title: HT_3W_3

city: Daejeon

first: Ji-Sun

last: Park

address: 125, Gwahak-ro

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
CLC Genomics Workbench 12.0 software is used for basecalling
Sequenced reads were trimmed and aligned to PGSC_DM_v3.4 transcripts using CLC Genomics Workbench 12.0 software with mapping options as follow: mismatch cost, 2; insertion cost, 3; deletion cost, 3; length fraction, 0.8; similarity fraction, 0.8.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by the software with the following options: "count paired reads as two".
Genome_build: PGSC_DM_v3.4 transcripts
Supplementary_files_format_and_content: Excel files containing name, functional annotation, region, fold change, P-value, and total count numbers.

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: The Solanum tuberisum L. cv. Desiree was propagated in petri dish with a diameter of 11.5 cm and a height of 2 cm containing MS medium (Duchefa) supplemented with 30 g/L sucrose and 8 g/L plant agar (Duchefa). Plantlets were grown under 16h light/8h dark conditions at constant temperature of 24 oC and light intensity of 100 micro mol m-2 s-1. To prepare the plantlets for tuberization, lateral buds were induced from the stem nodes in MS-agar plates for 2 weeks. The lateral buds were then excised and incubated in MS-agar plates for 4 weeks. Apical buds were subcultured every 2 weeks. To synchronize growth stages, apical buds were incubated in MS-agar plates for an additional week after the final subculture. Plantlets were then transferred to soil. Growth conditions of plantlets in soil are as follows: 12h light/12h dark; light intensity of 153 micro mol m-2 s-1.

extract_protocol:
Upper 5 leaves were harvested for RNA isolation. Total RNA were extracted from 50 mg of frozen ground tissues using RNeasy Plant Mini kit (QIAGEN).
Five micrograms of each RNA sample were used to generate a strand-specific library containing inserts of approximately 150–200 bp in size. PolyA RNA is captured by oligodT beads (Thermo Scientific, USA) and fragmented. The first-strand cDNA as synthesized by Superscript III reverse transcriptase (Invitrogen,USA) using dNTP, whereas the second-strand cDNA was generated using a dUTP mix. After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase (Enzymatics, USA). Indexed cDNA libraries were prepared by PCR amplification.

treatment_protocol: Plants were grown at NT and HT for 3 and 8 weeks.

tag: cultivar

value: Desiree

value: Leaf

value: 35 oC light/29 oC dark; 12 h light/12 h dark

tag: period

value: 3 weeks


title: A1092

status: Public on Sep 28 2022

type: SRA

city: Leicester

first: Shu

last: Ye

state: Leicestershire

address: British Heart Foundation Cardiovascular Research Centre, Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital

country: United Kingdom

institute: University of Leicester

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was checked with FastQC. Adapters were trimmed with BBMap.
Reads were mapped with STAR v2.7.1a
SAMtools v1.9 was used for processing aligned reads.
Rsubread was used to obtain raw read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Table and individual files of raw gene counts in all samples

molecule: total RNA

organism: Homo sapiens

source_name: Vascular Smooth Muscle Cells

extract_protocol:
Total RNA was extracted from an aliquot of passage-3 VSMCs stored with the use of the Biobasic EZ-10 DNAaway RNA miniprep kit (Biobasic), according to the manufacturer’s protocol with additional wash steps to ensure complete removal of residual salts from the samples
A strand specific library with rRNA removal was prepared from total RNA of each of the 1,499 VSMC samples, and 150bp paired-end sequencing at 30 million read depth was performed.

tag: source tissue

value: Umbilical cord artery

tag: cell type

value: Vascular Smooth Muscle Cells


title: TA - Immobile scRNA-seq

city: Urbana

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

country: USA

institute: University of Illinois at Champaign-Urbana

data_processing:
Fastq.gz files were generated and demultiplexed with 10X Genomic’s Cell Ranger 3.0.2. Each sample’s R1 and R2 fastq files were run through cellranger count using a custom reference made from Gencode M21 gene set and --expect-cells=5000 to call cells and de-duplicate individual reads to unique UMI counts per gene.
The UMI counts were then read into R (v 3.6.3) using Seurat (v. 3.1.4) (Stuart et al., 2019). Genes were filtered out if they did not have at least 1 UMI in at least 10 cells combined between the two samples. Cells with ≥ 50% mitochondrial UMIs were filtered out and then additional QC was performed based on the number of UMIs and genes detected. Cells that had > 4 median absolute deviations of the total UMI counts were excluded as possible doublets and cells were filtered out if they had fewer than 250 genes detected.
Cluster analysis was performed with the Seurat package. First, normalization was performed using the SCTransform method then linear dimensional reduction was done using Principal Components Analysis and the first 40 PCs were used as input to find clusters using a k-nearest neighbor graph and also for non-linear dimensional reduction using tSNE. Cell type identification was completed using candidate marker genes curated from the literature and the top unique genes for each cluster.
Within each cluster, differential expression testing was evaluated between Mobile and Immobile cells using the non-parametric Wilcoxon Rank Sum test.
Genome_build: Gencode M21
Supplementary_files_format_and_content: 10X Genomics cellranger count's filtered_feature_bc_matrix output in HDF5 format

organism: Mus musculus

source_name: tibialis anterior muscle

extract_protocol:
TAs were pooled according to treatment (Mobile vs. Immobile). The cleaned muscles were minced and then enzymatically digested for ~60 minutes at 37°C. The tissue solution was filtered (70 μm and 40 μm) to obtain mononuclear cell suspension, and the filtrate was centrifuged at 300 RCF for 5 minutes. Supernatant was decanted, and cell pellet was resuspended in PBS with 5% FBS.
Two single-cell libraries (one for the pooled mobile TAs and the other for the pooled immobile TAs) were constructed with the Chromium Single-Cell Gene Expression Kit Version 3 and sequenced on two 2x150nt SP lanes in a NovaSeq 6000.

treatment_protocol: Mice were subjected to unilateral hindlimb immobilization for two weeks by putting one tine of a staple into the plantar of the right foot and the other tine inserted into the distal gastrocnemius, which restrained the foot in full dorsiflexion and immobilized the tibialis anterior (TA) muscle at a shortened position. On day 14 of immobilization the TA muscles from mobile (“Mobile”; control) and previously immobilized (“Immobile”) limbs were excised and washed in cold 1X PBS with penicillin-streptomycin antibiotic.

tag: Sex

value: male

tag: strain

tag: age

value: 14 weeks

tag: treatment

value: immobile

tag: tissue

value: Pool of 6 tibialis anterior muscles from the right leg that had been immobilized


title: REF6-HA-6h_rep2

city: Beijing

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology

library_source: genomic

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
The correlation coefficients between biological replicates were examined using deepTools version 3.1.3 utility multiBamSummary, and subsequently biological replicates were merged with SAMtools version 1.9
For data visualization, bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
ChIP-seq peaks were identified using MACS2 version 2.1.2 with default parameters. Narrow peaks were called for REF6-HA ChIP-seq data. The q-value cutoff for peak calling was 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: Normalized REF6-HA coverage files. Data is generated from merged replicates except for Col control

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: REF6-HA 6h imbibed seeds

growth_protocol: After-ripened ref6-1;REF6-HA seeds (seeds harvested and stored at room temperature for at least three months) were sown on 1/2 MS medium,and subsequently subjected for germination in long days at ~22°C,and collected at different imbibition time points

extract_protocol:
For REF6-HA binding ChIP, chromatin was resuspended with ChIP lysis buffer (50mM HEPES (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.5% SDS, and 1×protease inhibitor cocktail (Sigma, S8830)) and sheared to generate 200-500bp fragments with Bioruptor (Diagenode) for 30 cycles (30s/on, 30s/off) at high power. Sheared chromatin was diluted four times with ChIP dilution buffer (50mM HEPES (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.01% SDS, and 1×protease inhibitor cocktail (Sigma, S8830)) and subjected to immunoprecipitation with anti-HA antibody (CST, 3724). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction

value: seeds

tag: time

tag: ecotype

value: Col

tag: genotype

tag: chip antibody

value: anti-HA antibody (CST, 3724)


title: HT_3W_2

country: South Korea


title: A1095


title: REF6-HA-24h_rep1

source_name: REF6-HA 24h imbibed seeds


title: Rep1, BF, RNAseq, jbp2, SKO

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology

data_processing:
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  paired-end_file_1.fasta - 2 paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Selection of minus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_minus_strand.bw --filterRNAstrand=forward --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Selection of plus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_plus_strand.bw --filterRNAstrand=reverse --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files showing distribution of polyadenylated transcripts across the T. brucei genome

molecule: polyA RNA

organism: Trypanosoma brucei brucei

source_name: Lister 427

growth_protocol: Bloodstream form cells were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA was extracted from 1-4 x 10^7 cells using Trizol (Thermo Fisher Scientific) according to the manufacturer's protocol. The RNA was treated with DNase and then purified using Phenol/Chloroform/Isoamyl alcohol pH 4.
Libraries were constructed using NEBNEXT Ultra II Directional RNA Library Prep kit (NEB) with a Poly-A mRNA magnetic isolation module (NEB).

tag: developmental stage

value: bloodstream form

tag: cell line

value: Lister 427

value: jbp2 SKO


title: HT_8W_3

value: 8 weeks


title: HT_3W_1

value: Desiree


title: A1087


title: A1093


title: A1090


title: Rep1, BF, JBP2, input

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

growth_protocol: Bloodstream form cells were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). Procyclic form T. brucei 427 cells were grown at 27oC in SDM-79 medium supplemented with hemin, 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
3-5 x 10^8 cells were harvested and fixed with 0.8% formaldehyde (final concentration) for 20 min at room temperature. Cells were lysed and sonicated for 30 cycles (30 s on, 30 s off; high setting) in a Bioruptor sonicator (Diagenode) in the presence of 0.2% SDS. Inputs (0.8% of total volume/sample) were taken before incubating the rest of the cell lysates overnight with 10 µg anti-GFP antibody (A-11122, Invitrogen) and Protein G Dynabeads. The beads were washed first in the presence of 500 mM NaCl, and then in the presence of 250 mM LiCl. The DNA was eluted from the beads with 1% SDS and treated with RNAse and Proteinase K. Finally, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
Immunoprecipitated and input DNA was blunt ended using a Quick Blunting Kit (NEB). DNA was then purified using AMPure beads (Beckman Coulter) with a beads:DNA ratio of 1.6:1 (v/v). DNA was A-tailed using Klenow Fragment exo (NEB) and NEXTflex adapters (Bioo Scientific) were ligated to the DNA fragments using a Quick Ligation Kit (NEB). Samples were purified twice with AMPure beads:DNA ratio of 1:1 (v/v), and DNA was then amplified by PCR (14-18 cycles). Following PCR, DNA was purified with AMPure beads:DNA ratio of 0.65:1 (v/v), and the resulting supernatant was taken for a 0.7:1 bead:sample purification (v/v). Finally, two 1:1 (v/v) DNA:AMPure beads purifications were performed. The DNA amount in each library was quantified using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution in each library was assessed using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).

tag: yfp-tagged protein


title: Rep1, BF, RNAseq, jbp2, DKO

value: jbp2 DKO


title: A1091


title: HT_8W_2

value: Leaf

value: 35 oC light/29 oC dark; 12 h light/12 h dark


title: Rep1, BF, RNAseq, set27, DKO

value: set27 DKO


title: A1088

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: A1085


title: NT_8W_1

value: 22 oC light/16 oC dark; 12 h light/12 h dark


title: NT_8W_2


title: Sprague Dawley rats, spared nerve injury (SNI) group, biol rep 3

city: Xi’an

first: YanYan

last: Chen

state: Jiangsu

address: Shiji Road

institute: Shaanxi University of Chinese Medicine

data_processing:
Oligo dT enrichment of mRNA, fragmentation of mRNA, reverse transcription of cDNA, ligation of adaptor, sequencing on Illumina platform
Conversion of sequencing image signals into text signals by CASAVA Base Calling
Sequencing data quality control with fastp 0.19.5
Gene expression values of the transcripts were computed by StringTie
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: L3-L6 spinal cord tissue

extract_protocol:
Total RNA was isolated from the L3-L6 spinal cord tissue of the rats using RNeasy Plus kit followed by a genomic DNA removal step
Illumina TruseqTM RNA sample prep Kit was used to generate sequencing libraries

value: L3-L6 spinal cord tissue

value: WT

value: spared nerve injury model, oral administrated with normal saline


title: Sprague Dawley rats, paeoniflorin-liquiritin combination (PLM) group, biol rep 3

value: spared nerve injury model, oral administrated with 20.65 mg/mL paeoniflorin and 3.100 mg/mL liquiritin


title: REF6-HA-6h_rep1

value: seeds

value: Col

value: anti-HA antibody (CST, 3724)


title: Sprague Dawley rats, spared nerve injury (SNI) group, biol rep 2


title: HT_8W_1


title: REF6-HA-0h_rep1

source_name: REF6-HA 0h imbibed seeds


title: A1083


title: Sprague Dawley rats, paeoniflorin-liquiritin combination (PLM) group, biol rep 2

value: spared nerve injury model, oral administrated with 20.65 mg/mL paeoniflorin and 3.99 mg/mL liquiritin


title: Sprague Dawley rats, spared nerve injury (SNI) group, biol rep 1


title: A1082


title: A1081


title: NT_3W_3

value: 3 weeks


title: Sprague Dawley rats, paeoniflorin-liquiritin combination (PLM) group, biol rep 1

value: spared nerve injury model, oral administrated with 20.65 mg/mL paeoniflorin and 3.98 mg/mL liquiritin


title: A1084


title: NT_3W_2

value: Desiree


title: Sprague Dawley rats, sham-operated (JA) group, biol rep 3

value: sham-operated, oral administrated with normal saline


title: A1086


title: NT_3W_1

value: Leaf


title: A1080


title: Sprague Dawley rats, sham-operated (JA) group, biol rep 2


title: Sprague Dawley rats, sham-operated (JA) group, biol rep 1


title: NT_8W_3

value: 8 weeks


title: Pre patient 31 [Sample 62]

type: RNA

city: Providence

first: Jennifer

middle: Renee

last: Ribeiro

state: RI

address: 200 Chestnut St.

department: Obstetrics and Gynecology

institute: Women and Infants Hospital of Rhode Island

description: low count genes were filtered out for a total of 750 genes detected on the panel

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing: The resulting data file in RCC format was used for data analysis in the nCounter Advanced Analysis Software. Raw data in RCC format was uploaded to nSolver for automated normalization, background subtraction, and quality control (QC) check.

label: fluorescent barcode

extract_protocol: Pre-treatment and post-treatment cases were reviewed to select an optimal formalin-fixed, paraffin-embedded tissue block for each case. An optimal pre-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present.   An optimal post-treatment block contained maximum tumor cellularity (minimum of 20%) with no lymph node tissue present, and with evidence of a lymphocytic response. For each block, ten unstained sections of 4-5 micron thickness were cut and placed on Avantix uncharged slides. An eleventh slide was cut at 4-5 microns, stained with hematoxylin and eosin, cover-slipped and reviewed to confirm the appropriate tissue was still present. FFPE sections were scraped into tubes for RNA isolation using an RNeasy FFPE Kit (Qiagen, 73504) according to manufacturer’s instructions. RNA concentration and quality was measured by NanoDrop

treatment_protocol: patients samples were obtained from naïve tumors during biopsy, or during interval debulking sugery after neoadjuvant treatment with carboplatin and paclitaxel chemotherapy

value: primary high grade serous ovarian cancer biopsy

tag: histology

value: high grade serous ovarian cancer

tag: Stage

value: IIIC

value: female

tag: platinum-free interval

tag: progression status as of 4/25/22

value: yes


title: SNCA TG Cerebellum H3K27ac

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq bamcoverage bigwig files were generated using aligned bam files
Assembly: hg19
Supplementary files format and content: bigwig coverage files

source_name: Cerebellum

extract_protocol:
Brain tissues were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: Cerebellum

tag: condition

value: Human SNCA transgene

tag: antibody

value: anti-H3K27ac (Cell signaling, D5E4)


title: A1079

tag: source tissue

value: Umbilical cord artery

tag: cell type

value: Vascular Smooth Muscle Cells


title: Pre patient 30 [Sample 61]

source_name: primary high grade serous ovarian cancer

value: IIIB

tag: Sex

tag: age


title: Pre patient 29 [Sample 60]

tag: tissue


title: SNCA EnKO Cortex H3K4me3

source_name: Cortex

value: Cortex

value: Human SNCA transgene enhancer KO

value: anti-H3K4me3 (Cell signaling, C42D8)


title: A1078


title: A1077


title: A1076


title: SNCA TG-L Cortex H3K4me3

value: Human SNCA transgene low level


title: SNCA EnKO Cortex H3K27ac


title: Pre patient 28 [Sample 59]


title: Pre patient 27 [Sample 58]


title: WT_3h.2_control for DacA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

description:
Slide Format: 8 x 60 K
Slide Layout: IS-62976-8-V2
Design ID: 75764

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: PCC6803, WT, 3 h HC, replicate 2

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid cultures in buffered BG11 media at 30°C under constant light with an intensity of 130 µmol photons m-2 s-1 and constant bubbling. The media for High Carbon (HC) and Low Carbon (LC) cultures was buffered with TES/KOH until a pH of 8 and 7. HC cultures were bubbled with CO2-enriched air (5%, v/v), while LC cultures with ambient air (0.04% CO2).

extract_protocol: RNA was prepared using a hot phenol-based protocol.

treatment_protocol: Cells were shifted to LC conditions at an OD750 of 0.8-1. Following the shift, the cultures were sampled after 3 h and 24 h for the transcriptome analysis by filtration.

value: WT

tag: treatment

value: 3 h high carbon conditions


title: A1074


title: Pre patient 26 [Sample 57]

value: primary high grade serous ovarian cancer biopsy

value: no


title: Pre patient 25 [Sample 56]

value: high grade serous ovarian cancer

value: IIIC


title: WT_3h.1_control for DacA

source_name: PCC6803, WT, 3 h HC, replicate 1

tag: genotype


title: SNCA TG-L Cortex  H3K27ac


title: WT_24h.1_control for DacA

source_name: PCC6803, WT, 24 h HC, replicate 1

value: 24 h high carbon conditions


title: WT_24h.2_control for DacA

source_name: PCC6803, WT, 24 h HC, replicate 2


title: A1073


title: SNCA TG Cortex  H3K27ac


title: A1075


title: SNCA EnKO Input

value: Input


title: A1072


title: Pre patient 24 [Sample 55]

value: female

value: yes


title: Pre patient 23 [Sample 54]


title: A1071

value: Umbilical cord artery


title: SNCA TG-L Input


title: DisA_3h.1

source_name: PCC6803, DacA, 3 h HC, replicate 1

value: delta-dacA


title: DisA_24h.2

source_name: PCC6803, DacA, 24 h HC, replicate 2


title: WT_0h.2_control for DacA

source_name: PCC6803, WT, LC, replicate 2

value: low carbon conditions


title: WT_0h.1_control for DacA

source_name: PCC6803, WT, LC, replicate 1


title: Pre patient 20 [Sample 51]

value: IV


title: A1070

source_name: Vascular Smooth Muscle Cells

value: Vascular Smooth Muscle Cells


title: Pre patient 21 [Sample 52]


title: Pre patient 22 [Sample 53]

value: IIIA


title: DisA_3h.2

source_name: PCC6803, DacA, 3 h HC, replicate 2


title: A1068


title: THAP1+/-_Striatum_Rep3

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of RNA-seq data in fastq files were assessed using QoRTs (v1.2.37) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using HISAT2 (v2.2.1) allowing gapped alignments to account for splicing against a custom-built genome composed of the Ensembl Rat RGSC6.0 (rn6) and Alignment quality was analyzed using samtools (v1.12) and visually inspected in the Integrative Genome Viewer (v2.4.19).
Normalized read counts for all genes were obtained using DESeq (V1.22.1).
Genome_build: rn6
Supplementary_files_format_and_content: tabular files counted mapped reads of each gene

source_name: Striatum

extract_protocol:
Striatum regions were dissected, flash frozen on dry ice. Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen).
A total of 100ng total RNA was subjected to polyA enrichment and cDNA libraries preparation using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, #E7760L).

tag: strain

value: Sprague Dawley Rat

value: Striatum


title: DisA_0h.1

source_name: PCC6803, DacA, LC, replicate 1


title: SNCA TG Input

value: Cortex

value: Human SNCA transgene


title: WT_24h.2

value: WT


title: DisA_0h.2

source_name: PCC6803, DacA, LC, replicate 2


title: Pre patient 19 [Sample 50]

value: primary high grade serous ovarian cancer biopsy

value: high grade serous ovarian cancer


title: THAP1+/-_Striatum_Rep2


title: A1067


title: THAP1+/-_Striatum_Rep4


title: A1069


title: A1060


title: THAP1+/-_Striatum_Rep1


title: WT_24h.1

value: 24 h high carbon conditions


title: Pre patient 17 [Sample 48]

value: IIIC


title: Pre patient 18 [Sample 49]

value: female


title: Wild-type_Striatum_Rep4

value: Wild-type


title: WT_3h.1

value: 3 h high carbon conditions


title: Pre patient 16 [Sample 47]

value: yes


title: WT_3h.2


title: Wild-type_Striatum_Rep3


title: A1054

value: Umbilical cord artery


title: A1059


title: A1047


title: OS 3

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was further processed with an in-house program called ACGT101-miR (LC Sciences, Houston, TX) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats. Unique sequences with lengths of 18-26 nts were subsequently mapped to specific-species precursors in miRBase 21.0 by BLAST searching to identify known miRNAs and novel 3p- and 5p-derived miRNAs. Lengths varying at both 3’- and 5’-ends and one mismatch inside of the sequence were allowed in the alignment.
MiRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test. The significance threshold was set to be 0.01 and 0.05 in each test.
Assembly: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V21.0
Supplementary files format and content: identified miRNAs with details (reads,location,length,etc)

organism: Sus scrofa

source_name: umbilical cord blood

extract_protocol:
In brief, dilute plasma ﬂuid with an equal volume of PBS and centrifuge 30 min at 2,000 × g, 4◦C, to remove cell. Then, carefully transfer supernatant to ultracentrifuge tubes or bottles without pellet contamination, centrifuge 45 min at 12,000 × g, 4◦C. Next, filter the suspension through a 0.22-µm ﬁlter, and collect in a fresh ultracentrifuge tube or bottle, centrifuge 2h at 160,000 × g, 4◦C. Pour off the supernatant. Resuspend the pellet in 250µl PBS and Store at −80◦C until use.
Three MS and threeOS piglets were used for library construction. Approximately 1 μg of total RNA was used to prepare the small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina). Single-end sequencing (36 bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) was performed following the recommended protocol.

treatment_protocol: Ready to concentration 15% EDTA anticoagulant solution, join 2 drops in the 5 ml syringe every time before collecting umbilical cord blood. When piglet was born, puts it under the heat lamp, a man picked up the umbilical cord, another discerned the UA and UV in light quickly, with syringe in draw blood vessels. After, upside down to make them blending fully timely, packing in 2 ml centrifuge tube, 1 ml per tube, for the next step.

tag: tissues

value: umbilical cord of OS

tag: content

value: exosome

tag: breed

value: Yorkshire


title: OS 2


title: Pre patient 15 [Sample 46]

tag: histology


title: A1048

value: Vascular Smooth Muscle Cells


title: Wild-type_Striatum_Rep1

value: Sprague Dawley Rat

value: Striatum


title: Wild-type_Striatum_Rep2


title: WT_0h.1

value: low carbon conditions


title: A1046


title: Pre patient 14 [Sample 45]

tag: Stage


title: WT_0h.2

value: WT


title: Pre patient 13 [Sample 44]

value: primary high grade serous ovarian cancer biopsy

tag: platinum-free interval


title: DisA_24h.1

source_name: PCC6803, DacA, 24 h HC, replicate 1

value: delta-dacA


title: SbtB_24h.1

source_name: PCC6803, SbtB, 24 h HC, replicate 1

value: delta-sbtB

value: 24 h high carbon conditions


title: Pre patient 12 [Sample 43]

source_name: primary high grade serous ovarian cancer

value: high grade serous ovarian cancer

value: IIIC

value: female

tag: progression status as of 4/25/22


title: SbtB_3h.1

source_name: PCC6803, SbtB, 3 h HC, replicate 1

value: 3 h high carbon conditions


title: SbtB_3h.2

source_name: PCC6803, SbtB, 3 h HC, replicate 2


title: SbtB_24h.2

source_name: PCC6803, SbtB, 24 h HC, replicate 2


title: A1045

value: Umbilical cord artery


title: Pre patient 11 [Sample 42]

value: yes


title: OS 1

value: umbilical cord of OS

value: exosome


title: SbtB_0h.2

source_name: PCC6803, SbtB, LC, replicate 2


title: SbtB_0h.1

source_name: PCC6803, SbtB, LC, replicate 1


title: MS 3

value: umbilical cord of MS

value: Yorkshire


title: A1044

value: Vascular Smooth Muscle Cells


title: MS 2


title: A1043


title: Pre patient 10 [Sample 41]


title: MS 1


title: A1041


title: A1042


title: A1040


title: CR5

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mm10 genome
Deduplication (UMI is in read 2) was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 has the UMI)
Reads were counted using Refseq annotations (1000 bases of the 3’ UTR), using HTSeq-Counts, and corrected for UMI saturation.
Normalization was performed using DESeq2
Assembly: mm10
Supplementary files format and content: Excel file includes the DESeq2 normalized counts

source_name: Mammary Gland

growth_protocol: Six week old female mice (~21 gram) were housed under a 12-hr light/dark cycle and fed ad libitum

extract_protocol:
Poly(A) RNA was extracted from 15,000 non-epithelial cells of an individual mouse #4 mammary glands using the Dynabeads mRNA DIRECT purification kit (Thermo Fisher, Waltham, MA) according to the manufacturer’s protocol.
A bulk adaptation of the MARS-Seq protocol was used to generate RNA-Seq libraries.
Briefly, 30 ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter, Indianapolis, IN), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Libraries were quantified by Qubit and TapeStation as well as by qPCR for ActB housekeeping gene.

treatment_protocol: CR was proceeded for 8 weeks by receiving 65% of the food consumed by their ad libitum-fed counterparts on the previous day.

value: Mammary Gland

value: Non-epithelial

value: FVB/N

value: Calorie restricted


title: Pre patient 9 [Sample 40]

value: primary high grade serous ovarian cancer biopsy

value: IV


title: CR4


title: CR3


title: Pre patient 7 [Sample 38]

value: high grade serous ovarian cancer

value: IIIB


title: Pre patient 6 [Sample 37]

value: IIIC

value: female


title: A1039

value: Umbilical cord artery


title: A1038


title: Pre patient 8 [Sample 39]

value: yes


title: Pre patient 5 [Sample 36]

value: no


title: Pre patient 4 [Sample 35]


title: A1035


title: CR1


title: A1036


title: A1037


title: Pre patient 1 [Sample 32]


title: Pre patient 3 [Sample 34]


title: A1034


title: Control3


title: Control4


title: Control5


title: A1032


title: A1033


title: Control2


title: A1031


title: 1108 - Tg-Pl - 12 mois

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

data_processing:
Demultiplexing was realised with Bcl2fastq 2.17.1.14 software with 0 mismatch
Reads were trimmed using Cutadapt 1.9.1 software  : error rate = 10%; overlap = 3 ; quality cutoff = 30 ; min sequence length = 25; max N = 0.3
Alignment was realised using Tophat v2.1.0 software
Assembly: mm10
Supplementary files format and content: gene expression is estimated using Cufflinks v2.1.1 software.
Supplementary files format and content: Cufflinks finally computes overall normalized gene expression in terms of FPKM (Fragments Per Kilobases of exon per Million mapped reads).
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Microglia

extract_protocol:
Total RNA were extracted from laser capture microdissected samples using the micro Rneasy kit from Qiagen
mRNA preamplification was realised by using SMART-Seq v4 Ultra Low Input RNA (Clontech) from 200pg total RNA
32 Dual indexed Librairies were performed using kit Nextera XT (Illumina) from 500 pg cDNAs

value: 12 months

value: Microglia

tag: distance from_amyloid_plaques

value: <75 um from plaque


title: Pre patient 2 [Sample 33]


title: Post patient 29 [Sample 29]

value: primary high grade serous ovarian cancer


title: Post patient 31 [Sample 31]


title: Periodontal ligament tissue periodontitis

city: london

first: Paul

last: Sharpe

address: Craniofacial Development & Stem cell bio, Guy's Tower Floor 27

institute: King's college London

data_processing:
Count matrices were generated from the fastq files via CellRanger pipeline using Ensembl 97 genome annotation.
Ambient and background RNA from the count matrices were first removed using CellBender remove‐background tool.
Only cells expressing >1000 features and having mitochondria gene content of less than 5% of total cell content were maintained.
Batch effect was removed by Seurat CCA approach. Integrated data were subsequently scaled and PCA was performed, followed by UMAP for embedding and Louvain clustering on knn graph.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: PTIS.TXT: Processed raw count matrix.

extract_protocol:
Tooth were extracted and digested with collagenase P. Single cells suspensions were fed into 10X Chromium.
Library was generated with Chromium Single Cell 3' v3 Kit.

tag: diagnosis

value: periodontitis

value: periodontal ligament


title: Post patient 30 [Sample 30]


title: A1030

tag: source tissue

value: Vascular Smooth Muscle Cells


title: 1032 - Tg-Pl - 12 mois

tag: cell type


title: 1107 - Tg-Pl - 12 mois


title: 1033 - Tg-Pl - 12 mois


title: Post patient 27 [Sample 27]

tag: Sex


title: Post patient 28 [Sample 28]

tag: age


title: A1029


title: 1108 - Tg-Pa - 12 mois

value: >100 um from plaque


title: CR2

tag: tissue

value: Mammary Gland

value: Non-epithelial

value: FVB/N

value: Calorie restricted


title: A1028


title: 1033 - Tg-Pa - 12 mois


title: 1107 - Tg-Pa - 12 mois


title: Lung FENDRR Flox - M294

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with zUMIs 2.4.5 (STAR for alignment)
Cells filtered with >5% of transcriptome from intron-spanning reads; <4% mitochondrial origin; at least 1000 unique genes
ensembl gene IDs translated to HGNC only when a 1:1 translation was feasible using the R package biomaRt
Genome_build: ensemble mouse reference genome GRCm38 release 96
Supplementary_files_format_and_content: MouseAging.raw.counts.mtx: gene expression UMI count matrix of all intron and exon spanning transcripts are in sparse matrix format, generated with R package 'Matrix' and writeMM() function; MouseAging.genes.tsv:  tsv of  of corresponding gene identities for the count matrix; MouseAging.barcodes.tsv: tsv of corresponding cell barcode identities for the count matrix

source_name: Whole Lung Dissociate

extract_protocol:
passed through 40 uM strainer
10X Genomics 3 prime v2

treatment_protocol: Enzymatic and Mechanical Digestion

value: C57BL/6J FENDRR Flox

value: lung

value: FENDRR Flox

value: 117 weeks

value: male


title: A1026

source_name: Vascular Smooth Muscle Cells

value: Umbilical cord artery


title: A1027


title: Post patient 25 [Sample 25]

value: high grade serous ovarian cancer

value: IIIC

value: female

value: yes


title: Post patient 23 [Sample 23]

value: primary high grade serous ovarian cancer

value: IIIB


title: Lung FENDRR Flox - F421

value: 23 weeks


title: Lung FENDRR Flox - M418


title: A1025

value: Vascular Smooth Muscle Cells


title: 1032 - Tg-Pa - 12 mois

value: 12 months

value: Microglia

value: >100 um from plaque


title: Post patient 24 [Sample 24]


title: Lung FENDRR Flox - F420

value: C57BL/6J FENDRR Flox


title: Post patient 22 [Sample 22]

value: IIIA


title: 1170 - NTg - 12 mois

value: Not relevant (control)


title: Post patient 26 [Sample 26]

value: no


title: Lung FENDRR Flox - M419

value: lung

value: FENDRR Flox

value: male


title: Post patient 20 [Sample 20]

value: high grade serous ovarian cancer

value: IV


title: A1023

value: Umbilical cord artery


title: Lung FENDRR Flox - F342

value: 103 weeks


title: A1024


title: Lung FENDRR Flox - M343


title: A1022


title: 1101 - NTg - 12 mois


title: Lung FENDRR Flox - F293

value: 120 weeks

value: female


title: 1171 - NTg- 12 mois


title: 1100 - NTg - 12 mois


title: A1021

value: Vascular Smooth Muscle Cells


title: Post patient 21 [Sample 21]

value: primary high grade serous ovarian cancer


title: Post patient 19 [Sample 19]

value: IIIC

value: yes


title: A1020


title: 1190 - Tg-Pl - 8 mois

value: 8 months

value: Microglia

value: <75 um from plaque


title: 1129 - Tg-Pl - 8 mois


title: CAMTA1 Knockout SH-SY5Y cells rep3

city: Zhengzhou

first: Yang

last: Liu

state: Henan

address: No.100 science avenue

department: Medical Genetics

institute: Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor seguence, and masked for low-complexity or low-quality sequence.
then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size(RPKM)were calculated using a protocol from Chepelev et al, Nucleic Acids Research, 2009.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: neuroblastoma cells

growth_protocol: WT SH-SY5Y and CAMTA1 KO SH-SY5Y  cells were routinely generated .

extract_protocol:
The RNA was using standard extraction methods to extract RNA from  cells
RNA librariies were prepared for sequensing using standand illuminia protocols

treatment_protocol: crispr/cas9 tec was used to knockout CAMTA1

value: brain

value: neuroblastoma cells

value: CAMTA1 knockout

tag: cell line


title: 1088 - Tg-Pl - 8 mois

tag: genotype


title: Post patient 17 [Sample 17]


title: 1089 - Tg-Pl - 8 mois


title: CAMTA1 Knockout SH-SY5Y cells rep1


title: A1018


title: A1017


title: Post patient 15 [Sample 15]


title: Post patient 18 [Sample 18]


title: 1190 - Tg-Pa - 8 mois

value: >100 um from plaque


title: A1004


title: Post patient 16 [Sample 16]

value: high grade serous ovarian cancer


title: Wild Type SH-SY5Y rep1

value: wildtype


title: Post patient 13 [Sample 13]


title: Post patient 14 [Sample 14]


title: Post patient 12 [Sample 12]


title: A1019

value: Umbilical cord artery


title: A1002


title: CAMTA1 Knockout HEK293T cells rep2

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor seguence, and masked for low-complexity or low-quality sequence.
then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size(RPKM)were calculated using a protocol from Chepelev et al, Nucleic Acids Research, 2009.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Human embryonic kidney cells

growth_protocol: WT HEK293T and CAMTA1 KO HEK293T  cells were routinely generated .

value: Human renal epithelial cell line

tag: genotype/variation

value: CAMTA1 Knockout


title: CAMTA1 Knockout SH-SY5Y cells rep2


title: 1129 - Tg-Pa - 8 mois


title: 1088 - Tg-Pa - 8 mois


title: CAMTA1 Knockout HEK293T cells rep1


title: Wild Type SH-SY5Y rep2


title: Wild Type SH-SY5Y rep3


title: A1000

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was checked with FastQC. Adapters were trimmed with BBMap.
Reads were mapped with STAR v2.7.1a
SAMtools v1.9 was used for processing aligned reads.
Rsubread was used to obtain raw read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Table and individual files of raw gene counts in all samples


title: 1089 - Tg-Pa - 8 mois


title: A1001


title: Post patient 11 [Sample 11]

value: female


title: Wild Type HEK293T cells rep2

value: wild type


title: Wild Type HEK293T cells rep1


title: THAP1+/- SP1-/- SHSY5Y Rep2

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of RNA-seq data in fastq files were assessed using QoRTs (v1.2.37) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using HISAT2 (v2.2.1) allowing gapped alignments to account for splicing against a custom-built genome composed of the Ensembl Homo Sapiens GRCh37 (hg19) and Alignment quality was analyzed using samtools (v1.12) and visually inspected in the Integrative Genome Viewer (v2.4.19).
Normalized read counts for all genes were obtained using DESeq (V1.22.1).
Genome_build: hg19
Supplementary_files_format_and_content: tabular files counted mapped reads of each gene

source_name: SHSY5Y cells

growth_protocol: SH-SY5Y cells were cultured in DMEM medium with 10% FBS and 1% Glutmax at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were generated using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, #E7760L)

value: SHSY5Y cells


title: Post patient 10 [Sample 10]

value: primary high grade serous ovarian cancer

value: IIIC


title: Post patient 9 [Sample 9]

value: IV

value: yes


title: 1090 - NTg - 8 mois

value: 8 months

value: Microglia

value: Not relevant (control)


title: 1115 - NTg - 8 mois


title: THAP1+/- SP1-/- SHSY5Y Rep1


title: Post patient 8 [Sample 8]


title: THAP1 iPSCs C5-3

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37)
Reads were aligned using STAR (v2.5.2b) allowing gapped alignments to account for splicing against a custom-built genome composed of the Ensembl Homo Sapiens GRCh37
Alignment quality was analyzed using samtools (v1.1) and visually inspected in the Integrative Genome Viewer (v2.4.19)
Normalized read counts for all genes were obtained using edgeR (v3.18.1)
Genome_build: hg19
Supplementary_files_format_and_content: tsv files counted mapped reads of each gene

source_name: iPSCs

growth_protocol: Midbrain dopaminergic (mDA) neurons were differentiated from iPSCs according to the previously reported protocols (Reinhardt et al., 2013). iPSCs were first derived into neural precursor cells (NPCs) using Neurobasal / DMEM / F12 media supplemented with 10 μM SB431542 (Sigma, S4317), 1 μM Dorsomorphin (Sigma, P5499), 3 μM CHIR99021 (Axon, 1386), and  500 mM Purmorphamine (Sigma, SML0868) for 4 days. After derivation of neural epithelial structures (NESCs), SB431542 and Dorsomorphin were removed and Ascorbic Acid (150 μM, Sigma, A8960) was added to the culture media. NESCs were manually picked and enzymatically purified for a minimum of 5 passages before undergoing characterisation and being hereafter referred to as NPCs. After obtained NPCs, midbrain dopaminergic neurons were differentiated by using Neurobasal / DMEM / F12 media supplemented with 1 μM Purmorphamine, 200 μM Ascorbic Acid, and 100 ng/mL FGF8b (Peprotech, 100-25) for 8 days. From day 8 to day 9, culture media was changed to Neurobasal / DMEM / F12 supplemented with 0.5 μM Purmorphamine and 200μM Ascorbic Acid. From day 10, culture media was changed to Neurobasal / DMEM / F12 media supplemented with BDNF (10 ng/Ml; Peprotech, 450-02), GDNF (10 ng/mL; Peprotech, 450-10), TGFβ3 (1 ng/mL; Peprotech, 100-21), cAMP (500μM; Applichem, A0455) and Ascorbic Acid (200μM). The cells were maintained in this medium until the designated experimental timepoint (d45).

value: iPSC differentiated mDA Neurons

value: THAP1 c.197_198delAG


title: THAP1+/- SHSY5Y Rep1


title: 1087 - NTg - 8 mois


title: THAP1 iPSCs C5-1


title: THAP1 iPSCs C5-2


title: THAP1+/- SHSY5Y Rep2


title: Post patient 7 [Sample 7]

value: high grade serous ovarian cancer

value: IIIB


title: 1116 - NTg - 8 mois


title: THAP1 iPSCs C3-3


title: 1130 - Tg - 4 mois

value: 4 months

value: >100 um from plaque


title: Post patient 6 [Sample 6]


title: 1212 - Tg - 4 mois


title: Wild-type SHSY5Y Rep2

value: Wild-type


title: THAP1 iPSCs C3-2


title: 1193 - Tg - 4 mois


title: Wild-type SHSY5Y Rep1


title: THAP1 iPSCs C3-1


title: 1192 - Tg - 4 mois


title: SHSY5Y SP1 ChIP-seq Rep2

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of ChIP-seq data in fastq files were assessed using QoRTs (v1.2.37). Raw reads were aligned to the hg19 genome assembly using BWA (v0.7.17). Alignment quality was analyzed and unmapped reads were filtered using samtools (v1.12).
ChIP-seq peaks calling were analyzed using MACS2 (v2.1.1.20160309)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

extract_protocol:
Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

tag: conditions

tag: antibody

value: anti-SP1 (Cell signaling, D4C3)


title: Post patient 3 [Sample 3]

value: female


title: Post patient 5 [Sample 5]

value: no


title: Post patient 4 [Sample 4]

value: primary high grade serous ovarian cancer


title: Control iPSCs C2-3


title: SHSY5Y SP1 ChIP-seq Rep1

value: SHSY5Y cells


title: Post patient 2 [Sample 2]

value: IIIC


title: 1039 - NTg - 4 mois


title: SHSY5Y THAP1 ChIP-seq Rep2

value: anti-THAP1 (Proteintech, 12584-1-AP)


title: Control iPSCs C2-2


title: THAP1+/- SHSY5Y H3K4me3 Rep2

value: anti-H3K4me3 (Cell signaling, C42D8)


title: Control iPSCs C1-3


title: T-HESC in vitro decidualization, timepoint 144 hrs, Replicate 2 [Set5_6days_Rep2]

city: Cambridge

first: Lajos

last: Kalmar

address: Tennis Court Road

institute: MRC Toxicology Unit, University of cambridge

data_processing:
Data was analyzed using snakePipes with standard parameters (Vivek Bhardwaj et al. Bioinformatics 2019).
The pipeline employs STAR aligner to map the reads to the human genome (genome build hg38).
FeatureCounts was utilized to count the number of reads per annotated gene using gencode gtf file (release 27).
Assembly: hg38
Supplementary files format and content: Tab separated .txt file containing the raw gene counts

source_name: telomerase-transformed human endometrial stromal cells (T-HESC)

growth_protocol: Cells were maintained in complete growth medium supplemented with 10% charcoal-treated FBS (Sigma, St Louis, MO) according to the manufacturer's instructions. Ascorbic Acid at a final concentration of 50 μg/mL was added to the culture medium every 3 to 4 days.

extract_protocol:
RNA was harvested at each time point using TRIzol (Invitrogen) according to the manufacturer's instructions.
TruSeq Stranded mRNA, according to the manufacturer protocol.

treatment_protocol: To induce decidualization,  T-HESCs were stimulated at timepoints 0 hrs and 72 hrs with cAMP [0.5 mM] and medroxyprogesterone acetate (MPA) [1 μM]  (Sigma, St Louis, MO).

tag: treatment

value: cAMP [0.5mM], MPA [1μM]; stimulus added at timepoint 0 hrs and 72hrs


title: T-HESC in vitro decidualization, timepoint 72 hrs, Replicate 1 [Set5_72_Rep1]

value: telomerase-transformed human endometrial stromal cells (T-HESC)

value: cAMP [0.5mM], MPA [1μM]; stimulus added at timepoint 0 hrs


title: T-HESC in vitro decidualization, timepoint 144 hrs, Replicate 1 [Set5_6days_Rep1]


title: 1038 - NTg - 4 mois

value: Microglia

value: Not relevant (control)


title: THAP1+/- SHSY5Y H3K4me3 Rep1


title: SHSY5Y THAP1 ChIP-seq Rep1


title: Wild-type SHSY5Y H3K4me3 Rep2


title: Control iPSCs C1-1

value: iPSC differentiated mDA Neurons


title: Post patient 1 [Sample 1]

tag: histology

value: high grade serous ovarian cancer

value: yes


title: Healthy Control-2

city: Farmington

first: Mohammed

last: Toufiq

state: Connecticut

address: 10 Discovery Drive, Farmington, CT 06032

department: Research Department

institute: The Jackson Laboratory for Genomic Medicine

description:
Healthy Control-2
Healthy Control-2

data_processing:
The RNA extracted from the samples of the patients and controls were submitted to the Genomics Core at Sidra Medicine for RNA-Seq analysis. Library preparation was performed using the TruSeq Illumina RNA Library Prep kit. Libraries were quantified using the KAPA HiFi Library quantification kit on a Roche LightCycler 480 (Roche, Basel, Switzerland). Cluster generation was performed on a cBot instrument. Samples were sequenced on Illumina HiSeq 4000. Processing of RNASeq data was done using the bcbio rnaseq pipeline (bcbio version 1.2.3). Prior to alignment, a quality check of raw data was done using FastQC version 0.11.9. Alignment was done using STAR (version 2.6.1d) and reads were mapped to the hg38 genome. After alignment, Samtools 1.3 was used to collect metrics on BAM files, which were further used to generate a multiQC report. FeatureCounts (version 2.0.0) was used to estimate the expression counts of each gene. Sample read counts were adjusted for library size and normalized using the Trimmed Mean of M-values (TMM) method using Bioconductor package EdgeR (version 3.34.1). Data were log2 transformed. Fold Change (FC) was calculated between patients and their respective controls using EdgeR. Genes with log2 FC of +2 and -2 were used for downstream pathway analysis with Ingenuity Pathway Analysis (version 01-18-05) and the Bioconductor package Complex Heatmap (version 2.8.0). ggplot2 library (version 3.3.5) was used for visualization and plotting.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized logcpm for every gene and every sample

source_name: Whole Blood

extract_protocol:
PBMCs were stored at -80 °C with QIAzol lysis reagent for later extraction of miRNA and RNA according to the manufacture's protocol (miRNeasy Mini kit, QIAGEN)
Library preparation was performed using the TruSeq Illumina RNA Library Prep kit. Libraries were quantified using the KAPA HiFi Library quantification kit on a Roche LightCycler 480 (Roche, Basel, Switzerland). Cluster generation was performed on a cBot instrument. Samples were sequenced on Illumina HiSeq 4000

value: PBMC

tag: gender

value: Male

tag: race

value: not provided

tag: patient id

value: Healthy Control

tag: time since symptom onset

tag: years since diagnosis


title: Meningeal T cells 1

city: New Brunswick, NJ 089

first: Qi

last: Yang

state: New Jersey

address: 89 French St

institute: Rutgers

description: no treatment

data_processing:
Primary analysis was performed using the Cellrange pipeline. Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v5.1.0 pipelines. The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines. These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
The following Chromium i7 multiplex barcodes were used : H11 for M1, and G11 for M2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx and tsv for processed data, bam for each sample

source_name: Sorted meningeal T cells from the wildtype mice

growth_protocol: primary cells

extract_protocol:
Meningeal MAIT cells, CD4 T cells and CD8+ T cells were sorted by fluorescence activated cell sorting (FACS), and mixed at 1:4:4 ratio. Cell mixature was randomly divided into two parts (M1 and M2).
Library was generated using chromium 5' gene expression kit (10X Genomics) accoding to the manufacturer's instruction.

treatment_protocol: 7 month C57BL/6 mice, no treatment

tag: strain

value: 7 mos


title: Meningeal T cells 2

description: no treatment


title: Control iPSCs C2-1

tag: cell type

value: Wild-type


title: T-HESC in vitro decidualization, timepoint 48 hrs, Replicate 2 [Set5_48_Rep2]


title: HP1

data_processing:
Primary analysis was performed using the Cellrange pipeline. Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v5.1.0 pipelines. The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines. These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
The following Chromium i7 multiplex barcodes were used : B3 for HP1, and D3 for HP2
Genome_build: mm10
Supplementary_files_format_and_content: mtx and tsv for processed data, bam for each sample

source_name: single live cells sorted from hippocampus from Mr1+/+ mice

extract_protocol: Hippocampal cells were isolated using Thermo Scientific Pierce Primary Neuron Isolation Kit (Product No. 88280). Cells were stained with DAPI and Draq5. Live cells were sorted by fluorescence activated cell sorting as DAPI- Draq5+ events. Library was generated using chromium 5' gene expression kit (10X Genomics) according to the manufacturer's instruction.

treatment_protocol: 7 month Mr1+/+ and Mr1-/- mice, no treatment


title: 1135 - NTg - 4 mois

value: 4 months

tag: distance from_amyloid_plaques


title: THAP1+/- SHSY5Y H3K27ac Rep1

value: SHSY5Y cells

value: anti-H3K27ac (Cell signaling, D5E4)


title: T-HESC in vitro decidualization, timepoint 72 hrs, Replicate 2 [Set5_72_Rep2]


title: 1037 - NTg - 4 mois

tag: age


title: Wild-type SHSY5Y H3K27ac Rep1


title: Case-1

description:
Patient-1
Patient-1

value: Female

value: Pakistan

tag: diagnosis

value: FBS

value: 2 Years


title: THAP1+/- SHSY5Y H3K27ac Rep2


title: T-HESC in vitro decidualization, timepoint 36 hrs, Replicate 1 [Set5_36_Rep1]

value: telomerase-transformed human endometrial stromal cells (T-HESC)

value: cAMP [0.5mM], MPA [1μM]; stimulus added at timepoint 0 hrs


title: THAP1+/- SHSY5Y Input Rep2


title: Healthy Control-1

description:
Healthy Control-1
Healthy Control-1


title: T-HESC in vitro decidualization, timepoint 18 hrs, Replicate 1 [Set5_18_Rep1]


title: Wild-type SHSY5Y Input Rep1


title: Wild-type SHSY5Y H3K4me3 Rep1

value: anti-H3K4me3 (Cell signaling, C42D8)


title: K4

city: Stanford

first: Pieter

last: Both

state: California

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50).
Trimmed reads were mapped to mm10 mouse genome with STAR (mismatch cutoff 4% of read length, no non-canonical junction alignments).
Exonic reads uniquely mapped were summarized over genes with the featureCounts module of the Subread package.
Raw counts were analyzed with DESeq2.
Genome_build: mm10

source_name: hindlimb muscles

growth_protocol: MuSCs were FACS-purified from hindlimb muscle of mice at 2-4 months of age.

extract_protocol:
Total RNA was extracted from FACS-purified MuSCs with Nucleospin RNA XS kit (Machery-Nagel)
RNA was reverse transcribed using oligo(dT) primers with the SMARTer Ultra Low Input system (Takara). The cDNA was then sheared with a Covaris S2 ultrasonicator. End repair, multiplexed adapter ligation and 13–15 cycles of library amplification were performed using the Ovation Ultralow Multiplex system (NuGEN)

value: male

value: 2-4 months

tag: sorting markers

value: muscle stem cells

value: ketones


title: K3


title: P2

value: PBS


title: K1


title: P1


title: T-HESC in vitro decidualization, timepoint 36 hrs, Replicate 2 [Set5_36_Rep2]


title: T-HESC in vitro decidualization, timepoint 0 hrs (control), Replicate 2 [Set5_0_Rep2]

value: No


title: T-HESC in vitro decidualization, timepoint 48 hrs, Replicate 1 [Set5_48_Rep1]


title: CTCF ChIP-seq

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
ChIP-seq data analysis was performed in Galaxy platform (Galaxy Version 1.2.0) (https://usegalaxy.org/).
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq peaks were identified using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with all peaks information

source_name: SH-SY5Y cells

value: SH-SY5Y cells

value: Wild-type

value: anti-CTCF(Cell signaling, D31H2)


title: T-HESC in vitro decidualization, timepoint 0 hrs (control), Replicate 1  [Set5_0_Rep1]


title: Sample 224_R

status: Public on Sep 27 2022

city: Worcester

first: Silvia

last: Corvera

state: MA

address: 373 Platantion Street

department: Molecular Medicine

institute: UMASS Medical School

description: Human-Mouse Hybrid

data_processing:
RNA was extracted from white and thermogenic implants using the TRIzol method. Library preparation was performed using the TruSeq cDNA library construction (Illumina). Samples were processed on the Illumina HiSeq 550 sequencing system with the NextSeq 500/550 High Output kit v2.5 (Illumina, Cat. No. 20024906). The generated fastq files were loaded into the DolphinNext platform (https://dolphinnext.umassmed.edu/, June 2020) and the Bulk RNA sequencing pipeline was used. The .fastq files were aligned to both the human (hg38) and the mouse (mm10) genome. The resulting alignments were processed using the R-package XenofilteR to classify reads as either of human or mouse origin. Reference (https://github.com/PeeperLab/XenofilteR, June 2020) for more details on XenofilteR source code. Once aligned, the files were run through RSEM for normalization.
Assembly: hg38 & mm10

organism:
Homo sapiens
Mus musculus

source_name: Adipose Tissue Graft

extract_protocol:
RNA was extracted using the TRIzol protocol from Invitrogen
Library preparation was performed using the TruSeq cDNA library construction (Illumina) following manufacturer protocol

treatment_protocol: Adipogenesis was induced by treating cells for 3 days and subsequently maintained for an additional 14 days. A subset of cells was chronically stimulated at 10 days of differentiation for 7 days with forskolin to induce thermogenesis. Differentiated and forskolin treated cells were implanted into immunodefficient mice for 8 weeks.

tag: condition

value: Thermogenic Implant

tag: tissue

value: Adipose Tissue Graft

value: Primary Adipocytes

tag: genotype

value: WT

value: MDI + FSK


title: T-HESC in vitro decidualization, timepoint 24 hrs, Replicate 2 [Set5_24_Rep2]

value: telomerase-transformed human endometrial stromal cells (T-HESC)


title: T-HESC in vitro decidualization, timepoint 6 hrs, Replicate 1 [Set5_6_Rep1]

value: cAMP [0.5mM], MPA [1μM]; stimulus added at timepoint 0 hrs


title: HP2

source_name: single live cells sorted from hippocampus from Mr1-/- mice

value: 7 mos


title: Control iPSCs C1-2

value: iPSC differentiated mDA Neurons


title: P4

value: male

value: 2-4 months


title: T-HESC in vitro decidualization, timepoint 24 hrs, Replicate 1 [Set5_24_Rep1]


title: THAP1+/- SHSY5Y Input Rep1

value: SHSY5Y cells

tag: conditions

tag: antibody


title: Sample 220_R

description: Human-Mouse Hybrid

value: White Implant

tag: treatment

value: MDI


title: Case-2

description:
Patient-2
Patient-2

value: PBMC

tag: gender

value: Male

value: Sudan

value: FBS

value: 2 Years


title: Wild-type SHSY5Y Input Rep2

value: Wild-type


title: THAP1 KD GATA2 ChIP-seq

value: SH-SY5Y cells

value: THAP1 knock-down

value: anti-GATA2 (Santa Cruz Biotechnology, CG2-96)


title: P3

value: muscle stem cells

value: PBS


title: 754_PM_Repetition_6 [SAMPLE 69]

city: Starkville

first: Esteban

last: Galeano

state: Mississippi

address: 775 Stone Blvd, 351 Thompson Hall, Mississippi State

institute: Mississippi State University

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions. For the normalization it uses the average of the TIF housekeeping gene. The three technical replicates ( PgGA2ox1, PgGA3ox1, PgGA20ox1) and two technical replicates (PgDELLA1 and PgGID1) were averaged for each sample, for the subsequent analysis. Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Matrix normalized worksheet reports normalized signal (against TIF housekeeping gene).

label: SYBR Green

organism: Picea glauca

source_name: Plants without treatment

label_protocol: PCR reactions were performed in 10 mL, containing SYBR Green master mix [0.2 mM dNTPs, 0.3 U Platinum Taq Polymerase (Invitrogen, Waltham, USA), 0.25X SYBR Green, and 0.1X ROX], 50 ng of cDNA and 300 nM of each primer. Three technical replicates for each reaction were analyzed on an ABI PRISM 7900HT Sequence Detection System (Applied Biosystems, Waltham, USA) where the first step was 95°C for 2 min followed by 40 cycles of 95°C for 15 s and 60 °C for 1 min. The qRT-PCR experiments were done at the Molecular Biology Service Unit, University of Alberta.

growth_protocol: On January 20, 2020 seedlings were removed from cold storage and planted into 2L pots filled with Sunshine Mix #4  (Sungro, Vilna, Alberta, Canada) and grown at the Biological Sciences greenhouse, University of Alberta, for their second growing season, between January 28 and April 28, 2020 (Day 92 of the experiment). Plants were grown under natural light supplemented by cool-white fluorescent lamps (400 µmol m-2 s-1) and provided with a 16/8 photoperiod and maximum day and night temperatures of 25°C and 18°C, respectively.

extract_protocol: Using 0.5 g of ground apical internode, total RNA was extracted using the ‘Purelink RNA Mini Kit’, ‘Plant RNA Isolation Aid’ and ‘PureLink DNAse’ (Thermo Scientific Inc, Waltham, USA), following the manufacturer’s instructions The cDNA synthesis was performed using a total of 0.5 μg RNA from each sample, with the Superscript III reverse transcriptase (Thermo Scientific Inc, Waltham, USA). The PgGA2ox1, PgGA3ox1, PgGA20ox1, PgDELLA1 and PgGID1 genes were selected based on previous studies (Kayal et al. 2011, Galeano and Thomas 2020).

treatment_protocol: No treatment were applied to the seedlings.

tag: sample type

value: Control

value: Needles

tag: breeding strategy

value: polymix pollination (PM)


title: K2

value: male

value: 2-4 months

value: ketones


title: T-HESC in vitro decidualization, timepoint 18 hrs, Replicate 2 [Set5_18_Rep2]

value: telomerase-transformed human endometrial stromal cells (T-HESC)

value: cAMP [0.5mM], MPA [1μM]; stimulus added at timepoint 0 hrs


title: 193*1045_CC_Repetition_3 [SAMPLE 66]

value: Test

value: controlled cross (CC)


title: Wild-type SHSY5Y H3K27ac Rep2

value: SHSY5Y cells

value: anti-H3K27ac (Cell signaling, D5E4)


title: 754_PM_Repetition_5 [SAMPLE 64]


title: 754_OP_Repetition_6 [SAMPLE 63]

value: open pollination (OP)


title: 129_PM_Repetition_3 [SAMPLE 62]


title: Sample 221_R

description: Human-Mouse Hybrid

value: White Implant

value: Adipose Tissue Graft

value: Primary Adipocytes

value: WT

value: MDI


title: 154_OP_Repetition_2 [SAMPLE 59]

value: Control

value: Needles


title: 754_OP_Repetition_5 [SAMPLE 57]


title: 96_OP_Repetition_3 [SAMPLE 58]


title: 754_PM_Repetition_3 [SAMPLE 56]

value: polymix pollination (PM)


title: Sample 221_L

description: Human-Mouse Hybrid


title: Sample 223_R

description: Human-Mouse Hybrid

value: Thermogenic Implant

value: MDI + FSK


title: 193_PM_Repetition_3 [SAMPLE 68]


title: 154_OP_Repetition_3 [SAMPLE 65]


title: 122*1047_CC_Repetition_3 [SAMPLE 54]


title: 138_PM_Repetition_3 [SAMPLE 53]


title: 122_OP_Repetition_3 [SAMPLE 50]


title: 122_PM_Repetition_3 [SAMPLE 55]


title: 193_OP_Repetition_3 [SAMPLE 49]


title: T-HESC in vitro decidualization, timepoint 6 hrs, Replicate 2 [Set5_6_Rep2]

value: telomerase-transformed human endometrial stromal cells (T-HESC)


title: 129_OP_Repetition_3 [SAMPLE 45]


title: 138_OP_Repetition_3 [SAMPLE 47]


title: 138_PM_Repetition_2 [SAMPLE 46]


title: 927_OP_Repetition_6 [SAMPLE 61]


title: Sample 219_L

description: Human-Mouse Hybrid


title: Sample 223_L

description: Human-Mouse Hybrid


title: 927*991_CC_Repetition_2 [SAMPLE 60]


title: 754_OP_Repetition_4 [SAMPLE 51]


title: 927*991_CC_Repetition_3 [SAMPLE 67]


title: 122_OP_Repetition_2 [SAMPLE 36]


title: 154_OP_Repetition_1 [SAMPLE 43]


title: 138*752_CC_Repetition_3 [SAMPLE 52]


title: 927_PM_Repetition_3 [SAMPLE 44]


title: 754*966_CC_Repetition_3 [SAMPLE 37]


title: 193*1045_CC_Repetition_2 [SAMPLE 48]


title: 754_OP_Repetition_3 [SAMPLE 40]


title: 193*1045_CC_Repetition_1 [SAMPLE 31]


title: 193_OP_Repetition_2 [SAMPLE 33]


title: 138*752_CC_Repetition_2 [SAMPLE 28]


title: 138_OP_Repetition_2 [SAMPLE 30]


title: 122_PM_Repetition_2 [SAMPLE 35]


title: 138_PM_Repetition_1 [SAMPLE 29]


title: 129_OP_Repetition_2 [SAMPLE 27]


title: G648_MNase_NP40_55m_(20220614_TB_Mv_G648_Mnase_55m)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: MNase-seq of G648 after 55 min in NP40

data_processing:
Genome_build: G648_genome.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence: Marseillevirus marseillevirus G648 (Genome_G648.fasta) or Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI (pUC19-601x7_KpnI.fasta). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

organism: Marseillevirus marseillevirus

source_name: MNase-seq

tag: source

value: DNA from MNase-digested chromatin


title: G648_MNase_NP40_7m_(20220614_TB_Mv_G648_Mnase_7m)

description: MNase-seq of G648 after 7 min in NP40


title: 96_OP_Repetition_2 [SAMPLE 42]


title: G648_MNase_NP40_7h_(20220614_TB_Mv_G648_Mnase_7h)

description: MNase-seq of G648 after 7 hr in NP40


title: 129_PM_Repetition_2 [SAMPLE 26]

value: Test


title: 927_OP_Repetition_5 [SAMPLE 24]


title: G648_MNase_NP40_18h_(20220614_TB_Mv_G648_Mnase_18h)

description: MNase-seq of G648 after 18 hr in NP40


title: 754_PM_Repetition_2 [SAMPLE 38]


title: G648_MNase_NP40_3m_(20220614_TB_Mv_G648_Mnase_3m)

description: MNase-seq of G648 after 3 min in NP40


title: 96_OP_Repetition_1 [SAMPLE 20]


title: 927_OP_Repetition_4 [SAMPLE 23]


title: G648_MNase_NP40_2_5m_(20220614_TB_Mv_G648_Mnase_2_5h)

description: MNase-seq of G648 after 2.5 min in NP40


title: 754_OP_Repetition_2 [SAMPLE 39]


title: 129*756_CC_Repetition_3 [SAMPLE 25]

value: controlled cross (CC)


title: G648_MNase_NP40_1m_(20220614_TB_Mv_G648_Mnase_1m)

description: MNase-seq of G648 after 1 min in NP40


title: 754_PM_Repetition_4 [SAMPLE 41]


title: 122*1047_CC_Repetition_2 [SAMPLE 34]


title: 754_OP_Repetition_1 [SAMPLE 19]


title: 122_PM_Repetition_1 [SAMPLE 15]


title: 193_OP_Repetition_1 [SAMPLE 13]


title: 927*991_CC_Repetition_1 [SAMPLE 21]


title: 754*966_CC_Repetition_2 [SAMPLE 17]


title: 138*752_CC_Repetition_1 [SAMPLE 10]


title: 129*756_CC_Repetition_2 [SAMPLE 8]


title: 927_PM_Repetition_2 [SAMPLE 22]


title: G648_MNase_NP40_20m_(20220614_TB_Mv_G648_Mnase_20m)

description: MNase-seq of G648 after 20 min in NP40


title: 193_PM_Repetition_2 [SAMPLE 32]


title: 122_OP_Repetition_1 [SAMPLE 16]


title: 927_OP_Repetition_3 [SAMPLE 7]


title: 129_OP_Repetition_1 [SAMPLE 5]


title: 129_PM_Repetition_1 [SAMPLE 9]


title: 754_PM_Repetition_1 [SAMPLE 18]


title: 129*756_CC_Repetition_1 [SAMPLE 4]


title: 754*966_CC_Repetition_1 [SAMPLE 6]


title: 138_OP_Repetition_1 [SAMPLE 11]


title: 927_PM_Repetition_1 [SAMPLE 1]


title: 193_PM_Repetition_1 [SAMPLE 12]


title: 122*1047_CC_Repetition_1 [SAMPLE 14]


title: 927_OP_Repetition_2 [SAMPLE 3]


title: 927_OP_Repetition_1 [SAMPLE 2]


title: 7_2

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

data_processing:
RNA-seq reads were aligned to tiger puffer genome and annotation (assembly fTakRub1.2) using HISAT2 (version 2.0.4).
The aligned short reads were counted using RSEM (version 1.2.12).
Genome_build: assembly fTakRub1.2
Supplementary_files_format_and_content: Excel file include FPKM for each sample.

organism: Takifugu alboplumbeus

source_name: Ventral part of telenchephalon, hypothalamus and pituitary

growth_protocol: Wild male grass puffers were obtained from the spawning site, Minamichita, Japan.

extract_protocol:
Total RNA of ventral part of telenchephalon, hypothalamus and pituitary were isolated with elimination of DNA contamination using DNase.
mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE100 strand specific sequencing libraries.
Strand-specific RNA-seq

treatment_protocol: After bringing live puffers back to the laboratory, brain region containing ventral part of telenchephalon, hypothalamus and pituitary was collected at around 19:00 (JST).

tag: sampling point

value: Full moon, July 2020

tag: Sex

value: male


title: 7_1


title: 8_3

value: Waning moon, July 2020


title: 8_1


title: 7_3


title: 6_3

value: Waxing moon, June 2020


title: 5_3

value: New moon, June 2020


title: 8_2


title: 6_1


title: 6_2


title: 5_1


title: 4_3

value: Waning moon, June 2020


title: 2_1

value: Waxing moon, May 2020


title: 4_2


title: 3_1

value: Full moon, June 2020


title: 5_2


title: 3_2


title: 3_3


title: 2_2


title: 4_1


title: 601_Xl3_MPE_(20220819_TB_601_Xl3_MPE_20220801)

description:
MPE-seq of Xenopus on 601x7_12bp-linker_pUC19 1:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI

data_processing:
Genome_build: pUC19-601x7_KpnI.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence: Marseillevirus marseillevirus G648 (Genome_G648.fasta) or Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI (pUC19-601x7_KpnI.fasta). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

organism: synthetic construct

source_name: MPE-seq

value: DNA from MPE-digested chromatin


title: 2_3


title: 1_2

value: New moon, May 2020


title: 601_Xl3_MNase_XL_(20220819_TB_601_Xl3_Mnase_20220801)

description:
MNase-seq of Xenopus on 601x7_12bp-linker_pUC19 1:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl1_MNase_(20220819_TB_601_Xl1_Mnase_20220729)

description:
MNase-seq of Xenopus on 601x7_12bp-linker_pUC19 1:4 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl2_MPE_(20220819_TB_601_Xl2_MPE_20220801)

description:
MPE-seq of Xenopus on 601x7_12bp-linker_pUC19 1:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv6_MNase_(20220819_TB_601_Mv6_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 5:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv5_MPE_(20220819_TB_601_Mv5_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 2:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl1_MPE_(20220819_TB_601_Xl1_MPE_20220801)

description:
MPE-seq of Xenopus on 601x7_12bp-linker_pUC19 1:4 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 1_3


title: 1_1


title: 601_Mv5_MNase_(20220819_TB_601_Mv5_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 2:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl4_MNase_(20220819_TB_601_Xl4_Mnase_20220729)

description:
MNase-seq of Xenopus on 601x7_12bp-linker_pUC19 3:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl4_MPE_(20220819_TB_601_Xl4_MPE_20220801)

description:
MPE-seq of Xenopus on 601x7_12bp-linker_pUC19 3:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv3_MPE_(20220819_TB_601_Mv3_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 1:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv3_MNase_(20220819_TB_601_Mv3_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 1:1 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Xl2_MNase_(20220819_TB_601_Xl2_Mnase_20220729)

description:
MNase-seq of Xenopus on 601x7_12bp-linker_pUC19 1:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv4_MPE_(20220819_TB_601_Mv4_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 3:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv4_MNase_(20220819_TB_601_Mv4_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 3:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv2_MPE_(20220819_TB_601_Mv2_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 1:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv1_MPE_(20220819_TB_601_Mv1_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 1:4 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv2_MNase_(20220819_TB_601_Mv2_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 1:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv6_MPE_(20220819_TB_601_Mv6_MPE_20220801)

description:
MPE-seq of T19 on 601x7_12bp-linker_pUC19 5:2 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: 601_Mv1_MNase_(20220819_TB_601_Mv1_Mnase_20220729)

description:
MNase-seq of T19 on 601x7_12bp-linker_pUC19 1:4 histone:DNA ratio
Widom 601 7-copy array with 12-bp linkers in pUC19 cleaved with BamHI and KpnI


title: BXD84_HFD

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD84 mice fed on high fat diet in a fed state

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner.

data_processing: Intensities were processed using the apt-probeset-summarize script from the Array Power Tool suite (version 2.11.3, https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip) with the gc-sst-rma-sketch standard method. Data processing code deposited at https://doi.org/10.5281/zenodo.4899683.

label: biotin

source_name: liver, high fat diet

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (part number 4411974) according to manufactures protocols, then 5500ng of cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice were housed 5 per cage, by strain and diet, in isolator cages with individual air filtration (500 cm2, GM500, Tecniplast) and provided water ad libitum.

extract_protocol: Total RNA was extracted from tissue samples using trizol. RNA concentration was assessed using a Nanodrop. RNA extracts from approximately 5 animals were pooled at equal mass concentration, representing a total of roughly 360 animals. Pooled RNA extracts were then cleaned up using the Qiagen RNEasy kit.

treatment_protocol: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks of age until euthanasia, about half of the mice were fed ad libitum a high-fat diet (HFD) and the rest continued to be fed a chow diet. To avoid multiple sacrifices at night, the light/dark cycle of the mice was inverted two weeks before the sacrifice to ensure their adaptation. At 29 weeks of age, mice were fasted overnight (their day) and refed with their respective diet for 4 hours before sacrifice. Mice were euthanized with isoflurane anesthesia. Tissue samples were then excised and stored in liquid nitrogen. Standard rodent chow (CD): 18% kCal fat, 24% kCal protein and 58% kCal of carbohydrates (Harlan, 2018, Indianapolis, IN, USA). High-fat diet (HFD): 60.3% kCal fat, 18.3% kCal protein and 21.4% kCal of carbohydrates (Harlan, 06414, Indianapolis, IN, USA).

tag: strain

value: 29 weeks

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until euthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: fat:60.3% kCal, protein:18.3% kCal, carbohydrate:21.4% kCal

value: Teklad Custom Diet TD.06414, Envigo, Indianapolis, IN, USA

value: liver

value: ng/ul

tag: rin


title: BXD81_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD81 mice fed on chow diet in a fed state

source_name: liver, chow diet

value: male

tag: age

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: fat:18% kCal, protein:24% kCal, carbohydrate:58% kCal

value: Teklad Global 18% Protein Rodent Diet 2018 , Envigo, Indianapolis, IN, USA


title: DBA/2J_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male DBA/2J mice fed on chow diet in a fed state


title: BXD89_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD89 mice fed on chow diet in a fed state


title: C57BL/6J_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male C57BL/6J mice fed on chow diet in a fed state


title: BXD100_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD100 mice fed on high fat diet in a fed state


title: BXD87_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD87 mice fed on high fat diet in a fed state


title: BXD75_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD75 mice fed on chow diet in a fed state


title: BXD87_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD87 mice fed on chow diet in a fed state


title: BXD79_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD79 mice fed on high fat diet in a fed state


title: BXD89_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD89 mice fed on high fat diet in a fed state


title: BXD100_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD100 mice fed on chow diet in a fed state


title: BXD90_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD90 mice fed on high fat diet in a fed state


title: BXD79_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD79 mice fed on chow diet in a fed state


title: BXD73_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD73 mice fed on high fat diet in a fed state


title: BXD66_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD66 mice fed on high fat diet in a fed state


title: BXD67_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD67 mice fed on chow diet in a fed state


title: BXD77_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD77 mice fed on chow diet in a fed state


title: BXD75_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD75 mice fed on high fat diet in a fed state


title: BXD81_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD81 mice fed on high fat diet in a fed state


title: BXD69_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD69 mice fed on high fat diet in a fed state


title: BXD73_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD73 mice fed on chow diet in a fed state


title: BXD90_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD90 mice fed on chow diet in a fed state


title: DBA/2J_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male DBA/2J mice fed on high fat diet in a fed state


title: C57BL/6J_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male C57BL/6J mice fed on high fat diet in a fed state


title: BXD77_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD77 mice fed on high fat diet in a fed state


title: BXD69_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD69 mice fed on chow diet in a fed state


title: BXD66_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD66 mice fed on chow diet in a fed state


title: BXD84_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD84 mice fed on chow diet in a fed state


title: BXD67_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD67 mice fed on high fat diet in a fed state


title: BXD64_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD64 mice fed on high fat diet in a fed state


title: BXD64_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD64 mice fed on chow diet in a fed state


title: BXD53_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD53 mice fed on chow diet in a fed state


title: BXD49_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD49 mice fed on high fat diet in a fed state


title: BXD51_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD51 mice fed on high fat diet in a fed state


title: BXD63_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD63 mice fed on chow diet in a fed state


title: BXD48a_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD48a mice fed on chow diet in a fed state


title: BXD55_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD55 mice fed on high fat diet in a fed state


title: BXD55_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD55 mice fed on chow diet in a fed state


title: BXD51_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD51 mice fed on chow diet in a fed state


title: BXD62_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD62 mice fed on high fat diet in a fed state


title: BXD48a_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD48a mice fed on high fat diet in a fed state


title: BXD39_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD39 mice fed on high fat diet in a fed state


title: BXD63_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD63 mice fed on high fat diet in a fed state


title: BXD53_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD53 mice fed on high fat diet in a fed state


title: BXD40_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD40 mice fed on chow diet in a fed state


title: BXD48_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD48 mice fed on chow diet in a fed state


title: BXD45_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD45 mice fed on high fat diet in a fed state


title: BXD43_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD43 mice fed on chow diet in a fed state


title: BXD62_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD62 mice fed on chow diet in a fed state


title: BXD39_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD39 mice fed on chow diet in a fed state


title: BXD45_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD45 mice fed on chow diet in a fed state


title: BXD43_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD43 mice fed on high fat diet in a fed state


title: BXD48_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD48 mice fed on high fat diet in a fed state


title: BXD49_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD49 mice fed on chow diet in a fed state


title: BXD40_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD40 mice fed on high fat diet in a fed state


title: BXD34_CD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD34 mice fed on chow diet in a fed state


title: BXD34_HFD

description: Gene expression data from pooled RNA extract of liver samples collected on 29 weeks old male BXD34 mice fed on high fat diet in a fed state


title: KIF_4+#2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Colon

extract_protocol: For flow-cytometrically sorted samples, cells  were isolated by first enzymatically digesting distal colon tissue and then purified by fluorescence-activated cell sorting (two times to achieve enhanced purity). A total of  1,000  CD4+ T cells (DAPI- CD19- CD4+ TCRβ+) were sorted using the BD Aria IIinto TCL buffer (QIAGEN) with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

value: Colon

tag: cell line

value: CD4+ T cells isolated from Germ-Free monocolinzed with EcN kfiCD mutant Colonic tissue

tag: cell type

value: CD4+ T cells

value: Germ-free + E.coli Nissle kfiCD D14


title: ECN_4+#1

value: CD4+ T cells isolated from Germ-Free monocolinzed with EcN Colonic tissue

value: Germ-free + E.coli Nissle wild-type D14


title: KIF_4+#1


title: ECN_4+#2


title: ECN_4+#3


title: GF_4+#3

value: CD4+ T cells isolated from Germ-Free Colonic tissue

value: Germ-free


title: GF_4+#1