title: 549-CT-12h

city: Seoul

first: Hyeon-Cheol

last: Lee

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

country: South Korea

institute: BPgene Co., Ltd.

description: RNAseq for CT-transfected BT-549 cell at 12h incubation

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling and quality check using FastQC v0.11.7
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.38, and mapped to hg38 whole genome using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Transcript assembly and abundance estimation using StringTie v2.1.3b
Statistical significance of the differential expression data was determined using DESeq2
Gene-enrichment and functional annotation analysis and pathway analysis for significant gene list were performed based on gProfiler
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values
Supplementary files format and content: Matrix table with raw gene counts

source_name: 12h after transfection CT mRNA

growth_protocol: Human triple-negative breast cancer cell lines (BT-549)  were cultured in Plasmax™ cell culture medium (Xymbio) supplemented with 2.5% dialyzed FBS (Gibco) and 1X Penicillin-Streptomycin (Gibco). Cells were maintained at 37 °C under 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was isolated from cells using TRIzol solution. After RNA extraction, it was quantified at a concentration of 1 μg.
Libraries were prepared according to TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E accompanying the TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Cells were plated 24 h before transfection in a 6-well plate at 5x105 cells/well. Cells were transfected 1.25 µg of mRNA complexed with Lipofectamine® MessengerMAX (Invitrogen) diluted in Opti-MEM medium (Gibco) to obtain a total volume of 200 µl. The transfection mix was added to the cells and cells were incubated at 37 °C, 5% of CO2 incubator during a time period depending on the experiment.

tag: type

value: Epithelial cells

value: TNBC cells

value: Transfection of CT mRNA for 12h


title: D6F, H3K27ac, rep4

status: Public on May 07 2022

type: SRA

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

country: Germany

institute: Univeritätsklinikum Erlangen

library_source: genomic

data_processing:
Quality control of samples using FastQC version 0.11.8
Read trimming using TrimGalore 0.6.4, and if necessary Cutadapt 2.8 and again FastQC
Read alignment using Bowtie2 version 2.3.4.3 default settings
generation of bam files and merging of files by samtools 1.9
generation of bigwig files and correlation plots by Deeptools 3.1.2
visualisation by IGV 2.6.3 and pyGenometracks 3.6
peak calling using MACS2 2.1.2.1
further data analysis by bedtools 2.28.0, mixtools 1.2.0, ggplot2 3.3.2, scanpy 1.8.1
Assembly: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary files format and content: bigwigfiles filtered by quality > 28, normalized using RPKM

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: cell culture

growth_protocol: 3D7::ABCG2-GFP P. falciparum parasites were cultivated at 5 % haematocrit in complete culture medium (RPMI-1640 complete medium (Gibco, Thermo Fisher Scientific) complemented with 25 mM HEPES pH 7.3 and 20 µg/ml gentamycin (Thermo Fisher Scientific) and supplemented with 0.25 %  AlbuMAX II Lipid-Rich BSA (Thermo Fisher Scientific) and 5 % human AB Rh+ serum purchased from the Bavarian Red Cross Service (BRK). The parasites were propagated in erythrocytes of blood group 0+ (purchased from BRK) in a gas environment of 1 % O2, 5 % CO2, and 94 % N2 at 37 °C.  Developing gametocytes were magnetically purified using MACS columns and separated by sex using flow cytometry. Male gametocytes were GFP low and female gametocytes GFP high. Mitotracker was used to sort for viable cells.

extract_protocol:
Parasites were crosslinked at a final concentration of 1% PFA for 10 min at 37°C and subsequently quenched with 125 mM glycine for 5 min on ice. The cells were then spun down and lysed using 0.075% saponin in PBS. After lysis the cells were washed twice with PBS and then resuspended in cold lysisbuffer (10 mM Hepes pH 7.9, 10 mM KCl, 0.1 mM EDTA pH 8.0, 0.1 mM EGTA pH 8.0, 1 mM DTT, 1x Protease Inhibitor (Roche); 1ml per 5*10^7 cells). The mix was then transferred to a tissue grinder and incubated on ice for 30 min. Then Igepal was added to a final concentration of 0.25% and cells were lysed with 100 strokes. The resulting free nuclei were again pelleted and lysed by SDS lysis buffer (1 % SDS, 10 mM EDTA, 50 mM Tris pH 8.1, 1x Protease Inhibitor). The DNA was then sheared by sonication (2 times 8 min with 30s ON 30s OFF cycles). The sheared material was spun and the supernatant was transferred and diluted 1:10 with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 150 mM NaCl). The diluted chromatin was then precleared by BSA-blocked agarose G beads (GE Healthcare) for 1h. Subsequently 50µl material were set aside as input. For the IP 15µl agarose G beads were used per antibody per sample. The IP was incubated under agitation at 4°C over night and thereafter washed sequentially with different buffers: Low Salt Wash Buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), then High Salt Wash Buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), then LiCl Wash Buffer (0.25 M LiCl, 1 % Igepal, 1 % Sodium-Desoxycholat, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), then twice at RT with TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). The immunoprecipitated chromatin was eluted from the beads with 100 µl Elution Buffer (2 % SDS, 200 mM NaHCO3) for 15 min at RT, twice. The Input sample was also diluted to the same volume with Elution Buffer. 500 mM NaCl were added for decrosslinking (45 °C over night). Finally, the proteins were digested by addition of 2 µl Proteinase K (Thermo Fisher Scientific) for 1 h at 37 °C, and DNA was purified using the MinElute Kit (QIAGEN 28006).
Libraries were generated using the Accel-NGS (TM) 2S Plus DNA Library Kit for Illumina platforms (SWI Swift Bioscience) and Accel-NGS (TM) 2S Indexing Kit (SWI Swift Bioscience) according to the manufacturer's guidelines. AmpureXP beads (Beckman Coulter) were used for the purification steps and the amplification step was performed with 15 cycles using the KAPA Hifi PCR kit (KK2101; Roche) according to published procedures (PMID: 26067602).
directional paired-end ChIP-Seq

treatment_protocol: Gametocytogenesis was induced by stressing the parasites through lowering the hematocrit and cultivation in partially spent medium. Asexual parasites were selectively inhibited by addition of N-acetyl-D-glucosamine, from day 0 to day 6 of gametocytogenesis. Gametocytes were enriched magnetically on a MACS CS column on day 3 and FACS sorted using GFP only or GFP and Mitrotracker Deep Red (as defined below) directly before nuclei were harvested. Asexual parasites were not sorted.

tag: parasite line

tag: sort strategy

value: GFP high, mitotracker

tag: Sex

value: female

tag: chip antibody

value: anti-H3K27ac, Abcam ab4729


title: D6F, H3K9me3, rep4

value: anti-H3K9me3, Active Motif 39161


title: Osteoclast-Control-2

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
cDNA and sequencing libraries were processed with FastQC (v0.1.1.8), TrimGalore (v0.6.4) and Kallisto (v0.46.0) using the mouse transcriptome index (mus musculus GRCm38.96).
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: osteoclasts

extract_protocol:
Primary periosteal stem cells were collected by FACS sorting as described previously (Debnath et al., Nature 2018). In vitro osteoclastogenesis was performed as previously reported (Tsukasaki et al., JBMR 2017). Total RNA was extracted from periosteal steal stem cells and osteoclasts using the Maxwell 16 LEV simply RNA Tissue Kit (Promega) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ion Torrent Proton protocols

tag: strain

tag: tissue

value: In vitro cultured osteoclasts (72h after RANKL stimulation)

tag: age

value: 11 weeks old


title: 549-CT-24h

description: RNAseq for CT-transfected BT-549 cell at 24h incubation

organism: Homo sapiens

source_name: 24h after transfection CT mRNA

tag: cell type

tag: cell line

tag: treatment

value: Transfection of CT mRNA for 24h


title: 549-NT5M-24h

description: RNAseq for NT5M-transfected BT-549 cell at 24h incubation

source_name: 24h after transfection NT5M mRNA

value: Transfection of NT5M mRNA for 24h


title: Root, P024, low P, rep2 [LP_P024_2]

city: Montpellier

first: Christophe

last: Maurel

address: 2 place Pierre Viala

department: Water, signaling and hydraulic architecture

country: France

institute: Institute for Plant Sciences of Montpellier (IPSiM)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp tool  (parameter: --qualified_quality_phred 20 --unqualified_percent_limit 50 –n_base_limit 10)
Trimmed sequence reads were mapped to B73_RefGen_v4, release 44 using hisat2
Read count extraction were performed using htseq-count (parameter: --mode union)
Assembly: Zea_mays.B73_RefGen_v4, release 44
Supplementary files format and content: Tab-separated text files include read count values for each sample
Supplementary files format and content: Tab-separated text files include FPKM values for each sample

organism: Zea mays

source_name: Root

extract_protocol:
RNA was harvested using innuPREP Plant RNA Kit (Analytik Jena AG, Jena, Germany).
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: Root

tag: genotype

value: low P


title: 549-CT-6h

description: RNAseq for CT-transfected BT-549 cell at 6h incubation

source_name: 6h after transfection CT mRNA

value: Transfection of CT mRNA for 6h


title: D6F, H2A.Z, rep4

value: anti-H2A.Z, Petter et al. 2011


title: Root, P415, high P, rep3 [HP_P415_3]

value: high P


title: 549-NT5M-12h

description: RNAseq for NT5M-transfected BT-549 cell at 12h incubation

source_name: 12h after transfection NT5M mRNA

value: Transfection of NT5M mRNA for 12h


title: 549-NT5M-6h

description: RNAseq for NT5M-transfected BT-549 cell at 6h incubation

source_name: 6h after transfection NT5M mRNA

value: Epithelial cells

value: Transfection of NT5M mRNA for 6h


title: 549-cdN-24h

description: RNAseq for CdN-transfected BT-549 cell at 24h incubation

source_name: 24h after transfection cdN mRNA

value: TNBC cells

value: Transfection of CdN mRNA for 24h


title: 549-cdN-12h

description: RNAseq for CdN-transfected BT-549 cell at 12h incubation

source_name: 12h after transfection cdN mRNA

value: Transfection of CdN mRNA for 12h


title: 549-CON-24h

description: RNAseq for BT-549 cell at 24h incubation

source_name: 24h control

value: No transfection


title: D6F, Input, rep4

value: GFP high, mitotracker

value: female


title: Ring, H3K27ac, rep3

value: not sorted

tag: developmental stage

value: ring/asexual

value: anti-H3K27ac, Abcam ab4729


title: 549-cdN-6h

description: RNAseq for CdN-transfected BT-549 cell at 6h incubation

source_name: 6h after transfection cdN mRNA

value: Transfection of CdN mRNA for 6h


title: Ring, H3R17me2, rep3

value: anti-H3R17me2, Abcam ab8284


title: Root, P415, high P, rep1 [HP_P415_1]

value: Root


title: Root, P415, high P, rep2 [HP_P415_2]


title: 549-CON-12h

description: RNAseq for BT-549 cell at 12h incubation

source_name: 12h control


title: 549-CON-6h

description: RNAseq for BT-549 cell at 6h incubation

source_name: 6h control


title: Ring, H3K9me3, rep3

value: anti-H3K9me3, Active Motif 39161


title: Root, P024, low P, rep1 [LP_P024_1]

value: low P


title: Ring, H3K4me3, rep3

value: anti-H3K4me3, Abcam ab8580


title: Root, F7, high P, rep3 [HP_F7_3]

value: high P


title: Root, F7, high P, rep2 [HP_F7_2]


title: Ring, H2A.Z, rep3

value: anti-H2A.Z, Petter et al. 2011


title: Root, F7, high P, rep1 [HP_F7_1]


title: Root, P024, high P, rep2 [HP_P024_2]


title: Root, P024, high P, rep3 [HP_P024_3]


title: hAOEC cells - 10 Gy radiation - 72h - set1 [10Gy72h_1]

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The sequencing error rate of base is calculated from Phred score (Qphred) based on Equation 1, while the Phred score is predicted from a probability model during base calling.
Raw reads filtering conditions are as follows:    (1) Remove reads containing adaptors;    (2) Remove reads containing N > 10% (N represents base that could not be determined);    (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
The clean reads are aligned to the reference genome by HISAT2. HTSeq was used to distribute reads on known RNAs. StringTie was used to assemble the sequences on the reference genome.
DeSeq2 was used for differential expression analysis.
genome build: hg38

source_name: primary human Aortic endothelial cells purchased from 'Cell Applications Inc, San Diego, CA''

growth_protocol: hAOEC cells were grown in EC Growth Media (Cat # 213-500, Cell Apllication Inc.)

extract_protocol:
Cells were washed lysed directly in Trizol. Phenol-chloroform extraction and total RNA isolation was performed as per manufacturer's guidelines using miRNeasy kit (Qiagen).
lncRNA sequencing was performed by Novogene (Novogene, Sacramento, CA) using the TruSeq Stranded Total RNA With Illumina Ribo-Zero Plus rRNA Depletion kit (Illumina, US) following manufacturer’s instructions. Sequencing runs were performed on Novaseq 6000 S4 system (Illumina, US). Briefly, Poly-A tailed RNA was purified from total RNA using poly-T oligo attached magnetic beads. The purified RNA was fragmented and reverse-transcribed into first strand cDNA using random primers. Second strand cDNA synthesis was performed using dUTP to preserve strand specific information. 3’-ends were repaired with adenylation. Adapters were ligated for strand selection and sequencing priming. PCR amplification was followed by purification. The quality of the amplified library was assessed on Bioanalyzer, and libraries were quantified on Qubit Fluorometer (Themo Fisher Scientific, US). Sequencing reactions were performed to generated 150 bp paired-end reads.

treatment_protocol: Cells were grown to ∼100% confluence in 60-mm2 tissue culture dishes. Fresh media was added prior to radiation. Radiated cells were returned to incubators for 24h or 72h.

value: primary human Aortic endothelial cells (hAOEC)

tag: tissue souce

value: Aorta

tag: biomaterial provider

value: Cell Applications Inc, San Diego, CA

value: 10 Gy radiation

tag: treatment time


title: D6F, H3R17me2, rep3

value: GFP high, no mitotracker


title: hAOEC cells - 10 Gy radiation - 72h - set2 [10Gy72h_2]


title: hAOEC cells - 8 Gy radiation - 72h - set1 [8Gy72h_1]

value: 8 Gy radiation


title: hAOEC cells - 8 Gy radiation - 72h - set3 [8Gy72h_3]


title: hAOEC cells - 8 Gy radiation - 72h - set2 [8Gy72h_2]


title: hAOEC cells - 2 Gy radiation - 72h - set3 [2Gy72h_3]

value: 2 Gy radiation


title: hAOEC cells - 10 Gy radiation - 72h - set3 [10Gy72h_3]


title: Ring, Input, rep3

value: not sorted

value: ring/asexual


title: hAOEC cells - 2 Gy radiation - 72h - set1 [2Gy72h_1]


title: hAOEC cells - 2 Gy radiation - 72h - set2 [2Gy72h_2]


title: Root, P024, high P, rep1 [HP_P024_1]


title: hAOEC cells - 1 Gy radiation - 72h - set3 [1Gy72h_3]

value: 1 Gy radiation


title: hAOEC cells - 4 Gy radiation - 72h - set1 [4Gy72h_1]

value: 4 Gy radiation


title: D6F, H3K4me3, rep3

value: female


title: hAOEC cells - 10 Gy radiation - 72h - set3 [10Gy72h_3_miRNA]

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts. In this step, clean data (clean reads) were obtained by  removing reads containing ploy-N, with 5’ adapter contaminants, without 3’  adapter or the insert tag, containing ploy A or T or G or C and low quality reads  from raw data. At the same time, Q20, Q30, and GC-content of the raw data were  calculated. Then, chose a certain range of length from clean reads to do all the  downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et  al., 2009) without mismatch to analyze their expression and distribution on the  reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0  was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and  srna-tools-cli were used to obtain the potential miRNA and draw the secondary  structures. Custom scripts were used to obtain the miRNA counts as well as base  bias on the first position of identified miRNA with certain length and on each  position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA,  tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker,  Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through  the following criteria (Zhou et al., 2010):  Normalization formula: Normalized expression = mapped readcount/Total  reads*1000000. Differential expression analysis of two conditions/groups was performed using  the DESeq R package (1.8.3).
genome build: hg38

extract_protocol:
Cells were washed lysed directly in Trizol. Phenol-chloroform extraction and total RNA isolation was performed as per manufacturer's guidelines using miRNeasy kit (Qiagen).
The small RNA libraries were prepared using the Qiaseq miRNA Library Preparation Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. Briefly, a universal preadenylated DNA adapter is added to the 3’ ends and an RNA adapter is ligated to the 5’ end. cDNA was synthesized using 3’-adapter as the primer. cDNA was subsequently cleaned up using magnetic beads and libraries were amplified and different 6-nt indices were included for each sample to enable sample identification after multiplexing. Library sizes were assessed using Bioanalyzer and average library sizes were around 180 bp. Samples were pooled and sequenced on Illumina Hiseq X sequencer generating 10 million single end reads per sample.

value: 10 Gy radiation - 72h


title: D6F, H3K27ac, rep3

value: anti-H3K27ac, Abcam ab4729


title: hAOEC cells - 1 Gy radiation - 72h - set2 [1Gy72h_2]


title: D6F, H3K9me3, rep3

value: anti-H3K9me3, Active Motif 39161


title: hAOEC cells - 1 Gy radiation - 72h - set1 [1Gy72h_1]


title: D6F, H2A.Z, rep3


title: hAOEC cells - 4 Gy radiation - 72h - set2 [4Gy72h_2]


title: Schizont, H3K9me3, rep2

value: schizont/asexual


title: Schizont, Input, rep2


title: hAOEC cells - 4 Gy radiation - 72h - set3 [4Gy72h_3]


title: D6F, Input, rep3


title: hAOEC cells - unirradiated - 72h control2 [0Gy72h_2]

value: unirradiated

value: 72h control


title: hAOEC cells - 8 Gy radiation - 72h - set3 [8Gy72h_3_miRNA]

value: primary human Aortic endothelial cells (hAOEC)

value: Aorta

value: 8 Gy radiation - 72h


title: Ring, H2A.Zac, rep4

value: anti-H2A.Zac, Azizan et al. in preparation


title: Schizont, H2A.Zac, rep1


title: hAOEC cells - 8 Gy radiation - 72h - set2 [8Gy72h_2_miRNA]

value: Cell Applications Inc, San Diego, CA


title: alx1;alx3 sibling 3

city: Boston

first: Eric

last: Liao

state: MA

address: CRMT, Simches Research Center, CPZN 4400, 185 Cambridge Street

institute: MGH

description: alx1;alx3 siblings

data_processing:
Germline: alignment of adapter-trimmed (Skewer v0.1.123) 2x150 (paired-end; PE) bp strand-specific Illumina reads to the Danio rerio GRCz11genome (assembly accession GCF_000002035.6) was achieved with the Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software; CRISPANTs: 2x75bp (paired-end; PE) strandspecific Illumina Reads were trimmed to remove Illumina adapter sequences and low-quality sequence with Trimmomatic (v. 0.36) (Bolger et al., 2014). Reads were aligned to GRCz11genome using STAR (v 2.7.1a) (Dobin et al., 2013) with custom built index based on Ensembl v91 gene annotations
Germline: Expression estimation was performed with RSEM v1.3.0 (RNASeq by Expectation Maximization); CRISPANTs: Gene expression counts were extracted using featureCounts from the subread package (v 2.0) (Liao et al., 2013) using Ensembl v91 gene annotations.
Assembly: Danio rerio GRCz11genome (assembly accession GCF_000002035.6)
Supplementary files format and content: RSEM.genes.results (Germline)
Supplementary files format and content: counts_RNAseq_danRer10_alx1_3_KO_2.txt (CRISPANTs)

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryo

growth_protocol: Germline: zebrafish embryos were incubated in E3 embryo medium at 29C until 5 days post-fertilization; CRISPANTs:  zebrafish embryos were incubated in E3 embryo medium at 29C until 72 hours post-fertilization

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and genomic DNA contamination was removed using the DNase Max Kit (Qiagen).
Germline: cDNA libraries were prepared using the TruSeq stranded mRNA library preparation protocol with poly-A selection; CRISPANTs: libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with NEBNext® Poly(A) mRNA Magnetic Isolation Module

value: whole embryo

tag: group

value: Germline samples


title: hAOEC cells - 10 Gy radiation - 72h - set2 [10Gy72h_2_miRNA]


title: alx1;alx3 sibling 2

description: alx1;alx3 siblings


title: alx1;alx3 sibling 1

description: alx1;alx3 siblings


title: hAOEC cells - 10 Gy radiation - 24h - set2 [10Gy24h_2]

value: 10 Gy radiation


title: alx1;alx3 sibling 4

description: alx1;alx3 siblings


title: hAOEC cells - 8 Gy radiation - 72h - set1 [8Gy72h_1_miRNA]


title: hAOEC cells - 10 Gy radiation - 24h - set3 [10Gy24h_3]


title: hAOEC cells - unirradiated - 72h control1 [0Gy72h_1]


title: Ring, Input, rep4

value: not sorted

value: ring/asexual


title: hAOEC cells - 4 Gy radiation - 72h - set3 [4Gy72h_3_miRNA]

value: 4 Gy radiation - 72h


title: hAOEC cells - 10 Gy radiation - 24h - set1 [10Gy24h_1]


title: Ring, H2A.Z, rep2

value: anti-H2A.Z, Petter et al. 2011


title: alx1;alx3/+ sibling 4


title: hAOEC cells - 10 Gy radiation - 72h - set1 [10Gy72h_1_miRNA]

value: 10 Gy radiation - 72h


title: hAOEC cells - 4 Gy radiation - 72h - set2 [4Gy72h_2_miRNA]


title: alx1;alx3/+ sibling 3


title: hAOEC cells - 4 Gy radiation - 72h - set1 [4Gy72h_1_miRNA]


title: Ring, Input, rep2


title: alx1;alx3/+ sibling 2


title: hAOEC cells - unirradiated - 72h control3 [0Gy72h_3]


title: hAOEC cells - 2 Gy radiation - 72h - set3 [2Gy72h_3_miRNA]

value: 2 Gy radiation - 72h


title: Ring, H3K27ac, rep1

value: anti-H3K27ac, Abcam ab4729


title: alx1;alx3/+ sibling 1


title: hAOEC cells - 2 Gy radiation - 72h - set2 [2Gy72h_2_miRNA]


title: alx1 sibling 4

description: alx1 siblings


title: hAOEC cells - 8 Gy radiation - 24h - set1 [8Gy24h_1]

value: 8 Gy radiation


title: hAOEC cells - 2 Gy radiation - 72h - set1 [2Gy72h_1_miRNA]


title: alx1 sibling 3

description: alx1 siblings


title: hAOEC cells - 8 Gy radiation - 24h - set2 [8Gy24h_2]


title: hAOEC cells - 4 Gy radiation - 24h - set2 [4Gy24h_2]

value: 4 Gy radiation


title: Ring, H2A.Z, rep1


title: alx1 sibling 1

description: alx1 siblings


title: hAOEC cells - 4 Gy radiation - 24h - set1 [4Gy24h_1]

value: primary human Aortic endothelial cells (hAOEC)


title: hAOEC cells - 2 Gy radiation - 24h - set3 [2Gy24h_3]

value: Aorta

value: 2 Gy radiation


title: Ring, Input, rep1


title: hAOEC cells - 1 Gy radiation - 72h - set2 [1Gy72h_2_miRNA]

value: 1 Gy radiation - 72h


title: hAOEC cells - unirradiated - 72h control3 [0Gy72h_3_miRNA]

value: Cell Applications Inc, San Diego, CA

value: unirradiated - 72h control


title: hAOEC cells - 1 Gy radiation - 72h - set3 [1Gy72h_3_miRNA]


title: Ring, H3R17me2, rep1

value: anti-H3R17me2, Abcam ab8284


title: Ring, H3K9me3, rep1

value: anti-H3K9me3, Active Motif 39161


title: hAOEC cells - 8 Gy radiation - 24h - set3 [8Gy24h_3]


title: Schizont, Input, rep1

value: not sorted

value: schizont/asexual


title: hAOEC cells - 2 Gy radiation - 24h - set2 [2Gy24h_2]


title: GD6F, H2A.Z, rep2

value: GFP high, no mitotracker

value: female


title: hAOEC cells - 4 Gy radiation - 24h - set3 [4Gy24h_3]


title: KcngRGC_3

city: San Francisco

first: Xin

last: Duan

department: Ophthalmology

institute: UCSF

description:
scRNA-seq
Combined_excit_counts.csv

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger (v3.0.2, 10X Genomics).
Sample alignment to mouse genome GRCm38 (mm10) with the count function from Cell Ranger (v3.0.2, 10X Genomics).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Csv files including count matrix, sample metadata, and marker gene list from pan-RGC tracing and differential RGC tracing.

source_name: Superior Colliculus

extract_protocol:
The contralateral superior colliculi corresponding to four high-coverage eyes without damage were prepared through an electrophysiology slice protocol. Each mouse was transcardially perfused with ice-cold, carbogenated cutting solution (78.3 mM NaCl, 2.3 mM KCl, 33.8 mM Choline-Cl, 0.45 mM CaCl2, 6.4 mM MgCl2, 1.1 mM NaH2PO4, 23 mM NaHCO3, 20 mM D-Glucose, 0.5 mM L-glutamine, pH 7.4). Coronal slices of 500µm thick were cut with a vibratome (Leica VT1200S) in ice-cold carbogenated cutting solution and then immediately transferred into ice-cold, carbogenated ACSF (125 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 1 mM MgCl2.6H2O, 2 mM CaCl2, 20 mM D-Glucose, pH 7.4). Slices containing the superior colliculus were transferred to a Petri-dish with ice-cold carbogenated ACSF. The mCherry-positive superficial superior colliculus hemisphere was microdissected under a fluorescence dissection microscope. The dissected regions were transferred into resuspension buffer (Hibernate-A supplemented with B27, 25% glucose, 0.01% BSA, 1% Glutamax, and 0.1mg/mL DNaseI). The mCherry negative SC hemisphere was dissected and processed in parallel to prepare an unstained sample (negative control) for FACS gating. Resuspension buffer was then exchanged with papain solution (2mg/mL papain, 0.1mg/mL DNaseI in Hibernate-Calcium), and the dissected tissue was digested in papain for 25min at 37°C. Following incubation, papain solution was exchanged with trituration buffer (Hibernate-A supplemented with B27, 25% glucose, 0.1% BSA). Tissue pieces were subsequently gently triturated using a 200ul pipette tip to obtain a single-cell suspension. Tissue debris was allowed to settle for 1 min at room temperature, and the supernatant was transferred to a new microcentrifuge tube and centrifuged at 300g for 5 min at 4°C. The supernatant was then exchanged with 1 ml resuspension buffer. The resulting cell suspension was gently pipetted and filtered with a 70µm filter to remove cell clumps.
FACS sorting was performed on a BD FACSAriaII Cell Sorter with a 100 µm nozzle. DAPI was added before sorting at a concentration of 3ng/mL. FACS was used to select cells with low DAPI fluorescence and high mCherry fluorescence. The native (mCherry-negative, without injections) sample was used to establish gating for mCherry. Sorted cells were immediately processed for cDNA library preparation.
Library preparation was performed by the UCSF Institute of Human Genetics Core Facility, using 10X Chromium Single 3Prime Reagent Kits according to the manufacturer’s protocols. Library length and concentration were quantified using a Bioanalyzer (Agilent). A sequencing depth of 50,000 read pairs/cell was targeted for library preparation as recommended by 10x Genomics. Paired-end sequencing was performed on an Illumina NovaSeq. The Cell Ranger pipeline, run by the UCSF Institute of Human Genetics Computational Core, was used to generate FASTQ files, perform an alignment with the mm10 mouse genome assembly, and generate feature-barcode matrices.

value: Adult

value: Pooled male and female

value: Superior Colliculus


title: hAOEC cells - unirradiated - 72h control2 [0Gy72h_2_miRNA]


title: hAOEC cells - unirradiated - 72h control1 [0Gy72h_1_miRNA]


title: hAOEC cells - 1 Gy radiation - 72h - set1 [1Gy72h_1_miRNA]


title: GD6F, H3R17me2, rep1

source_name: cell culture


title: GD6F, Input, rep2


title: hAOEC cells - 1 Gy radiation - 24h - set3 [1Gy24h_3]

value: 1 Gy radiation


title: KcngRGC_1

description:
scRNA-seq
Combined_excit_counts.csv


title: hAOEC cells - 10 Gy radiation - 24h - set3 [10Gy24h_3_miRNA]

value: 10 Gy radiation - 24h


title: hAOEC cells - 1 Gy radiation - 24h - set2 [1Gy24h_2]

value: primary human Aortic endothelial cells (hAOEC)


title: CartRGC_3

description:
scRNA-seq
Combined_excit_counts.csv

value: Cart-Cre


title: GD6F, H3K27ac, rep1

value: anti-H3K27ac, Abcam ab4729


title: hAOEC cells - 1 Gy radiation - 24h - set1 [1Gy24h_1]

value: Aorta


title: CartRGC_2

description:
scRNA-seq
Combined_excit_counts.csv


title: GD6F, H3K4me3, rep1

value: anti-H3K4me3, Abcam ab8580


title: CartRGC_1

description:
scRNA-seq
Combined_excit_counts.csv


title: hAOEC cells - unirradiated - 24h control3 [0Gy24h_3]

value: Cell Applications Inc, San Diego, CA

value: unirradiated

value: 24h control


title: hAOEC cells - unirradiated - 24h control2 [0Gy24h_2]


title: GD6F, H2A.Z, rep1

value: anti-H2A.Z, Petter et al. 2011


title: KcngRGC_2

description:
scRNA-seq
Combined_excit_counts.csv


title: hAOEC cells - 10 Gy radiation - 24h - set2 [10Gy24h_2_miRNA]


title: hAOEC cells - 8 Gy radiation - 24h - set3 [8Gy24h_3_miRNA]

value: 8 Gy radiation - 24h


title: hAOEC cells - 10 Gy radiation - 24h - set1 [10Gy24h_1_miRNA]


title: GD6F, Input, rep1

value: GFP high, no mitotracker


title: hAOEC cells - 2 Gy radiation - 24h - set1 [2Gy24h_1]

value: 2 Gy radiation


title: hAOEC cells - 8 Gy radiation - 24h - set2 [8Gy24h_2_miRNA]


title: hAOEC cells - unirradiated - 24h control1 [0Gy24h_1]


title: CartRGC_4

description:
scRNA-seq
Combined_excit_counts.csv

value: Adult


title: PanRGC_3

description:
scRNA-seq
Pan_mWmC_counts.csv

value: Pooled male and female


title: hAOEC cells - 4 Gy radiation - 24h - set3 [4Gy24h_3_miRNA]

value: 4 Gy radiation - 24h


title: PanRGC_2

description:
scRNA-seq
Pan_mWmC_counts.csv

value: Superior Colliculus


title: GD6F, H3K9me3, rep1

value: female

value: anti-H3K9me3, Active Motif 39161


title: PanRGC_4

description:
scRNA-seq
Pan_mWmC_counts.csv


title: hAOEC cells - 8 Gy radiation - 24h - set1 [8Gy24h_1_miRNA]

value: primary human Aortic endothelial cells (hAOEC)


title: PanRGC_1

description:
scRNA-seq
Pan_mWmC_counts.csv


title: Exp_63DOX(-)

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using RPKM.
RPKM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol, gene ID and RPKM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Cells differentiated into gastric-lineage, without DOX

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.E).

value: differentiated cells from hiPSCs

value: hiPSC line 3AB4

value: overexpressing CDX2, without DOX


title: hAOEC cells - 4 Gy radiation - 24h - set2 [4Gy24h_2_miRNA]

value: Aorta

value: Cell Applications Inc, San Diego, CA


title: hAOEC cells - 2 Gy radiation - 24h - set3 [2Gy24h_3_miRNA]

value: 2 Gy radiation - 24h


title: hAOEC cells - 4 Gy radiation - 24h - set1 [4Gy24h_1_miRNA]


title: Exp49_DOX(+)

source_name: Cells differentiated into gastric-lineage, with DOX

value: overexpressing CDX2, with DOX


title: Exp54_DOX(-)


title: alx1; alx3 CRISPANTs 1

description:
alx1; alx3 CRISPANTs
counts_RNAseq_danRer10_WT_alx1_3CRISPANTs.txt

value: whole embryo

value: CRISPANTs samples

value: alx1; alx3


title: alx1; alx3 CRISPANTs 4


title: alx1; alx3 CRISPANTs 3


title: alx1; alx3 CRISPANTs 6


title: alx1; alx3 CRISPANTs 2


title: Exp49_DOX(-)


title: Exp_63DOX(+)


title: alx1; alx3 CRISPANTs 5


title: hAOEC cells - 1 Gy radiation - 24h - set3 [1Gy24h_3_miRNA]

value: 1 Gy radiation - 24h


title: hAOEC cells - 1 Gy radiation - 24h - set2 [1Gy24h_2_miRNA]


title: WT control for alx1;alx3 CRISPANTs 6

description:
WT
counts_RNAseq_danRer10_WT_alx1_3CRISPANTs.txt

value: WT control for alx1;alx3


title: mutant rep3

city: Chonqing

first: Xi

last: Zeng

address: Gaotanyan main street NO.30

department: Department of Microbiology and Biochemical Pharmacy

country: China

institute: Army Medical University

data_processing:
FastQC (version v0.11.5) was used for raw data quality control.
Trimmomatic (version 0.36) was applied to filter out the adaptor and low-quality reads.
Filtered reads were mapped to the Acinetobacter baumannii genome Acinetobacter_baumannii_GCA_000786735.1(ASM78673v1) by STAR (version 2.5.3a) and evaluated by RSeQC (version 2.6).
The reads count for each gene was calculated using featureCounts (Version 1.5.1).
Genome_build: GCA_000786735.1(ASM78673v1)
Supplementary_files_format_and_content: read count

organism: Acinetobacter baumannii

source_name: thallus

growth_protocol: LAC-4 mutant and wild-type strains were cultured in 20ml TSB until OD600=0.6~0.8, and then the bacteria were collected and resuspended in 1ml PBS.

extract_protocol:
Total RNAs were extracted from bacteria samples using TRIzol (Invitrogen) and DNA was digested by DNaseI after RNA extraction. A260/A280 was examined with NanodropTM One spectrophotometer (Thermo Fisher Scientific Inc) to determine RNA quality. RNA Integrity was confirmed by 1% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
Total RNAs (2 μg) were used for to prepare sequencing library using KC-Total RNA-seq Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina).

value: LAC-4 mutant


title: Slc2a1,Slc2a3, Slc2a5, Slc2a6, Slc2a8-deleted cells rep 2

city: Tucson

first: Deepta

last: Bhattacharya

state: AZ

address: 1656 East Mabel St

department: Immunobiology

institute: University of Arizona

data_processing:
Reads were mapped and transcript abundance estimated using Salmon v.1.5.1 on the Galaxy server
Assembly: Gencode M28 transcriptome
Supplementary files format and content: Salmon generated ".tabular" files containing TPM values for all transcripts

extract_protocol:
NucleoSpin RNA XS (Macherey Nagel)
SMARTseq V4 (Takara Bio) by Novogene

value: multiple myeloma

value: transduced with vectors expressing Slc2a1, Slc2a3, Slc2a5, Slc2a6, or Slc2a8 gRNA


title: Control cells rep 2

value: WT

value: transduced with vector expressing Rosa26 gRNA


title: Control cells rep 3


title: Slc2a1,Slc2a3, Slc2a5, Slc2a6, Slc2a8-deleted cells rep 1


title: Slc2a1,Slc2a3, Slc2a5, Slc2a6, Slc2a8-deleted cells rep 3


title: WT control for alx1;alx3 CRISPANTs 5


title: Exp54_DOX(+)

value: differentiated cells from hiPSCs


title: mutant rep2


title: WT control for alx1;alx3 CRISPANTs 4


title: hAOEC cells - 1 Gy radiation - 24h - set1 [1Gy24h_1_miRNA]

value: primary human Aortic endothelial cells (hAOEC)


title: Control cells rep 1


title: hAOEC cells - unirradiated - 24h control3 [0Gy24h_3_miRNA]

value: unirradiated - 24h control


title: mutant rep1


title: WT control for alx1;alx3 CRISPANTs 3


title: Slc2a1-deleted cells rep 3

value: Slc2a1 KO

value: transduced with vector expressing Slc2a1 gRNA


title: hAOEC cells - unirradiated - 24h control2 [0Gy24h_2_miRNA]

value: Aorta

value: Cell Applications Inc, San Diego, CA


title: control rep3

value: wildtype


title: hAOEC cells - unirradiated - 24h control1 [0Gy24h_1_miRNA]


title: Slc2a1-deleted cells rep 1


title: Slc2a1-deleted cells rep 2


title: WT control for alx1;alx3 CRISPANTs 2

value: whole embryo

value: CRISPANTs samples


title: WT control for alx1;alx3 CRISPANTs 1


title: control rep1


title: hAOEC cells - 2 Gy radiation - 24h - set1 [2Gy24h_1_miRNA]

value: 2 Gy radiation - 24h


title: Liv_19mo_AL_36B

status: Public on May 06 2022

city: Dallas

first: Victoria

last: Acosta

state: TX

address: 6001 Forest Park Lane

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Sequencing libraries were constructed in house following TruSeq RNA Sample preparation protocol (Illumina). RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to M14 GENCODE (protein coding only) version of mouse genome from www.gencodegenes.org. Raw reads were quantified using featureCounts tool from Rsubread package followed by RPKM calculation using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment.
M14 from GENCODE

source_name: Liver aged ad lib

growth_protocol: C57BL/6J male mice (8 week-old) were individually housed in standard polycarbonate mouse cages (Fischer Scientific, Cat. Nos. 01-288-1B and 01-288-21) containing a 4.75 in diameter stainless steel running wheel inside isolation cabinets containing 12 cages each. Temperature and humidity levels were monitored, and the mice were housed under an LD12:12 cycle (green LEDs, ~100 lux at the level of the cage floor). Water was provided ad libitum throughout the study.

extract_protocol:
RNA was extracted using 1mL of Trizol reagent and Zymo column kit according to manufactor's instructions.
mRNA-seq libraries were prepared in house following TruSeq RNA Library Preparation Kit (Illumina) manufacturer's instructions.

treatment_protocol: Feeding and wheel-running access   Mice were fed with round pellets of 300mg each containing 3.65 Kcal/g (Dustless Precision Pellets, Rodent, Purified, F0075, BioServ, Flemington, NJ, USA). The composition of the pellets is equivalent to regular mouse chow. Food access was controlled by an automated feeder system designed in our lab with Phenome Technologies Inc., Skokie, IL, USA that precisely controls the duration, amount and timing of food access (Acosta-Rodriguez et al., Cell Metabolism 2017). After six weeks of recording under ad libitum food access, mice were randomly assigned to one of 6 feeding conditions: 24h access ad libitum (AL) and 5 caloric restricted groups with acees to 70% of ad libitum levels. Two of the CR groups had access at the beginning of the dark (CR-night) or light (CR-day) phase, in which they consumed their allotment as a single meal within < 2h (resembling classic CR protocols). Other 3 groups had food spread-out 12 hours during the dark (CR-night-12h) or light (CR-day-12h) by releasing small meals of 300mg pellet every 90min or over 24 hours (CR-spread) by releasing one 300mg pellet every 160min. Mice were weighed in the morning and cages were changed every 21 days, and bedding was checked for any evidence of food spillage. We used ClockLab Chamber Control Software v3.401 (Actimetrics Inc., Wilmette, IL, USA) to program and record feeding events.   Wheel-running behavior was recorded throughout the study using ClockLab Data Acquisition System v3.209 (Actimetrics Inc., Wilmette, IL, USA). All mice were monitored in real-time in these conditions  until the time points for the tissue collections (see tissue collection, n=24 per feeding per age). Samples were collected, snap frozen and stored at -80ºC until RNA extraction.

tag: mouse strain

tag: knockout

value: Liver

value: Male

tag: light condition

value: 12h light / 12h dark

tag: feeding

value: Ad libitum

value: 19 months-old


title: T6S_2_3 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum only (Ta3)

city: Tai，an

first: Haiyan

last: Wang

state: Shandong

address: 61 Daizong Street

institute: Shandong Agricultural University

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: GDDH13_v1.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Malus domestica

source_name: apple rootstock (M9T337) roots

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

value: apple rootstock (M9T337) roots

value: apple rootstock (M9T337) root with 6S-2 spore suspension inoculum only (Ta)


title: CK_1 apple rootstock (M9T337) root inoculated with PDB medium (CK1)

value: apple rootstock (M9T337) root inoculated with PDB medium (CK)


title: Liv_19mo_AL_40B

value: WT

tag: Sex


title: T6S_2_C_1 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum first and then inoculated with MR5 (TaFp1)

value: apple rootstock (M9T337) root with 6S-2 spore suspension inoculum first and then inoculated with MR5 (TaFp)


title: T6S_2_1 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum only (Ta1)


title: T6S_2_C_2 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum first and then inoculated with MR5 (TaFp2)


title: T6S_2_2 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum only (Ta2)


title: CK_C_3 apple rootstock (M9T337) root inoculated with PDB medium first and then inoculated with MR5 (Fp3)

value: apple rootstock (M9T337) root inoculated with PDB medium first and then inoculated with MR5 (Fp)


title: CK_C_2 apple rootstock (M9T337) root inoculated with PDB medium first and then inoculated with MR5 (Fp2)


title: T6S_2_C_3 apple rootstock (M9T337) root with 6S-2 spore suspension inoculum first and then inoculated with MR5 (TaFp3)


title: CK_2 apple rootstock (M9T337) root inoculated with PDB medium (CK2)


title: CK_3 apple rootstock (M9T337) root inoculated with PDB medium (CK3)


title: CK_C_1 apple rootstock (M9T337) root inoculated with PDB medium first and then inoculated with MR5 (Fp1)


title: Liv_19mo_AL_28B


title: control rep2

tag: strain


title: Liv_19mo_AL_24B

tag: tissue


title: Liv_19mo_AL_20B

tag: age


title: Liv_19mo_AL_16B


title: Liv_19mo_AL_00B


title: Liv_19mo_AL_40A


title: Liv_19mo_AL_44A


title: Liv_19mo_AL_12B


title: Liv_19mo_AL_08B


title: Liv_19mo_AL_04B


title: Liv_19mo_AL_32B


title: Liv_19mo_AL_36A


title: Liv_19mo_AL_28A


title: Liv_19mo_AL_24A


title: Liv_6mo_CR-spread_24B

source_name: Liver young CR-spread

value: CR-spread

value: 6 months-old


title: Liv_6mo_CR-spread_44B


title: Liv_6mo_CR-spread_36B


title: Liv_6mo_CR-spread_40B


title: Liv_19mo_AL_20A


title: Liv_6mo_CR-spread_44A


title: Liv_19mo_AL_04A


title: Liv_19mo_AL_16A


title: Liv_19mo_AL_08A


title: Liv_6mo_CR-spread_20B


title: Liv_19mo_AL_12A


title: Liv_6mo_CR-spread_40A


title: Liv_6mo_CR-spread_28B


title: Liv_19mo_AL_32A


title: Liv_19mo_AL_00A


title: Liv_6mo_CR-spread_32B


title: alx1 sibling 2

description: alx1 siblings

value: Germline samples


title: Liv_6mo_CR-spread_12B


title: Liv_6mo_CR-spread_16B


title: Liv_6mo_CR-spread_32A


title: Ring, H3K4me3, rep1

tag: parasite line

tag: sort strategy

value: not sorted

value: ring/asexual

tag: chip antibody

value: anti-H3K4me3, Abcam ab8580


title: Liv_6mo_CR-spread_24A

value: Liver


title: Liv_6mo_CR-spread_36A

value: Male


title: Liv_6mo_CR-spread_28A

value: 12h light / 12h dark


title: Liv_6mo_CR-spread_00B


title: Liv_6mo_CR-spread_08B


title: Liv_6mo_CR-spread_04B


title: Liv_6mo_CR-spread_08A


title: Liv_6mo_CR-spread_00A


title: Liv_6mo_CR-day-2h_32B

source_name: Liver young CR-day-2h


title: Liv_6mo_CR-day-2h_44B


title: Liv_6mo_CR-spread_20A


title: Liv_6mo_CR-spread_04A


title: Liv_6mo_CR-day-2h_36B


title: Liv_6mo_CR-day-2h_24B


title: Liv_6mo_CR-day-2h_16B


title: Liv_6mo_CR-day-2h_04B


title: Liv_6mo_CR-day-2h_36A


title: Liv_6mo_CR-day-2h_12B


title: Liv_6mo_CR-day-2h_20B


title: Liv_6mo_CR-day-2h_00B


title: Liv_6mo_CR-spread_12A


title: Liv_6mo_CR-spread_16A


title: Liv_6mo_CR-day-2h_44A


title: Liv_6mo_CR-day-2h_32A


title: Liv_6mo_CR-day-2h_20A


title: Liv_6mo_CR-day-2h_24A


title: Liv_6mo_CR-day-2h_28A


title: Liv_6mo_CR-day-2h_12A


title: Liv_6mo_CR-day-2h_28B


title: Liv_6mo_CR-day-2h_40B


title: Liv_6mo_CR-day-2h_04A


title: Liv_6mo_CR-day-2h_08B


title: Liv_6mo_CR-day-2h_40A


title: Liv_6mo_CR-day-2h_16A


title: Liv_6mo_CR-day-2h_08A


title: Liv_6mo_CR-day-2h_00A


title: Liv_6mo_CR-night-2h_32B

source_name: Liver young CR-night-2h


title: Liv_6mo_CR-night-2h_28B


title: Liv_6mo_CR-night-2h_24B


title: Liv_6mo_CR-night-2h_16B


title: Liv_6mo_CR-night-2h_44B


title: Liv_6mo_CR-night-2h_36B


title: Liv_6mo_CR-night-2h_04B


title: Liv_6mo_CR-night-2h_08B


title: Liv_6mo_CR-night-2h_40B


title: Liv_6mo_CR-night-2h_40A


title: Liv_6mo_CR-night-2h_12B


title: Liv_6mo_CR-night-2h_20A


title: Liv_6mo_CR-night-2h_12A


title: Liv_6mo_CR-night-2h_20B


title: Liv_6mo_CR-night-2h_32A


title: Liv_6mo_CR-day-12h_28B

source_name: Liver young CR-day-12h


title: Liv_6mo_CR-night-2h_08A


title: Liv_6mo_CR-day-12h_24B


title: Liv_6mo_CR-night-2h_36A


title: Liv_6mo_CR-night-2h_00A


title: Liv_6mo_CR-day-12h_32B


title: Liv_6mo_CR-day-12h_20B


title: Liv_6mo_CR-night-2h_00B


title: Liv_6mo_CR-day-12h_08B


title: Liv_6mo_CR-night-2h_44A


title: Liv_6mo_CR-day-12h_44A


title: Liv_6mo_CR-night-2h_28A


title: Liv_6mo_CR-night-2h_04A


title: Liv_6mo_CR-night-2h_24A


title: Liv_6mo_CR-day-12h_00B


title: Liv_6mo_CR-night-2h_16A


title: Liv_6mo_CR-day-12h_12B


title: Liv_6mo_CR-day-12h_40B


title: Liv_6mo_CR-day-12h_36B


title: Liv_6mo_CR-day-12h_44B


title: Liv_6mo_CR-day-12h_16B


title: Liv_6mo_CR-day-12h_04B


title: Liv_6mo_CR-day-12h_40A


title: Liv_6mo_CR-day-12h_32A


title: Liv_6mo_CR-day-12h_36A


title: Liv_6mo_CR-day-12h_16A


title: Liv_6mo_CR-day-12h_20A


title: Liv_6mo_CR-day-12h_12A


title: Liv_6mo_CR-day-12h_24A


title: Liv_6mo_CR-day-12h_28A


title: Liv_6mo_CR-day-12h_04A


title: Liv_6mo_CR-day-12h_00A


title: Liv_6mo_CR-night-12h_32B

source_name: Liver young CR-night-12h


title: Liv_6mo_CR-night-12h_20B


title: Liv_6mo_CR-day-12h_08A


title: Liv_6mo_CR-night-12h_24B


title: Liv_6mo_CR-night-12h_36B


title: Liv_6mo_CR-night-12h_00B


title: Liv_6mo_CR-night-12h_40B


title: Liv_6mo_CR-night-12h_44B


title: Liv_6mo_CR-night-12h_24A


title: Liv_6mo_CR-night-12h_28A


title: Liv_6mo_CR-night-12h_32A


title: Liv_6mo_CR-night-12h_36A


title: Liv_6mo_CR-night-12h_08B


title: Liv_6mo_AL_36B

source_name: Liver young ad lib

value: Ad libitum


title: Liv_6mo_CR-night-12h_16B


title: Liv_6mo_AL_20B


title: Liv_6mo_CR-night-12h_04B


title: Liv_6mo_CR-night-12h_40A


title: Liv_6mo_AL_24B


title: Liv_6mo_AL_16B


title: Liv_6mo_CR-night-12h_20A


title: Liv_6mo_CR-night-12h_28B


title: Liv_6mo_AL_44B


title: Liv_6mo_CR-night-12h_12B


title: Liv_6mo_AL_40B


title: Liv_6mo_CR-night-12h_04A


title: Liv_6mo_AL_12B


title: Liv_6mo_CR-night-12h_12A


title: Liv_6mo_AL_28B


title: Liv_6mo_CR-night-12h_16A


title: Liv_6mo_CR-night-12h_44A


title: Liv_6mo_CR-night-12h_08A


title: Liv_6mo_AL_32B


title: Liv_6mo_AL_08B


title: Liv_6mo_AL_44A


title: Liv_6mo_AL_04B


title: MEF rep1 (ATAC-seq)

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

institute: CRCL

description:
MEF_peaks.narrowPeak
MEF_peaks.txt
MEF_summits.bed
consensus_peak.bed
consensus_peak.counts

data_processing:
Sequencing reads are aligned to the Ensembl mouse reference version 93 using bwa mem version 0.7.15
BAM files are Encode blacklist filtered and quality filtered at mapping quality 10.
Peaks are called with MACS2 version 2.1.1.20160309. Replicates are joined at this stage.
Peaks are merged with homer's mergePeak command for a consensus peak set
Coverage in consensus peak set is determined with multiBamCov from Bedtools2 version 2.25.0
Genome_build: mm9
Supplementary_files_format_and_content: peak counts and bed files

source_name: mouse embryonic fibroblasts

growth_protocol: MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Transformed cells were cultivated in the same medium than MEF.

extract_protocol:
Cells were freeze in medium containing 5% DMSO. ATAC-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo and FACS-cell sorted after 5 days.

tag: cell type

value: mouse embryonic fibroblast (MEF)

tag: treatment

value: control mouse embryonic fibroblasts


title: Liv_6mo_AL_12A


title: Liv_6mo_AL_40A


title: Liv_6mo_AL_28A


title: Liv_6mo_AL_08A


title: Liv_6mo_AL_04A


title: MEF, Repro d5 rep1 (ATAC-seq)

data_processing:
Sequencing reads are aligned to the Ensembl mouse reference version 93 using bwa mem version 0.7.15
BAM files are Encode blacklist filtered and quality filtered at mapping quality 10.
Peaks are called with MACS2 version 2.1.1.20160309. Replicates are joined at this stage.
Peaks are merged with homer's mergePeak command for a consensus peak set
Coverage in consensus peak set is determined with multiBamCov from Bedtools2 version 2.25.0
Genome_build: mm9
Supplementary_files_format_and_content: peak counts

growth_protocol: MEF were generated from E13.5 mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol.

treatment_protocol: MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo.

value: 5 days of Repro (doxycycline treatment to induce OSKM expression)


title: Liv_6mo_AL_20A


title: Liv_6mo_AL_36A


title: Liv_6mo_CR-night-12h_00A


title: iPS rep 1 (ATAC-seq)

description:
iPS_peaks.narrowPeak
iPS_peaks.txt
iPS_summits.bed
consensus_peak.bed
consensus_peak.counts

value: induced pluripotent stem cells derived from MEF OSKM doxycycline-inducible


title: Liv_6mo_AL_00B

value: WT


title: MEF, Transfo d5 rep2 (ATAC-seq)

value: 5 days of Transfo (viral induction of K-RasG12V + cMyc + shp53)


title: TC rep 1 (ATAC-seq)

description:
transformed_cell_peaks.narrowPeak
transformed_cell_peaks.txt
transformed_cell_summits.bed
consensus_peak.bed
consensus_peak.counts

value: transformed cells derived from MEF expressing K-RasG12V + cMyc + shp53


title: Liv_6mo_AL_16A


title: Liv_6mo_AL_00A


title: Liv_6mo_AL_32A


title: Liv_6mo_AL_24A


title: MEF, Repro d5 rep2 (ATAC-seq)


title: MEF, Transfo d5 rep1 (ATAC-seq)


title: MEF rep2 (ATAC-seq)


title: H9B28_B28_CTL

city: Irvine

first: Seyed

middle: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3 519 Ring Rd

department: Developmental and Cellular Biology

institute: University of California, Irvine

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to mm10 using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Kallisto was used to map the fastq files to the mm10 genome
Protein coding and long non-coding RNA genes with greater than 1 TPM in both replicates in at least four cells were kept. TPMs were quantile normalized for all heatmaps and figures
Genome_build: mm10
Supplementary_files_format_and_content: tsv output tab-delimited text files with abundance measures in counts and TPM; Supplementary file contains tab-separated file with expression values for all samples

source_name: Crh-IRES-Cre; Ai14 tdTomato

extract_protocol:
Cell prep protocol: Dissection. P10-P12 pups were killed via decapitation and brains were removed immediately on ice. The brain was trimmed to a smaller block containing hypothalamus and was placed into a slush of EBSS. The block was then sliced on a vibratome to obtain at 1.5mm slice posterior of the anterior commissure. The slice was then trimmed under a dissection microscope to remove thalamus and cortex. Dissociation. The trimmed slices were placed immediately into papain and gently triturated ~15 times with a pipette to break up tissue before being placed on a heated (37C) orbital shaker for 30 minutes. Digested tissue was then homogenized by triturating with pipette ~ 50 times until there were no visible tissue chunks. Homogenate was spun at 500 x g for 15 minutes at room temperature. Supernatant was removed and cells were resuspended in 500uL 2% FBS in PBS. FACS. Samples were run on the aria fusion. Immediately prior to sort, cell suspension was run through a 70uM filter and washed with 500uL 2% FBS in PBS.  Cells were sorted into 8 well strip tubes and immediately spun down at 4C and frozen on dry ice.
RNA from single cells was converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (FC-121-1030, Illumina). Libraries were sequenced on the Illumina NextSeq500 platform using paired-end 43 bp mode.

treatment_protocol: Animal protocol: The simulated poverty limited bedding and nesting paradigm (LBN) consisted of limiting nesting and bedding materials in cages between P2-P9 as described previously. For the LBN group, a plastic-coated mesh platform was placed ~2.5cm above the floor of a standard cage. Cobb bedding was reduced to cover the cage floor sparsely, and one-half of a single nestlet was provided for nesting material on the platform. CTL dams and litters resided in standard cages containing ample cob bedding and one whole nestlet for nesting. This paradigm causes maternal care to be fragmented and unpredictable 48,52, provoking chronic stress in the pups 55. CTL and experimental cages were undisturbed during P2–P9, housed in temperature-controlled rooms (22°C). For RNA sequencing pups remained on the LBN paradigm until tissue was collected P10-P12. For experiments in adulthood, experimental groups were transferred to standard cages on P10 and were weaned on P21. Animals were housed by sex with littermates.

value: CRH-expressing neuron

tag: genotype

value: Crh-IRES-Cre; Ai14 tdTomato

tag: condition

value: CTL

tag: weight

tag: age at collection

tag: protocol

value: RNA

tag: library prep

value: Nextera XT DNA Library Prep Kit (FC-131-1096, Illiumina)


title: H8L17_L17_ELA

value: ELA


title: H9L15_L15_ELA


title: H9L17_L17_ELA


title: H9B21_B21_CTL


title: H8L15_L15_ELA


title: H8L16_L16_ELA


title: H8B21_B21_CTL


title: H8B23_B23_CTL


title: H9L16_L16_ELA


title: H8B28_B28_CTL


title: H9B23_B23_CTL


title: H7L17_L17_ELA


title: H7L16_L16_ELA


title: H7B28_B28_CTL


title: H7B23_B23_CTL


title: H6B28_B28_CTL


title: H5L17_L17_ELA


title: H6L10_L10_ELA


title: H6L16_L16_ELA


title: H5L16_L16_ELA


title: H5B34_B34_CTL


title: H7B34_B34_CTL


title: H7B21_B21_CTL


title: H6B34_B34_CTL


title: H5B23_B23_CTL


title: H5B28_B28_CTL


title: H5B20_B20_CTL


title: H4L17_L17_ELA


title: H4L16_L16_ELA


title: H4L10_L10_ELA


title: H4B28_B28_CTL


title: H4B34_B34_CTL


title: H6B23_B23_CTL


title: H3L10_L10_ELA


title: H3L16_L16_ELA


title: H3L13_L13_CTL


title: H4B23_B23_CTL


title: H3B23_B23_CTL


title: H2L16_L16_ELA


title: H3B34_B34_CTL


title: H1L17_L17_ELA


title: H2B19_B19_CTL


title: H1L16_L16_ELA


title: H2B34_B34_CTL


title: H12L15_L15_ELA


title: H1B34_B34_CTL


title: H1L13_L13_CTL


title: H2L13_L13_CTL


title: H12B28_B28_CTL


title: H2L17_L17_ELA


title: H12L17_L17_ELA


title: H12L11_L11_ELA


title: H3L17_L17_ELA


title: H11L17_L17_ELA


title: H11L15_L15_ELA


title: H11L16_L16_ELA


title: H12L16_L16_ELA


title: H2L11_L11_ELA


title: H10L15_L15_ELA


title: H10L16_L16_ELA


title: H10B28_B28_CTL


title: H1L11_L11_ELA


title: H10L17_L17_ELA


title: H10B21_B21_CTL


title: H10L11_L11_ELA


title: G9L11_L11_ELA


title: G9L16_L16_ELA


title: G9L17_L17_ELA


title: G9L13_L13_CTL


title: G9B34_B34_CTL


title: G9B21_B21_CTL


title: G8L13_L13_CTL


title: G8L16_L16_ELA


title: H11B28_B28_CTL


title: G8B21_B21_CTL


title: G7L13_L13_CTL


title: G8L11_L11_ELA


title: G7L16_L16_ELA


title: G8B34_B34_CTL


title: G6L16_L16_ELA


title: G7B34_B34_CTL


title: G6L13_L13_CTL


title: G6L10_L10_ELA


title: G6L11_L11_ELA


title: G6B34_B34_CTL


title: G5L16_L16_ELA


title: G5L13_L13_CTL


title: G8L17_L17_ELA


title: G5B34_B34_CTL


title: G4L13_L13_CTL


title: G5L10_L10_ELA


title: G4L16_L16_ELA


title: G4L11_L11_ELA


title: G3L16_L16_ELA


title: G4L10_L10_ELA


title: G5L11_L11_ELA


title: G7L11_L11_ELA


title: G7L10_L10_ELA


title: G3L16S1_L16_ELA


title: G3L13_L13_CTL


title: G3B34_B34_CTL


title: G2L16S1_L16_ELA


title: G2L11_L11_ELA


title: G2B19_B19_CTL


title: G1L16_L16_ELA


title: G1L16S1_L16_ELA


title: G3L11_L11_ELA


title: G2L13_L13_CTL


title: G12L16_L16_ELA


title: G3L10_L10_ELA


title: G2L16_L16_ELA


title: G12L13_L13_CTL


title: G2B34_B34_CTL


title: G1B34_B34_CTL


title: G4B34_B34_CTL


title: G12L11_L11_ELA


title: G11L17_L17_ELA


title: G11L16_L16_ELA


title: G11L13_L13_CTL


title: G12L17_L17_ELA


title: G10L16_L16_ELA


title: G10B34_B34_CTL


title: G11B34_B34_CTL


title: G10L11_L11_ELA


title: G1L11_L11_ELA


title: G1L13_L13_CTL


title: G10B21_B21_CTL


title: F9L16S1_L16_ELA


title: F9L16_L16_ELA


title: F9L11_L11_ELA


title: G10L17_L17_ELA


title: G12B34_B34_CTL


title: F9B33_B33_CTL


title: G10L13_L13_CTL


title: F8L11_L11_ELA


title: G11L11_L11_ELA


title: F8B21_B21_CTL


title: F7L16S1_L16_ELA


title: F7L16_L16_ELA


title: F9B21_B21_CTL


title: F8L16_L16_ELA


title: F7L13_L13_CTL


title: F6L16_L16_ELA


title: F7L11_L11_ELA


title: F6L13_L13_CTL


title: F7B33_B33_CTL


title: F6L16S1_L16_ELA


title: F6L11_L11_ELA


title: F6L10_L10_ELA


title: F6B33_B33_CTL


title: F5L10_L10_ELA


title: F8L16S1_L16_ELA


title: F4B33_B33_CTL


title: F9L13_L13_CTL


title: F7L10_L10_ELA


title: F3L11_L11_ELA


title: F2L16_L16_ELA


title: F3B26_B26_CTL


title: F2L16S1_L16_ELA


title: F5L16_L16_ELA


title: F5L16S1_L16_ELA

description: R2 fastq file was not available at time of submission, only R1 fastq submitted.


title: F5B33_B33_CTL


title: F5L11_L11_ELA


title: F1L16_L16_ELA


title: F5B26_B26_CTL


title: F3L16S1_L16_ELA


title: F4L16_L16_ELA


title: F4L16S1_L16_ELA


title: F1B33_B33_CTL


title: F1B26_B26_CTL


title: F4L11_L11_ELA


title: F4L10_L10_ELA


title: F4B26_B26_CTL


title: F12L11_L11_ELA


title: F3L16_L16_ELA


title: F3L10_L10_ELA


title: F3B33_B33_CTL


title: F2B33_B33_CTL


title: F2L11_L11_ELA


title: F12B34_B34_CTL


title: F1L11_L11_ELA


title: F1L16S1_L16_ELA


title: F2B26_B26_CTL


title: F2B19_B19_CTL


title: F11L13_L13_CTL


title: F10L16S1_L16_ELA


title: F10L16_L16_ELA


title: F11L16S1_L16_ELA


title: F12L16S1_L16_ELA


title: F12L16_L16_ELA


title: F10L11_L11_ELA


title: E9L16_L16_ELA


title: F12L13_L13_CTL


title: F10L13_L13_CTL


title: E9B38_B38_CTL


title: F11L11_L11_ELA


title: F11L16_L16_ELA


title: F11B34_B34_CTL


title: E8L16_L16_ELA


title: F10B34_B34_CTL


title: F10B21_B21_CTL


title: E9L11_L11_ELA


title: E8L11_L11_ELA


title: E8B33_B33_CTL


title: E8B38_B38_CTL


title: E9B21_B21_CTL


title: E8B26_B26_CTL


title: E9B33_B33_CTL


title: E9B26_B26_CTL


title: E8B21_B21_CTL


title: E7L16_L16_ELA


title: E7B38_B38_CTL


title: E7L10_L10_ELA


title: E7B26_B26_CTL


title: E7B33_B33_CTL


title: E7L11_L11_ELA


title: E5L17_L17_ELA


title: E6L10_L10_ELA


title: E6L11_L11_ELA


title: E6B33_B33_CTL


title: E5L10_L10_ELA


title: E4L17_L17_ELA


title: E4B26_B26_CTL


title: E4L11_L11_ELA


title: E4B20_B20_CTL


title: E6B26_B26_CTL


title: E5L11_L11_ELA


title: E5L16_L16_ELA


title: E5B26_B26_CTL


title: E5B33_B33_CTL


title: E6L17_L17_ELA


title: E6L16_L16_ELA


title: E2B25_B25_CTL


title: E2B19_B19_CTL


title: E2L11_L11_ELA


title: E2B33_B33_CTL


title: E3L17_L17_ELA


title: E3L11_L11_ELA


title: E3B33_B33_CTL


title: E4B33_B33_CTL


title: E3B26_B26_CTL


title: E2B38_B38_CTL


title: E3L16_L16_ELA


title: E2L17_L17_ELA


title: E12L16_L16_ELA


title: E3B19_B19_CTL


title: E1L11_L11_ELA


title: E1B33_B33_CTL


title: E12L11_L11_ELA


title: E1B25_B25_CTL


title: E11L16_L16_ELA


title: E12B26_B26_CTL


title: E12B33_B33_CTL


title: E11L11_L11_ELA


title: E1L17_L17_ELA


title: E11B33_B33_CTL


title: E12B38_B38_CTL


title: E11B38_B38_CTL


title: E12L16S1_L16_ELA


title: E11B26_B26_CTL


title: E10L16_L16_ELA


title: E10B21_B21_CTL


title: E11B38S2_B38_CTL


title: D9B38_B38_CTL


title: D9L16_L16_ELA


title: E10L11_L11_ELA


title: E10B33_B33_CTL


title: E10B38_B38_CTL


title: E10B26_B26_CTL


title: D8B21_B21_CTL


title: D7L17_L17_ELA


title: D9B32_B32_CTL


title: D9B25_B25_CTL


title: D7L10_L10_ELA


title: D9B21_B21_CTL


title: D7B32_B32_CTL


title: D8L9_L9_ELA


title: D9L17_L17_ELA


title: D9L11_L11_ELA


title: D7B25_B25_CTL


title: D6L11_L11_ELA


title: D8B38_B38_CTL


title: D8L16_L16_ELA


title: D7L11_L11_ELA


title: D6B32_B32_CTL


title: D8B32_B32_CTL


title: E10B38S2_B38_CTL


title: D8B25_B25_CTL


title: D8L17_L17_ELA


title: D7L16_L16_ELA


title: D5L17_L17_ELA


title: D8L11_L11_ELA


title: D5L16_L16_ELA


title: D5L10_L10_ELA


title: D7L9_L9_ELA


title: D4L7_L7_ELA


title: D4L16_L16_ELA


title: D7B38_B38_CTL


title: D6L16_L16_ELA


title: D6B38_B38_CTL


title: D4B25_B25_CTL


title: D5B38_B38_CTL


title: D3L7_L7_ELA


title: D6B20_B20_CTL


title: D3L17_L17_ELA


title: D3B32_B32_CTL


title: D3B38_B38_CTL


title: D6L17_L17_ELA


title: D5B25_B25_CTL


title: D5B32_B32_CTL


title: D4L11_L11_ELA


title: D6B25_B25_CTL


title: D5L11_L11_ELA


title: D3B25_B25_CTL


title: D2L11_L11_ELA


title: D4B20_B20_CTL


title: D4B32_B32_CTL


title: D2B32_B32_CTL


title: D4B38_B38_CTL


title: D4L17_L17_ELA


title: D1B25_B25_CTL


title: D3B19_B19_CTL


title: D12L16_L16_ELA


title: D12B38_B38_CTL


title: D12B25_B25_CTL


title: D2L7_L7_ELA


title: D3L11_L11_ELA


title: D11L11_L11_ELA


title: D2B38_B38_CTL


title: D11B38_B38_CTL


title: D11B25_B25_CTL


title: D1L17_L17_ELA


title: D2L17_L17_ELA


title: D1L11_L11_ELA


title: D10B38_B38_CTL


title: D10L11_L11_ELA


title: D2B25_B25_CTL


title: D10B21_B21_CTL


title: D2B19_B19_CTL


title: D10B33_B33_CTL


title: D1B32_B32_CTL


title: D2L16_L16_ELA


title: D11B33_B33_CTL


title: C9L16_L16_ELA


title: D1B38_B38_CTL


title: D11L16_L16_ELA


title: D12L11_L11_ELA


title: D12L17_L17_ELA


title: C9B25_B25_CTL


title: C8L17_L17_ELA


title: D12B33_B33_CTL


title: D10L16_L16_ELA


title: D10L17_L17_ELA


title: C7L17_L17_ELA


title: C8B21_B21_CTL


title: C9L11_L11_ELA


title: C7L7_L7_ELA


title: D10B25_B25_CTL


title: C7L16_L16_ELA


title: C9L17_L17_ELA


title: C7B32_B32_CTL


title: C9B38_B38_CTL


title: D11L17_L17_ELA


title: C7B25_B25_CTL


title: C6L11_L11_ELA


title: C8L11_L11_ELA


title: C8B32_B32_CTL


title: C6B38_B38_CTL


title: C6B20_B20_CTL


title: C6B25_B25_CTL


title: C6B32_B32_CTL


title: C9B32_B32_CTL


title: C6L17_L17_ELA


title: C8B38_B38_CTL


title: C9B21_B21_CTL


title: C7B38_B38_CTL


title: C8B25_B25_CTL


title: C5B38_B38_CTL


title: C8L16_L16_ELA


title: C5B20_B20_CTL


title: C7L10_L10_ELA


title: C5L17_L17_ELA


title: C6L16_L16_ELA


title: C5L16_L16_ELA


title: C4B32_B32_CTL


title: C4B38_B38_CTL


title: C9L7_L7_ELA


title: C5B25_B25_CTL


title: C7L11_L11_ELA


title: C4L17_L17_ELA


title: C5B32_B32_CTL


title: C3L17_L17_ELA


title: C2L11_L11_ELA


title: C2L12_L12_ELA


title: C2L17_L17_ELA


title: C2B32_B32_CTL


title: C5L11_L11_ELA


title: C3B38_B38_CTL


title: C1L7_L7_ELA


title: C4L7_L7_ELA


title: C2B38_B38_CTL


title: C2B19_B19_CTL


title: C1B38_B38_CTL


title: C4L11_L11_ELA


title: C4L12_L12_ELA


title: C4B20_B20_CTL


title: C12L16_L16_ELA


title: C4L16_L16_ELA


title: C1L12_L12_ELA


title: C1B32_B32_CTL


title: C3L11_L11_ELA


title: C3L12_L12_ELA


title: C3B32_B32_CTL


title: C12B38_B38_CTL


title: C12L17_L17_ELA


title: C3B19_B19_CTL


title: C1L17_L17_ELA


title: C1L11_L11_ELA


title: C12B25_B25_CTL


title: C12B32_B32_CTL


title: C11L17_L17_ELA


title: C12L11_L11_ELA


title: C11B38_B38_CTL


title: C11L16_L16_ELA


title: C11L11_L11_ELA


title: C11B25_B25_CTL


title: C11L7_L7_ELA


title: C10L7_L7_ELA


title: C11B32_B32_CTL


title: hrlp-2, rep2

city: Singapore

first: Yu

last: Zhang

state: Singapore

address: 1 Research Link national university of singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Paired-end raw reads were trimmed by removing reads with PHRED scores below 20 or with length shorter than 25 nt
Trimmed data were aligned to the reference genome TAIR10 using STAR 2.7.3a with default parameters
Filtered gene counts were normalized to the counts per million (CPM) values
Assembly: genome TAIR10
Supplementary files format and content: Text files include normalized gene count

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 23 ± 2°C, long days (16 hr light/8 hr dark)

extract_protocol:
The aerial parts of 9-day-old wild-type and hrlp-2 seedlings grown under LDs were harvested for total RNA extraction using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used to construct the library

value: seedlings

tag: phenotype

value: HRLP knock out

value: 23 +- 2 degrees C, long days


title: WT, rep2

value: Col


title: hrlp-2, rep1


title: hrlp-2, rep3


title: WT, rep3


title: WT, rep1


title: C10L16_L16_ELA


title: C10L17_L17_ELA


title: C10B32_B32_CTL


title: B9L17_L17_ELA


title: C10B25_B25_CTL


title: C10B38_B38_CTL


title: B9B36_B36_CTL


title: B9B38_B38_CTL


title: B9B21_B21_CTL


title: B9B32_B32_CTL


title: miRNA449a experiment no. 4

type: RNA

city: Hannover

first: Marlies

last: Eilers

address: Kurze Halbe 12

institute: Medizinische Hochschule Hannover

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6,0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of GEx hybridization buffer (Agilent) was added to the fragmentation mixture and hybridized to SurePrintG3 8x60k Human Gene Expression Arrays (#G4851C, Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm. Profile: AgilentHD_GX_1Color

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid:072363_D_F_20150612 to obtain background subtracted and spatially detrended Processed Signal intensities. These values were then transformed with base 2 log and normalized with Shift to 75 Percentile followed by Baseline Transformation on basis of the median of all samples.

source_name: HCC38 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the Low-Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with a Nanophotometer (Implen) and the Bioanalyzer (Agilent).

growth_protocol: Cell culture in RPMI-1640-Medium (#R8758,Sigma, 10 % FKS, 4,5 mg/mL Glucose, 2,4 mg/mL Hepes, 0,11 mg/mL Natriumpyruvat and 100U/ml Penicillin/Streptomycin). Incubation at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA-Extraction with Direct-zol RNA Mini Prep Kit (Zymo Research) following the manufacturers instructions incl. Dnase digestion. RNA was quantified using a Nanophotometer (Implen) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Transient Transfection with 50nM AllStars Negative Control siRNA or 50nM mimic449a and Hiperfect Transfection Reagent (all Qiagen) with 250.000 cells/well in 6-well-plates for 48h hours following the manufacturers instructions.

tag: cell line

tag: transfected with


title: B9L12_L12_ELA


title: C10B21_B21_CTL


title: C10L11_L11_ELA


title: B8L12_L12_ELA


title: B8L11_L11_ELA


title: Treated2, T4nv, Natalizumab

first: Nikolaos

last: Patsopoulos

address: 60 Fenwood Road

institute: BRIGHAM AND WOMEN'S HOSPITAL

data_processing:
Paired-end raw ATAC-seq reads were trimmed using Ngmerge using default parameters
The reads were then aligned to GRCh38 using Bowtie2 version 2.3.5
The resulting SAM files were converted and sorted into BAM format using samtools version 1.5
Reads with MAPQ<10 and reads that were aligned to mitochondria were filtered out using samtools
duplicate reads were removed using picard version 2.20.6
peaks were called using MACS2 version 2.2.5 51 with default parameters and --keep-dup all --nomodel –nolambda
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

source_name: peripheral blood

extract_protocol:
Cells were flow-sorted directly into cold tagmentation buffer (10 uL TD, 2 uL 2% IGEPAL CA-630, 6 uL nuclease-free H2O, 2 uL TDE1 per sample), followed by incubation at 37℃ for 30 min with shaking at 500 RPM. DNA was extracted QIAGEN MinElute PCR purification kit according to the manufacturer's protocol
Samples were amplified with KAPA HiFi kits and Illumina Nextera indices. The amplified material was cleaned with the QIAGEN MinElute PCR purification kit and quantified using KAPA library quantification kits

value: peripheral blood

tag: Sex

value: F

value: Natalizumab


title: Treated2, T4ra, Natalizumab

tag: tissue


title: Treated2, traB, Natalizumab

value: traB

tag: age


title: Treated2, cMBc, Natalizumab

value: cMBc


title: AllStars control experiment no. 4

value: AllStars Negative Control siRNA


title: miRNA449a experiment no. 3


title: AllStars control experiment no. 3


title: B8L17_L17_ELA


title: AllStars control experiment no. 2


title: Treated2, T4em, Natalizumab


title: miRNA449a experiment no. 2


title: B8B31_B31_CTL


title: B8L7_L7_ELA


title: B8B36_B36_CTL


title: B8B21_B21_CTL


title: B8B38_B38_CTL


title: miRNA449a experiment no. 1


title: B7L7_L7_ELA


title: AllStars control experiment no. 1


title: B9L11_L11_ELA


title: Treated1, traB, Interferon_beta_1a


title: Treated1, T4ra, Interferon_beta_1a


title: Treated1, T4nv, Interferon_beta_1a


title: B7L12_L12_ELA


title: Treated2, T4cm, Natalizumab


title: B7L11_L11_ELA


title: B7L10_L10_ELA


title: Treated1, cMBc, Interferon_beta_1a


title: B7L17_L17_ELA


title: Treated3, traB, Glatiramer_acetate


title: Treated3, T4ra, Glatiramer_acetate


title: B6L17_L17_ELA


title: Treated3, T4em, Glatiramer_acetate


title: Treated3, T4nv, Glatiramer_acetate


title: Treated1, T4em, Interferon_beta_1a


title: B7B38_B38_CTL


title: B6L12_L12_ELA


title: Treated1, T4cm, Interferon_beta_1a


title: Treated3, cMBc, Glatiramer_acetate


title: Untreated1, cMBc, Untreated

value: Untreated


title: B6B38_B38_CTL

value: CRH-expressing neuron


title: Untreated2, cMBc, Untreated


title: Untreated2, traB, Untreated


title: B7B36_B36_CTL

value: Crh-IRES-Cre; Ai14 tdTomato


title: B5L11_L11_ELA


title: Treated3, T4cm, Glatiramer_acetate


title: B7B31_B31_CTL

value: CTL


title: Untreated6, cMBc, Untreated


title: B6L11_L11_ELA

value: RNA


title: B5L12_L12_ELA

value: Nextera XT DNA Library Prep Kit (FC-131-1096, Illiumina)


title: B5L17_L17_ELA

value: ELA


title: B5L14_L14_ELA


title: Untreated1, traB, Untreated


title: B6B31_B31_CTL


title: Untreated1, T4ra, Untreated


title: B6L10_L10_ELA


title: Untreated3, cMBc, Untreated


title: Untreated4, T4ra, Untreated


title: B6L7_L7_ELA


title: B5B38_B38_CTL


title: Untreated4, T4nv, Untreated


title: B5B36_B36_CTL


title: Untreated2, T4nv, Untreated


title: Untreated3, T4nv, Untreated


title: B4L12_L12_ELA


title: B4L14_L14_ELA


title: Untreated5, T4nv, Untreated


title: B5L10_L10_ELA


title: Untreated3, T4ra, Untreated


title: B3L17_L17_ELA


title: Untreated3, T4em, Untreated


title: B4L17_L17_ELA


title: Untreated2, T4em, Untreated


title: Untreated1, T4em, Untreated


title: B4L11_L11_ELA


title: Untreated6, T4em, Untreated


title: B4B20_B20_CTL


title: Untreated2, T4ra, Untreated


title: B3L11_L11_ELA


title: Untreated6, T4nv, Untreated


title: Untreated4, T4em, Untreated


title: Untreated5, T4em, Untreated


title: B3L14_L14_ELA


title: B3B36_B36_CTL


title: B3B38_B38_CTL


title: Untreated3, T4cm, Untreated


title: Untreated2, T4cm, Untreated


title: B4B38_B38_CTL


title: B3B19_B19_CTL


title: Untreated4, T4cm, Untreated


title: B2L17_L17_ELA


title: B2L12_L12_ELA


title: B2L14_L14_ELA


title: Untreated5, T4cm, Untreated


title: Untreated6, T4cm, Untreated


title: Untreated1, T4nv, Untreated


title: Untreated1, T4cm, Untreated


title: B3L12_L12_ELA


title: B2L11_L11_ELA


title: B1L17_L17_ELA


title: GC080717_H03

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

data_processing:
Single-end sequencing was performed using an Illumina HiSeq 4000 device
After adapter removal, 50bp-long raw reads were aligned to the reference genome hg38 using splice-aware aligner HISAT2
Absolute gene counts were generated using HTSeq based on the Ensemble83 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

extract_protocol:
After collection, the blood samples were stored in PAXgene tubes at ambient temperature for at least 24 hours, and then stored at -80°C until extraction. Total RNA was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH).
Library preparation was done using the Lexogen QuantSeq mRNA kit according to the manufacturer’s instructions

tag: ar

tag: abmrh

tag: tcmr

tag: polyoma (no

tag: dsa


title: B2B36_B36_CTL

tag: genotype


title: B2B19_B19_CTL

tag: condition


title: GC080717_G04


title: B2B38_B38_CTL

tag: weight


title: GC080717_H06


title: GC080717_H05


title: GC080717_G03


title: GC080717_H02


title: GC080717_H01


title: B1L12_L12_ELA

tag: age at collection


title: GC080717_F06


title: GC080717_H04


title: GC080717_G01


title: GC080717_G06


title: GC080717_G02


title: GC080717_F05


title: B1B36_B36_CTL

tag: protocol


title: GC080717_G05


title: S100a10_bacTRAP_Flx_Sh_anxious_TRAP_Rep3

city: NY

first: Revathy

middle: Uthaiah

last: Chottekalapanda

state: NY

address: 1230 York Avenue

department: Laboratory of Molecular and Cellular neuroscience

institute: The Rockefeller University

description:
TRAP15
TRAP15

data_processing:
The raw sequencing files in FASTQ format were aligned in the Mus musculus assembly 10 reference genome using TopHat version 2.0.11 with the parameter of only 1 multiple hit allowed.
Cufflinks version 2.2.1 was utilized to calculate the fragments per kilobase of transcript per Million mapped reads (FPKM) for all genes in each sample.
Differential expression was done using edgeR version 3.8.6.
P values were calculated and adjusted for multiple testing using the Benjamini-Hochberg procedure.
Pathway analysis was performed using GO and Ingenuity Pathway Analysis (Qiagen).
Assembly: mm10 (GRCm38)
Supplementary files format and content: reads.counts.*.txt: Read counts.
Supplementary files format and content: *.csv: Enrichment IP/input (DESeq2).
Library strategy: TRAP-Seq

source_name: TRAP IP RNA of pooled cortices from three mice with transgenic expression of EGFPL10a

extract_protocol:
Cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). RNA from Immunoprecipitated (IP'ed) and input samples were purified with the RNeasy plus micro kit (Qiagen) following manufacturer's protocol.
2.5 ng RNA from TRAP IP or input was reverse transcribed using the NuGEN Ovation RNA-Seq System V2. Libraries for sequencing were generated using 500ng of cDNA using Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocols.
Samples were sequenced in two independent lanes on an Illumina NextSeq 500 sequencer using the 75-bp paired-end sequencing.

treatment_protocol: Mice were administered 0.167g/L fluoxetine in drinking water for 21 days.

tag: strain

tag: brain region

value: Cortex

tag: cell type

value: Layer5a S100a10 neurons

tag: housing

value: single housed (Sh)

tag: treatment

value: Fluoxetine (Flx)

tag: behavior

value: anxious

tag: sample type

value: Immunoprecipitation (IP)


title: B1B38_B38_CTL

tag: tissue

tag: library prep


title: S100a10_bacTRAP_Vehicle_Sh_TRAP_Rep3

description:
TRAP11
TRAP11

value: Vehicle

value: normal


title: S100a10_bacTRAP_Flx_Sh_anxious_TRAP_Rep4

description:
TRAP16
TRAP16


title: S100a10_bacTRAP_Vehicle_Sh_TRAP_Rep4

description:
TRAP12
TRAP12


title: S100a10_bacTRAP_Flx_Sh_TRAP_Rep3

description:
TRAP13
TRAP13


title: GC080717_F04

tag: ar

tag: abmrh

tag: tcmr


title: GC080717_F03

tag: polyoma (no

tag: dsa


title: GC080717_F01


title: S100a10_bacTRAP_Vehicle_Gh_TRAP_Rep4

description:
TRAP10
TRAP10

value: group housed (Gh)


title: S100a10_bacTRAP_Vehicle_Gh_TRAP_Rep3

description:
TRAP9
TRAP9


title: S100a10_bacTRAP_Flx_Sh_anxious_TRAP_Rep1

description:
TRAP7
TRAP7


title: GC080717_E06


title: S100a10_bacTRAP_Flx_Sh_TRAP_Rep2

description:
TRAP6
TRAP6


title: S100a10_bacTRAP_Flx_Sh_TRAP_Rep1

description:
TRAP5
TRAP5


title: GC080717_E04


title: S100a10_bacTRAP_Vehicle_Gh_TRAP_Rep2

description:
TRAP2
TRAP2


title: B1L11_L11_ELA

tag: genotype

tag: condition

tag: weight


title: S100a10_bacTRAP_Flx_Sh_TRAP_Rep4

description:
TRAP14
TRAP14

tag: strain


title: GC080717_E05


title: S100a10_bacTRAP_Vehicle_Gh_TRAP_Rep1

description:
TRAP1
TRAP1

tag: brain region


title: GC080717_F02


title: GC080717_E03


title: S100a10_bacTRAP_Flx_Sh_anxious_TRAP_Rep2

description:
TRAP8
TRAP8

tag: cell type


title: S100a10_bacTRAP_Vehicle_Sh_TRAP_Rep1

description:
TRAP3
TRAP3

tag: housing


title: S100a10_bacTRAP_Vehicle_Sh_TRAP_Rep2

description:
TRAP4
TRAP4

tag: treatment


title: GC080717_D06


title: S100a10_bacTRAP_Flx_Sh_anxious_input_Rep4

description:
INPUT16
INPUT16

data_processing:
The raw sequencing files in FASTQ format were aligned in the Mus musculus assembly 10 reference genome using TopHat version 2.0.11 with the parameter of only 1 multiple hit allowed.
Cufflinks version 2.2.1 was utilized to calculate the fragments per kilobase of transcript per Million mapped reads (FPKM) for all genes in each sample.
Differential expression was done using edgeR version 3.8.6.
P values were calculated and adjusted for multiple testing using the Benjamini-Hochberg procedure.
Pathway analysis was performed using GO and Ingenuity Pathway Analysis (Qiagen).
Assembly: mm10 (GRCm38)
Supplementary files format and content: reads.counts.*.txt: Read counts.
Supplementary files format and content: *.csv: Enrichment IP/input (DESeq2).

source_name: Whole cortex input RNA pooled from three mice with transgenic expression of EGFPL10a

tag: behavior

value: Input


title: S100a10_bacTRAP_Flx_Sh_input_Rep3

description:
INPUT13
INPUT13

tag: sample type


title: GC080717_E02


title: GC080717_D02


title: GC080717_E01


title: S100a10_bacTRAP_Vehicle_Sh_input_Rep3

description:
INPUT11
INPUT11


title: S100a10_bacTRAP_Vehicle_Gh_input_Rep3

description:
INPUT9
INPUT9


title: S100a10_bacTRAP_Flx_Sh_anxious_input_Rep2

description:
INPUT8
INPUT8


title: GC080717_C04


title: GC080717_D03


title: S100a10_bacTRAP_Vehicle_Sh_input_Rep4

description:
INPUT12
INPUT12


title: S100a10_bacTRAP_Flx_Sh_input_Rep4

description:
INPUT14
INPUT14


title: GC080717_D01


title: S100a10_bacTRAP_Vehicle_Gh_input_Rep4

description:
INPUT10
INPUT10


title: GC080717_C02


title: GC080717_C06


title: S100a10_bacTRAP_Flx_Sh_anxious_input_Rep1

description:
INPUT7
INPUT7


title: S100a10_bacTRAP_Flx_Sh_input_Rep2

description:
INPUT6
INPUT6


title: S100a10_bacTRAP_Flx_Sh_anxious_input_Rep3

description:
INPUT15
INPUT15


title: GC080717_C01


title: GC080717_D05


title: GC080717_B06


title: GC080717_D04


title: S100a10_bacTRAP_Vehicle_Gh_input_Rep2

description:
INPUT2
INPUT2


title: S100a10_bacTRAP_Vehicle_Sh_input_Rep2

description:
INPUT4
INPUT4


title: GC080717_C05


title: GC080717_B04


title: S100a10_bacTRAP_Flx_Sh_input_Rep1

description:
INPUT5
INPUT5


title: GC080717_C03


title: S100a10_bacTRAP_Vehicle_Sh_input_Rep1

description:
INPUT3
INPUT3


title: GC080717_B03


title: S100a10_bacTRAP_Vehicle_Gh_input_Rep1

description:
INPUT1
INPUT1


title: GC080717_B05


title: GC080717_B02


title: Liv_19mo_CR-spread_44B

source_name: Liver aged CR-spread

tag: mouse strain

tag: knockout

value: WT

tag: tissue

value: Liver

tag: Sex

value: Male

tag: light condition

value: 12h light / 12h dark

tag: feeding

value: CR-spread

tag: age

value: 19 months-old


title: Liv_19mo_CR-spread_40B


title: GC080717_B01

tag: ar

tag: abmrh

tag: tcmr

tag: polyoma (no

tag: dsa


title: Liv_19mo_CR-spread_36B


title: GC080717_A05


title: GC080717_A03


title: GC080717_A06


title: GC080717_A04


title: Liv_19mo_CR-spread_32B


title: Liv_19mo_CR-spread_28B


title: GC080717_A01


title: GC080717_A02


title: Liv_19mo_CR-spread_16B


title: GC080716_H04


title: Liv_19mo_CR-spread_04B


title: Liv_19mo_CR-spread_44A


title: GC080716_H06


title: GC080716_H02


title: Liv_19mo_CR-spread_20B


title: Liv_19mo_CR-spread_24B


title: Liv_19mo_CR-spread_12B


title: GC080716_H05


title: GC080716_G04


title: Liv_19mo_CR-spread_28A


title: Liv_19mo_CR-spread_24A


title: GC080716_G02


title: Liv_19mo_CR-spread_00B


title: GC080716_H03


title: Liv_19mo_CR-spread_40A


title: GC080716_H01


title: Liv_19mo_CR-spread_20A


title: GC080716_G03


title: GC080716_G01


title: Liv_19mo_CR-spread_08A


title: GC080716_G06


title: GC080716_F06


title: GC080716_G05


title: Liv_19mo_CR-spread_36A


title: Liv_19mo_CR-spread_12A


title: Liv_19mo_CR-spread_32A


title: Liv_19mo_CR-spread_04A


title: GC080716_F04


title: Liv_19mo_CR-day-2h_44B

source_name: Liver aged CR-day-2h


title: Liv_19mo_CR-day-2h_40B


title: Liv_19mo_CR-day-2h_36B


title: GC080716_F01


title: GC080716_F05


title: Liv_19mo_CR-spread_00A


title: GC080716_F03


title: GC080716_F02


title: Liv_19mo_CR-day-2h_20B


title: Liv_19mo_CR-spread_16A


title: GC080716_D03


title: Liv_19mo_CR-day-2h_28B


title: Liv_19mo_CR-day-2h_44A


title: Liv_19mo_CR-day-2h_24B


title: GC080716_E04


title: GC080716_E05


title: Liv_19mo_CR-day-2h_32B


title: GC080716_D01


title: Liv_19mo_CR-day-2h_40A


title: Liv_19mo_CR-day-2h_16B


title: GC080716_C06


title: GC080716_E02


title: GC080716_E03


title: Liv_19mo_CR-day-2h_08B


title: GC080716_E01


title: GC080716_D05


title: Liv_19mo_CR-day-2h_12B


title: Liv_19mo_CR-day-2h_28A


title: GC080716_D06


title: Liv_19mo_CR-day-2h_32A


title: GC080716_D04


title: GC080716_C03


title: GC080716_C02


title: Liv_19mo_CR-day-2h_04B


title: Liv_19mo_CR-day-2h_20A


title: GC080716_C01


title: Liv_19mo_CR-day-2h_12A


title: Liv_19mo_CR-day-2h_00B


title: GC080716_D02


title: GC080716_E06


title: GC080716_B05


title: Liv_19mo_CR-day-2h_08A


title: GC080716_B04


title: Liv_19mo_CR-day-2h_00A


title: Liv_19mo_CR-night-2h_44B

source_name: Liver aged CR-night-2h


title: Liv_19mo_CR-day-2h_36A


title: GC080716_A06


title: Liv_19mo_CR-night-2h_36B


title: GC080716_B01


title: GC080716_C04


title: GC080716_C05


title: Liv_19mo_CR-day-2h_24A


title: Liv_19mo_CR-night-2h_28B


title: GC080716_A04


title: GC080716_B06


title: Liv_19mo_CR-spread_08B


title: GC080716_A01


title: Liv_19mo_CR-day-2h_04A


title: Liv_19mo_CR-night-2h_00B


title: GC080716_B03


title: GC080715_H02


title: GC080715_H03


title: Liv_19mo_CR-night-2h_44A


title: GC080715_H04


title: GC080716_A05


title: Liv_19mo_CR-night-2h_20B


title: Liv_19mo_CR-night-2h_40B


title: Liv_19mo_CR-day-2h_16A


title: Liv_19mo_CR-night-2h_24B


title: GC080716_A03


title: GC080716_B02


title: GC080716_A02


title: Liv_19mo_CR-night-2h_12B


title: GC080715_G06


title: Liv_19mo_CR-night-2h_32B


title: Liv_19mo_CR-night-2h_16B


title: GC080715_G05


title: Liv_19mo_CR-night-2h_28A


title: GC080715_H06


title: Liv_19mo_CR-night-2h_08B


title: Liv_19mo_CR-night-2h_20A


title: Liv_19mo_CR-night-2h_24A


title: Liv_19mo_CR-night-2h_12A


title: GC080715_H01


title: Liv_19mo_CR-night-2h_04A


title: Liv_19mo_CR-night-2h_04B


title: Liv_19mo_CR-night-2h_00A


title: GC080715_H05


title: GC080715_G04


title: Liv_19mo_CR-night-2h_32A


title: GC080715_G03


title: GC080715_F04


title: GC080715_G01


title: GC080715_E06


title: Liv_19mo_CR-night-2h_40A


title: Liv_19mo_CR-night-2h_36A


title: GC080715_F05


title: Liv_19mo_CR-night-2h_08A


title: Liv_19mo_CR-day-12h_40B

source_name: Liver aged CR-day-12h


title: Liv_19mo_CR-day-12h_32B


title: GC080715_F06


title: GC080715_F03


title: Liv_19mo_CR-night-2h_16A


title: GC080715_E05


title: Liv_19mo_CR-day-12h_20B


title: GC080715_F02


title: GC080715_E01


title: Liv_19mo_CR-day-12h_12B


title: Liv_19mo_CR-day-12h_36B


title: GC080715_D05


title: Liv_19mo_CR-day-12h_28B


title: GC080715_F01


title: Liv_19mo_CR-day-12h_44B


title: GC080715_E03


title: Liv_19mo_CR-day-12h_44A


title: GC080715_D01


title: Liv_19mo_CR-day-12h_32A


title: GC080715_C06


title: GC080715_D06


title: GC080715_E02


title: GC080715_D04


title: GC080715_C05


title: Liv_19mo_CR-day-12h_24B


title: Liv_19mo_CR-day-12h_16B


title: Liv_19mo_CR-day-12h_40A


title: GC080715_E04


title: Liv_19mo_CR-day-12h_04B


title: Liv_19mo_CR-day-12h_08B


title: Liv_19mo_CR-day-12h_24A


title: Liv_19mo_CR-day-12h_20A


title: Liv_19mo_CR-day-12h_28A


title: Liv_19mo_CR-day-12h_00B


title: GC080715_C04


title: Liv_19mo_CR-day-12h_36A


title: Liv_19mo_CR-day-12h_16A


title: GC080715_B06


title: Liv_19mo_CR-day-12h_12A


title: GC080715_B05


title: GC080715_C02


title: GC080715_D02


title: GC080715_C01


title: GC080715_G02


title: GC080715_B04


title: Liv_19mo_CR-day-12h_08A


title: GC080715_B02


title: GC080715_B03


title: Liv_19mo_CR-night-12h_32B

source_name: Liver aged CR-night-12h


title: GC080715_C03


title: GC080715_A06


title: Liv_19mo_CR-night-12h_28B


title: Liv_19mo_CR-night-12h_40B


title: Liv_19mo_CR-night-12h_36B


title: Liv_19mo_CR-day-12h_00A


title: Liv_19mo_CR-night-12h_44B


title: Liv_19mo_CR-night-12h_16B


title: GC080715_A02


title: GC080715_A04


title: Liv_19mo_CR-night-12h_24B


title: Liv_19mo_CR-day-12h_04A


title: GC080715_A03


title: GC080715_A01


title: Liv_19mo_CR-night-12h_08B


title: GC080715_A05


title: Liv_19mo_CR-night-12h_20B


title: GC080714_H04


title: GC080714_H05


title: GC080714_H06


title: Liv_19mo_CR-night-12h_04B


title: Liv_19mo_CR-night-12h_00B


title: GC080715_D03


title: GC080714_H03


title: Liv_19mo_CR-night-12h_40A


title: GC080714_H02


title: Liv_19mo_CR-night-12h_12B


title: Liv_19mo_CR-night-12h_36A


title: GC080714_H01


title: GC080714_G06


title: GC080714_G04


title: Liv_19mo_CR-night-12h_28A


title: GC080714_G05


title: GC080715_B01


title: GC080714_G03


title: Liv_19mo_CR-night-12h_24A


title: Liv_19mo_CR-night-12h_20A


title: Liv_19mo_CR-night-12h_16A


title: GC080714_G02


title: Liv_19mo_CR-night-12h_12A


title: GC080714_F06


title: Liv_19mo_CR-night-12h_08A


title: GC080714_G01


title: Liv_19mo_CR-night-12h_44A


title: Liv_19mo_CR-night-12h_00A


title: Liv_19mo_CR-night-12h_04A


title: GC080714_F05


title: GC080714_F04


title: GC080714_F03


title: GC080714_F02


title: Liv_19mo_AL_44B

source_name: Liver aged ad lib

value: Ad libitum


title: GC080714_F01


title: GC080714_E06


title: GC080714_E04


title: GC080714_E05


title: Liv_19mo_CR-night-12h_32A


title: B1B29_B29_CTL

value: CRH-expressing neuron

tag: genotype

value: Crh-IRES-Cre; Ai14 tdTomato

tag: condition

value: CTL

tag: weight

tag: age at collection

tag: protocol

value: RNA

tag: library prep

value: Nextera XT DNA Library Prep Kit (FC-131-1096, Illiumina)


title: B12B38_B38_CTL


title: B12L7_L7_ELA

value: ELA


title: GC080714_E01


title: GC080714_E03


title: B12B36_B36_CTL


title: B12L12_L12_ELA


title: B11L7_L7_ELA


title: B12B32_B32_CTL


title: GC080714_D05


title: B11L12_L12_ELA


title: GC080714_D04


title: GC080714_D03


title: B11L11_L11_ELA


title: B11L17_L17_ELA


title: GC080714_D02


title: GC080714_E02


title: GC080714_C05


title: GC080714_C06


title: B11B38_B38_CTL


title: B12L11_L11_ELA


title: B12L17_L17_ELA


title: B11B32_B32_CTL


title: B11B21_B21_CTL


title: B10L11_L11_ELA


title: B10L17_L17_ELA


title: B10L7_L7_ELA


title: GC080714_C04


title: B10B38_B38_CTL


title: GC080714_D01


title: B11B36_B36_CTL


title: GC080714_C03


title: GC080714_B06


title: B10B36_B36_CTL


title: GC080714_C01


title: GC080714_B04


title: GC080714_D06


title: GC080714_B03


title: B10B32_B32_CTL


title: GC080714_B02


title: B10B21_B21_CTL


title: GC080714_B01


title: A9L17_L17_ELA


title: A9L11_L11_ELA


title: GC080714_A05


title: GC080714_A06


title: B10L12_L12_ELA


title: A9B36_B36_CTL


title: GC080714_C02


title: GC080714_B05


title: A9L12_L12_ELA


title: GC080714_A03


title: GC080714_A02


title: GC080714_A04


title: GC080713_H05


title: A8L17_L17_ELA


title: A9B29_B29_CTL


title: A8L11_L11_ELA


title: A8B38_B38_CTL


title: A9B21_B21_CTL


title: A8L12_L12_ELA


title: A8B36_B36_CTL


title: GC080714_A01


title: A8B29_B29_CTL


title: GC080713_G06


title: A8B21_B21_CTL


title: GC080713_H02


title: A9B38_B38_CTL


title: GC080713_H01


title: A7L11_L11_ELA


title: GC080713_H04


title: GC080713_G05


title: A7B36_B36_CTL


title: GC080713_G04


title: GC080713_H03


title: A7B38_B38_CTL


title: GC080713_H06


title: A7L10_L10_ELA


title: A7L12_L12_ELA


title: A6L10_L10_ELA


title: GC080713_G02


title: A7L17_L17_ELA


title: GC080713_E05


title: GC080713_G03


title: A7B29_B29_CTL


title: A6B38_B38_CTL


title: A6B29_B29_CTL


title: GC080713_F05


title: GC080713_G01


title: GC080713_E04


title: GC080713_F04


title: A6L17_L17_ELA


title: GC080713_E02


title: A5L12_L12_ELA


title: GC080713_E01


title: A6L11_L11_ELA


title: GC080713_F01


title: GC080713_F02


title: GC080713_F06


title: GC080713_D06


title: A6L12_L12_ELA


title: GC080713_F03


title: A5B38_B38_CTL


title: GC080713_E06


title: GC080713_D03


title: A5L17_L17_ELA


title: A6B36_B36_CTL


title: GC080713_D01


title: A5L11_L11_ELA


title: GC080713_E03


title: A5B36_B36_CTL


title: A4L11_L11_ELA


title: A4L17_L17_ELA


title: GC080713_C04


title: GC080713_D04


title: GC080713_D05


title: A5L10_L10_ELA


title: GC080713_C06


title: A3L17_L17_ELA


title: GC080713_C05


title: A4B29_B29_CTL


title: GC080713_C02


title: GC080713_C03


title: A5B29_B29_CTL


title: A4L10_L10_ELA


title: A3L12_L12_ELA


title: GC080713_D02


title: GC080713_B05


title: A3L11_L11_ELA


title: A4L12_L12_ELA


title: A3B38_B38_CTL


title: GC080713_B06


title: A3B36_B36_CTL


title: GC080713_B04


title: A4B38_B38_CTL


title: GC080713_B03


title: A3B19_B19_CTL


title: GC080713_B02


title: GC080713_B01


title: A2L17_L17_ELA


title: GC080713_C01


title: GC080713_A06


title: A2L12_L12_ELA


title: GC080713_A05


title: GC080713_A04


title: A2L11_L11_ELA


title: A2B38_B38_CTL


title: GC080712_H06


title: GC080713_A02


title: GC080713_A01


title: A1L11_L11_ELA


title: A2B29_B29_CTL


title: A1L17_L17_ELA


title: A1B38_B38_CTL


title: GC080712_H05


title: A1B29_B29_CTL


title: A3B29_B29_CTL


title: GC080712_H03


title: GC080712_H02


title: A12L12_L12_ELA


title: A12L17_L17_ELA


title: GC080712_H01


title: GC080712_H04


title: A12B38_B38_CTL


title: A1B36_B36_CTL


title: A1L12_L12_ELA


title: GC080712_G06


title: A12L11_L11_ELA


title: A11L11_L11_ELA


title: GC080712_F05


title: GC080712_F02


title: GC080712_G04


title: GC080712_G05


title: GC080712_E06


title: GC080712_G03


title: A12B36_B36_CTL


title: A10L11_L11_ELA


title: A12B29_B29_CTL


title: A11L12_L12_ELA


title: GC080712_G01


title: GC080712_F03


title: A10L17_L17_ELA


title: A10B36_B36_CTL


title: A11B38_B38_CTL


title: A11B21_B21_CTL


title: GC080712_F06


title: A10L12_L12_ELA


title: A10B29_B29_CTL


title: A11B29_B29_CTL


title: GC080712_F01


title: A11L17_L17_ELA


title: GC080712_G02


title: GC080712_E01


title: A11B36_B36_CTL


title: GC080712_E03


title: GC080712_F04


title: GC080712_E05


title: GC080712_E04


title: GC080712_D05


title: GC080712_D04


title: GC080712_E02


title: A10B38_B38_CTL


title: WT34-BSL_S7

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

institute: Duke-NUS Medical School

description:
Sorted mouse Lung fibroblasts WT BSL
counts_mouse_stim

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 or mouse genome mm10 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 92 and Mus musculus mm10 Ensembl release 86
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: Lung Fibroblasts

growth_protocol: see above

extract_protocol:
Total RNA was extracted from either the snap-frozen liver tissues or HSCs lysate using Trizol (Invitrogen) followed by RNeasy column (Qiagen) purification.
Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol:
Primary fibroblasts from IL11RA1 wildtype mice (Passage 4) at baseline
see above

tag: strain

tag: treatment

value: BSL

tag: rin


title: WT32-TGFB_S2

description:
Sorted mouse Lung fibroblasts WT TGFB
counts_mouse_stim

treatment_protocol:
Primary fibroblasts from IL11RA1 wildtype mice (Passage 4) were stimulated with 5ng/ml of TGFbeta for 24h
see above

value: TGFB


title: WT33-BSL_S4


title: WT33-TGFB_S5


title: WT34-TGFB_S8


title: A10B21_B21_CTL

tag: tissue


title: K30-TGFB_S17

description:
Sorted mouse Lung fibroblasts KO TGFB
counts_mouse_stim

treatment_protocol:
Primary fibroblasts from IL11RA1 null mice (Passage 4) were stimulated with 5ng/ml of TGFbeta for 24h
see above


title: GC080712_C06


title: GC080712_D01


title: GC080712_D03


title: GC080712_D02


title: K30-BSL_S16

description:
Sorted mouse Lung fibroblasts KO BSL
counts_mouse_stim

treatment_protocol:
Primary fibroblasts from IL11RA1 null mice (Passage 4) at baseline
see above


title: WT32-BSL_S1


title: GC080712_C05


title: K29-TGFB_S14


title: GC080712_C04


title: GC080712_C03


title: K29-BSL_S13


title: K28-TGFB_S11


title: K28-BSL_S10


title: GC080712_D06


title: GC080712_C01


title: Saline_3

description:
Whole Lung 3wks Saline treatment (Mouse)
counts_mouse_ab

source_name: Lung

treatment_protocol:
Whole lung tissue lysate of mice treated with vehicle
see above

value: Saline


title: GC080712_C02