title: bacterial culture_20h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 20 hours; biological replicate #4
Sample name: 20h4


title: HSC-MPP-c

status: Public on Mar 27 2019

type: SRA

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: transcriptomic

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat software.
RNA-Seq: The mapping parameter ‘-g 1’ was used to allow one alignment to the reference for a given read
RNA-Seq: The featureCounts software was used to count reads on the basis of the RefSeq gene model. CPM and RPKM expression values were calculated using a script in R
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: CPM and RPKM values from RNA sequencing

molecule: polyA RNA

organism: Homo sapiens

source_name: HSC-MPP (Bulk of 100 cells)

extract_protocol:
cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

treatment_protocol: Cells from human bone marrow of healthy adult donors were isolated by FACS

tag: cell type

value: HSC-MPP

tag: tissue

value: Bone marrow

tag: disease

value: healthy

tag: phenotype

value: Lin- CD34+ CD38- CD45RA-


title: bacterial culture_20h biol rep1

city: Madison

first: Tippapha

last: Pisithkul

state: Wisconsin

address: 1550 Linden Drive

department: Bacteriology

country: USA

institute: UW-Madison

description:
B. subtilis grown in a biofilm-inducing medium for 20 hours; biological replicate #1
Sample name: 20h1

data_processing:
Bacillus subtilis NCIB3610 chromosome (GenBank accession number: CP020102.1) and plasmid pBS32 (GenBank accession number: NZ_CP020103.1) were concatenated into a single FASTA file.
100 base single-end reads were aligned to the sequences in the resulting FASTA file using BWA-MEM version 0.7.15
Alignment files were prepared using SAMtools, version 1.3.1
The number of reads aligning to each coding sequence was determined using the summarize overlaps function from the R package GenomicAlignments, with the arguments ignore.strand = TRUE and mode = “IntersectionNotEmpty”.
Read count normalization and calculation of differential expression was performed using a combination of the R package edgeR and the voomWithQualityWeights function from the R package limma.
Calculation of false discovery rate was performed by the method of Benjamini and Hochberg.
Genome_build: Bacillus subtilis NCIB3610 chromosome (GenBank accession number: CP020102.1) and plasmid pBS32 (GenBank accession number: NZ_CP020103.1)
Supplementary_files_format_and_content: RPKMs

molecule: total RNA

organism: Bacillus subtilis

source_name: bacterial culture

growth_protocol: Bacillus subtilis strain NCIB3610 was maintained on Luria-Bertani (LB) agar plates. Floating biofilms (pellicles) were grown in modified MSgg medium adjusted to pH 6.8 ± 0.05. The modified MSgg contains 2% (v/v) glycerol, 1% (w/v) glutamate, 5 mM potassium phosphate (pH 7), 5 mM MOPS (pH 7), 2 mM MgCl2, 700 uM CaCl2, 50 uM MnCl2, 50 uM FeCl3, 1 uM ZnCl2, and 2 uM thiamine. Pellicles were grown in a 12-well polystyrene plate format at 37°C. Each well contained 4.5 mL culture volume with a custom-made stainless-steel mesh. Samples were collected every 4 hours from 8 to 32 hours after inoculation (in a 1:1000 dilution) from a late exponential LB culture (OD600 ~ 1.0-1.5) into MSgg.

extract_protocol:
Planktonic cells and/or pellicles (4 biological replicates per sample) were washed in -20°C cold methanol (50% (v/v) final concentration) and subject to centrifugation. The supernatant was discarded while the pellet was immediately freeze-dried using liquid nitrogen and stored at -80°C until extraction. To extract RNA, the pellet (volume of approximately 100 μL) was thawed on ice and resuspended in 200 μL of lysozyme-TE (10 mM Tris-Cl, pH 7.5; 1mM EDTA, pH 8) by vortexing before a 20 min-incubation at 37°C. RNA in the resultant mixture was extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) as per manufacturer’s instructions. Residual DNA was enzymatically removed using DNase (RNase-Free DNase Set; QIAGEN).
Total RNA was verified for purity and integrity via the NanoDrop2000 Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that meet the Illumina sample input guidelines were then prepared according the TruSeq® RNA Preparation Guide. For each sample’s TruSeq RNA library preparation, 1 μg of total RNA was ribosomally reduced using the RiboZeroTM rRNA Removal (Bacteria) kit (Illumina, San Diego, CA, USA). rRNA-depleted samples were purified with Agencourt RNAClean XP Beads (Beckman Coulter, Indianapolis, IN, USA). Subsequently, rRNA-depleted samples were fragmented using divalent cations under elevated temperature and immediately reversed transcribed into double-stranded (ds) cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. The ds cDNA was purified by paramagnetic beads, end-repaired by T4 DNA polymerase and Klenow DNA Polymerase, and phosphorylated by T4 polynucleotide kinase. The blunt ended cDNA was purified by paramagnetic beads and then incubated with Klenow DNA Polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments. DNA fragments were ligated to Illumina adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated products were purified by paramagnetic beads. Products of the ligation were PCR-amplified with PhusionTM DNA Polymerase using Illumina's genomic DNA primer set and purified by paramagnetic beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were standardized to 2μM. Cluster generation was performed using standard Cluster Kits (v3) and the Illumina cBot. Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer. Images were analyzed using the standard Illumina Pipeline, version 1.8.2.

tag: strain

tag: treatment

value: grown in a biofilm-inducing medium

tag: developmental stage

value: biofilm

tag: time


title: bacterial culture_16h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 16 hours; biological replicate #4
Sample name: 16h4


title: bacterial culture_20h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 20 hours; biological replicate #2
Sample name: 20h2


title: CMP-CD114-c

source_name: CMP-CD114 (Bulk of 100 cells)


title: bacterial culture_16h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 16 hours; biological replicate #3
Sample name: 16h3


title: CMP-CD114-b


title: bacterial culture_16h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 16 hours; biological replicate #2
Sample name: 16h2


title: CMP-CD114-d


title: CMP-CD114-a


title: MEP_93_33513487

source_name: MEP

value: MEP


title: bacterial culture_16h biol rep1

description:
B. subtilis grown in a biofilm-inducing medium for 16 hours; biological replicate #1
Sample name: 16h1


title: bacterial culture_12h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 12 hours; biological replicate #3
Sample name: 12h3


title: MEP_92_33511483


title: bacterial culture_12h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 12 hours; biological replicate #4
Sample name: 12h4


title: CMP-CD131-d

source_name: CMP-CD131 (Bulk of 100 cells)


title: bacterial culture_12h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 12 hours; biological replicate #2
Sample name: 12h2


title: MEP_89_33512485


title: bacterial culture_12h biol rep1

description:
B. subtilis grown in a biofilm-inducing medium for 12 hours; biological replicate #1
Sample name: 12h1


title: MEP_86_33509479


title: MEP_84_33495563


title: bacterial culture_8h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 8 hours; biological replicate #3
Sample name: 8h3

value: planktonic


title: CMP-CD131-a


title: MEP_83_33512483


title: bacterial culture_8h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 8 hours; biological replicate #4
Sample name: 8h4


title: MEP_384_34441574


title: MEP_81_33509478


title: bacterial culture_8h biol rep1

description:
B. subtilis grown in a biofilm-inducing medium for 8 hours; biological replicate #1
Sample name: 8h1


title: bacterial culture_8h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 8 hours; biological replicate #2
Sample name: 8h2


title: MEP_382_34438605


title: MEP_381_34436600


title: MEP_90_33515487


title: MEP_378_34449559


title: MEP_379_34438604


title: MEP_380_34439576


title: muSOX replicate 1

city: Amherst

first: Mandy

last: Muller

state: MA

address: 639 North Pleasant Street, 101 Morrill IVN

department: Microbiology

institute: University of Massachusetts, Amherst

data_processing:
Using Galaxy, reads were then aligned to the human genome (hg38) by Bowtie2
differential expression analysis were performed using Cufflink and Cuffdiff2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include average (over replicates) FPKM values for each Sample

growth_protocol: 293T cells (ATCC) were grown in DMEM (Invitrogen) supplemented with 10% FBS, routinely passaged and transfected using PolyJet

extract_protocol:
RNA extraction by Trizol
Poly A selection, RNA check on Bioanalyzer and standard library prep

tag: cell line

tag: genotype/variation

value: muSOX


title: SOX Replicate 2

value: SOX


title: BGLF5 Replicate 1


title: vhs Replicate 2

value: vhs


title: muSOX Replicate 2


title: BGLF5 replicate 2


title: vhs Replicate 1


title: MEP_286_33963975


title: MEP_285_33963973


title: Mock Replicate 2

value: Mock


title: SOX Replicate 1


title: MEP_284_33961993


title: MEP_282_33945044


title: MEP_186_34585643


title: MEP_190_34602620


title: MEP_181_34608595


title: MEP_185_34605606


title: MEP_182_34590650


title: MEP_180_34602617


title: MEP_178_34590648


title: GMP_77_33495562

source_name: GMP

value: GMP


title: GMP_74_33491559


title: GMP_70_33513483


title: GMP_68_33515482


title: GMP_76_33493551


title: GMP_69_33492565


title: GMP_67_33492564


title: GMP_66_33505540


title: GMP_65_33505539


title: Mock Replicate 1


title: GMP_374_34452526


title: GMP_375_34460512


title: GMP_373_34438602


title: ChIPseq of clr4D ade6+, replicate 2, H3K9 ChIPs input

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
smallRNA-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
Genome_build: Spombe.ASM294v2.24
Supplementary_files_format_and_content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures was grown exponentially in YES media at 30 degrees celsius

extract_protocol:
Exponentially growing S.pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).

tag: genotype

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ clr4D


title: MEP_281_33964950


title: ChIPseq of paf1+ ade6si3, replicate 3, H3K9 ChIPs input

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 2, H3K9 ChIPs input

value: h-  leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3 paf1-Q264Stop::kanMX


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 1, H3K9 ChIPs input


title: GMP_371_34450568


title: GMP_370_34450567


title: GMP_369_34462517


title: MEP_177_34605604


title: GMP_280_33949005


title: ChIPseq of paf1+ ade6si3, replicate 1, H3K9 ChIPs input


title: ChIPseq of paf1+ ade6+, replicate 3, H3K9 ChIPs input


title: ChIPseq of paf1+ ade6+, replicate 2, H3K9 ChIPs input


title: GMP_279_33954991


title: GMP_278_33955990


title: ChIPseq of clr4D ade6+, replicate 1, H3K9 ChIPs input


title: GMP_376_34437604


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 3, H3K9 ChIPs input


title: GMP_277_33947044


title: ChIPseq of clr4D ade6+, replicate 1, H3K9me3


title: ChIPseq of clr4D ade6+, replicate 2, H3K9me3


title: GMP_276_33949003


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 3, H3K9me3


title: GMP_275_33957991


title: GMP_174_34600612


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 2, H3K9me3


title: ChIPseq of paf1+ ade6si3, replicate 3, H3K9me3


title: GMP_173_34590647


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 1, H3K9me3


title: GMP_170_34586643


title: ChIPseq of paf1+ ade6si3, replicate 2, H3K9me3


title: GMP_169_34585638


title: ChIPseq of paf1+ ade6+, replicate 3, H3K9me3


title: GMP_165_34608590


title: ChIPseq of paf1+ ade6+, replicate 2, H3K9me3


title: GMP_164_34584645


title: GMP_166_34600607


title: ChIPseq of paf1+ ade6si3, replicate 2, H3K9 ChIPs input


title: ChIPseq of paf1+ ade6+, replicate 1, H3K9 ChIPs input


title: ChIPseq of paf1+ ade6si3, replicate 1, H3K9me3


title: GMP_163_34608587


title: ChIPseq of paf1+ ade6+, replicate 1, H3K9me3


title: ChIPseq of clr4D ade6+, replicate 2, H3K9me2


title: GMP_161_34597608


title: ChIPseq of clr4D ade6+, replicate 1, H3K9me2


title: CMP_62_33493549

source_name: CMP

value: CMP


title: GMP_162_34586642


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 3, H3K9me2


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 2, H3K9me2


title: CMP_61_33496545


title: ChIPseq of paf1-Q264Stop ade6si3, replicate 1, H3K9me2


title: ChIPseq of paf1+ ade6si3, replicate 3, H3K9me2


title: CMP_60_33504518


title: CMP_58_33488570


title: CMP_56_33498543


title: NMG_5

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Microglia of C57BL/6JRj mice

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.38 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

organism: Mus musculus

source_name: Brain

extract_protocol: All Methods listed in Van Hove et al.  A single-cell atlas of non-parenchymal brain macrophages reveals unique transcriptional identities that are shaped by ontogeny and tissue environment.  Nature Neuroscience. 2019.

value: Microglia


title: ChIPseq of paf1+ ade6+, replicate 3, H3K9me2


title: ChIPseq of paf1+ ade6si3, replicate 2, H3K9me2


title: ChIPseq of paf1+ ade6si3, replicate 1, H3K9me2


title: ChIPseq of paf1+ ade6+, replicate 2, H3K9me2


title: CMP_57_33495559

value: Bone marrow


title: CMP_59_33511482

value: healthy


title: CMP_55_33493547


title: ChIPseq of paf1+ ade6+, replicate 1, H3K9me2


title: OsRUS1-OX rep2

city: Guangzhou

first: Xuewen

last: Hou

state: Guangdong

address: NO 483 Wushan Road, Tianhe District

department: Department of Plant Sciences, College of Life Sciences

country: China

institute: South China Agricultural University

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, then mapped to rice whole genome using Tophat v2.0.12 with parameters mismatch = 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Expected number of Fragments Per Kilobase of transcript sequence per Millions (FPKM) were calculated using a protocol from Trapnell, Cole, et al., Nature Biotechnology, 2010.
Genome_build: Oryza sativa Japonica Group (assembly Build 4.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa

source_name: flag leaves

growth_protocol: Rice plants were cultivated in the experimental field under natural growth conditions. Field management adhered to normal agricultural practices.

extract_protocol:
Total RNAs of ZH-11 and OsRUS1-OX flag leaves were extracted using the TIANGEN RNAprep Pure Plant Kit, and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 3 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When ZH-11 and OsRUS1-OX plants were at the heading stage, the flag leaves were collected on a sunny summer day (11:00 am, WT with expanded leaves, OsRUS1-OX with rolled leaves) with triplicate. Samples were flash frozen in liquid nitrogen, then stored in -80℃ until use.

tag: cultivar

value: flag leaves

tag: condition

value: 11 am, sunlight, leaf rolled


title: CMP_51_33488567


title: CMP_52_33491553


title: CMP_54_33491554


title: CMP_50_33512480


title: OsRUS1-OX rep1


title: CMP_48_33514481


title: WT rep1

value: 11 am, sunlight, leaf expanded


title: CMP_49_33498542


title: WT rep3


title: WT rep2


title: CMP_45_33512479


title: CMP_41_33479588


title: CMP_43_33510477


title: CMP_42_33488566


title: OsRUS1-OX rep3


title: CMP_38_33499550


title: CMP_39_33495554


title: CMP_37_33485603


title: CMP_368_34449558


title: CMP_367_34458527


title: CMP_40_33485605


title: CD64Cre/+  x Irf8fl/fl choroid plexux

description: CD64Cre/+  x Irf8fl/fl choroid plexux of CD64Cre/+ x Irf8fl/fl mice

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq
Demultiplexed data was then processed using the Cell Ranger count pipeline
8bp I7 sample barcode
26bp read1 (16bp Chromium barcode and 10bp UMI)
98bp read2 (transcript)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output CellRanger Count) for each sample

source_name: choroid plexus

value: CD64Cre/+  x Irf8fl/fl

value: choroid plexux

value: CD64Cre/+ x Irf8fl/fl

tag: platform

value: 10x Genomics

tag: number of cells


title: 16 months APP/PS1 whole brain

description: 16 months APP/PS1 whole brain of APPPS1 B6-Tg(Thy1-APPswe; Thy1-PS1 L166P) mice

source_name: brain

value: whole brain


title: 16 months WT whole brain

description: 16 months WT whole brain of APPPS1 B6-Tg(Thy1-APPswe; Thy1-PS1 L166P) mice

value: WT


title: 9 months APP/PS1 whole brain

description: 9 months APP/PS1 whole brain of APPPS1 B6-Tg(Thy1-APPswe; Thy1-PS1 L166P) mice


title: WT whole brain

description: WT whole brain of C57BL/6JRj mice


title: CMP_366_34451542


title: CMP_365_34449557


title: WT enriched subdural meninges

description: WT enriched subdural meninges of C57BL/6JRj mice

source_name: enriched subdural meninges

value: enriched subdural meninges


title: CMP_36_33480575


title: WT dura

description: WT dura of C57BL/6JRj mice

source_name: dura mater

value: dura


title: CMP_47_33495556


title: CD64+/+ x Irf8fl/fl  choroid plexus

description: CD64+/+ x Irf8fl/fl  choroid plexus of CD64+/+ x Irf8fl/fl mice

value: CD64+/+ x Irf8fl/fl

value: choroid plexus


title: Lmx1b-conditional-control_103031-001-005

city: Amsterdam

first: Marten

middle: Piet

last: Smidt

state: NH

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UVA

description:
neuronal material
103031-001-005

data_processing:
adapter trimming and quality filtering
aligments (tophat 1.0.14/Bowtie 2.1.0)
mRNAseq readcounting (Htseq-count 0.6.1p1)
differential expression analysis ko vs wt
Deseq 1.10.1 (R) for selection of differential expressed genes (0)
Genome_build: Mus musculus (GRCm38p4 Fasta and GFT format)
Supplementary_files_format_and_content: txt file, all genes with statistics

source_name: Midbrain dissected material E14.5

extract_protocol:
Dissected midbrain material from E14.5 mouse embryo’s, total RNA extraction (trizol)
RNAseq library construction from Total RNA samples (1-6) (Illumina “preparing samples for sequencing of mRNA” Rev. A ,September 2008)

treatment_protocol: Lmx1b-fl/fl; Pitx3-Cre vs Lmx1b-wt/wt;Pitx3-Cre

value: midbrain

value: Lmx1b wt/wt;Pitx3-Cre

tag: background strain


title: CMP_358_34439572

value: CMP

value: Bone marrow


title: CMP_46_33499552

value: healthy


title: Lmx1b-conditional-control_103031-001-006

description:
neuronal material
103031-001-006


title: Lmx1b-conditional-control_103031-001-004

description:
neuronal material
103031-001-004


title: Lmx1b-conditional-ko_103031-001-003

description:
neuronal material
103031-001-003

value: Lmx1b fl/fl;Pitx3-Cre driven conditional ko


title: Lmx1b-conditional-ko_103031-001-002

description:
neuronal material
103031-001-002


title: CMP_355_34436599


title: CMP_357_34443589


title: CMP_356_34466439


title: CMP_354_34439582


title: Expt. 2 Injured Mouse (LPS), Type II Alveolar cells, technical rep. 2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
3241ATII5
count_matrix.tsv.gz
cell_metadata.tsv.gz

data_processing:
UMI count matrices were generated using the 10x genomics cellranger count(2.1.1) pipeline with default parameters. The count matrices were normalized by downsampling to the lowest read count libraries using cellranger aggr. The aggregated matrix was then further filtered to exclude cells not passing the following QC measures: at least 100 genes detected (UMI > 0), number of UMIs less than 3 times that standard deviation of UMIs expressed per sample, and proportion of UMIs derived from mitochondia less than 35%. Genes were also excluded  if they were not expressed in at least  3 cells (UMI count > 0). After filtering, this matrix was used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original non-downsampled UMI data was used for all analysis and is provided as the count_matrix.tsv.gz. EGFP counts were generated by mapping reads unaligned to the mm10 genome to the eGFP cDNA using bowtie2 (--very-sensitive-local mode).
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

source_name: Injured Type II Lung Epithelial Cells

growth_protocol: Animals were maintained in a pathogen-free environment on a 12 h light/dark cycle with full access to food and water.

extract_protocol:
Briefly, lungs were perfused with 10 ml of PBS at 20 cm H20, lavaged twice with 1 ml PBS + 5mM EDTA + 5 mM EGTA, twice with RPMI 1640 + 25 mM HEPES, and once with 4.5 U/ml elastase (Worthington #LS00229) in RPMI with 25 mM HEPES. Next, 2 ml of elastase 4.5 U/ml was instilled into the lungs, followed immediately with 500 ul of 1% low melting point agarose. Lungs were submerged into 2 ml elastase 4.5 U/ml and incubated for 45 m at 37⁰C. The trachea and bronchial tree were dissected off, and lung tissue was submerged in 5 ml ice cold FBS with 0.2 mg/ml DNAse (Sigma #DN25). Tissue was minced to ~0.5-1 mm3 fragments with scissors, shaken vigorously for 2 m, and filtered over 100, 40, and 20 um filters consecutively. Cell suspension was centrifuged at 350 g for 12 m at 4⁰C onto a percoll cushion. Cell pellet was resuspended in 30 ul DNAse (4 mg/ml), and 300 ul RPMI + 25 mM HEPES + 20% FBS was added. Cells were stained with anti-T1α PE-Cy7 (eBioscience #25-5381), anti-EPCAM-647 (Biolegend #118212), and CD45-A700 (ebioscience #56-0451-80) antibodies with FcBlock (BD Pharmingen #553142) for 60 m at 4⁰C. DAPI (Thermo #62248) 1 ug/ml was added. Cells were sorted on a Moflo XDP (Beckman). Gates were drawn based on FMO controls. DAPI- Tomato- GFP+ cells and DAPI- Tomato+ GFP- CD45- EpCAM+ T1α+ cells were collected. Cells were processed using the 10x chromium platform to generate single cell RNA-Seq libraries, which were sequenced on the Illumina HiSeq. Technical replicates are defined as the same cell suspension split into two separate wells for the 10x genomics single cell capture.
library construction protocol: 10x Genomics 3' end library kit

treatment_protocol: SPCCreERT2+/-;mTmG+/- mice were administered tamoxifen 20 mg/ml in corn oil at a dose of 0.25 mg / g body weight i.p. every other day for 3 doses at age 6 wk. At 12 wk of age, SPCCreERT2+/-;mTmG+/-  mice were treated with 40 μg LPS (E. coli 0111:B4; List Biological Laboratories) in 50 μl 0.9% saline by i.t. instillation or left untreated. Mice were euthanized 7 days later.

value: Injured Type II Lung Epithelial Cells


title: Lmx1b-conditional-ko_103031-001-001

description:
neuronal material
103031-001-001


title: CMP_352_34440599


title: CMP_353_34437611


title: Expt. 2 Injured Mouse (LPS), Type II Alveolar cells, technical rep. 1

description:
3241ATII4
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: CMP_363_34441571


title: Expt. 2 Control Mouse, Type II Alveolar cells

description:
3242ATII3
count_matrix.tsv.gz
cell_metadata.tsv.gz

source_name: Control Type II Lung Epithelial Cells

value: Control Type II Lung Epithelial Cells


title: CMP_350_34437599


title: Expt. 2 Control Mouse, Non-Type II Lung Epithelial cells, technical rep. 2

description:
3242ATI2
count_matrix.tsv.gz
cell_metadata.tsv.gz

source_name: Control Non-Type II Lung Epithelial Cells


title: CMP_348_34456546


title: Expt. 1 Injured Mouse (LPS), Type II Alveolar cells, technical rep. 1

description:
3162-ATII-4
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: CMP_349_34437610


title: Expt. 2 Control Mouse, Non-Type II Lung epithelial cells, technical rep. 1

description:
3242ATI1
count_matrix.tsv.gz
cell_metadata.tsv.gz

value: Control Non-Type II Lung Epithelial Cells


title: Expt. 1 Injured Mouse (LPS), Type II Alveolar cells, technical rep. 2

description:
3162-ATIII-5
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: CMP_346_34459534


title: CMP_347_34460506


title: CMP_359_34458525


title: Expt. 1 Control Mouse, Non-Type II lung epithelial cells, technical rep. 2

description:
3161-ATII-2
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: Expt. 1 Control Mouse, Type II Alveolar cells

description:
3161-ATII-3
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: Expt. 1 Control Mouse, Non Type II lung epithelial cells, technical rep. 1

description:
3161-ATII-1
count_matrix.tsv.gz
cell_metadata.tsv.gz


title: CMP_343_34437597


title: CMP_342_34462515


title: CMP_339_34452523


title: CMP_34_33492557


title: CMP_341_34451533


title: ctrl-1

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: In-vitro

growth_protocol: Male or female, 8-12 week old NOD.Cg-PrkdcscidIl2rgtmWjl/SzJ (NSG) mice were injected intravenously with 0.5e6 FFLuc-GFP NALM6 NALM6 leukaemia cell line. Four days later, 0.2e6, CAR T cells were administered i.v. by tail vein injection. NALM6 cells were stored in Trizol (LS) before RNA extraction. For in vitro and ex-vivo experiments, cells were cultured in RMPI/10%FBS.

extract_protocol:
RNA were extracted using Trizol standard protocol
After ribogreen quantification and quality control on bioAnalyser, 500ng of total RNA underwent library preparation using the Truseq Stranded Total RNA library preparation chemistry (Illumina), with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 51 million paired reads were generated per sample and the percent of mRNA bases was 58% on average.

treatment_protocol: Mice bearing NALM6 leukaemia cell line line were treated with 2e5 19BBζ CAR T cells


title: ctrl-2


title: M6-D6

source_name: ex-vivo

tag: mice strain

value: NOD.Cg-PrkdcscidIl2rgtmWjl/SzJ (NSG)


title: CMP_351_34441568

tag: cell type


title: ctrl-3


title: M7-D6


title: CMP_338_34439581

tag: tissue


title: M4-D6


title: CMP_336_34452522

tag: disease


title: CMP_335_34438610

tag: phenotype


title: CMP_334_34450564


title: M3-D6


title: M5-D6


title: M2-D6


title: CMP_333_34460504


title: M1-D6


title: CMP_332_34443583


title: M6-D0

source_name: Relapse

value: 19-BB[zeta] CAR T cells


title: M7-D0


title: CMP_331_34449561


title: CMP_330_34460503


title: M4-D0


title: CMP_337_34442586


title: M5-D0


title: CMP_33_33493543


title: CMP_327_34440597


title: M3-D0


title: CMP_328_34443582


title: CMP_326_34437609


title: M2-D0


title: M1-D0


title: CMP_324_34438609


title: CMP_323_34441565


title: CMP_322_34452518


title: CMP_321_34440596


title: Dox_Bortz_2

city: Cambridge

first: Peter

last: Tsvetkov

address: 455 Main St

institute: Whitehead Institute

data_processing:
RNASeq reads were aligned using STAR (v2.5.4b) using default parameters (except --sjdbOverhang 39 ) to the human genome (GRCh37) with Ensembl annotation (GRCh37.87) in gtf format.
featureCounts (v1.6.1) was used with default parameters except for -s 2 (reversely stranded)
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from featureCounts

source_name: breast

growth_protocol: T47D cells were grown to 70% confluency the shPSMD2 was induced with 0.2ug/ml of doxycycline for 3 days . Cells were then spit into media lacking Dox and after 24 hours treated with with either DMSO or 20nM Bortezomib. Samples were collecte dafter 16 hours for RNA extraction.

extract_protocol:
cells were collected and extracted using Trizol reagent.
RNAseq libraries were prepared using the TruSeq stranded polyA mRNA kits as described by the manufacturer (Illumina RS-122-2101).

treatment_protocol: Cells treated with DMSO or 20nM Bortezomib for 16 hours

tag: shRNA

value: Dox induced shPSMD2

tag: agent

value: 20nM Bortezomib


title: Dox_Bortz_1


title: Control_bortz_1

value: uninduced shPSMD2


title: CMP_32_33481574


title: Control_bortz_2


title: Control_bortz_3


title: Dox_3

value: DMSO


title: CMP_319_34456545


title: Dox_2


title: Dox_1


title: Control_3


title: CMP_317_34436592


title: CMP_314_34442583


title: CMP_312_34437608


title: CMP_325_34459533


title: Control_2


title: CMP_313_34462513


title: Dox_Bortz_3


title: Control_1


title: CMP_311_34441576


title: Delayed group - Bortezomib+Elesclomol 2

data_processing:
RNASeq reads were aligned using STAR (v2.5.4b )using default parameters (except --sjdbOverhang 39 ) to the human genome (GRCh37) with Ensembl annotation (GRCh37.87) in gtf format.
featureCounts (v1.6.1) was used with default parameters except for -s 2 (reversely stranded)
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from featureCounts

source_name: bone marrow

growth_protocol: MM.1S gfp+/luc+ were cultivated in RPMI supplemented with 10% FBS and 1%P/S media. 3 millions cells were injected intravenously in SCID-beige mice. Mice were randomly included in the study when their tumors reached 10^7 radians intensity by BLI measurents.

extract_protocol:
At mice paralysis, a bone marrow flushing from the femurs was performed. Cell pelletS were then frozen at -80C upon collection of all samples and later RNA was extracted using Trizol.
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold following manufacturer’s instructions (Illumina RS-122-2301).

treatment_protocol: Mice were randomly attributed a group of treatment (n=5 per group). Control group was IV injected once a week 200 uL saline solution; Bortezomib (0.25 mg/kg, 100 uL) was IP injected first day of the week, once a week until death of the animal. Elesclomol (25 mg/kg, 100 uL) was subcutaneously injected every 3rd day of the week until death of the animal. Elesclomol+Bortezomib group were treated similarly to previous groups. The delayed group started the Elesclomol treatment 14 days after the inclusion of the animal in the study. Endpoint of the study was dictated by either limb-paralysis of the animal or severe toxicity induced by the treatment as per Dana-Farber Animal policy.

tag: xenografts host mice

value: SCID-beige mice

value: Delayed group - Bortezomib+Elesclomol


title: Delayed group - Bortezomib+Elesclomol 3


title: Delayed group - Bortezomib+Elesclomol 1


title: Bortezomib+Elesclomol 3

value: Bortezomib+Elesclomol


title: CMP_308_34440595


title: CMP_31_33481573


title: CMP_320_34460513


title: CMP_310_34439580


title: CMP_307_34462512


title: Bortezomib+Elesclomol 2


title: CMP_318_34450562


title: Elesclomol 3

value: Elesclomol


title: CMP_303_34459523

value: CMP


title: CMP_304_34440602

value: Bone marrow


title: Elesclomol 1


title: CMP_302_34450561

value: healthy


title: CMP_300_34437591


title: Bortezomib 3

value: Bortezomib


title: CMP_30_33483585


title: Bortezomib 2


title: CMP_298_34452529


title: Bortezomib 1


title: PBS 1

value: PBS


title: PBS 2


title: CMP_297_34462511


title: Bortezomib+Elesclomol 1


title: CMP_299_34443595


title: CMP_296_34466434


title: CMP_293_34466444


title: Expression_vaccinee20_4th_vaccination

city: Sejong-ro,

first: Adnan

last: Khan

state: Please select

address: Jochiwon-eup, Yeongi-gun, Chungnam 30019

country: South Korea

institute: Korea University

description:
EXP:020-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

data_processing:
Illumina Casava1.7 software was used for basecalling.
Low-quality reads were filtered out according to the following criteria: (i) reads containing more than 10% of skipped bases, (ii) reads containing more than 40% of bases with quality scores less than 20, and (iii) reads with average quality scores of each read of less than 20. The whole filtering process was performed using in-house scripts.
Filtered reads were mapped to the mouse reference genome (Ensembl release 77), using the aligner STAR v.2.3.0e.
Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of Ensembl release.
Genes were considered differentially expressed when having a change of more than two-fold, with a p-value of less than or equal to 0.05., Genes or transcripts with reapeated expression of zero abundance were deleted.
bts635 (2013)).
Genome_build: mouse reference genome (Ensembl release 77)
Supplementary_files_format_and_content: tab-delimited text files include relative abundance (FPKM) of each gene for each Sample

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from blood samples using standard Ficoll-Paque (GE Healthcare, Little Chalfont UK) with density gradient centrifugation.
RNA libraries were prepared using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA)

tag: age

tag: gender

value: F

tag: vaccination administration

value: 4th vaccination

tag: response to vaccination (prnt50)

value: High

value: Peripheral blood derived mononuclear cells


title: Elesclomol 2

tag: cell line


title: CMP_294_34460500

source_name: CMP


title: Expression_vaccinee20_3rd_vaccination

description:
EXP:020-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: 3rd vaccination


title: Expression_vaccinee20_2nd_vaccination

description:
EXP:020-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: 2nd vaccination


title: CMP_292_34466443


title: Expression_vaccinee20_pre_vaccination

description:
EXP:020-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: Pre vaccination


title: CMP_291_34438606


title: Expression_vaccinee19_2nd_vaccination

description:
EXP:019-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: M


title: Expression_vaccinee19_3rd_vaccination

description:
EXP:019-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee18_4th_vaccination

description:
EXP:018-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_29_33499549


title: Expression_vaccinee19_pre_vaccination

description:
EXP:019-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_289_34437588


title: PBS 3

value: SCID-beige mice


title: Expression_vaccinee18_3rd_vaccination

description:
EXP:018-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_272_33954988


title: Expression_vaccinee18_2nd_vaccination

description:
EXP:018-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_28_33492556


title: CMP_270_33965944


title: Expression_vaccinee17_3rd_vaccination

description:
EXP:017-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: Low


title: Expression_vaccinee18_pre_vaccination

description:
EXP:018-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_27_33480573


title: Expression_vaccinee17_4th_vaccination

description:
EXP:017-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_295_34456543


title: CMP_269_33961985


title: Expression_vaccinee17_pre_vaccination

description:
EXP:017-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee17_2nd_vaccination

description:
EXP:017-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_290_34437589


title: CMP_266_33953972


title: CMP_265_33967953


title: Expression_vaccinee16_3rd_vaccination

description:
EXP:016-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_267_33967954


title: Expression_vaccinee16_4th_vaccination

description:
EXP:016-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_264_33969942


title: CMP_263_33964947


title: Expression_vaccinee15_4th_vaccination

description:
EXP:015-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_262_33965942


title: Expression_vaccinee15_3rd_vaccination

description:
EXP:015-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_261_33957989


title: CMP_271_33961987


title: Expression_vaccinee15_pre_vaccination

description:
EXP:015-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_260_33950009


title: Expression_vaccinee14_4th_vaccination

description:
EXP:014-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_257_33966943


title: CMP_259_33946021


title: Expression_vaccinee14_3rd_vaccination

description:
EXP:014-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_258_33950007


title: CMP_256_33962981


title: Expression_vaccinee13_3rd_vaccination

description:
EXP:013-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee14_2nd_vaccination

description:
EXP:014-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee13_2nd_vaccination

description:
EXP:013-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee14_pre_vaccination

description:
EXP:014-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_255_33954983


title: Expression_vaccinee16_pre_vaccination

description:
EXP:016-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_25_33496541


title: CMP_250_33959992


title: CMP_253_33965938


title: CMP_252_33957987


title: Expression_vaccinee16_2nd_vaccination

description:
EXP:016-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_251_33954982


title: Expression_vaccinee13_pre_vaccination

description:
EXP:013-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee13_4th_vaccination

description:
EXP:013-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee12_4th_vaccination

description:
EXP:012-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee15_2nd_vaccination

description:
EXP:015-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_249_33954981


title: Expression_vaccinee12_3rd_vaccination

description:
EXP:012-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee12_2nd_vaccination

description:
EXP:012-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: CMP_248_33967950


title: Expression_vaccinee12_pre_vaccination

description:
EXP:012-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: CMP_247_33955984


title: Expression_vaccinee11_4th_vaccination

description:
EXP:011-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_244_33945034


title: Expression_vaccinee11_3rd_vaccination

description:
EXP:011-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee11_pre_vaccination

description:
EXP:011-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_306_34439568


title: CMP_242_33966937


title: Expression_vaccinee10_2nd_vaccination

description:
EXP:010-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee11_2nd_vaccination

description:
EXP:011-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_237_33963963


title: CMP_243_33945033


title: CMP_240_33959990


title: Expression_vaccinee10_4th_vaccination

description:
EXP:010-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_239_33947036


title: CMP_236_33961977


title: CMP_238_33963964


title: Expression_vaccinee09_2nd_vaccination

description:
EXP:009-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee09_3rd_vaccination

description:
EXP:009-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee10_3rd_vaccination

description:
EXP:010-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee09_4th_vaccination

description:
EXP:009-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_246_33966939


title: CMP_234_33959987


title: Expression_vaccinee09_pre_vaccination

description:
EXP:009-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_245_33957986


title: Expression_vaccinee08_4th_vaccination

description:
EXP:008-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: Expression_vaccinee10_pre_vaccination

description:
EXP:010-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_233_33959986


title: CMP_23_33491549


title: CMP_223_33967945


title: Expression_vaccinee08_3rd_vaccination

description:
EXP:008-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: CMP_235_33967946


title: cordBlood_TNrev_rep3

type: RNA

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description: Gene expression of naive CD8 T cells from human cord blood, activated then maintained for 8 days in 25ng/ml IL-7

hyb_protocol: 600 ng of labeled RNA was hybridized to SurePrint G3 Human 8x60K microarray slides (Agilent)

scan_protocol: Slides were scanned with a High Resolution C Scanner (Agilent), using a scan resolution of 3 mm

data_processing: Feature extraction was performed using Feature Extraction Software (Agilent) using default parameters

source_name: Cord blood, naïve CD8, Anti-CD3 activated, 25ng/ml IL-7  replicate 3

label_protocol: 25ng of each source sample RNA was labeled with Cy3 dye using the Low Input Quick Amp Labelling Kit (Agilent). A specific activity of greater than 6.0 was confirmed by measurement with a spectrophotometer

growth_protocol: TN cells were enriched by immunomagnetic separation. Activation and de-differentiation was carried out in RPMI 1640 supplemented with 10% foetal bovine serum. Cultures were incubated  at 37 C in a humidified incubator with 5% CO2.

extract_protocol: RNA extraction was performed using RNeasy columns (Qiagen, Hilden, Germany). Source RNA was confirmed as high quality by use of a Bioanalyzer 2100 (Agilent). RNA Integrity Numbers of 6.0 were confirmed for all samples using a RNA 6000 Pico Chip kit (Agilent) Technologies, Santa Clara, CA, USA)

treatment_protocol: Gene expression analysis was performed on cells from 3 human cord blood samples, i.e. 3 freshly enriched CD8+ TN samples and 3 samples of CD8+ TN cells which had been activated with anti CD3 plus 300 U/ml IL-2, and after 6 days maintained for further 13 days in  25 ng/mL IL-7

value: Cord Blood

value: activated CD8 T cells reverted to a naive-like phenotype


title: CMP_221_33965937

value: CMP


title: Expression_vaccinee07_4th_vaccination

description:
EXP:007-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: HEART Input control

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

data_processing:
Base calling
RNAseq Plugin Ion Torrent
Alignment
Bowtie 2
Galaxy Version 2.3.2.2 Default settings
Peak Calling
MACS2 callpeak
Galaxy Version 2.1.1.20160309.3 Upper Mfold bound 50 Bandwidth 300bp peaks detection based on q-value FDR 0.05
Genome_build: Mouse mm10 (GRCm38 dec 2011)
Supplementary_files_format_and_content: bigwig

source_name: HsaCrexThraTag

extract_protocol: Qiagen RNA easy, Ion ChIP-Seq Library Preparation on the Ion Proton System including Ion Xpress Plus Fragment Library Preparation Kit

treatment_protocol: Heart was obtained HSA-Cre x ThraTag transgenic mice at post-natal day 15. This transgenic model expresses a tagged version of the TRalpha1 nuclear receptor only in cardiomyocytes.

value: Post-natal day 15

tag: genotype/variation

value: HsaCrexThraTag


title: Expression_vaccinee08_pre_vaccination

description:
EXP:008-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt


title: HEART [chAP17]

tag: antibody

value: Tralpha


title: HEART [chAP16]


title: cordBlood_TN_rep2

description: Gene expression of naïve CD8 T cells from human cord blood

source_name: Cord blood, naïve CD8, replicate 2

value: naive CD8+ T cells


title: cordBlood_TN_rep3

source_name: Cord blood, naïve CD8, replicate 3


title: cordBlood_TNrev_rep1

source_name: Cord blood, naïve CD8, Anti-CD3 activated, 25ng/ml IL-7  replicate 1


title: cordBlood_TNrev_rep2

source_name: Cord blood, naïve CD8, Anti-CD3 activated, 25ng/ml IL-7  replicate 2


title: fWBI Animal 5, Hippocampus

city: Winston-Salem

first: Rachel

middle: N

last: Andrews

state: North Carolina

address: Medical Center Boulevard

department: Pathology, Section on Comparative Medicine

institute: Wake Forest University

description:
Sample 44
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

data_processing:
Raw read quality was assessed by FASTQC analysis (Babraham Bioinformatics). Uniquely mapped reads ranged from 21M-36M reads per sample.
Reads with >Q20 quality score were aligned to the Ensembl Macaca mulatta genome build Mmul_1 using the STAR aligner.
Gene counts determined by featureCounts software.
Differentially expressed genes (DEGs) were identified by DESeq2, irradiated groups were compared to thorax-only irradiated controls.
Genome_build: Mmul_1
Supplementary_files_format_and_content: Counts_All.txt: Tab-delimited matrix of raw counts generated by featureCounts.

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Animals were humanely euthanized in accordance with the American Veterinary Medical Association’s Guidelines on Euthanasia by deep anesthesia with pentobarbital, followed by exsanguination and perfusion of the vascular system with 2 liters of cold normal saline. The brain was removed intact, and sectioned coronally in 4 mm intervals using a stainless steel brain matrix with cutting guides. Sections were immediately frozen on dry ice. 100 mg of brain tissue was homogenized in QIAzol lysis reagent, and aliquots of homogenized lysates equivalent to 40 mg tissue were extracted for total RNA using the RNeasy Microarray Tissue Mini kit (Qiagen). Extracted RNA was DNase-treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research), then assessed for RNA quality using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies). RIN values for the RNA samples ranged from 7.1 to 9.3.
Total RNA was used to prepare cDNA libraries using the Illumina® TruSeq Stranded Total RNA with Ribo-Zero Gold Preparation kit (Illumina Inc.) and the SciClone NGS Work Station (Perkin Elmer).

tag: brain sub-region tissue

value: Hippocampus

tag: irradiation group

value: Fractionated whole brain irradiation

tag: radiation dose to brain

value: 40 Gy, (8x5 Gray fractions)

tag: animal

value: fWBI Animal 5


title: fWBI Animal 4, White Matter

description:
Sample 42
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: White matter, centrum semiovale

value: fWBI Animal 4


title: CMP_222_33947034

tag: cell type

tag: tissue

value: Bone marrow

value: healthy


title: CMP_220_33946015

tag: disease

tag: phenotype


title: fWBI Animal 5, Prefrontal Cortex

description:
Sample 43
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Dorsolateral prefrontal cortex, Brodmann Area 46


title: fWBI Animal 4, Hippocampus

description:
Sample 41
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_22_33485600


title: Expression_vaccinee07_3rd_vaccination

description:
EXP:007-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: M

value: 3rd vaccination

value: Peripheral blood derived mononuclear cells


title: cordBlood_TN_rep1

source_name: Cord blood, naïve CD8, replicate 1

value: Cord Blood


title: Expression_vaccinee07_2nd_vaccination

description:
EXP:007-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: 2nd vaccination


title: fWBI Animal 5, White Matter

description:
Sample 45
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: HEART [chAP15]

value: Post-natal day 15

value: HsaCrexThraTag


title: fWBI Animal 3, Hippocampus

description:
Sample 38
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: fWBI Animal 3


title: Expression_vaccinee08_2nd_vaccination

description:
EXP:008-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: High


title: CMP_219_33948999

value: CMP


title: fWBI Animal 3, White Matter

description:
Sample 39
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Fractionated whole brain irradiation

value: 40 Gy, (8x5 Gray fractions)


title: Expression_vaccinee07_pre_vaccination

description:
EXP:007-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: Pre vaccination


title: fWBI Animal 4, Prefrontal Cortex

description:
Sample 40
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: fWBI Animal 4


title: Expression_vaccinee06_4th_vaccination

description:
EXP:006-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: F

value: 4th vaccination

value: Low


title: CMP_216_33945031

value: Bone marrow

value: healthy


title: fWBI Animal 1, Hippocampus

description:
Sample 32
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Hippocampus

value: fWBI Animal 1


title: CMP_218_33961975


title: CMP_215_33954976


title: Expression_vaccinee06_2nd_vaccination

description:
EXP:006-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: 2nd vaccination

value: Peripheral blood derived mononuclear cells


title: fWBI Animal 2, Hippocampus

description:
Sample 35
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: fWBI Animal 2


title: TBI Animal 5, White Matter

description:
Sample 30
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: White matter, centrum semiovale

value: Total body irradiation

value: TBI Animal 5


title: fWBI Animal 2, Prefrontal Cortex

description:
Sample 34
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Dorsolateral prefrontal cortex, Brodmann Area 46

value: Fractionated whole brain irradiation


title: fWBI Animal 2, White Matter

description:
Sample 36
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: 40 Gy, (8x5 Gray fractions)


title: Expression_vaccinee06_pre_vaccination

description:
EXP:006-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: Pre vaccination


title: fWBI Animal 1, White Matter

description:
Sample 33
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: Expression_vaccinee06_3rd_vaccination

description:
EXP:006-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: F

value: 3rd vaccination


title: TBI Animal 5, Prefrontal Cortex

description:
Sample 28
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_214_33955981

value: CMP


title: fWBI Animal 1, Prefrontal Cortex

description:
Sample 31
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_213_33948998

value: Bone marrow


title: TBI Animal 5, Hippocampus

description:
Sample 29
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: Expression_vaccinee05_4th_vaccination

description:
EXP:005-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: M

value: 4th vaccination


title: TBI Animal 4, White Matter

description:
Sample 27
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: 7.2 Gray

value: TBI Animal 4


title: TBI Animal 3, White Matter

description:
Sample 24
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: TBI Animal 3


title: CMP_212_33959985

value: healthy


title: TBI Animal 4, Hippocampus

description:
Sample 26
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Hippocampus


title: fWBI Animal 3, Prefrontal Cortex

description:
Sample 37
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: fWBI Animal 3


title: Expression_vaccinee05_3rd_vaccination

description:
EXP:005-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: Peripheral blood derived mononuclear cells


title: CMP_211_33967942


title: TBI Animal 4, Prefrontal Cortex

description:
Sample 25
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Dorsolateral prefrontal cortex, Brodmann Area 46

value: Total body irradiation


title: CMP_210_33966935


title: TBI Animal 3, Hippocampus

description:
Sample 23
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: TBI Animal 2, Prefrontal Cortex

description:
Sample 19
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: 6.75 Gray

value: TBI Animal 2


title: TBI Animal 3, Prefrontal Cortex

description:
Sample 22
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: TBI Animal 2, White Matter

description:
Sample 21
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: White matter, centrum semiovale


title: Expression_vaccinee05_2nd_vaccination

description:
EXP:005-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: 2nd vaccination


title: TBI Animal 2, Hippocampus

description:
Sample 20
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: TBI Animal 1, Hippocampus

description:
Sample 17
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: TBI Animal 1


title: Expression_vaccinee04_4th_vaccination

description:
EXP:004-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: F


title: CMP_209_33965935

value: CMP

value: Bone marrow


title: CMP_21_33484591


title: Expression_vaccinee05_pre_vaccination

description:
EXP:005-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: M

value: Pre vaccination


title: TBI Animal 1, White Matter

description:
Sample 18
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: Expression_vaccinee04_2nd_vaccination

description:
EXP:004-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: TBI Animal 1, Prefrontal Cortex

description:
Sample 16
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_208_33962975


title: Control Animal 5, Hippocampus

description:
Sample 14
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Thoracic irradiation only, control

value: 0.1 Gray

value: Control Animal 5


title: Expression_vaccinee04_pre_vaccination

description:
EXP:004-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Control Animal 5, White Matter

description:
Sample 15
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: Expression_vaccinee19_4th_vaccination

description:
EXP:019-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: 4th vaccination


title: Control Animal 4, White Matter

description:
Sample 12
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Control Animal 4


title: Expression_vaccinee02_4th_vaccination

description:
EXP:002-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: High

value: Peripheral blood derived mononuclear cells


title: Control Animal 4, Hippocampus

description:
Sample 11
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Hippocampus


title: CMP_204_33962973

value: healthy


title: CMP_206_33955979


title: Control Animal 4, Prefrontal Cortex

description:
Sample 10
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Dorsolateral prefrontal cortex, Brodmann Area 46


title: Control Animal 3, White Matter

description:
Sample 9
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: White matter, centrum semiovale

value: Control Animal 3


title: Expression_vaccinee02_3rd_vaccination

description:
EXP:002-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: F

value: 3rd vaccination


title: Expression_vaccinee04_3rd_vaccination

description:
EXP:004-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: Expression_vaccinee02_2nd_vaccination

description:
EXP:002-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: 2nd vaccination


title: CMP_202_33953967

value: CMP

value: Bone marrow


title: Control Animal 3, Prefrontal Cortex

description:
Sample 7
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Thoracic irradiation only, control


title: Control Animal 3, Hippocampus

description:
Sample 8
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: 0.1 Gray


title: CMP_203_33942019


title: Expression_vaccinee02_pre_vaccination

description:
EXP:002-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt
Gene_age_distributed_4th_vaccinees.txt
Dose_dependent_gene_with_PRNTab.txt

value: Pre vaccination


title: Control Animal 2, Hippocampus

description:
Sample 5
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Control Animal 2


title: Control Animal 2, White Matter

description:
Sample 6
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_207_33955980


title: Control Animal 1, White Matter

description:
Sample 3
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Control Animal 1


title: Control Animal 5, Prefrontal Cortex

description:
Sample 13
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Control Animal 5


title: CMP_201_33967937


title: Expression_vaccinee01_3rd_vaccination

description:
EXP:001-3:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: Low

value: Peripheral blood derived mononuclear cells


title: Control Animal 1, Prefrontal Cortex

description:
Sample 1
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt


title: CMP_20_33492554

value: healthy


title: Expression_vaccinee01_4th_vaccination

description:
EXP:001-4:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt

value: 4th vaccination


title: Expression_vaccinee01_2nd_vaccination

description:
EXP:001-2:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_199_33942016


title: Expression_vaccinee01_pre_vaccination

description:
EXP:001-1:FPKM
expression.transcripts.txt
expression.genes.txt
Up_DEGs_HRs_vs_NRs+LRs.txt
Up_DEGs_HRs.txt


title: CMP_198_33967936


title: CMP_200_33942018


title: CMP_197_33967935


title: CMP_196_33965933


title: Control Animal 1, Hippocampus

description:
Sample 2
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Hippocampus


title: Control Animal 2, Prefrontal Cortex

description:
Sample 4
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt

value: Dorsolateral prefrontal cortex, Brodmann Area 46


title: CMP_195_33942015


title: RME632_Blastocyst_ZFP708KO_2: Maternal ZFP708 Knockout Blastocysts RNA-Seq (rep2)

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Raw reads were aligned to the mm9 genome using STAR 2.4.2a (using options --sjdbGTFfile Mus_musculus.Ensembl.NCBIM37.65.gtf --sjdbOverhang $((lng - 1)) --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --twopassMode Basic).
Bam files were sorted with samtools sort and indexed with samtools index.
The number of reads mapping to each gene was quantified with htseq-count (using options --order=pos --format=bam --stranded=reverse) on features from the gtf file Mus_musculus.Ensembl.NCBIM37.65.gtf.
The raw counts of reads were then imported to DEseq2 in R to perform the differential expression analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts from DeSeq2

source_name: Maternal ZFP708 Knockout Blastocysts

growth_protocol: Embryos were isolated at indicate times and directly processed for RNA-seq. All datasets are produced from single embryos except blastocysts, for which 10 embryos were pooled for each replicate. Embryonic stem cells were cultured under standard LIF/FCS conditions.

extract_protocol: total RNA extraction

treatment_protocol: no treatment

tag: genotype

value: ZFP708 maternal null

value: Maternal ZFP708 Knockout Blastocysts


title: CMP_194_33959978

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat software.
RNA-Seq: The mapping parameter ‘-g 1’ was used to allow one alignment to the reference for a given read
RNA-Seq: The featureCounts software was used to count reads on the basis of the RefSeq gene model. CPM and RPKM expression values were calculated using a script in R
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: CPM and RPKM values from RNA sequencing


title: SAMPLE 9: Astragalus membranaceus H3

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description: replicate 3

hyb_protocol: Standard Illumina HT-12 beadchips hybridization protocol

scan_protocol: Illumina HiScan standard scanning protocol

data_processing: The raw intensity values were background corrected by RMA, normalized by quantile normalization and then transformed into log2 scale in R

label: biotin

source_name: Astragalus membranaceus 3

label_protocol: Standard Illumina HT-12 beadchips label protocol

growth_protocol: Cells were seeded at the denity of 1x10^6 per10-cm dish.

extract_protocol: RNA was extracted with Trizol reagent. The cDNA was synthesized from total RNA primed with T7 Oligo(dT) and amplified by an Illumina TotalPre RNA Amplification Kit (Ambion, Austin, USA).

treatment_protocol: Codonopsis pilosula and Astragalus embranaceus Aqueous Extracts were add 24 after seeding.

value: hepatocellular carcinoma


title: SAMPLE 8: Astragalus membranaceus H2

description: replicate 2

source_name: Astragalus membranaceus 2


title: SAMPLE 7: Astragalus membranaceus H1

description: replicate 1

source_name: Astragalus membranaceus 1


title: SAMPLE 6: Codonopsis pilosula D4

description: replicate 3

source_name: Codonopsis pilosula 3


title: RME631_Blastocyst_ZFP708KO_1: Maternal ZFP708 Knockout Blastocysts RNA-Seq (rep1)


title: CMP_193_33954972

extract_protocol:
cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

value: CMP


title: RME633_Blastocyst_ZFP708KO_3: Maternal ZFP708 Knockout Blastocysts RNA-Seq (rep3)


title: RME628_Blastocyst_WT_1: WT Blastocysts RNA-Seq (rep1)

source_name: WT Blastocysts

value: wild type

value: WT Blastocysts


title: RME629_Blastocyst_WT_2: WT Blastocysts RNA-Seq (rep2)


title: CMP_18_33485598

value: Bone marrow


title: RME803_2C_MUT_7: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 7

source_name: Maternal ZFP708 Knockout 2-Cell Embryo

value: Maternal ZFP708 Knockout 2-Cell Embryo


title: RME803_2C_MUT_8: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 7


title: T10_H322

first: Jian

last: Zhang

address: 1838 Guangzhou Blvd North

department: Department of Medical Genetics

institute: Southern Medical University

description: Gene expression in H322 cell line

hyb_protocol: Array hybridization, washing, scanning, data extraction and analyses were performed as previously described (Keita et al., 2013).

source_name: H322 cell line

label_protocol: Fluorescently labeled cDNA targets were generated from 10 μg of total RNA from each corresponding A549s cell clone following user’s manual. Agilent Gene Expression Hybridization Kit was used for hybridization according to the manufacturer’s instruction.

extract_protocol: riefly, total RNA from control and GALNT10 siRNA knockdown A549s cells were extracted in triplicates using GeneJET RNA Purification kit (Thermo Scientific) following the manufacturer’s protocol and quantified by NanoDrop spectrophotometer. The quality of the RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent).


title: SAMPLE 4: Codonopsis pilosula D1

description: replicate 1

source_name: Codonopsis pilosula 1


title: T10_A549Si

description: Gene expression of GALNT10 knockdown in A549 cell line

scan_protocol: Array hybridization, washing, scanning, data extraction and analyses were performed as previously described (Keita et al., 2013).

source_name: GALNT10 knockdown in  A549 cell line


title: T10_H322_OE

description: Gene expression of GALNT10 over-expression in H322 cell line

data_processing: Array hybridization, washing, scanning, data extraction and analyses were performed as previously described (Keita et al., 2013).

source_name: GALNT10 over-expressing in H322 cell line


title: SAMPLE 2: Ctrl C2

description: replicate 2

source_name: ctrl 2


title: SAMPLE 3: Ctrl C3

description: replicate 3

source_name: ctrl 3


title: HSD F2 female derived from HSD F0 male rep04

city: New Delhi

first: Manoj

middle: Ramesh

last: Teltumbade

state: Delhi

address: Mathura Road, Near Sukhdev Vihar, bus depo

country: India

institute: Institute of Genomics and Integrative Biology

description:
Drosophila_F2_Female_T04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was analysed using R/Bioconductor affy and limma packages. Quantile Normalization and RMA background correction was used.

organism: Drosophila melanogaster

source_name: whole fly, 14 days of treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3’ IVT Express Kit).

growth_protocol: 30 adult virgin females (and unmated males) Oregon R flies per vial fed respective diet for 14 days at 25C temperature. Media vials changed after 7 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Microarray Tissue Handbook).

treatment_protocol: At the end of treatment, flies were anesthetized using CO2 and collected in Trizol.

value: whole fly

tag: generation

tag: diet fed

value: HSD

tag: diet of ancestral f0 males

value: HSD F0 male

tag: strain/background

value: Oregon R

value: female

value: 14 days

tag: developmental stage

value: adult

tag: batch


title: RME801_2C_MUT_6: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 6


title: SAMPLE 5: Codonopsis pilosula D2

description: replicate 2

source_name: Codonopsis pilosula 2

tag: cell line


title: RME800_2C_MUT_5: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 5


title: CMP_17_33495553

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

institute: Weatheral Institute of Molecular Medicine

source_name: CMP

value: healthy


title: RME630_Blastocyst_WT_3: WT Blastocysts RNA-Seq (rep3)


title: T10_A549

description: Gene expression in A549 cell line

source_name: A549 cell line


title: RME799_2C_MUT_4: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 4


title: HSD F2 female derived from HSD F0 male rep03

description:
Drosophila_F2_Female_T03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: gender

tag: age


title: RME796_2C_MUT_1: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 1


title: RME798_2C_MUT_3: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 3


title: CMP_160_34608585


title: RME797_2C_MUT_2: Maternal ZFP708 Knockout 2-Cell Embryo RNA-seq rep 2


title: RME795_2C_WT_7: WT 2-Cell Embryo RNA-seq rep 7

source_name: WT 2-Cell Embryo

value: WT 2-Cell Embryo


title: RME792_2C_WT_4: WT 2-Cell Embryo RNA-seq rep 4


title: CMP_158_34584640


title: RME794_2C_WT_6: WT 2-Cell Embryo RNA-seq rep 6


title: HSD F2 female derived from HSD F0 male rep02

description:
Drosophila_F2_Female_T02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: RME790_2C_WT_2: WT 2-Cell Embryo RNA-seq rep 2


title: CMP_16_33481570


title: RME793_2C_WT_5: WT 2-Cell Embryo RNA-seq rep 5


title: RME791_2C_WT_3: WT 2-Cell Embryo RNA-seq rep 3


title: CMP_156_34602613


title: CMP_155_34593622


title: HSD F2 female derived from HSD F0 male rep01

description:
Drosophila_F2_Female_T01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F2 female derived from HSD F0 male rep04

description:
Drosophila_F2_Female_S04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD


title: CD F2 female derived from HSD F0 male rep03

description:
Drosophila_F2_Female_S03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_152_34597605


title: CD F2 female derived from HSD F0 male rep02

description:
Drosophila_F2_Female_S02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F2 female derived from HSD F0 male rep01

description:
Drosophila_F2_Female_S01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: RME788_ZYG_MUT_7: Maternal ZFP708 Knockout Zygote RNA-seq rep 7

source_name: Maternal ZFP708 Knockout Zygote

value: ZFP708 maternal null

value: Maternal ZFP708 Knockout Zygote


title: RME787_ZYG_MUT_6: Maternal ZFP708 Knockout Zygote RNA-seq rep 6


title: CMP_153_34584637

value: CMP


title: CMP_150_34595626


title: RME783_ZYG_MUT_2: Maternal ZFP708 Knockout Zygote RNA-seq rep 2


title: RME781_ZYG_WT_7: WT Zygote RNA-seq rep 7

source_name: WT Zygote

value: wild type

value: WT Zygote


title: RME782_ZYG_MUT_1: Maternal ZFP708 Knockout Zygote RNA-seq rep 1


title: RME789_2C_WT_1: WT 2-Cell Embryo RNA-seq rep 1


title: CMP_149_34585633

value: Bone marrow


title: SAMPLE 1: Ctrl C1

description: replicate 1

source_name: ctrl 1

value: hepatocellular carcinoma


title: RME785_ZYG_MUT_4: Maternal ZFP708 Knockout Zygote RNA-seq rep 4


title: CMP_15_33492553


title: HSD F2 male derived from HSD F0 male rep04

description:
Drosophila_F2_Male_R04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: male


title: HSD F2 male derived from HSD F0 male rep03

description:
Drosophila_F2_Male_R03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

value: HSD F0 male


title: RME786_ZYG_MUT_5: Maternal ZFP708 Knockout Zygote RNA-seq rep 5


title: RME779_ZYG_WT_5: WT Zygote RNA-seq rep 5


title: RME784_ZYG_MUT_3: Maternal ZFP708 Knockout Zygote RNA-seq rep 3


title: RME778_ZYG_WT_4: WT Zygote RNA-seq rep 4


title: RME776_ZYG_WT_2: WT Zygote RNA-seq rep 2


title: HSD F2 male derived from HSD F0 male rep02

description:
Drosophila_F2_Male_R02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: Oregon R


title: RME777_ZYG_WT_3: WT Zygote RNA-seq rep 3


title: RME774_GV_MUT_7: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep7

source_name: Maternal ZFP708 Knockout GV Oocyte

value: Maternal ZFP708 Knockout GV Oocyte


title: CMP_148_34588648


title: RME773_GV_MUT_6: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep6


title: CD F2 male derived from HSD F0 male rep04

description:
Drosophila_F2_Male_Q04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: 14 days

value: adult


title: HSD F2 male derived from HSD F0 male rep01

description:
Drosophila_F2_Male_R01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_147_34605596

value: healthy


title: RME780_ZYG_WT_6: WT Zygote RNA-seq rep 6


title: CD F2 male derived from HSD F0 male rep02

description:
Drosophila_F2_Male_Q02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD


title: CMP_146_34585631


title: RME770_GV_MUT_3: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep3

value: ZFP708 maternal null


title: RME771_GV_MUT_4: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep4


title: CMP_145_34595624


title: CMP_14_33485597


title: RME772_GV_MUT_5: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep5


title: CD F2 male derived from HSD F0 male rep01

description:
Drosophila_F2_Male_Q01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F2 male derived from HSD F0 male rep03

description:
Drosophila_F2_Male_Q03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: HSD F2 female derived from CD F0 male rep04

description:
Drosophila_F2_Female_P04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD F0 male

value: female


title: RME768_GV_MUT_1: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep1


title: RME767_GV_WT_7: WT GV Oocyte RNA-seq rep 7

source_name: WT GV Oocyte

value: wild type

value: WT GV Oocyte


title: RME769_GV_MUT_2: Maternal ZFP708 Knockout GV Oocyte RNA-seq rep2


title: RME766_GV_WT_6: WT GV Oocyte RNA-seq rep 6


title: RME775_ZYG_WT_1: WT Zygote RNA-seq rep 1

value: WT Zygote


title: CMP_136_34590639

value: CMP

value: Bone marrow


title: HSD F2 female derived from CD F0 male rep02

description:
Drosophila_F2_Female_P02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly


title: RME764_GV_WT_4: WT GV Oocyte RNA-seq rep 4


title: CMP_135_34597600


title: HSD F2 female derived from CD F0 male rep03

description:
Drosophila_F2_Female_P03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD


title: CMP_134_34608583


title: CMP_133_34597599


title: RME761_GV_WT_1: WT GV Oocyte RNA-seq rep 1


title: RME762_GV_WT_2: WT GV Oocyte RNA-seq rep 2


title: HSD F2 female derived from CD F0 male rep01

description:
Drosophila_F2_Female_P01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_131_34605591


title: RME756_ZFP708-2: FLAG-ZFP708 OE Embryonic Stem Cell RNA-seq rep 2

source_name: FLAG-ZFP708 OE Embryonic Stem Cells

value: ZFP708 overexpression

value: FLAG-ZFP708 OE Embryonic Stem Cells


title: RME757_ZFP708-3: FLAG-ZFP708 OE Embryonic Stem Cell RNA-seq rep 3


title: RME755_ZFP708-1: FLAG-ZFP708 OE Embryonic Stem Cell RNA-seq rep 1


title: CMP_130_34608582


title: RME763_GV_WT_3: WT GV Oocyte RNA-seq rep 3


title: CD F2 female derived from CD F0 male rep02

description:
Drosophila_F2_Female_O02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: Oregon R


title: CD F2 female derived from CD F0 male rep04

description:
Drosophila_F2_Female_O04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: 14 days


title: CD F2 female derived from CD F0 male rep03

description:
Drosophila_F2_Female_O03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: adult


title: RME754_ESC-3: E14 Embryonic Stem Cell RNA-seq rep 3

source_name: E14 Embryonic Stem Cells

value: E14 Embryonic Stem Cells


title: RME765_GV_WT_5: WT GV Oocyte RNA-seq rep 5


title: CMP_13_33479587

value: healthy


title: RME753_ESC-2: E14 Embryonic Stem Cell RNA-seq rep 2


title: RME752_ESC-1: E14 Embryonic Stem Cell RNA-seq rep 1


title: CMP_129_34595621


title: HSD F2 male derived from CD F0 male rep03

description:
Drosophila_F2_Male_N03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: male


title: RME751_ZFP708_KO-3: ZFP708 maternal/zygotic mESC RNA-seq rep 3

source_name: ZFP708 maternal/zygotic Embryonic Stem Cells

value: ZFP708 maternal/zygotic null


title: HSD F2 male derived from CD F0 male rep02

description:
Drosophila_F2_Male_N02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD F0 male


title: CMP_128_34600600


title: CMP_127_34586630


title: CMP_126_34602603


title: RME749_ZFP708_KO-1: ZFP708 maternal/zygotic mESC RNA-seq rep 1

value: ZFP708 maternal/zygotic Embryonic Stem Cells


title: HSD F2 male derived from CD F0 male rep04

description:
Drosophila_F2_Male_N04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_124_34598607


title: RME747_ZFP708_WT-2: control mESC RNA-seq rep 2

source_name: Embryonic Stem Cells

value: wild type

value: Embryonic Stem Cells


title: RME748_ZFP708_WT-3: control mESC RNA-seq rep 3


title: CMP_123_34583629

value: CMP


title: RME750_ZFP708_KO-2: ZFP708 maternal/zygotic mESC RNA-seq rep 2


title: CD F2 female derived from CD F0 male rep01

description:
Drosophila_F2_Female_O01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD

value: female


title: RME746_ZFP708_WT-1: control mESC RNA-seq rep 1


title: Mammary gland cow nb 1058 restricted group

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

institute: INRA

description: Biological replicate 1 of 6

hyb_protocol: After purification (Qiagen RNeasy Mini Kit), 1,65 µg of Cy3 labeled cRNA were hybridized onto G2519F-023647 Bovine (V2) Gene Expression Microarray, 4x44K (Agilent, USA) with hybridization buffer (Agilent Gene Expression Hybridization Kit) according to the manufacturer’s instructions. After 17h of hybridization, slides were washed with the Gene Expression Wash Pack.

scan_protocol: Microarrays were scanned with Agilent G2505 scanner.

data_processing: Data were extracted with Feature Extraction 11,0 software (Agilent, USA) (no background subtraction).

organism: Bos taurus

source_name: Mammary gland biopsy Restricted

label_protocol: 100 ng of total RNA extracted were amplified and fluorescently labelled to produce Cy3 cRNA using the Low Input Quick Amp Labeling one color Kit (Agilent, USA) in the presence of spike-in one color control.

growth_protocol: Twelve cows were studied at early lactation stage,

extract_protocol: Total RNA was prepared through homogenization of approximately 50 mg of mammary gland tissue according to manufacture protocol of mirVana miRNA extraction kit (Invitrogen Life Technologies, Cergy Pontoise, France)

treatment_protocol: At 24 ± 3 d in milk, multiparous cows were either allowed to continue ad libitum intake of a lactation diet (CON, n = 6), or the ration was diluted with barley straw (48% DM) for 4 d (RES, n = 6). On d 3, one healthy rear mammary quarter was infused with 50 µg of LPS. mammary gland biopsies were performed 24 h after LPS challenge

tag: physiological stage

value: early lactation stage, multiparous.

tag: breed

value: Holstain cow

tag: diet

value: Restricted


title: CD F2 male derived from CD F0 male rep04

description:
Drosophila_F2_Male_M04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: Oregon R


title: HSD F2 male derived from CD F0 male rep01

description:
Drosophila_F2_Male_N01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

value: 14 days

value: adult


title: CD F2 male derived from CD F0 male rep03

description:
Drosophila_F2_Male_M03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: male


title: Mammary gland cow nb 1015 restricted group

description: Biological replicate 1 of 6


title: Mammary gland cow nb 7043 restricted group

description: Biological replicate 1 of 6


title: CD F2 male derived from CD F0 male rep02

description:
Drosophila_F2_Male_M02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: Mammary gland cow nb 0078 restricted group

description: Biological replicate 1 of 6


title: Mammary gland cow nb 1018 restricted group

description: Biological replicate 1 of 6


title: CMP_121_34602602

tag: cell type

value: Bone marrow

value: healthy


title: CMP_122_34601606

tag: tissue


title: HSD F1 female derived from HSD F0 male rep04

description:
Drosophila_F1_Female_L04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD F0 male


title: Mammary gland cow nb 0049 restricted group

description: Biological replicate 1 of 6


title: Mammary gland cow nb 0055 control group

description: Biological replicate 1 of 6

source_name: Mammary gland biopsy Control

value: Control


title: CME958: INPUT (G)

data_processing:
Raw reads were aligned to mm9 genome using Bowtie2 (default parameters), before sorting the bam files with samtools sort.
Bigwig files were generated with the bamCoverage fonction of deeptools2.0, using the options --normalizeUsing RPKM --binSize 25 --smoothLength 100.
Peaks were called with Macs2 callpeak (default parameters).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files showing the reads coverage

source_name: HA-ZFP708 OE Embryonic Stem Cells (1)

growth_protocol: Embryonic stem cells were cultured under standard LIF/FCS conditions.

extract_protocol:
ChIP was performed as previously described {Guccione:2007dy}. Chromatin was fragmented using a BRANSON Digital Sonifier (#S540D) to 250-1000bp fragments, precleared and incubated with antibodies overnight. Antibody/chromatin complexes were incubated for 50% Protein-G Sepharose slurry and washed before elution/decrosslinking in 1% SDS and 0.1 M NaHCO3. DNA was column purified with QIAquick PCR purification Kit, Qiagen.
ChIP DNA concentrations were measured with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB), following manufacturer’s instructions. PCR conditions were adjusted to starting material concentrations and final elution volumes were reduced. Libraries were quantified by Bioanalyzer (High Sensitivity DNA Kit, Agilent) and PCR (KAPA Library Quantification Kit for Illumina, Roche). ChIP-Seq libraries were pooled and sequenced on the NextSeq500, as a single end (76bp) run

value: mouse embryonic stem cells

tag: antibody


title: CME959: HA-ChIP-seq (G)

value: alpha-HA, Abcm, ab9110, 5 ug


title: CMP_120_34605588

value: CMP

tag: disease

tag: phenotype


title: HSD F1 female derived from HSD F0 male rep03

description:
Drosophila_F1_Female_L03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

source_name: whole fly, 14 days of treatment

tag: generation

value: female


title: CME937: TRIM28 ChIP-seq (F)

source_name: FLAG-ZFP708-KDEL OE Embryonic Stem Cells (1)

value: alpha-TRIM28, Abcam ab10484, 5ug


title: Mammary gland cow nb 8027 control group

description: Biological replicate 1 of 6

value: early lactation stage, multiparous.

value: Holstain cow


title: CMP_12_33499548

source_name: CMP


title: Mammary gland cow nb 0015 control group

description: Biological replicate 1 of 6


title: CMP_118_34590632


title: CME935: TRIM28 ChIP-seq (D)


title: CMP_119_34602601


title: CME936: INPUT (F)


title: CMP_117_34589620


title: CMP_154_34596639


title: CD F2 male derived from CD F0 male rep01

description:
Drosophila_F2_Male_M01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: diet fed

value: CD

value: CD F0 male


title: HSD F1 female derived from HSD F0 male rep01

description:
Drosophila_F1_Female_L01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

tag: diet of ancestral f0 males

value: Oregon R

value: 14 days


title: Mammary gland cow nb 1076 control group

description: Biological replicate 1 of 6


title: Mammary gland cow nb 1024 control group

description: Biological replicate 1 of 6


title: CMP_115_34595615

value: Bone marrow


title: HSD F1 female derived from HSD F0 male rep02

description:
Drosophila_F1_Female_L02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: strain/background

value: adult


title: CD F1 female derived from HSD F0 male rep03

description:
Drosophila_F1_Female_K03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD F0 male

tag: developmental stage


title: Mammary gland cow nb 9040 control group

description: Biological replicate 1 of 6

value: Control


title: CD F1 female derived from HSD F0 male rep04

description:
Drosophila_F1_Female_K04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: batch


title: CD F1 female derived from HSD F0 male rep02

description:
Drosophila_F1_Female_K02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F1 female derived from HSD F0 male rep01

description:
Drosophila_F1_Female_K01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CME934: INPUT (D)

value: mouse embryonic stem cells


title: CME572: H3K9me3 ChIP-seq (B)

source_name: FLAG-ZFP708 OE Embryonic Stem Cells (1)

value: alpha-H3K9me3, Abcam, ab8898, 3 ug


title: CMP_116_34597598

value: CMP

value: healthy


title: CME575: H3K9me3 ChIP-seq (E)


title: CME571: FLAG ChIP-seq (B)

value: alpha-FLAG, Sigma, F3165, 5ug


title: D155: PTFC treatment (liver_hight fat dieat 24 weeks and PTFC treatment for 18 weeks_rep3)

city: Hangzhou

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

hyb_protocol: The pre-hybridization of MOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.

source_name: liver

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: The mice were exposed to continuous light and 12:12 h light/dark cycle, and provided with food and water ad libitum.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: A total of 24 healthy male SPFC57BL/6 mice aged 6–8 weeks were purchased from Shanghai Sippr-BKLaboratory Animal Co. Ltd. (production license: SCXK (Hu) 2013-0016). All the mice were randomly divided into three groups after one week of adaptive feeding as follows: (i) control group (ND group, 6 mice), which was normally fed with feedstuff (21.5% protein, 12.3% fat, and 66.2% carbohydrate) produced by Jiangsu Synergic Bioengineering Co., Ltd.; (ii) high-fat diet groups (HFD group, 12 mice) were given high-fat diet (comprising 21.6% protein, 36.1% fat, 42.3% carbohydrate; 82.75% basal diet + 10% lard, 2% cholesterol, 0.25% bile salt, and 5% egg yolk powder; feedstuff was produced by Jiangsu Synergic Bioengineering Co., Ltd.)for 16-week (6 mice) and 24-week (6 mice) respectively; (iii) HFD + PTFC group (6 mice) was fed with high-fat diet for six weeks, and intragastric administration of PTFC at 50 mg kg1 d1 was performed for 18 weeks. The normal and the model groups were administered with an equal volume of 0.9% sodium chloride,exposed to continuous light and 12:12 h light/dark cycle, andprovided with food and water ad libitum. Mice in 16-week HFD group were sacriﬁced at the end of week 16. Mice in each group were sacriﬁced at the end of week 24. The mice were fasted on water for 12 h the night before later treatment. Under anesthesia, blood samples were extracted intraocularly, and liver specimens were collected. The right liver lobe was extracted and ﬁxed in 10% neutral formalde-hyde for pathological observation, and the other liver tissues werestored at -70 ℃ for RNA extraction.

value: male

tag: strain

value: liver

tag: development stage

value: 31~33-week age


title: HSD F1 male derived from HSD F0 male rep03

description:
Drosophila_F1_Male_J03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: gender

tag: age


title: D152: PTFC treatment (liver_hight fat dieat 24 weeks and PTFC treatment for 18 weeks_rep2)


title: CMP_113_34599596


title: CME574: FLAG ChIP-seq (E)


title: CME570: TRIM28 ChIP-seq (B)

value: alpha-TRIM28, Abcam ab10484, 5ug


title: CMP_114_34588641