
title format: donor.allergen.dose


title: d150.Ctr.0 [103265-001-123]

description:
103265-001-123
title format: donor.allergen.dose


title: d150.Soy.50 [103265-001-119]

description:
103265-001-119
title format: donor.allergen.dose


title: d150.Soy.10 [103265-001-115]

description:
103265-001-115
title format: donor.allergen.dose


title: d150.Soy.50 [103265-001-117]

description:
103265-001-117
title format: donor.allergen.dose


title: d150.Soy.50 [103265-001-116]

description:
103265-001-116
title format: donor.allergen.dose


title: d150.Soy.10 [103265-001-114]

description:
103265-001-114
title format: donor.allergen.dose


title: d150.Soy.10 [103265-001-113]

description:
103265-001-113
title format: donor.allergen.dose


title: d150.Soy.10 [103265-001-112]

description:
103265-001-112
title format: donor.allergen.dose


title: d133.Pea.10 [103362-001-028]

description:
103362-001-028
title format: donor.allergen.dose


title: d150.WB.50 [103265-001-109]

description:
103265-001-109
title format: donor.allergen.dose


title: d150.WB.50 [103265-001-110]

description:
103265-001-110
title format: donor.allergen.dose


title: d150.WB.50 [103265-001-108]

description:
103265-001-108
title format: donor.allergen.dose


title: d150.WB.50 [103265-001-107]

description:
103265-001-107
title format: donor.allergen.dose


title: d150.Soy.50 [103265-001-120]

description:
103265-001-120
title format: donor.allergen.dose


title: d150.Soy.50 [103265-001-118]

description:
103265-001-118
title format: donor.allergen.dose


title: d150.Soy.10 [103265-001-111]

description:
103265-001-111
title format: donor.allergen.dose


title: d150.WB.10 [103265-001-105]

description:
103265-001-105
title format: donor.allergen.dose


title: d149.Soy.50 [103265-001-093]

description:
103265-001-093
title format: donor.allergen.dose


title: d149.Ctr.0 [103265-001-098]

description:
103265-001-098
title format: donor.allergen.dose


title: d150.WB.10 [103265-001-101]

description:
103265-001-101
title format: donor.allergen.dose


title: d150.WB.10 [103265-001-104]

description:
103265-001-104
title format: donor.allergen.dose


title: d149.Soy.50 [103265-001-095]

description:
103265-001-095
title format: donor.allergen.dose


title: d149.Ctr.0 [103265-001-096]

description:
103265-001-096
title format: donor.allergen.dose


title: d150.WB.10 [103265-001-103]

description:
103265-001-103
title format: donor.allergen.dose


title: d149.Ctr.0 [103265-001-099]

description:
103265-001-099
title format: donor.allergen.dose


title: d149.Ctr.0 [103265-001-100]

description:
103265-001-100
title format: donor.allergen.dose


title: d150.WB.10 [103265-001-102]

description:
103265-001-102
title format: donor.allergen.dose


title: d149.Soy.50 [103265-001-092]

description:
103265-001-092
title format: donor.allergen.dose


title: d149.Soy.50 [103265-001-091]

description:
103265-001-091
title format: donor.allergen.dose


title: d149.Soy.10 [103265-001-090]

description:
103265-001-090
title format: donor.allergen.dose


title: d149.Soy.10 [103265-001-088]

description:
103265-001-088
title format: donor.allergen.dose


title: d149.Soy.10 [103265-001-089]

description:
103265-001-089
title format: donor.allergen.dose


title: d149.Soy.10 [103265-001-087]

description:
103265-001-087
title format: donor.allergen.dose


title: d150.WB.50 [103265-001-106]

description:
103265-001-106
title format: donor.allergen.dose


title: d134.Lup.50 [103362-001-083]

description:
103362-001-083
title format: donor.allergen.dose


title: d149.WB.10 [103265-001-080]

description:
103265-001-080
title format: donor.allergen.dose


title: d149.WB.50 [103265-001-083]

description:
103265-001-083
title format: donor.allergen.dose


title: d149.WB.50 [103265-001-082]

description:
103265-001-082
title format: donor.allergen.dose


title: d149.WB.50 [103265-001-084]

description:
103265-001-084
title format: donor.allergen.dose


title: d149.WB.50 [103265-001-085]

description:
103265-001-085
title format: donor.allergen.dose


title: d149.Ctr.0 [103265-001-097]

description:
103265-001-097
title format: donor.allergen.dose


title: d149.WB.10 [103265-001-078]

description:
103265-001-078
title format: donor.allergen.dose


title: d149.WB.10 [103265-001-077]

description:
103265-001-077
title format: donor.allergen.dose


title: d149.WB.10 [103265-001-079]

description:
103265-001-079
title format: donor.allergen.dose


title: d149.WB.10 [103265-001-076]

description:
103265-001-076
title format: donor.allergen.dose


title: d149.Soy.10 [103265-001-086]

description:
103265-001-086
title format: donor.allergen.dose


title: d145.Ctr.0 [103265-001-075]

description:
103265-001-075
title format: donor.allergen.dose


title: d145.Ctr.0 [103265-001-071]

description:
103265-001-071
title format: donor.allergen.dose


title: d145.Ctr.0 [103265-001-072]

description:
103265-001-072
title format: donor.allergen.dose


title: d145.Ctr.0 [103265-001-073]

description:
103265-001-073
title format: donor.allergen.dose


title: d145.Ctr.0 [103265-001-074]

description:
103265-001-074
title format: donor.allergen.dose


title: d145.Soy.50 [103265-001-068]

description:
103265-001-068
title format: donor.allergen.dose


title: d145.Soy.50 [103265-001-070]

description:
103265-001-070
title format: donor.allergen.dose


title: d145.Soy.50 [103265-001-069]

description:
103265-001-069
title format: donor.allergen.dose


title: d145.Soy.50 [103265-001-066]

description:
103265-001-066
title format: donor.allergen.dose


title: d145.Soy.10 [103265-001-065]

description:
103265-001-065
title format: donor.allergen.dose


title: d145.Soy.50 [103265-001-067]

description:
103265-001-067
title format: donor.allergen.dose


title: d145.Soy.10 [103265-001-062]

description:
103265-001-062
title format: donor.allergen.dose


title: d145.Soy.10 [103265-001-064]

description:
103265-001-064
title format: donor.allergen.dose


title: d145.Soy.10 [103265-001-063]

description:
103265-001-063
title format: donor.allergen.dose


title: d145.Soy.10 [103265-001-061]

description:
103265-001-061
title format: donor.allergen.dose


title: d145.WB.50 [103265-001-059]

description:
103265-001-059
title format: donor.allergen.dose


title: d145.WB.50 [103265-001-060]

description:
103265-001-060
title format: donor.allergen.dose


title: d145.WB.50 [103265-001-058]

description:
103265-001-058
title format: donor.allergen.dose


title: d145.WB.50 [103265-001-056]

description:
103265-001-056
title format: donor.allergen.dose


title: d145.WB.10 [103265-001-055]

description:
103265-001-055
title format: donor.allergen.dose


title: d145.WB.10 [103265-001-054]

description:
103265-001-054
title format: donor.allergen.dose


title: d145.WB.50 [103265-001-057]

description:
103265-001-057
title format: donor.allergen.dose


title: d145.WB.10 [103265-001-052]

description:
103265-001-052
title format: donor.allergen.dose


title: d145.WB.10 [103265-001-051]

description:
103265-001-051
title format: donor.allergen.dose


title: d143.Ctr.0 [103265-001-050]

description:
103265-001-050
title format: donor.allergen.dose


title: d145.WB.10 [103265-001-053]

description:
103265-001-053
title format: donor.allergen.dose


title: d143.Ctr.0 [103265-001-049]

description:
103265-001-049
title format: donor.allergen.dose


title: d143.Ctr.0 [103265-001-048]

description:
103265-001-048
title format: donor.allergen.dose


title: d143.Ctr.0 [103265-001-047]

description:
103265-001-047
title format: donor.allergen.dose


title: d143.Soy.50 [103265-001-044]

description:
103265-001-044
title format: donor.allergen.dose


title: d143.Ctr.0 [103265-001-046]

description:
103265-001-046
title format: donor.allergen.dose


title: d143.Soy.50 [103265-001-045]

description:
103265-001-045
title format: donor.allergen.dose


title: d143.Soy.50 [103265-001-042]

description:
103265-001-042
title format: donor.allergen.dose


title: d143.Soy.50 [103265-001-041]

description:
103265-001-041
title format: donor.allergen.dose


title: mter-4_4

status: Public on Mar 18 2021

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Trim low quality reads and apapters. Trimmomatic V0.39 - ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
Remove ribosomal RNA. SortmeRNA
map to the reference genome. HISAT2 V2.1.0.
Count reads on features. htseq-count
Genome_build: C. elegans - WBCEL235
Supplementary_files_format_and_content: HTSeq - count files are tge output from the data pre-processing steps outlined above.

organism: Caenorhabditis elegans

source_name: Young Adult

growth_protocol: Wild-type and mter-4 mutant embryos were grown to young adults on NGM plates seeded with E. coli HB101 at 20C.

extract_protocol:
Frozen pellets of animals were freeze/thawed 5x using liquid nitrogen. Samples were then refrozen and sent to BGI for RNA extraction and DNBseq PE100
BGI performed standard RNA extraction from Trizol
DNBSeq library preparation from BGI for their propriatary sequencing platform.

treatment_protocol: No treatments were done - young adult animals were collected in Trizol and frozen on dry ice.

tag: tissue

value: Young adult whole animals

tag: genotype


title: d143.Soy.10 [103265-001-039]

description:
103265-001-039
title format: donor.allergen.dose


title: d143.Soy.10 [103265-001-038]

description:
103265-001-038
title format: donor.allergen.dose


title: d143.Soy.10 [103265-001-036]

description:
103265-001-036
title format: donor.allergen.dose


title: d143.WB.50 [103265-001-035]

description:
103265-001-035
title format: donor.allergen.dose


title: d143.Soy.10 [103265-001-037]

description:
103265-001-037
title format: donor.allergen.dose


title: d143.WB.50 [103265-001-032]

description:
103265-001-032
title format: donor.allergen.dose


title: d143.WB.50 [103265-001-034]

description:
103265-001-034
title format: donor.allergen.dose


title: d143.WB.10 [103265-001-029]

description:
103265-001-029
title format: donor.allergen.dose


title: d143.WB.50 [103265-001-031]

description:
103265-001-031
title format: donor.allergen.dose


title: d143.WB.10 [103265-001-030]

description:
103265-001-030
title format: donor.allergen.dose


title: d143.WB.10 [103265-001-028]

description:
103265-001-028
title format: donor.allergen.dose


title: d143.WB.10 [103265-001-026]

description:
103265-001-026
title format: donor.allergen.dose


title: d143.WB.10 [103265-001-027]

description:
103265-001-027
title format: donor.allergen.dose


title: d124.Ctr.0 [103265-001-024]

description:
103265-001-024
title format: donor.allergen.dose


title: d124.Ctr.0 [103265-001-021]

description:
103265-001-021
title format: donor.allergen.dose


title: d124.Ctr.0 [103265-001-025]

description:
103265-001-025
title format: donor.allergen.dose


title: d124.Soy.50 [103265-001-020]

description:
103265-001-020
title format: donor.allergen.dose


title: d124.Ctr.0 [103265-001-022]

description:
103265-001-022
title format: donor.allergen.dose


title: d124.Ctr.0 [103265-001-023]

description:
103265-001-023
title format: donor.allergen.dose


title: d143.Soy.50 [103265-001-043]

description:
103265-001-043
title format: donor.allergen.dose


title: d124.Soy.50 [103265-001-018]

description:
103265-001-018
title format: donor.allergen.dose


title: d124.Soy.50 [103265-001-017]

description:
103265-001-017
title format: donor.allergen.dose


title: d143.WB.50 [103265-001-033]

description:
103265-001-033
title format: donor.allergen.dose


title: d124.Soy.50 [103265-001-016]

description:
103265-001-016
title format: donor.allergen.dose


title: d124.Soy.10 [103265-001-015]

description:
103265-001-015
title format: donor.allergen.dose


title: d124.Soy.10 [103265-001-013]

description:
103265-001-013
title format: donor.allergen.dose


title: d124.Soy.10 [103265-001-014]

description:
103265-001-014
title format: donor.allergen.dose


title: d124.Soy.10 [103265-001-012]

description:
103265-001-012
title format: donor.allergen.dose


title: d124.Soy.10 [103265-001-011]

description:
103265-001-011
title format: donor.allergen.dose


title: d124.WB.50 [103265-001-010]

description:
103265-001-010
title format: donor.allergen.dose


title: d124.WB.50 [103265-001-008]

description:
103265-001-008
title format: donor.allergen.dose


title: d124.WB.50 [103265-001-007]

description:
103265-001-007
title format: donor.allergen.dose


title: d124.WB.50 [103265-001-009]

description:
103265-001-009
title format: donor.allergen.dose


title: d143.Soy.10 [103265-001-040]

description:
103265-001-040
title format: donor.allergen.dose


title: d124.WB.10 [103265-001-002]

description:
103265-001-002
title format: donor.allergen.dose


title: d124.WB.10 [103265-001-003]

description:
103265-001-003
title format: donor.allergen.dose


title: d124.WB.10 [103265-001-001]

description:
103265-001-001
title format: donor.allergen.dose


title: d124.Soy.50 [103265-001-019]

description:
103265-001-019
title format: donor.allergen.dose


title: 097-286_V5

city: Seattle

first: Lamar

last: Ballweber Fleming

state: WA

address: 1100 Fairview Ave N

department: VIDD

country: USA

institute: Fred Hutchinson Cancer Res Ctr

data_processing:
Reads aligning to rDNA,tRNA, mtrDNA using BOWTIE2 were filtered.
Reads not aligning to rDNA,tRNA,mtrDNA were aligned using STAR (v2.37a, Index Homo Sapiens (human-hg38 genome assembly, whole genome
Aligned reads quantified to annoation model Partek E/M) using GENCODE Genes release 26
Features were filtered excluding features where maximum counts was <=20.0
Data were normalized by adding 1 to all counts and using the TMM normalization method implemented with Partek-flow software version 9.0.20.0622
Genome_build: human-hg38 genome assembly
Supplementary_files_format_and_content: csv

source_name: PBMC

extract_protocol:
QIAGEN Rneasy
Illumina stranded mRNA TruSEQ

treatment_protocol: PBMC in RNA cellprotect

tag: visit

tag: treatmentarm

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)

tag: bmi

value: FALSE


title: 097-286_V4


title: d124.WB.10 [103265-001-004]

description:
103265-001-004
title format: donor.allergen.dose


title: 097-257_V6

value: TRUE


title: 097-286_V6


title: 097-277_V5


title: 097-286_V3


title: 097-277_V6


title: 097-277_V4


title: 097-277_V3


title: 097-257_V5


title: 097-257_V3


title: 097-226_V5


title: 097-257_V4


title: 097-226_V3


title: 097-226_V4


title: 097-226_V6


title: 097-204_V6


title: 097-204_V3


title: 097-187_V6


title: 097-187_V4


title: 097-204_V4


title: 097-187_V5


title: d124.WB.10 [103265-001-005]

description:
103265-001-005
title format: donor.allergen.dose


title: d124.WB.50 [103265-001-006]

description:
103265-001-006
title format: donor.allergen.dose


title: 097-179_V6


title: 097-179_V3


title: 097-187_V3


title: 097-176_V4


title: 097-176_V6


title: R71C09_dam:kdm5_2

city: Bronx

first: Hayden

middle: A. M.

last: Hatch

state: New York

address: 1300 Morris Park Avenue, Ullmann 809

department: Dominick P. Purpura Department of Neuroscience; Department of Genetics

institute: Albert Einstein College of Medicine

description: Targeted DamID

library_source: genomic

data_processing:
Library strategy: DamID
Libraries were sequenced on a BGISEQ-500 platform with 50 bp read length and 20 M clean reads.
For Targeted DamID analyses, sequencing data were aligned to release 6 of the Drosophila melanogaster genome and processed using damidseq_pipeline as previously described (Marshall et al., 2016; Marshall & Brand, 2017).
Peaks were called using find_peaks (using the parameters fdr=0.01, min_quant=0.9) (Marshall et al., 2016) on the averaged replicates, and genes overlapping peaks identified using peaks2genes (Marshall et al., 2016).
Genome_build: dm6 (BDGP6, Ensembl release 98)
Supplementary_files_format_and_content: xlsx spreadsheets including genes bound by KDM5

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: NPCs/immature neurons

growth_protocol: To profile KDM5 occupancy in GMCs and immature neurons of WL3/pupae, UAS-LT3-dam or UAS-LT3-dam-kdm5 flies were crossed with tubulin-Gal80[ts]; R71C09-Gal4 flies and allowed to lay eggs for 12-14 hrs at 25 ºC. Embryos were transferred to 18 ºC for 9 days and subsequently moved to 29 ºC for 3 days.

extract_protocol:
Tissue processing for all TaDa experiments was performed as previously described in Marshall et al., 2016 with the following modifications. A total of 40 pupae of each genotype were homogenized in 500 mM EDTA followed by DNA extraction using the Zymo Quick-DNA Miniprep Plus Kit. DpnI digestion, PCR adaptor ligation, DpnII digestion, and PCR amplification were performed as described. DNA was sonicated using a Diagenode Bioruptor for 8-10 cycles (5-min at high power, 30-s on/30-s off) and analyzed using an Agilent Bioanalyzer. DamID adaptor removal and DNA cleanup were performed as described and samples were submitted to BGI Genomics for library construction and sequencing.
Libraries were prepared at BGI Genomics following a ChIP-seq workflow. DNA fragments were first end-repaired and dA-tailed using End Repair and A-Tailing (ERAT) enzyme. Adaptors were then ligated for sequencing and ligated DNA purified using AMPure beads. DNA was then PCR amplified with BGI primers for 8 cycles and PCR purified with AMPure beads. DNA was then homogenized, circularized, digested, and again purified. DNA was then prepared into proprietary DNA nanoballs (DNB™) for sequencing.

tag: developmental stage

value: Third instar larvae/pupae

value: NPCs/immature neurons


title: R71C09_dam:kdm5_3

description: Targeted DamID


title: 097-176_V5


title: R71C09_dam:kdm5_4

description: Targeted DamID


title: R71C09_dam_2

description: Targeted DamID


title: 097-174_V4


title: R71C09_dam:kdm5_6

description: Targeted DamID


title: R71C09_dam_3

description: Targeted DamID


title: R71C09_dam:kdm5_5

description: Targeted DamID


title: R71C09_dam:kdm5_1

description: Targeted DamID


title: 097-174_V3


title: 097-176_V3


title: 097-174_V5


title: 097-174_V6


title: 097-166_V5


title: RNA_Med1_P10_BAT_AKO

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

organism: Mus musculus

growth_protocol: ChIP-seq: Primary brown preadipocytes were isolated from interscapular BAT of newborn Med1f/f;CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid

extract_protocol:
ChIP-seq: Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
ChIP-seq: Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).
ATAC-Seq: 5 × 10^4 freshly collected cells were aliquoted into a new tube and spun down at 500 × g for 5 min at 4 °C. The cell pellet was incubated in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega) on ice for 3 min and was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were collected by centrifugation at 500 × g for 10 min at 4 °C, then resuspended in 50 µl of transposition reaction buffer (25 µl 2x Tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). The reaction was incubated at 37 °C for 30 min with mixing (1000 r.p.m.) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
ATAC-Seq: DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols
RNA-Seq: Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
RNA-Seq: Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.
nascent RNA-Seq: 10^6 cells were labeled with 0.5 mM ethylene uridine for 30 min at 37 °C. After RNA extraction, 1 μg total RNA was depleted of rRNA using the NEBNext rRNA Depletion kit (NEB). To capture nascent RNA, the sample was biotinylated by the Click-iT Nascent RNA Capture Kit (ThermoFisher, C10365) according to the manufacturer’s instructions.
nascent RNA-Seq: Double-stranded cDNAs were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Library construction was done using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: ChIP-seq: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: strain background

value: 129S4/SvJae - C57BL/6 mixed

tag: genotype/variation

value: Brown adipose tissue


title: 097-179_V4


title: 097-166_V4


title: 097-166_V3


title: 097-166_V6


title: WT DRG 7D 3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using Ensembl GRCm38 as reference
Normalization (VST), removed unwanted variation (k=1) by RUVseq, quantitation and differential expression analysis using limma
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized read count

source_name: L3-L5 DRGs

extract_protocol: L3-L5 DRGs were removed from PBS perfused mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent.

value: dorsal root ganglia (DRG)

tag: sample type

value: 7 day following sciatic nerve injury

tag: injury condition

value: mid-thigh sciatic nerve crush

tag: strain

tag: sample storage

value: DRGs stored in Trizol


title: RNA_Med1_P10_WAT_AKO

value: Inguinal white adipose tissue


title: WT DRG 7D 2


title: 097-154_V5


title: WT DRG 7D 1


title: 097-154_V4


title: WT DRG 3D 3

value: 3 day following sciatic nerve injury


title: 097-136_V5


title: WT DRG 3D 1


title: 097-154_V3


title: 097-136_V3


title: 097-134_V6


title: WT DRG 1D 1

value: 1 day following sciatic nerve injury


title: 097-134_V5


title: 097-134_V4


title: WT DRG sham 3

value: sham operated mice


title: RNA_Med1_P10_BAT_WT


title: R71C09_dam_1

description: Targeted DamID


title: 097-129_V5


title: 097-154_V6


title: 097-129_V4


title: FNIP1-TGKO rep2

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

description:
Gastrocnemius muscle total RNA from FNIP1-TGKO mouse
FNIP1-TGKO biological rep2

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Gastrocnemius muscle from FNIP1-TGKO mouse

extract_protocol:
Gastrocnemius muscle  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gastrocnemius muscle

tag: age

value: 8 weeks of age

value: FNIP1-TGKO mouse


title: 097-134_V3


title: WT DRG sham 1


title: FNIP1-TGKO rep1

description:
Gastrocnemius muscle total RNA from FNIP1-TGKO mouse
FNIP1-TGKO biological rep1


title: WT DRG 3D 2


title: 097-107_V6

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)

value: FALSE


title: FNIP1-KO rep1

description:
Gastrocnemius muscle total RNA from FNIP1 knock-out mouse
FNIP1-KO biological rep1

source_name: Gastrocnemius muscle from FNIP1-KO mouse

value: FNIP1 knock-out mouse


title: FNIP1-KO rep2

description:
Gastrocnemius muscle total RNA from FNIP1 knock-out mouse
FNIP1-KO biological rep2


title: 097-107_V5


title: WT rep2

description:
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for FNIP1 knock-out
Wildtype biological rep2

source_name: Gastrocnemius muscle from wild-type mouse

value: Wild-type mouse - control mouse for FNIP1 knock-out


title: 097-129_V3

value: TRUE


title: RNA_Med1_P10_WAT_WT

value: 129S4/SvJae - C57BL/6 mixed


title: WT rep1

description:
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for FNIP1 knock-out
Wildtype biological rep1


title: 097-107_V4


title: 097-100_V6


title: 097-129_V6


title: RNA-Seq-siKDM5C-CTL-MCF-7-rep2

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

molecule: polyA RNA

growth_protocol: MCF-7 cells were cultured in DMEM medium supplemented with 10% FBS and 1%penicillin and streptomycin

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: Before experiment, MCF-7 cells were knockdown by siRNA(CTL) or siRNA specifically targeting KDM5C or ZMYND8 and medium was changed to phenol red free DMEM plus 5% charcoal-stripped FBS and 1% penncilin and streptomycin. On the second day, cells were treated with the same way as described above and maintained for another two days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 6hrs.

tag: cell line

value: Michigan Cancer Foundation-7 (MCF-7) cells

tag: genotype/varaition

tag: treatment

value: control


title: RNA-Seq-siKDM5C-E2-MCF-7-rep2


title: 097-100_V4


title: WT DRG sham 2

value: dorsal root ganglia (DRG)


title: RNA-Seq-siCTL-CTL-MCF-7-rep2

value: siCTL


title: 097-098_V6


title: 097-098_V5


title: WT DRG 1D 3

value: mid-thigh sciatic nerve crush

value: DRGs stored in Trizol


title: 097-100_V3


title: KDM5C-E2-MCF-7

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: MCF-7 cells were cultured in DMEM medium supplemented with 10% FBS and 100 units/mL penicillin/100 ug/mL streptomycin

extract_protocol:
For ChIP assays, cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 mins at RT (for KDM5C (Bethyl Laboratory, A301-034A), ZMYND8 (Bethyl Laboratory, A302-090A)) or fixed with 1% glutaraldehyde for 10mins at RT(for CDK9 (CST, 2316S) ChIP). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 200-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 3 hrs. After washing and elution, formaldehyde or DSG and formaldehyde fixed chromatin was treated at 65 ℃ overnight whereas glutaraldehyde fixed chromatin was treated with 0.2mg/mL proteinase K at 55℃ for two hours then 65℃ overnight with interval shaking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Before experiment, medium was changed to phenol red free DMEM plus 5% charcoal-stripped FBS and 1% penncilin and streptomycin to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.

tag: chip antibody

value: Bethyl Laboratory; A301-034A


title: 097-098_V4


title: 097-098_V3


title: ZMYND8-CTL-MCF-7

value: Bethyl Laboratory; A302-090A


title: WT DRG 1D 2

tag: tissue

value: 1 day following sciatic nerve injury


title: Mock (NV1LS2)

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Library strategy: sDRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using Macs v2.2.5 with default parameters except for --nomodel. We then merged peaks from all samples. HTseq-count v0.11.2 was then used to count the total number of reads in each merged peak.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: sDRIP-seq bedGraph files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).

source_name: NTREA-2 D1

growth_protocol: NTERA-2 D1 cells were obtained from ATCC and grown in high-glucose Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin / streptomycin. Cells were seeded 1-2 days prior to experiments and were grown to 40-60% confluency

extract_protocol:
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Extracted DNA was subjected to mock or enzymatic treatments (RNase H1, RNase III, RNase T1, or RNase T1+RNase III) prior to immunoprecipitation with the S9.6 antibody.

tag: cell type

value: testicular embryonal carcinoma cell line

value: NTREA-2 D1

value: Mock


title: Mock (NV1LS1)


title: 097-074_V6

tag: visit

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)

value: FALSE


title: ZMYND8-E2-MCF-7


title: 097-107_V3

tag: treatmentarm


title: 097-074_V5

tag: bmi


title: 097-074_V3


title: 097-074_V4


title: RNA-Seq-siCTL-E2-MCF-7-rep2


title: RNase III (LS5I)

value: RNase III


title: KDM5C-CTL-MCF-7


title: 097-064_V6


title: Mock (LS5G)


title: 097-064_V5


title: RNase T1 (LS5D)

value: RNase T1


title: 097-064_V4


title: 097-064_V3


title: Mock (LS5C)


title: 097-057_V5


title: 097-057_V6


title: 097-100_V5

value: TRUE


title: RNase T1+III (LS5F)


title: 336

city: Dublin

first: William

middle: P.

last: Martin

state: - Select State/Province -

address: Diabetes Complications Research Centre, Conway Institute, University College Dublin

country: Ireland

institute: University College Dublin

data_processing:
Quality control of reads performed with fastqc.
Quality filtering of reads performed with trim_galore.
Alignment towards rn5 rat reference genome using STAR.
Quantification of aligned reads using featureCounts (Subread package).
Differential expression analysis using DESeq2.
Genome_build: rn5 (Rnor_5.0) rat reference genome
Supplementary_files_format_and_content: *_featureCounts.txt: Tab-delimited text files providing raw counts of aligned reads for each rat renal cortical sample.

organism: Rattus norvegicus

source_name: Renal cortex

extract_protocol:
RNA extraction from renal cortex was performed using an RNeasy Mini Kit (Qiagen). RNA was isolated according to manufacturer’s instructions. Renal cortical samples were preserved on dry ice prior to lysis steps. RNA samples were stored at -80 degrees Celsius until RNA-sequencing. RNA integrity was checked using a Bioanalyser system prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation kit: TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold.

value: Zucker Diabetic Sprague Dawley

value: 37 weeks

value: Renal cortex

tag: experimental group

value: RYGB surgery/Best Medical Therapy


title: 339


title: 097-057_V4


title: C3h10-102

city: jiang su

first: MIngshan

last: Li

state: su zhou

address: Industrial park

institute: suzhou university

data_processing:
Through Illumina platform, a large number of sample double-ended sequencing data were obtained.In view of the influence of data error rate on the results, Trimmomatic software was used to preprocess the quality of the original data, and the number of reads in the whole quality control process was statistically summarized.
We used hisat2 to sequence Clean Reads with the designated reference genome to obtain the position information on the reference genome or gene, as well as the sequence characteristic information specific to the sequenced samples.
We use reference transcripts as library and use sequence similarity alignment method to determine the expression abundance of each transcript in each sample.Use software for Bowtie2 2.2.9 with parameters -k30 -t and eXpress 1.5.1.with parameters --rf-stranded
Transcriptional expression was calculated using FPKM (Fragments Per KB Per Million Reads), which is the number of Fragments Per Million of Fragments from a transcript Per kilobase length.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MSC

extract_protocol:
the cells were incubated with 5x001e_AZA (Sigma Aldrich) at 20 micromol/L respectively and incubated for 72 hours. Then the cells were replaced with fresh growth media, and incubated in a CO2 incubator for another 21 days. The medium was replaced in every 2-3 days and morphological changes of the cells were observed at the same time.
For common animals, the RNA was digested with a Truseq Stranded Total RNA with Ribo-Zero Gold kit, and an interrupting reagent was added to break the RNA into short fragments.The broken RNA was used as a template to synthesize a cDNA strand with random primers of six bases, and then a two-strand synthesis reaction system was formulated to synthesize two-strand cDNA. During the synthesis of the two-strand cDNA strand, dUTP was substituted for dTTP, and then different ligaments were connected, and then a strand containing dUTP was digested by UNG enzymatic method, and only one strand of cDNA with different ligaments was retained.One strand of cDNA was purified using the kit;The end of the purified cDNA strand was repaired, A tail was added and sequenced, fragment size selection was performed, and PCR amplification was performed at last.After the constructed RNA library was qualified by Agilent 2100 BioAnalyzer, Illumina sequencer was used for sequencing.

value: treated with 5-AZA for 72 hours


title: C3h10-101


title: 097-057_V3


title: C3h10-1

value: untreated


title: RNase T1 (LS5H)


title: RNA-seq_24hr_rep3

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
Paired-end reads were aligned to mm10 genome/transcriptome by topHat with the following options: --no-discordant --no-mixed --library-type fr-firststrand –b2-very-sensitive
Only pairs where both reads aligned with MAPQ >= 11 were kept
Duplicated were removed by rmdup from samtools
Aligned reads were assigned to genes using featureCounts from Rsubread R/Bioconductor package

source_name: Naïve (CD44int/lo CD62Lhi) CD8+ T cells

growth_protocol: Naïve (CD44hi, CD62Lhi) OT-I CD8+ T cells were sorted purified from male mice (6-12 weeks old).

extract_protocol:
Total RNA was extracted using trizol/chloroform and purified using isopropanol, RNA was subjected DNAse-treatment
Poly mRNA selection, Illumina Library Prep mRNA

treatment_protocol: They were stimulated in vitro with 1uM SIINKFEL peptide and rhIL-2 (10U/mL) for 0, 3, 5 and 24 hours.

value: OT-I Transgenic Mouse

value: CD8 T cells

value: In vitro stimulation with SIINFEKL for 24hrs


title: 097-048_V6


title: 324


title: 097-048_V5


title: RNA-seq_5hr_rep3

value: In vitro stimulation with SIINFEKL for 5hrs


title: RNA-seq_24hr_rep1


title: 323


title: RNase T1+III (LS5J)

value: testicular embryonal carcinoma cell line

value: NTREA-2 D1

value: RNase T1+III


title: 320


title: RNA-seq_5hr_rep2


title: 312


title: 097-048_V4

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)

value: FALSE


title: RNA-seq_5hr_rep1


title: RNA-seq_3hr_rep3

value: In vitro stimulation with SIINFEKL for 3hrs


title: 097-048_V3


title: RNA-seq_3hr_rep2


title: RNA-seq_3hr_rep1


title: 350

value: RYGB surgery


title: 097-045_V5


title: RNA-seq_0hr_rep2

value: non-stimulated


title: C3h10-2


title: 346

value: Zucker Diabetic Sprague Dawley

value: 37 weeks


title: 097-045_V4


title: 307

value: Renal cortex

value: RYGB surgery/Best Medical Therapy


title: RNA-seq_0hr_rep3


title: 338


title: RNA-seq_24hr_rep2


title: 344


title: ATAC-seq_24hr_rep2

data_processing:
Nextera Transposase adaptors were removed using trim_galore in paired-end mode
Paired-end reads were aligned to mm10 genome using bowtie2 with the options: --very-sensitive-local --no-mixed –no-discordant
Only pairs where both reads aligned with MAPQ >= 10 were kept.
Duplicates were removed by MarkDuplicates from picard tools
Reads were converted into bedpe format
Reads overlapping mm10 blacklist regions or chrM were removed.
.bedpe files were converted to .bdg format using genomecov from bedtools
After appropriate scaling peaks were called by bdgpeakcall from MACS2
Genome_build: mm10
Supplementary_files_format_and_content: ATAC counts called for the consensus peak set

extract_protocol:
Nuclei were extracted with nuclei lysis buffer and nuclei were subjected to Tn5 digestion. DNA was extracted using Qiagen MinElute Extraction Kit
Libraries were constructed according to Buenrostro et al., 2015

value: In vitro, SIINFEKL for 24hrs


title: ATAC-seq_24hr_rep1

value: OT-I Transgenic Mouse


title: 097-040_V6

value: TRUE


title: 097-045_V3


title: ATAC-seq_3hr_rep2

value: In vitro, SIINFEKL for 3hrs


title: 326


title: TI_24hr_rep2

data_processing:
Paired-end reads were aligned to mm10 genome using bowtie2 with the following options: --very-sensitive --no-mixed --no-discordant
Only pairs where both reads were aligned with MAPQ >= 10 were kept
.sam files where converted to .bedpe files using bedtools
Reads overlapping mm10 blacklist regions were removed.
Narrow and broad peaks where called with MACS2 with -f BEDPE option
Genome_build: mm10
Supplementary_files_format_and_content: H0minusH3.bed: 0hr peaks with the peaks intersecting with the 3hr peaks removed
Supplementary_files_format_and_content: H0minusH5.bed: 0hr peaks with the peaks intersecting with the 5hr peaks removed
Supplementary_files_format_and_content: H0minusH24.bed: 0hr peaks with the peaks intersecting with the 24hr peaks removed
Supplementary_files_format_and_content: H3minusH0.bed: 3hr peaks with the peaks intersecting with the 0hr peaks removed
Supplementary_files_format_and_content: H5minusH0.bed: 5hr peaks with the peaks intersecting with the 0hr peaks removed
Supplementary_files_format_and_content: H24minusH0.bed: 24hr peaks with the peaks intersecting with the 0hr peaks removed

extract_protocol:
Lysates were clarified from sonicated crosslinked cells and H3K27me3-DNA complexes were isolated with antibody.
Libraries were constructed using 5-10ng ChIP-DNA using the NEBNext CHIP-seq Library Master Mix Set for Illumina (NEB #E6240L, New England BioLabs Inc).

value: In vitro, SIINFEKL

tag: antibody


title: RNA-seq_0hr_rep1

value: CD8 T cells


title: ATAC-seq_3hr_rep1


title: TI_5hr_rep1


title: TI_5hr_rep2


title: 319


title: 097-045_V6


title: 337


title: 330


title: TI_24hr_rep1


title: TI_3hr_rep2


title: 097-040_V4


title: ATAC-seq_0hr_rep1

value: Non-stimulated


title: TI_3hr_rep1


title: 097-040_V3


title: TI_0hr_rep2


title: TI_0hr_rep1


title: H2K27me3_ChIP-seq_24hr_rep2


title: 097-029_V6


title: 309


title: 308


title: 097-029_V4


title: 097-029_V5


title: 097-029_V3


title: 097-040_V5


title: ATAC-seq_0hr_rep2


title: H2K27me3_ChIP-seq_0hr_rep2


title: 097-026_V6


title: H2K27me3_ChIP-seq_0hr_rep1

value: H3K27me3 Millipore (cat # 07-449; lot #


title: H2K27me3_ChIP-seq_3hr_rep1


title: 097-026_V4


title: 097-026_V3


title: 097-023_V6

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)


title: 097-023_V5

value: FALSE


title: 097-023_V4


title: H2K27me3_ChIP-seq_5hr_rep1


title: H2K27me3_ChIP-seq_24hr_rep1


title: H2K27me3_ChIP-seq_3hr_rep2


title: 097-023_V3


title: H2K27me3_ChIP-seq_5hr_rep2


title: Hippocampus 16 weeks male Ts65Dn  control mice biological replicate5

type: RNA

city: Strasbourg

first: maria

middle: del mar

last: muñiz moreno

state: Alsace

address: 1 Rue Laurent Fries

department: Translational medicine and neurogenetics

country: France

institute: IGBMC

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

scan_protocol: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.CEL files

data_processing: All the pipeline was implemented using R and linux bash environments. The .CEL files  were further processed with limma to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithm producing the summaries at the transcript level. The quality control workflow was implemented in two steps: first on the raw data, and then after the rma normalization to asses the effect of normalization where we analysed the signal distribution, the Intensity-dependent bias, the homogeneity of the probe sets and the structure of the data using Spearman correlation plots, Hierarchical clustering, PCA, tSNE and OPLS plots. The raw intensity measures of the arrays where normalized using limma RMA normalization algorithm (Ritchie et al., 2015) producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package pd.mogene.1.0.st.v1 (Carvalho B., 2015) and further annotated using ENSEMBL BioMart databases from biomaRt R package (Durinck S et al., 2005; Durinck S et al., 2009) updated on 12/02/2018 against the mm10 genome assembly   The non-annotated probes and control probes were discharged from the analysis. Of 35556 probes, 27359 were annotated.  Following the normalization and quality control analysis pipeline, a total of 27359 probes mapping to 24213 genes were annotated of the 25018 genes that could be detected by the arrays. The differential expression analysis (DEA) was carried on using FCROS (Dembélé et al., 2014) method implemented in the R environment. For the Differential functional analysis (DFA) aiming to identify the functions and possibly infer the mechanistic changes in the pathways where these DEGs show a statistical meaningful difference between the two conditions trisomic vs. wild type on each mouse model, we used the generally applicable gene set enrichment for pathway analysis (GAGE) R package (gage) to carry on the functional expression analysis.

label: Biotin

source_name: Hippocampus, 16 weeks old male mouse

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: All the mice were bred under speciﬁc pathogen-free (SPF) conditions with free access to food and water in the Institut Clinique de la Souris (I.C.S.) animal facility. The light cycle was fixed to provide 12 h light and 12 h of darkness. Llights are on at 7:00 AM. Only animals coming from litters containing a minimum of two male pups were selected. After weaning, male mice were gathered by litters in the same cage.All the mice were maintained on C57BL/6N genetics background, except Ts65Dn that are maintained on F1 hybrid B6C3B background.

extract_protocol: Total RNA extraction were isolated from the full hippocampus (right + left) of mutant trisomic and  littermate controls (N = 5 per group) and flash frozen in liquid nitrogen. Total RNA was extracted using the RNeasy plus mini kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. The samples quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).

value: 16 weeks

value: Hippocampus

tag: Sex

value: Male

tag: background

value: F1 hybrid B6C3B

tag: model name

tag: sample taxid

tag: genotype

value: WT

tag: condition

tag: number


title: Hippocampus 16 weeks male Ts65Dn  control mice biological replicate4

tag: age


title: 097-020_V6


title: 097-026_V5


title: Hippocampus 16 weeks male Ts65Dn  mutant trisomic mice biological replicate5

value: Mut


title: 097-020_V5


title: Hippocampus 16 weeks male Ts65Dn  control mice biological replicate2


title: Hippocampus 16 weeks male Ts65Dn  control mice biological replicate1


title: Hippocampus 16 weeks male Ts65Dn  control mice biological replicate3


title: Hippocampus 16 weeks male Ts65Dn  mutant trisomic mice biological replicate4


title: Hippocampus 16 weeks male Tg(Dyrk1a)  control mice biological replicate4


title: Hippocampus 16 weeks male Ts65Dn  mutant trisomic mice biological replicate3


title: Hippocampus 16 weeks male Tg(Dyrk1a)  control mice biological replicate5


title: Hippocampus 16 weeks male Ts65Dn  mutant trisomic mice biological replicate1


title: 097-020_V4


title: Hippocampus 16 weeks male Tg(Dyrk1a)  control mice biological replicate2


title: 097-020_V3


title: Hippocampus 16 weeks male Tg(Dyrk1a)  mutant trisomic mice biological replicate5


title: Hippocampus 16 weeks male Tg(Dyrk1a)  control mice biological replicate1


title: MIA-21 corresponding

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description:
Run08-RAW.xlsx
J46N

hyb_protocol: The Gene expression assay was performed on the NanoString nCounter platform using the PanCancer Immune Profiling Panel (cat # 115000132). 12 FFPE samples (input of 200 ng to 300 ng based on DV200 value) were run per cartridge following the manufacturer’s protocol. Briefly, Excess probes are hybridized (overnight) at 65C to target RNA molecules to ensure that each target finds a probe pair. After hybridization, excess probes were washed away using the automated nCounter instrument.

scan_protocol: After hybridization washes, the cartridge was read using ncounter digital analyzer (an epifluorescene microscope with CCD capture technology that generates target molecule counts).

data_processing:
nSolver 4.0 software (NanoString Technologies) was applied for quality control with default setting, and all samples passed QC check. Background correction was performed with negative controls, followed by two-steps normalization using geometric mean of 6 positive controls and 40 housekeeping genes. Then global adjustment was achieved by quantile-normalization to remove any unwanted technical variations, which was followed by log2 transformation to obtain variance stabilization.
nSolver processed data are further quantile normalized and log2 transformed for all analysis

source_name: PreCancer of Lung

growth_protocol: The surgical specimens were subjected to FFPE blocks directly

extract_protocol: RNA was extracted from FFPE using the AllPrep DNA/RNA FFPE kit (QIAGEN, Netherlands) per the manufacturer’s instructions. FFPE samples with tumor area demarcated by a pathologist was manually macro-dissected to enrich for the demarcated tumor area before RNA extraction.  On average, three 10-micron thick sections were used for RNA extraction per patient. Each sample was run on the Agilent TapeStation 4200 to determine the DV200 value (degree of fragmentation of the sample based on the percentage of the sample with greater than 200 intact nucleotides) for the FFPE samples. All the FFPE samples had 11.4% to 91.6% of the RNA having greater than 200 intact nucleotides.

treatment_protocol: no treatment for these surgical specimens

value: Lung

tag: histology

value: N


title: Hippocampus 16 weeks male Tg(Dyrk1a)  control mice biological replicate3


title: Hippocampus 16 weeks male Tg(Dyrk1a)  mutant trisomic mice biological replicate2


title: Hippocampus 16 weeks male Tg(Dyrk1a)  mutant trisomic mice biological replicate4


title: Hippocampus 16 weeks male Ts65Dn  mutant trisomic mice biological replicate2


title: 097-013_V5


title: 097-013_V4


title: MIA-20

description:
Run08-RAW.xlsx
J45M

value: MIA


title: MIA-20 correspoding

description:
Run08-RAW.xlsx
J45N


title: Hippocampus 16 weeks male Tg(Dyrk1a)  mutant trisomic mice biological replicate1


title: 097-011_V6


title: Hippocampus 16 weeks male Tg(Dyrk1a)  mutant trisomic mice biological replicate3


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Yah model) replicate5


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Yah model) replicate3


title: MIA-19 corresponding

description:
Run08-RAW.xlsx
J44N


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Yah model) replicate2


title: MIA-21

description:
Run08-RAW.xlsx
J46M


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate5  (renalysis)


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Yah model) replicate4


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Dp1 model) replicate5


title: 097-011_V4


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate1 (renalysis)

description: Gene expression data from Dp1Rhr_Dp5Yah_WT


title: MIA-19

description:
Run08-RAW.xlsx
J44M


title: 097-011_V3


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate4  (renalysis)


title: MIA-18

description:
Run08-RAW.xlsx
J43M


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Yah model) replicate1


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate2  (renalysis)

description: Gene expression data from  Dp1Rhr_Dp5Yah_WT


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Dp1 model) replicate4


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Dp1 model) replicate3


title: AIS-11

description:
Run08-RAW.xlsx
J43S

value: AIS


title: AC-2

first: Fei

middle: jun

last: Gu

address: 138 Xianlin Avenue

institute: Nanjing University of traditional Chinese Medicine

data_processing:
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads  count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

source_name: tumor sample

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Tumor induction:CT26 cells were injected into syngeneic BALB/c mice
Sample treatment: model was given saline once a day (6 g / kg) and 'AC' treatment was given Astragalus and Curcuma phaeocaulis Valeton(2:1) once a day (6 g / kg).

tag: strain

value: BALB/c

tag: treatment

value: AC treated

value: colon tumor


title: AC-3

tag: tissue


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Dp1 model) replicate1


title: Hippocampus 16 weeks male Dp5Yah mutant trisomic mice biological (Dp5Dp1 model) replicate2


title: AC-1


title: MOL-3

value: model


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate5 (reanalysis)


title: AIS-10

description:
Run07-RAW.xlsx
J42S


title: AIS-10 corresponding

description:
Run07-RAW.xlsx
J42N


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate4 (reanalysis)


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate1 (reanalysis)


title: AIS-11,MIA-18 corresponding

description:
Run08-RAW.xlsx
J43N


title: MIA-17 corresponding

description:
Run07-RAW.xlsx
J41N


title: MOL-2


title: Hippocampus 16 weeks male Dp3Yah  control mice biological replicate5


title: MIA-17

description:
Run07-RAW.xlsx
J41M


title: MOL-1


title: CON-3

source_name: normal

value: Sham

value: healthy colon


title: AIS-9,MIA-16 corresponding

description:
Run07-RAW.xlsx
J40N


title: CON-2


title: MIA-16

description:
Run07-RAW.xlsx
J40M


title: CON-1


title: AIS-9

description:
Run07-RAW.xlsx
J40S


title: MIA-15 corresponding

description:
Run07-RAW.xlsx
J39N


title: Hippocampus 16 weeks male Dp3Yah  control mice biological replicate4


title: Hippocampus 16 weeks male Dp3Yah  control mice biological replicate2


title: Hippocampus 16 weeks male Dp3Yah  mutant trisomic mice biological replicate5


title: Hippocampus 16 weeks male Dp3Yah  mutant trisomic mice biological replicate3


title: MIA-15

description:
Run07-RAW.xlsx
J39M


title: Hippocampus 16 weeks male Dp3Yah  control mice biological replicate1


title: Hippocampus 16 weeks male Dp3Yah  control mice biological replicate3


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate2 (reanalysis)


title: Hippocampus 16 weeks male Dp3Yah  mutant trisomic mice biological replicate4


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate3  (renalysis)


title: Hippocampus 16 weeks male Dp3Yah  mutant trisomic mice biological replicate2


title: AAH-9,AIS-8 corresponding

description:
Run07-RAW.xlsx
J38N


title: AIS-8

description:
Run07-RAW.xlsx
J38S


title: Hippocampus 16 weeks male Dp1Yey  control mice biological replicate5


title: Hippocampus 16 weeks male Dp1Yey  control mice biological replicate2


title: Hippocampus 16 weeks male Dp1Yey  control mice biological replicate3


title: AAH-9

description:
Run07-RAW.xlsx
J38H

value: AAH


title: Hippocampus 16 weeks male Dp1Yey  control mice biological replicate1

value: 16 weeks


title: Hippocampus 16 weeks male Dp3Yah  mutant trisomic mice biological replicate1

value: Hippocampus


title: AIS-7

description:
Run06-RAW.xlsx
J36S


title: Hippocampus 16 weeks male Dp1Yey  mutant trisomic mice biological replicate5

value: Male


title: MIA-14 corresponding

description:
Run06-RAW.xlsx
J35N


title: Hippocampus 16 weeks male Dp1Yey  control mice biological replicate4


title: Hippocampus 16 weeks male Dp1Yey  mutant trisomic mice biological replicate3


title: MIA-14

description:
Run06-RAW.xlsx
J35M


title: Hippocampus 16 weeks male Dp1Yey  mutant trisomic mice biological replicate4


title: Hippocampus 16 weeks male Dp1Rhr  mutant trisomic mice biological replicate5


title: AIS-7 corresponding

description:
Run06-RAW.xlsx
J36N


title: Hippocampus 16 weeks male Dp1Rhr  mutant trisomic mice biological replicate1


title: Hippocampus 16 weeks male Dp1Yey  mutant trisomic mice biological replicate2


title: Hippocampus 16 weeks male Dp1Yey  mutant trisomic mice biological replicate1


title: MIA-13

description:
Run06-RAW.xlsx
J34M


title: MIA-13 corresponding

description:
Run06-RAW.xlsx
J34N


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate5


title: Hippocampus 16 weeks male Dp1Rhr  mutant trisomic mice biological replicate2


title: miRNA-TPP-rep2

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

description: miRNA Sample 58

data_processing:
For mRNA seq, reads were evaluated by FastQC v0.11.3 to detect major sequencing problems, and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA-seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 (GRCz10) genome
For mRNA seq, the Bioconductor package, edgeR v3.26.0, was used to normalize gene counts and determine differential expression
For miRNA, reads were evaluated by FastQC v0.11.3 to detect major sequencing problems, and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA-seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 (GRCz10) genome
For miRNA, the Bioconductor package, edgeR v3.26.0, was used to normalize miRNA gene counts and determine expression
Genome_build: GRz10 for mRNA
Supplementary_files_format_and_content: DGE_rlog_TMM_normalized_counts_FRC_mRNA.tab is a tab-delimited text files include TMM-normalized values for each Sample
Supplementary_files_format_and_content: Combined_HTSeq-count_table_FRC_mRNA.tab is a tab-delimited text files contain raw gene counts for every gene and every sample
Supplementary_files_format_and_content: DGE_rlog_transformed_counts_FRC_miRNA.tab is a tab-delimited text file with transformed miRNA counts for each sample
Supplementary_files_format_and_content: Count_matrix_FRC_miRNA.tab is a tab-delimited text file with miRNA counts for each sample

organism: Danio rerio

source_name: zebrafish whole embryos

extract_protocol:
FRC-exposed embryos were homogenzied in RNAzol (4 replicates per treatment) and total RNA was extracted using the Direct-zol MiniPrep kit. Total RNA was then processed for library preparation
mRNA and small RNA libraries were prepared using the PrepX™ mRNA and Illumina TruSeq Small RNA library kit respectively.
Illumina HiSeq 3000, single end, 100 bp for mRNA and 50 bp for small RNA

treatment_protocol: Embryos were treated with EC80 or limit concentrations of FRCs from 6 to 48 hpf.

tag: developmental stage

value: 48 h post fertilization

value: TPP


title: miRNA-TPP-rep1

description: miRNA Sample 57


title: miRNA-TiBP-rep4

description: miRNA Sample 52

value: TiBP


title: miRNA-TPP-rep4

description: miRNA Sample 60


title: miRNA-TiBP-rep2

description: miRNA Sample 50


title: miRNA-TiBP-rep3

description: miRNA Sample 51


title: miRNA-TiBP-rep1

description: miRNA Sample 49


title: miRNA-TPP-rep3

description: miRNA Sample 59


title: Hippocampus 16 weeks male Dp1Rhr  mutant trisomic mice biological replicate4

value: Mut


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate4

value: WT


title: Hippocampus 16 weeks male Dp1Rhr  mutant trisomic mice biological replicate3


title: MIA-12

description:
Run06-RAW.xlsx
J33M

value: Lung

value: MIA


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate1


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate3


title: 097-013_V6

data_processing:
Reads aligning to rDNA,tRNA, mtrDNA using BOWTIE2 were filtered.
Reads not aligning to rDNA,tRNA,mtrDNA were aligned using STAR (v2.37a, Index Homo Sapiens (human-hg38 genome assembly, whole genome
Aligned reads quantified to annoation model Partek E/M) using GENCODE Genes release 26
Features were filtered excluding features where maximum counts was <=20.0
Data were normalized by adding 1 to all counts and using the TMM normalization method implemented with Partek-flow software version 9.0.20.0622
Genome_build: human-hg38 genome assembly
Supplementary_files_format_and_content: csv

extract_protocol:
QIAGEN Rneasy
Illumina stranded mRNA TruSEQ

tag: visit

tag: treatmentarm

value: Tetanus mo(0) + ALVAC mo(1,2,4,7) & AIDSVAX B/E mo(4,7) + HepB mo(7.5,8.5,13)

value: FALSE


title: miRNA-TBPH-rep1

description: miRNA Sample 21

value: TBPH


title: miRNA-TBPH-rep2

description: miRNA Sample 22


title: miRNA-TCEP-rep1

description: miRNA Sample 69

value: TCEP


title: miRNA-TCEP-rep3

description: miRNA Sample 71


title: miRNA-TBPH-rep3

description: miRNA Sample 23


title: miRNA-TCEP-rep4

description: miRNA Sample 72


title: miRNA-TCEP-rep2

description: miRNA Sample 70


title: AAH-8,MIA-11,corresponding

description:
Run04-RAW.xlsx
J32N

value: N


title: AAH-8

description:
Run04-RAW.xlsx
J32H


title: miRNA-TBPH-rep4

description: miRNA Sample 24


title: AIS-6

description:
Run06-RAW.xlsx
J31S

value: AIS


title: MIA-12 corresponding

description:
Run06-RAW.xlsx
J33N


title: miRNA-TDBPP-rep3

description: miRNA Sample 47

value: TDBPP


title: miRNA-TDBPP-rep1

description: miRNA Sample 45


title: AIS-6 corresponding

description:
Run06-RAW.xlsx
J31N


title: miRNA-TDBPP-rep4

description: miRNA Sample 48


title: MIA-11

description:
Run04-RAW.xlsx
J32M


title: miRNA-TDBPP-rep2

description: miRNA Sample 46


title: AAH-7 corresponding

description:
Run05-RAW.xlsx
J30N


title: AAH-7

description:
Run05-RAW.xlsx
J30H

value: AAH


title: 097-013_V3

tag: bmi


title: AAH-5,AAH-6,AIS-5,MIA-10 corresponding

description:
Run05-RAW.xlsx
J27N


title: MIA-10

description:
Run05-RAW.xlsx
J27M


title: AAH-5

description:
Run05-RAW.xlsx
J27H


title: MIA-9 corresponding

description:
Run04-RAW.xlsx
J26N


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate2

value: 16 weeks

value: Hippocampus


title: Hippocampus 16 weeks male Dp1Rhr Dp5Yah  Dp5/Dp1  control mice biological replicate3 (reanalysis)

value: Male


title: miRNA-TCPP-rep4

description: miRNA Sample 28

value: 48 h post fertilization

value: TCPP


title: miRNA-TCPP-rep3

description: miRNA Sample 27


title: MIA-9

description:
Run04-RAW.xlsx
J26M


title: miRNA-TBBPA-DBPE-rep1

description: miRNA Sample 65


title: miRNA-BDE-47-rep1

description: miRNA Sample 41


title: miRNA-TCPP-rep2

description: miRNA Sample 26


title: miRNA-IPP-rep2

description: miRNA Sample 54

value: IPP


title: miRNA-BDE-47-rep2

description: miRNA Sample 42


title: miRNA-BDE-47-rep4

description: miRNA Sample 44


title: AIS-5

description:
Run05-RAW.xlsx
J27S


title: miRNA-TBBPA-rep2

description: miRNA Sample 18

value: TBBPA


title: miRNA-TBBPA-rep4

description: miRNA Sample 20


title: miRNA-TBBPA-rep3

description: miRNA Sample 19


title: miRNA-IPP-rep1

description: miRNA Sample 53


title: miRNA-TBBPA-DBPE-rep2

description: miRNA Sample 66


title: AIS-4 corresponding

description:
Run04-RAW.xlsx
J25N

value: Lung


title: miRNA-TCPP-rep1

description: miRNA Sample 25


title: miRNA-TBBPA-rep1

description: miRNA Sample 17


title: AIS-4

description:
Run04-RAW.xlsx
J25S


title: miRNA-BDE-47-rep3

description: miRNA Sample 43


title: miRNA-IPP-rep4

description: miRNA Sample 56


title: miRNA-TBBPA-DBPE-rep3

description: miRNA Sample 67


title: miRNA-TBBPA-DBPE-rep4

description: miRNA Sample 68


title: miRNA-Control-rep4

description: miRNA Sample 4

value: Control


title: miRNA-IPP-rep3

description: miRNA Sample 55


title: AAH-4 corresponding

description:
Run04-RAW.xlsx
J24N


title: miRNA-Control-rep3

description: miRNA Sample 3


title: miRNA-Control-rep1

description: miRNA Sample 1


title: AAH-4

description:
Run04-RAW.xlsx
J24H


title: mRNA-TCEP-rep3

description: mRNA Sample 71


title: mRNA-TCEP-rep2

description: mRNA Sample 70


title: MIA-7 corresponding

description:
Run03-RAW.xlsx
J22N


title: MIA-7

description:
Run03-RAW.xlsx
J22M

value: MIA


title: AAH-6

description:
Run05-RAW.xlsx
J27H


title: mRNA-TCEP-rep1

description: mRNA Sample 69


title: mRNA-TBBPA-DBPE-rep2

description: mRNA Sample 66


title: mRNA-TBBPA-DBPE-rep4

description: mRNA Sample 68


title: mRNA-TBBPA-DBPE-rep3

description: mRNA Sample 67


title: mRNA-TPP-rep4

description: mRNA Sample 60

value: TPP


title: mRNA-TPP-rep2

description: mRNA Sample 58


title: mRNA-TBBPA-DBPE-rep1

description: mRNA Sample 65


title: MIA-8

description:
Run04-RAW.xlsx
J23M


title: mRNA-TPP-rep1

description: mRNA Sample 57


title: miRNA-Control-rep2

description: miRNA Sample 2


title: mRNA-TCEP-rep4

description: mRNA Sample 72


title: MIA-6

description:
Run03-RAW.xlsx
J21M


title: mRNA-IPP-rep4

description: mRNA Sample 56


title: AAH-3,MIA-6 corresponding

description:
Run03-RAW.xlsx
J21N


title: mRNA-IPP-rep2

description: mRNA Sample 54


title: mRNA-IPP-rep1

description: mRNA Sample 53


title: mRNA-IPP-rep3

description: mRNA Sample 55


title: AIS-3 corresponding

description:
Run03-RAW.xlsx
J20N


title: MIA-8 corresponding

description:
Run04-RAW.xlsx
J23N


title: mRNA-TiBP-rep2

description: mRNA Sample 50

value: TiBP


title: mRNA-TiBP-rep3

description: mRNA Sample 51


title: mRNA-TPP-rep3

description: mRNA Sample 59


title: AAH-3

description:
Run03-RAW.xlsx
J21H


title: mRNA-TiBP-rep1

description: mRNA Sample 49


title: AIS-3

description:
Run03-RAW.xlsx
J20S


title: mRNA-TiBP-rep4

description: mRNA Sample 52


title: mRNA-TDBPP-rep2

description: mRNA Sample 46


title: mRNA-TDBPP-rep1

description: mRNA Sample 45


title: mRNA-TDBPP-rep4

description: mRNA Sample 48


title: AAH-2,AIS-2 corresponding

description:
Run03-RAW.xlsx
J19N


title: AIS-2

description:
Run03-RAW.xlsx
J19S


title: mRNA-TDBPP-rep3

description: mRNA Sample 47


title: MIA-5

description:
Run03-RAW.xlsx
J18M


title: AAH-2

description:
Run03-RAW.xlsx
J19H


title: mRNA-BDE-47-rep2

description: mRNA Sample 42


title: mRNA-BDE-47-rep4

description: mRNA Sample 44


title: AAH-1 corresponding

description:
Run02-RAW.xlsx
J17N


title: AAH-1

description:
Run02-RAW.xlsx
J17H


title: mRNA-BDE-47-rep1

description: mRNA Sample 41


title: mRNA-TBPH-rep3

description: mRNA Sample 23

value: TBPH


title: mRNA-TCPP-rep2

description: mRNA Sample 26


title: mRNA-TCPP-rep1

description: mRNA Sample 25


title: mRNA-TCPP-rep3

description: mRNA Sample 27


title: mRNA-TBPH-rep4

description: mRNA Sample 24


title: mRNA-TBPH-rep1

description: mRNA Sample 21


title: MIA-4 corresponding

description:
Run02-RAW.xlsx
J16N

value: N


title: MIA-4

description:
Run02-RAW.xlsx
J16M


title: mRNA-TBBPA-rep4

description: mRNA Sample 20


title: mRNA-BDE-47-rep3

description: mRNA Sample 43


title: mRNA-TBBPA-rep3

description: mRNA Sample 19


title: mRNA-TBBPA-rep2

description: mRNA Sample 18


title: MIA-3 corresponding

description:
Run02-RAW.xlsx
J15N


title: MIA-5 corresponding

description:
Run03-RAW.xlsx
J18N


title: mRNA-TBPH-rep2

description: mRNA Sample 22


title: mRNA-TCPP-rep4

description: mRNA Sample 28


title: mRNA-TBBPA-rep1

description: mRNA Sample 17


title: MIA-3

description:
Run02-RAW.xlsx
J15M


title: mRNA-Control-rep3

description: mRNA Sample 3


title: mRNA-Control-rep2

description: mRNA Sample 2


title: mRNA-Control-rep4

description: mRNA Sample 4


title: MIA-2 corresponding

description:
Run02-RAW.xlsx
J14N


title: mRNA-Control-rep1

description: mRNA Sample 1


title: MIA-2

description:
Run02-RAW.xlsx
J14M


title: MIA-1 corresponding

description:
Run02-RAW.xlsx
J13N


title: AIS-1 corresponding

description:
Run02-RAW.xlsx
J11N


title: MIA-1

description:
Run02-RAW.xlsx
J13M


title: tra1Q3_CASP_1

city: London

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to C. albicans whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Genome_build: Candida albicans SC5314 reference genome (assembly 21)
Supplementary_files_format_and_content: Raw gene counts table for every gene and every sample
Supplementary_files_format_and_content: Normalized counts text files for each gene for each sample

organism: Candida albicans

source_name: C. albicans RNA

growth_protocol: Overnight cultures were diluted to an OD600 = 0.1 and grown for two hours with or without treatment

extract_protocol:
RNA samples were then extracted using the Geneaid Presto Mini Yeast Kit No. RBYD050 following manufacturer's protocol
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

treatment_protocol: 10 ng/mL caspofungin

value: caspofungin


title: WT_CASP_2


title: WT_CASP_1


title: tra1Q3_ND_3

value: control


title: tra1Q3_ND_1


title: tra1Q3_CASP_2


title: WT_CASP_3


title: tra1Q3_ND_2


title: WT_ND_3


title: AIS-1

description:
Run02-RAW.xlsx
J11S

value: AIS


title: ADC-6 corresponding

description:
Run01-RAW.xlsx
J9N


title: ADC-6

description:
Run01-RAW.xlsx
J9C

value: ADC


title: Bax_Null_Atoh7_Null_rep2

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Bax Null; Atoh7 Null

data_processing:
Demux and generation of fastq files using default parameters from Cellranger v1.2.1 or v2.2.0 mkfastq; Alignment of .fastq files using Cellranger v1.2.1 or v2.2.0 count with refdata-cellranger-mm10 as a reference index; count matrices were manually aggregated and used as input to Monocle2 single cell RNAseq framework
Genome_build: mm10 (refdata-cellranger-mm10)
Supplementary_files_format_and_content: Expression Matrix of aggregated datasets
Supplementary_files_format_and_content: Gene features of aggregated datasets
Supplementary_files_format_and_content: Cell Feautres of aggregated datasets

source_name: Retinal Cells

extract_protocol: 10x Genomics 3' single cell RNAseq v2

value: E14 Bax/Atoh7 double mutant


title: Bax_Null_Atoh7_Null_rep1

description: Bax Null; Atoh7 Null


title: Bax_Null_rep2

description: Bax Null; Atoh7 WT

value: E14 Bax mutant


title: WT_ND_1


title: WT_ND_2


title: Nor rep2 [circRNA, lncRNA, mRNA]

city: Shenzhen

first: Yuqi

last: Wu

state: Guangdong

address: Xueyuan Road 1098

institute: Shenzhen University

description:
S_2N2
gene_sample_FPKM_with_symbol.txt

data_processing:
The paired-end sequencing mode of the Illumina Hiseq 3000 sequencing platform was used for high-throughput sequencing of multiple samples, and the Fastp software was used to remove the adapter sequence fragments and low-quality fragments. BWA software was used to compare the preprocessed data with the rRNA sequence database.
Use STAR software to compare the preprocessed sequence with the reference genome sequence of the sequenced species, and use RSEQC to count the data.
From Reads comparison to reference genome results, StringTie software is used to assemble the transcripts in the sample. According to the sequence coverage depth information of the connecting region between Exon region and Exon, construct the most likely mRNA structure and estimate its expression level.
According to the definition of lncRNA, a series of screenings were performed on the transcripts assembled by StringTie. Known long-chain non-coding transcript information comes from the Ensembl database.
For the previous STAR comparison results, CIRCexplorer2 software was used to predict the front and back positions of the circular RNA.
The expression of transcripts is calculated using FPKM (FPKM-Fragments Per Kilobase of transcript per Million fragments mapped).
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/rattus_norvegicus/dna/
Supplementary_files_format_and_content: gene_sample_FPKM_with_symbol.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Testicular tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Illumina® TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 3000 following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Testicular tissue

value: Sprague-Dawley

value: Normal


title: ADC-5

description:
Run01-RAW.xlsx
J8C


title: tra1Q3_CASP_3


title: Nor rep3 [circRNA, lncRNA, mRNA]

description:
S_2N3
gene_sample_FPKM_with_symbol.txt


title: DM rep3 [circRNA, lncRNA, mRNA]

description:
S_2D3
gene_sample_FPKM_with_symbol.txt

value: STZ-induced diabetes


title: Bax_Null_rep1

description: Bax Null; Atoh7 WT


title: DM rep2 [circRNA, lncRNA, mRNA]

description:
S_2D2
gene_sample_FPKM_with_symbol.txt


title: Subset_Tn

city: La Jolla

first: Stanislav

last: Dikiy

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

data_processing:
Trim adapter sequences, removed unpaired reads; Trimmomatic v0.36; options: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Align reads to genome; STAR v2.5.4b; options: --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.55 --outFilterMatchNmin 30 --alignIntronMax 1 --alignEndsType Local
Sort by name; samtools v1.10; options: sort -@ 4 -n
Fix mate information; samtools v1.10; options: fixmate -rm
Sort by coordinate; samtools v1.10; options: sort -@ 4
Remove duplicate reads; samtools v1.10; options: markdup -l 1500 -r -d 100
Sort by name; samtools v1.10; options: sort -@ 4 -n
Convert bam to bedgraph and scale for library size; bedtools v2.26.0; options bedtools genomecov -bg -scale -g mm10.genome
Convert bedgraph to bigWig; wigToBigWig; options: wigToBigWig -clip mm10.genome
Genome_build: mm10
Supplementary_files_format_and_content: bigWig format: continuous graph of aligned read density across genome (indexed)

source_name: lymph node and spleen

extract_protocol:
Combined protocol for extraction and library preparation, see below
cells were pelleted in a fixed rotor benchtop centrifuge at 500g for 5 minutes at 4°C. Cells were then washed in 1ml cold 1x PBS and pelleted again. Supernatant was aspirated and cells were resuspended in 50µl ice-cold cell lysis buffer (10mM Tris-Cl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40) to disrupt plasma membranes. Nuclei were pelleted at 1000g for 10 minutes. Supernatant was aspirated and nuclei were resuspended in 50µl transposition reaction mixture (25µl TD buffer; 2.5µl TDE1; 22.5µl ddH2O; llumina, 20034197). Samples were incubated in a ThermoMixer at 1100rpm for 45 minutes at 42°C. DNA was then purified using a MinElute PCR Purification Kit (QIAGEN, 28004), per manufacturer instructions. DNA was eluted in 10µl buffer EB. Libraries were then barcoded and amplified with NEBNext High-Fidelity Master Mix and primers from (Buenrostro et al., 2013) (50µl reaction with 10µl DNA and 2.5µl of 25µM primers – 1 cycle of 5min at 72°C, 30sec at 98°C; 5 cycles of 10sec at 98°C, 20sec at 63°C, 1min at 72°C). A qPCR on the product determined that an additional 7 cycles (10sec at 98°C, 20sec at 63°C, 1min at 72°C) were required. Library was purified and size selected with AMPure beads (Beckman Coulter, A63881): 45µl of PCR product was incubated with 18µl beads and supernatant was collected (beads bound larger >2000bp fragments). Supernatant (63µl) was then incubated with an additional 63µl of beads for 5 minutes, supernatant was removed, beads were washed 2x with 75% ethanol, and DNA was eluted into 50µl H2O by incubating for 2 minutes.

tag: cell type

value: Naive CD4 T cell

value: lymph node and spleen


title: Subset_aTreg

value: activated regulatory T cell


title: Bax_het_Atoh7_Null_rep2

description: Bax het; Atoh7 Null

value: E14 Atoh7 mutant


title: ADC-4 corresponding

description:
Run01-RAW.xlsx
J7N

value: Lung


title: Nor rep1 [circRNA, lncRNA, mRNA]

description:
S_2N1
gene_sample_FPKM_with_symbol.txt


title: ADC-4

description:
Run01-RAW.xlsx
J7C


title: ADC-3 correspomding

description:
Run01-RAW.xlsx
J5N


title: Bax_het_Atoh7_Null_rep1

description: Bax het; Atoh7 Null


title: Subset_DN4

source_name: thymus

value: Double negative #4 thymocyte

value: thymus


title: Vector control 2

city: Copenhagen

first: Cord

middle: Herbert

last: Brakebusch

address: Ole Maaløes Vej 5, Biocentret, Building: 1-3-14

country: Denmark

institute: Biotech Research and Innovation Centre

data_processing:
The software ZebraCall v2 (version 0.5.6.153) was used for base-calling
Reads were trimmed by removing those  (1) with adaptor sequences, (2) with > 10% unknown bases and (3) and those with low quality bases (of sequencing quality score of <5)
Bowtie2 was used to map the clean reads to reference gene and HISAT to the reference genome GRCh38.p11
Genes expression level is quantified by the software package RSEM (Li and Dewey 2011) and output as FPKM values
Differentially expressed genes were screened by NOISeq with the following criteria: Foldchange ≥2 and diverge probability ≥0.8.
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: txt file with raw gene counts in FPKM for every gene and every sample

extract_protocol:
Subconfluent cultures of cells were lysed and RNA extracted by standard protocol using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
Libraries were prepared by BGI genomics using standard protocol for the BGISEQ-500 platform

value: Epithelial

value: Mammary gland; derived from metastatic site

tag: cell line

value: Vector control


title: ADC-5 corresponding

description:
Run01-RAW.xlsx
J8N

value: N


title: C22-PD5-C9-TGF-3

city: Seoul

first: Ho-Geun

last: Yoon

address: 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: C22_siPDCD5_TGF-beta1 24h

growth_protocol: Mouse clara C22 cell line derived  from transgenic H-2Kb-tsA58 mice capable of being passaged as an immortalised cloned cell line in culture. Cells grow at 33 ºC in the presence of gamma-interferon, at 39ºC in the absence of gamma-interferon cells terminally differentiate.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Differentiated cells were starved serum for 2 hours, 20ng/ml TGF-beta1 was added and incubated for 24 hours.

value: Mouse lung clara cell line

tag: genotype/variation

value: TGF-beta1 24h


title: DM rep1 [circRNA, lncRNA, mRNA]

description:
S_2D1
gene_sample_FPKM_with_symbol.txt

value: Testicular tissue


title: ADC-2 corresponding

description:
Run01-RAW.xlsx
J3N


title: Subset_DP

value: Double positive thymocyte


title: Subset_DN3

value: Double negative #3 thymocyte


title: C22-PD5-C9-TGF-2


title: Vector control 1


title: CDC42BPA/CDC42BPB Double Knockout 2

value: CDC42BPA/CDC42BPB Double Knockout


title: ADC-2

description:
Run01-RAW.xlsx
J3C

value: ADC


title: CDC42BPA/CDC42BPB Double Knockout 1


title: C22-PD5-C9-TGF-1


title: Subset_DN1

value: Double negative #1 thymocyte


title: C22-PD5-C9-3

value: control


title: Subset_CD4SP

value: CD4 single positive thymocyte


title: ADC-1

description:
Run01-RAW.xlsx
J2C

value: Lung


title: CDC42BPB Knockout 1

value: CDC42BPB Knockout


title: C22-PD5-C9-2


title: CDC42BPA Knockout 1

value: CDC42BPA Knockout