title: G1E-ER4 24h - chiapet-SMC1A_rep2

city: Cambridge

first: Jonathan

last: Li

state: Massachusetts

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

data_processing:
The data were analyzed using Origami software (https://github.com/younglab/origami) under release tag alpha20160828
Each ChIA-PET data set was processed as follows: the reads were first trimmed and aligned using origami-alignment, which trims the ChIA-PET linker if present and aligns trimmed PETs. PETs not having a linker were discarded from further analysis. Each end of a PET with a linker sequence was separately mapped to the hg19 genome assembly using bowtie with the following options: -v 1 –k 1 –m 1. After alignment, the separated PETs were re-paired in the final BAM output. After repairing, all duplicated PETs within the data were removed, since these were believed to be PCR duplicates. Peaks were called on the re-paired ChIA-PET reads using MACS1 v1.4.2 with the following parameters: --nolambda –nomodel –p 1e-9.
mm9
chiapet interactions; each row indicates a pair of regions, total counts for the interaction, a p-value, and a score given by a Bayes mixutre model

growth_protocol: G1ER4 cells were cultured in Isocove’s modified Dulbecco’s medium (IMDM) supplemented with 15%  fetal calf serum (FCS), 100 units (U) /mL penicillin and 100 g/mL streptomycin (PS), 2 U/mL recombinant human erythropoietin (EPO), and 50 ng/ml mouse recombinant SCF or 1% conditioned medium from murine SCF producer cell line

extract_protocol: ChIA-PET was performed as previously described (Hnisz et al., Science, 2016) using G1-ER4 cells (150 million per replicate)

treatment_protocol: Differentiation was induced by adding beta-estradiol (Sigma, cat: E8875) at a final concentration of 10 nM for 24 hrs or as otherwise indicated

value: 10 nM beta-estradiol for 24h

tag: chip antibody

value: anti-SMC1 (Bethyl, cat:A300-055A)


title: DONOR D AMPK

status: Public on Jan 05 2024

type: RNA

city: Pittsburgh

first: Erica

last: Braverman

state: PA

address: 4401 Penn Ave

country: USA

institute: University of Pittsburgh

description: DONOR D AMPKG2

data_processing:
Normalization of the data was performed by the manufacturer's website (https://geneglobe.qiagen.com/us/analyze)
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control (i.e., AMPKg2/EV) ratios.

label: SYBR GREEN

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ T CELLS

label_protocol: One microgram of RNA was reverse transcribed to cDNA using the Biorad iScript cDNA Reaction Kit (per kit’s instructions). Using Biorad’s SYBR Green Master Mix reagent, 4 uL of cDNA was placed into 36 uL of water, master mix, and primers and the quantitative PCR reaction run in triplicate reactions of 10 uL each on an Applied Biosystem QuantStudio3 cycler with the standard protocol of 95C and 60C over 40x cycles.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell type

value: HUMAN CD4+ T CELLS

tag: plasmid

value: AMPKG2 PLASMID


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 2

type: SRA

city: Guangzhou

first: Jinyi

last: Wu

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

country: China

institute: Guangzhou Laboratory

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-2

library_source: transcriptomic single cell

data_processing:
For bulk RNA-seq data, raw reads of fastq format from this study were first processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw reads. Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. For single cell RNA-seq data, data of day 6 blastoids was pre-processed through Trimmomatic software to remove adapters and to drop low quality reads or short reads below 26 bps. Other single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq and scRNAseq (Smartseq2) count table: gene by cell expression matrix generated with STAR; scRNAseq (10X) count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: TJ 1# CI-hnESC

extract_protocol:
For bulk RNA-seq, total RNAs were collected and isolated from cells using RNAiso Plus (Takara). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina following manufacturer’s recommendations. For scRNA-seq, CI-hnESCs and day 2 aggregates were dissociated and sorted by flow cytometer for Smart-seq2 library construction and the libraries were sequenced on MGISEQ2000 (MGI Tech) platform to generate 100-bp paired-end reads. Day 3, day6 blastoids and the blastoids upon removing MEK/BRAF inhibition from Aggrewell were manually picked and polled with a mouth pipette, washed once with DPBS and then dissociated with 0.25% trypsin-EDTA (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Attached cultured bE14 blastoids were first rinsed once with DPBS and then treated with cold DPBS and incubated in 4°C for 10-20min to allow breaking of the matrix. When the samples became mobile under a microscope upon gentle shaking, the bE14 blastoids were transferred to a clean tube using a cut-tip and dissociated with 0.25% trypsin-EDTA at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cell

tag: cell line

value: TJ 1# CI-hnESC


title: TELC-D5-scRNA-rep2

city: guangzhou

first: Wenjuan

state: 广东

address: UCAS

department: GIBH

institute: UCAS

data_processing:
Raw sequencing reads were filtered and demultiplexed using PISA (v0.2). Filtered reads were aligned to hg38 genome reference using STAR (v2.7.3a) and sorted by sambamba (v0.7.0). Cell versus gene UMIs (Unique Molecular Identifiers) count matrices were generated by PISA.
Count matrices were processed using the Seurat package (v3.1.4) in R (v3.6.0). Genes expressed in less than three cells were filtered out. Cells with less than 15% mitochondrial reads, less than 500 genes and 3,000 UMIs detected were excluded from the further analysis. Doublet removal was performed by DoubletFinder with the default parameter.
Assembly: hg38
Supplementary files format and content: Tab-separated raw matrix file

source_name: Not applicable

growth_protocol: Human naïve PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express and plated at a density of 100,000 cell/well of 6-well plate on Geltrex in TE induction medium (1:1 mix of Neurobasal medium (Gibco) and DMEM/F12 (HyClone) supplemented with N2 (Gibco) and B27 (Gibco), penicillin-streptomycin (HyClone), Glutamax (Gibco), β-mercaptoethanol (Sigma), 1 µM PD0325901 (Axon) and 1 µM A83-01 (Selleck)) for five days. TELCs at day 5 were used for downstream analysis throughout this study. For generating expandable TSCs, TELCs at day 5 were dissociated into single cells with TrypLE and plated on Geltrex-coated six-well plates at a 1:4-1:8 split ratio in TSC medium (DMEM/F12 supplemented with N2 and B27, penicillin-streptomycin, Glutamax, β-mercaptoethanol, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF (PeproTech), 0.5 µM A83-01 (Selleck), 1 µM SB431542 (Selleck), 2 µM CHIR99021 (Axon), 0.8 mM VPA (Vetec) and 5 µM Y-27632 (Axon)) supplemented with 10 µM Y-27632.

extract_protocol:
Cells were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express (Gibco). After passing through 70 μM cell strainers, cell suspensions were converted to barcoded scRNA-seq libraries according to the manufacturer’s protocol.
scRNA-seq libraries were prepared using a DNBelab C Series Single-Cell Library Prep set(MGI,1000021082). Qubit ssDNA Assay kit (Thermo Fisher Scientific, Q10212) was used to quantify the sequencing library concentration.

tag: tissue

value: Not applicable

value: Human ESC derived-TELC-D5

tag: treatment

value: untreated(wild type)


title: DONOR D EV

description: DONOR D EV CONTROL

value: EV PLASMID


title: G1E-ER4 0h - chiapet-SMC1A_rep2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: 10 nM beta-estradiol for 0h


title: TELC-D5-scRNA-rep1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 1

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-1


title: G1E-ER4 0h - chiapet-SMC1A_rep1


title: Differentiated C3H10T1/2 cells, siYBX1, rep2

status: Public on Jan 04 2024

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

library_source: transcriptomic

data_processing:
The libraries were sequenced on the BGISEQ-500 platform and paired-end reads  were generated.
About 50M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 49M clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to GRCm39 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for all Sample

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent(Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V5 RNA-seq Library Prep following manufacturer's protocols.

treatment_protocol: Adipogenic differentiation was induced by treatment of confluent C3H10T1/2 preadipocytes with complete medium supplemented with 0.5 mM 3-isobutyl-1-methylxanthine (Sigma), 1 μM dexamethasone (Sigma), 850 nM insulin (Sigma), 1nM triiodothyronine (Sigma), 125 nM indomethacin (Sigma) and 1 μM rosiglitazone (MedChemExpress) for 2 days. Then, cells were changed to the complete medium supplemented with 1 nM T3, 850 nM insulin, and 1 μM rosiglitazone for another 2 days. Differentiated adipocytes at day 4 were transfected with specific siRNAs targeting YBX1 or control siRNA, and total RNA was extracted 48h after transfection for RNA-seq and bioinformatics analysis.

value: mesenchymal stem cells

tag: genotype

value: YBX1 knockdown

value: adipogenic differentiation


title: Differentiated C3H10T1/2 cells, siYBX1, rep3


title: Differentiated C3H10T1/2 cells, siYBX1, rep1


title: Differentiated C3H10T1/2 cells, siNC rep3

value: WT


title: Differentiated C3H10T1/2 cells, siNC rep2


title: M1833.8KT

city: Dallas

first: James

last: Brugarolas

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Internal Medicine

institute: University of Texas Southwestern Medical Center

data_processing:
The raw RNA-Seq data from mice underwent quality control tests using FastQC and MultiQC.
Bowtie2 was employed to quantify the abundance of ribosomal RNA (rRNA).
RNA-seq reads were aligned to the Mouse GRCm38 (mm10) reference genome using STAR (v2.5.2a).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Dysmorphic-Kidney

growth_protocol: All mice were housed in a barrier facility with sterile laminar flow cages maintained at 22°C, under a 12-hour light/dark cycle. Animals were provided unrestricted access to disinfected tap water and commercial food.

extract_protocol:
RNA was extracted from mouse FFPE samples using an in-house method developed by the NYGC. This method uses a thermostable protease in a novel digestion buffer with saponified medium-chain triglycerides for the efficient separation of high-quality RNA. Solid phase reversible immobilization beads (Beckman Coulter, #B23319) were used to purify nucleic acid.
RNA samples were processed using a Kapa Stranded Total RNA-seq Library Preparation Kit (Roche, #KK8484) without depletion of ribosomal RNA.

treatment_protocol: ASPSCR1-TFE3 LSL/+ mice were interbred with mice expressing Cre under the control of kidney lineage-specific promoters, Pax8 and Sglt2.

value: Dysmorphic-Kidney

value: Pax8-Cre; ASPSCR1-TFE3 LSL/+


title: Differentiated C3H10T1/2 cells, siNC rep1


title: M1833.7N

source_name: Normal-Embryonic Kidney

value: Normal-Embryonic Kidney


title: M1833.4KT


title: DONOR A AMPK

description: DONOR A AMPKG2


title: H0248.9N


title: G1E-ER4 24h - chiapet-SMC1A_rep1

value: 10 nM beta-estradiol for 24h

value: anti-SMC1 (Bethyl, cat:A300-055A)


title: H0248.6N


title: H0248.3KT


title: H0248.1KT


title: H0248.5KT


title: M1816N2

source_name: Normal-Kidney

value: Normal-Kidney


title: M1906N2


title: M1906N1


title: M1816N1


title: DONOR A EV

description: DONOR A EV CONTROL

value: HUMAN CD4+ T CELLS


title: H0038N2


title: H0372KT2

source_name: Tumor-Kidney

value: Tumor-Kidney

value: Sglt2-Cre; ASPSCR1-TFE3 LSL/+


title: H0372OT3

source_name: Tumor-Retro Orbit

value: Tumor-Retro Orbit


title: H0372KT1


title: H0038N1


title: H0322N


title: H0322OT2


title: H0322KT1


title: H0319BT3

source_name: Tumor-Brain

value: Tumor-Brain


title: H0319KT1


title: H0218N


title: H0319KT2


title: H0218OT3


title: H0218KT2


title: H0072BT3


title: H0055BT3


title: H0072OT4


title: H0072KT1


title: H0055N


title: H0055KT2


title: H0055KT1a


title: V1P KO/KO DNs RNA 2

city: Philadelphia

first: Craig

last: Bassing

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Raw RNA-Seq reads were trimmed using bbduk as part of bbmap (version 38.92) (https://sourceforge.net/projects/bbmap/). Reads were then aligned to mm10 using STAR (version 2.7.9a) (https://pubmed.ncbi.nlm.nih.gov/23104886/). bamCoverage from the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) yielded the bigwig coverage files and was run using flags to separate the coverage tracks by stranded-ness and to normalize to counts per million (cpm). Normalized bigwig coverage files were uploaded to the UCSC genome browser (https://pubmed.ncbi.nlm.nih.gov/12045153/).
Assembly: mm10
Supplementary files format and content: bigwig coverage files as produced by bamCoverage. The coverage is seperated into reads originating from the forward (fwd) or reverse (rev) strand.

source_name: Rag1-/- DN thymocytes

extract_protocol:
(B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice.
RNA sequencing library preparation was prepared using Rib0-Zero rRNA Removal Kit and TruSeq Stranded Total RNA library Prep kit following manufacturer’s protocol (Illumina, RS-122-2101)

value: Rag1-/- DN thymocytes


title: V1P KO/KO DNs RNA 1


title: V1C Scr/Scr DNs RNA 1


title: WT DNs RNA 3


title: V1C Scr/Scr DNs ChIP CTCF 2 input

data_processing:
For ChiP-Seq, paired-end reads were aligned to the mm10 genome using bowtie2 (version 2.4.5) (https://pubmed.ncbi.nlm.nih.gov/22388286/). Peak calling was done using the macs2 algorithm (version 2.2.7.1) (https://pubmed.ncbi.nlm.nih.gov/18798982/), with exception for the H3K9me2 mark where the edd (version 1.1.9) software (https://pubmed.ncbi.nlm.nih.gov/24782521/) was used to identify enriched domains. Bigwig files for the visualization in the UCSC genome browser were yielded by the bamCoverage tool inside the deeptools package (version 3.5.1) (https://pubmed.ncbi.nlm.nih.gov/27079975/) applying the RPGC normalization.
Assembly: mm10
Supplementary files format and content: bigwig files produced by bamCoverage and normalized by RPGC. For H3K9me2 the enriched domains as computed by edd as log ratio at 10k resolution are uploaded.

extract_protocol: DN thymocytes were isolated from Rag1-/- mice.

value: input


title: WT DNs RNA 1


title: WT DNs RNA 2


title: V1P KO/KO DNs ChIP H3K27ac 1 input


title: V1C Scr/Scr DNs RNA 2


title: H0319N


title: V1P KO/KO DNs ChIP CTCF 1 input


title: WT DNs ChIP H3K27ac 1 input


title: V1C Scr/Scr DNs ChIP CTCF and H3K27ac 1 input


title: V1P KO/KO DNs ChIP CTCF 2 input


title: V1C Scr/Scr DNs ChIP H3K9me2 1 input


title: WT DNs ChIP CTCF 2 input


title: V1C Scr/Scr DNs ChIP H3K9me2 and H3K27ac 2 input


title: WT DNs ChIP CTCF 1 input


title: H0218KT1


title: V1P KO/KO DNs ChIP H3K9me2 1 input


title: H0072KT2


title: V1C Scr/Scr DNs ChIP H3K27ac 1


title: WT DNs ChIP H3K9me2 1 input


title: WT DNs ChIP H3K9me2 2 input


title: V1P KO/KO DNs ChIP H3K27ac 2


title: V1C Scr/Scr DNs ChIP H3K27ac 2


title: WT DNs ChIP H3K27ac 2 input


title: WT DNs ChIP H3K27ac 1


title: V1C Scr/Scr DNs ChIP CTCF 2


title: V1C Scr/Scr DNs ChIP CTCF 1


title: WT DNs ChIP CTCF 1


title: V1P KO/KO DNs ChIP CTCF 1


title: WT DNs ChIP CTCF 2


title: V1C Scr/Scr DNs ChIP H3K9me2 2


title: V1C Scr/Scr DNs ChIP H3K9me2 1


title: V1P KO/KO DNs ChIP H3K9me2 1


title: WT DNs ChIP H3K9me2 2


title: V1P KO/KO DNs ChIP H3K9me2 2


title: V1P KO/KO DNs ChIP H3K9me2 and H3K27ac 2 input


title: WT DNs ChIP H3K9me2 1


title: V1C Scr/Scr DNs ArimaHiC 2

data_processing:
For HiC, paired end raw reads were mapped with bwa version (https://pubmed.ncbi.nlm.nih.gov/19451168/), treating forward and reverse reads separately, as described and implemented with the HiCExplorer command tool version 3.6 (https://pubmed.ncbi.nlm.nih.gov/29335486/). For Figure 1, we combined experimental data from conventional and Arima HiC because they had sufficient pairwise spearman correlations. For Figures 3 and 4, we down-sampled data from the genotype with the most reads to be equivalent to the number of reads from the genotype with the least reads. Visualization was done via UCSC genome browser (https://pubmed.ncbi.nlm.nih.gov/12045153/), using the interact format, and juicebox (https://pubmed.ncbi.nlm.nih.gov/29428417/). MUSTACHE version 1.2.0 (https://pubmed.ncbi.nlm.nih.gov/32998764/) was used to identify significant looping at resolutions 10K, 5K and 3K.
Assembly: mm10
Supplementary files format and content: Combined and down sampled .hic files

extract_protocol:
DN thymocytes were isolated from Rag1-/- mice.
The final conventional HiC library was generated with 5 PCR cycles using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Dual Index primers (NEB) for Illumina sequencing. For the Arima HiC the KAPA Hyper Prep Kit was used.


title: V1P KO/KO DNs ArimaHiC 2


title: V1C Scr/Scr DNs ArimaHiC 1


title: WT DNs ArimaHiC 6


title: WT DNs ChIP H3K27ac 2


title: WT DNs ConventionalHiC 4


title: WT DNs ConventionalHiC 2


title: WT DNs ArimaHiC 5


title: 7CR20HFD_PIT

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
Quality of sequencing for RNA reads were checked using FastQC. The adaptors and low-quality bases (Q < 20) were trimmed to a minimum of 36 base pairs using Trimmomatic (27). STAR was used to align Mus musculus GRCm39.104 reference genome with reads that passed quality control (28). To obtain raw counts, BAM files using Subread's features Count function were transformed to log2 counts per million (CPM) (29). Genes with a low expression were filtered out and libraries normalized by trimmed mean of M values (30). R package, Limma, using the voom “With Quality Weights” function was used for differential expression and linear modeling (31).  Genes with an FDR adjusted p-values < 0.055 and a Log2FC ≥ 0.58 (1.5-fold increase) were considered significant and designated as differentially expressed genes (DEGs).
Assembly: Mus musculus GRCm39.104
Supplementary files format and content: tab-delimited csv

source_name: Pituitary

growth_protocol: For the diet induced obesity (DIO) studies, additional offspring were generated using the CR20 model as described above (see 2.2). FED and CR20 offspring were weaned at PND21 and separated by sex. Offspring weight and length (nose to anus) were measured weekly from weaning to 8 weeks of age. Female pups were inspected daily from PND 21 until the day of vaginal opening to determine the timing of puberty.

extract_protocol:
At euthanasia, trunk serum, pituitaries, eWAT, and liver were collected.
Libraries for RNAseq were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina Inc) according to the manufacturer’s protocol.

treatment_protocol: At 8 weeks of age, pups from each dam were blindly assigned to either a CTRL or HFD feeding group. Offspring were introduced to either a 10% fat (CTRL) diet (Envigo, TD.110675) or a 45% high fat diet (HFD) (Envigo, TD.06415) which they consumed for 10 weeks or 16 weeks. For each sex, this resulted in four experimental groups with 5±1 mice/group: FED control (FED-CTRL); FED high fat diet (FED-HFD) and calorie restricted control (CR20-CTRL) and HFD (CR20-HFD).  Food intake, an average of food consumed divided by the number of mice per cage, and individual mouse weights were measured weekly for the duration of the experiment

value: Pituitary


title: V1P KO/KO DNs ChIP H3K27ac 1


title: 7CR20HFD_LIV

source_name: Liver

value: Liver


title: 7CR20HFD_FAT

source_name: Epididymal white adipose tissue(eWAT)

value: Epididymal white adipose tissue(eWAT)


title: WT DNs ConventionalHiC 3


title: WT DNs ConventionalHiC 1


title: V1P KO/KO DNs ChIP CTCF 2


title: 5CR20CTRL_PIT


title: 6CR20HFD_PIT


title: 4CR20CTRL_LIV


title: 6CR20HFD_FAT


title: V1P KO/KO DNs ArimaHiC 1


title: 4CR20CTRL_FAT


title: 49CR20CTRL_FAT


title: 4CR20CTRL_PIT


title: 49CR20CTRL_LIV


title: 49CR20CTRL_PIT


title: 5CR20CTRL_LIV


title: 47CR20CTRL_LIV


title: 47CR20CTRL_FAT


title: 48CR20CTRL_FAT


title: 47CR20CTRL_PIT


title: 48CR20CTRL_PIT


title: 46CR20HFD_PIT


title: 46CR20HFD_LIV


title: 48CR20CTRL_LIV


title: 46CR20HFD_FAT


title: 45CR20HFD_LIV


title: 45CR20HFD_PIT


title: 6CR20HFD_LIV


title: 42FEDCTRL_LIV


title: 41FEDCTRL_PIT


title: 45CR20HFD_FAT


title: 40FEDHFD_PIT


title: 41FEDCTRL_FAT


title: 42FEDCTRL_FAT


title: 42FEDCTRL_PIT


title: 5CR20CTRL_FAT


title: 40FEDHFD_LIV


title: 40FEDHFD_FAT


title: 33CR20CTRL_PIT


title: 32CR20HFD_LIV


title: 41FEDCTRL_LIV


title: 33CR20CTRL_LIV


title: 31CR20HFD_PIT


title: 32CR20HFD_PIT


title: 33CR20CTRL_FAT


title: 31CR20HFD_LIV


title: 32CR20HFD_FAT


title: 31CR20HFD_FAT


title: 24FEDCTRL_LIV


title: 23FEDHFD_LIV


title: 24FEDCTRL_FAT


title: 24FEDCTRL_PIT


title: 23FEDHFD_FAT


title: 23FEDHFD_PIT


title: 16FEDCTRL_PIT


title: 16FEDCTRL_FAT


title: 16FEDCTRL_LIV


title: 15FEDCTRL_PIT


title: PIF4-HA_Input_28C

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
The raw reads were treated with Cutadapt to remove adapters and reads with low sequencing quality.
The filtered reads were mapped to Arabidopsis thaliana genome(TAIR10) by bowtie2. SAMtools was used to remove PCR duplicates and low mapped quality reads.
MACS2 was used to find peaks. Differentially peaks were selected by using MAnorm. The peaks were annotated by using ChIPpeakAnno.
bamCoverage was used to normalized the reads through RPKM and computeMatrix was used to calculate enrichment signal.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium under continuous white light at 22°C for 6 days.

extract_protocol:
seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

treatment_protocol: treated at 28°C (warm conditions) or 22°C (normal conditions) for 6 h

tag: ecotype

value: seedlings


title: 15FEDCTRL_LIV


title: PIF4-HA_HA_28C

value: anti-HA


title: 15FEDCTRL_FAT


title: 14FEDCTRL_PIT


title: PIF4-HA_HA_22C


title: 14FEDCTRL_LIV


title: pif4_28C_rep2

description: all featureCounts.txt have 16 column, names are WT_22C_rep1, WT_22C_rep2, mrg1mrg2_22C_rep1, mrg1mrg2_22C_rep2, pif4_22C_rep1, pif4_22C_rep2, mrg1mrg2pif4_22C_rep1, mrg1mrg2pif4_22C_rep2, WT_28C_rep1, WT_28C_rep2, mrg1mrg2_28C_rep1, mrg1mrg2_28C_rep2, pif4_28C_rep1, pif4_28C_rep2, mrg1mrg2pif4_28C_rep1, mrg1mrg2pif4_28C_rep2

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the genome of Arabidopsis thaliana (TAIR10) using Hisat2.
SAMtools was used to obtain high mapping quality reads.
FeatureCounts was used to calculate the reads count of genes.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include featureCounts for each Sample

extract_protocol:
RNA was extracted using RNAprep pure Plant Kit (Tiangen Biotech).
RNA-seq library construction was performed according to the instructions of KAPA stranded mRNA-seq Kit (Kapa Biosystems).

treatment_protocol: 28°C treatments for 3 hours.

tag: cultivar

value: 28°C treatments for 3 hours

tag: time

value: Day 6


title: ST486 cells, circZDHHC11_sh2_exp1

city: Groningen

first: Joost

last: Kluiver

address: Hanzeplein 1

country: Netherlands

institute: UMCG

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 12.0.1.1

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: ST486 (BL cell line)

label_protocol: Cy3 and Cy5 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack, Cyanine 5 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

growth_protocol: ST486 was cultured in RPMI 1640 (Thermo Fisher, Waltham, MA, USA) containing 20% fetal bovine serum (Sigma, St. Louis, MO, USA).

extract_protocol: miRNeasy micro or mini kit (Qiagen, Hilden, Germany)

treatment_protocol: ST486 cells were infected with shRNAs (sh1 and sh2) against circZDHHC11 or control shRNA (NT1). Two independent experiments were performed using GFP+ sorted cells  (>98% purity) on day 5 (exp 1) or day 6 (exp 2) post-infection.

tag: disease state

value: Burkitt lymphoma


title: PIF4-HA_Input_22C


title: mrg1mrg2pif4_28C_rep2

value: mrg1 mrg2 pif4


title: ST486 cells, circZDHHC11_sh1_exp1


title: mrg1mrg2pif4_28C_rep1


title: ST486 cells, circZDHHC11_sh1_exp2


title: 13FEDHFD_PIT


title: ST486 cells, NT1_exp1


title: ST486 cells, NT1_exp2


title: pif4_28C_rep1


title: ST486 cells, circZDHHC11_sh2_exp2


title: 13FEDHFD_LIV


title: mrg1mrg2_28C_rep1

value: mrg1 mrg2


title: 14FEDCTRL_FAT


title: 12FEDHFD_LIV


title: 13FEDHFD_FAT


title: 12FEDHFD_FAT


title: WT_28C_rep2

value: WT


title: mrg1mrg2_28C_rep2


title: WT_28C_rep1


title: 12FEDHFD_PIT


title: mrg1mrg2pif4_22C_rep2

value: keep in 22°C


title: 11FEDHFD_LIV


title: 11FEDHFD_FAT


title: 10FEDHFD_PIT


title: mrg1mrg2pif4_22C_rep1


title: mrg1mrg2_22C_rep1


title: pif4_22C_rep2


title: pif4_22C_rep1


title: mrg1mrg2_22C_rep2


title: WT_22C_rep2


title: WT_22C_rep1


title: Muscle, unexercised, CHCHD4 Tg, rep 3

city: Bethesda

first: Paul

middle: M.

last: Hwang

address: 9000 Rockville Pike

institute: NHLBI

data_processing:
Raw data files (FASTQ format) were aligned to the Mouse GENCODE Gene Set
(Release M25) using STAR/2.7.8a with default parameters, and the expected counts
were quantified using RSEM/1.3.2.
Assembly: mm10
Supplementary files format and content: excel include raw count
Supplementary files format and content: excel include RSEM values

source_name: skeletal muscles

extract_protocol:
Tissue RNA was purified using the RNeasy kit (Qiagen)
RNA libraties was prepared using smarter mRNA-seq Libaray prep kit

value: skeletal muscles

value: CHCHD4 Tg

value: No training


title: Muscle, unexercised, CHCHD4 Tg, rep 1


title: Muscle, unexercised, WT, rep 4


title: Muscle, unexercised, WT, rep 3


title: Sample 4 No CpG

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina CASAVA software was used for basecalling.
Reads were aligned to the mouse genome by Rsubread version 1.18.0.
Read counts were summarized by Entrez Gene ID using the featureCounts and Rsubread's inbuilt mm10 RefSeq annotation.
Assembly: mm10 (NCBI build 38.1)
Supplementary files format and content: tab-delimited text files. Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. The supplementary file GenewiseCounts.txt.gz collates the genewise counts for all samples into one file.

source_name: CD8- dendritic cells

growth_protocol: No cell growth was applied. Dendritic cells were enriched and FACS sorted from the spleen of mice and were directly subject to cell lysis for RNA preparation.

extract_protocol:
FACS sorted cells were lysed for RNA preparation using the QIAGEN RNEasy plus mini-kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Enriched preparation of dendritic cells from the spleen of mice were subject to surface labelling by antibodies to proceed with FACS sorting. FACS sorted CD8 negative dendritic cells were then directly subject to cell lysis for RNA preparation.

value: CD8- dendritic cells

tag: strain

tag: sample


title: Muscle, unexercised, WT, rep 2


title: Muscle, unexercised, WT, rep 1


title: Sample 3 No CpG


title: Sample 4 CpG

value: CpG


title: 10FEDHFD_LIV


title: Sample 3 CpG


title: Sample 2 No CpG


title: Muscle, unexercised, CHCHD4 Tg, rep 2


title: Muscle, unexercised, CHCHD4 Tg, rep 4


title: Muscle, exercised, CHCHD4 Tg, rep 3

value: Treadmill training


title: Sample 2 CpG


title: Muscle, exercised, CHCHD4 Tg, rep 2


title: Muscle, exercised, CHCHD4 Tg, rep 1


title: B6 Wound Healing Cornea Epithelium

city: Wenzhou

first: Qiongjie

last: CAO

state: Zhejiang

address: 270 Xueyuan Road

institute: Wenzhou Medical University

description: Gene and lncRNA expression from Wound Healing Cornea Epithelium

hyb_protocol: The biotin-labelled cRNA (specific activity >10.0 pmol biotin /ug cRNA) was hybridized to Affymetrix transcriptome assay MTA 1.0 for 17 hours at 65Â°C in a rotating Affymetrix hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37Â°C GE Wash buffer 2, then dried immediately by brief centrifugation.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000, and the probe cell intensity data were summarized using the default settings of the Command Console Software (Affymetrix).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 ( Affymetrix) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: biotin

source_name: C57BL/6 mice, wound healing corneal epithelium, replicate1

label_protocol: The 2μg RNA samples were amplified and labeled into biotinylated cRNA, followed by hybridization onto the microarrays according to the manufacturer's instructions.

growth_protocol: Male and female C57BL/6 mice, aged 8 weeks, were anesthetized using intraperitoneal injections of a combination of ketamine (87 mg/kg) and xylazine (13 mg/kg).

extract_protocol: Total RNA was extracted by using the Trizol Reagent (Invitrogen) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The full thickness of the corneal epithelium, extending up to the corneal/limbal border, was removed using a 0.5-mm corneal rust ring remover. After approximately 48 hours, healing progressed until only 10% of the original wound area remained. Subsequently, the entire corneal epithelium was collected from both the injured and fellow eyes for RNA isolation.

value: corneal epithelium

value: injured


title: Muscle, exercised, CHCHD4 Tg, rep 4


title: CD103 low 2

data_processing:
Illumina CASAVA software was used for basecalling.
Reads were aligned to the mouse genome by subread version 1.4.6.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files. Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: CD8 dendritic cells

tag: cell population

value: CD103 low

value: Untreated

tag: date


title: CD103 negative 3

value: CD103 negative


title: B6 uninjured Cornea Epithelium

description: Gene and lncRNA expression from uninjured Cornea Epithelium

source_name: C57BL/6 mice, uninjured corneal epithelium, replicate 1

value: uninjured


title: Muscle, exercised, WT, rep 3


title: CD103 low 1


title: CD103 negative 2


title: Muscle, exercised, WT, rep 2


title: Marmoset_PRA_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression in parent-reared marmoset at aged stage

hyb_protocol: 0.6µg of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/µg cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 25µl containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25µl of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to marmoset microarray 8x60K (G4858A #84626, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 084626_D_F_20170124) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 14.9 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

organism: Callithrix jacchus

source_name: parent rearing, aged, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with TRIzol Reagent with the PureLink RNA Mini Kit (Thermo Fisher Scientific, USA) according to the manufacturer's instructions.

treatment_protocol: After birth, the marmosets underwent either human hand- or parental rearing for a duration of 3 months. Subsequently, they were housed together with their age-matched peers. To categorize the marmosets based on age, those falling within the age range of 13 to 19 months were classified as Young Marmosets, while those within the age range of 88 to 164 months were designated as Aged Marmosets

value: hippocampus tissue

tag: age

value: aged

value: parent rearing


title: KO_U4

city: ithaca

first: Luye

last: An

address: 618 tower road

department: biomedical sciences

institute: cornell university

data_processing:
Raw data were aligned to genome using package STAR with default parameters
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include reads per gene

source_name: dorsal skin

extract_protocol:
Fresh collected tissue was homogenized using liquid nitrogen and total RNA was extracted using Trizol standard protocol
0.5ug of total RNA was used for initital prep. mRNA was enriched using Poly A enrichment method. Library was preped using NEBNext Ultra II directional RNA library prep kit

value: dorsal skin

tag: Sex

value: male

tag: skin condition

value: telogen

value: Tnfrsf1a/b KO


title: CD103 negative 1


title: Muscle, exercised, WT, rep 1

value: skeletal muscles

value: WT


title: Marmoset_HRA_rep3

description: Gene expression in human hand-reared marmoset at aged stage

source_name: hand rearing, aged, replicate 3

tag: cell type

value: hand rearing


title: Marmoset_HRA_rep1

source_name: hand rearing, aged, replicate 1


title: lepto, 14 dpi

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

data_processing:
Demultiplexing and gene counting were performed using Cell Ranger software's "count" function (10X Genomics).
Assembly: Reference genome was constructed by adding the Pan troglodytes HBEGF gene to the mm10 genome using Cell Ranger software's "mkref" function (10X Genomics).
Supplementary files format and content: Normalized expression of each gene per cell. [csv <- GetAssayData(data, assay = "RNA", slot = "norm.data")]

source_name: meninges, leptomeninges

extract_protocol:
Tissues were isolated, digested with papain and Dnase I, and homogenized to yield cell suspensions for single-cell RNA-sequencing.
Libraries were constructed according to the manufacturer's protocol (10X Genomics).

treatment_protocol: Mice were treated with tamoxifen daily for three days to induce iDTR expression. Mice were naïve or immunized with MOG peptide to induce EAE.

value: meninges, leptomeninges

value: PdgfrbCreERT2/+, Rosa-iDTR+/-

tag: treatment 1

value: tamoxifen

tag: treatment 2

value: EAE, 14 dpi


title: KO_U2

tag: tissue


title: Marmoset_PRA_rep3

source_name: parent rearing, aged, replicate 3

tag: treatment


title: KO_U3

tag: genotype


title: Marmoset_HRY_rep1

description: Gene expression in human hand-reared marmoset at young stage

source_name: hand rearing, young, replicate 1

value: young


title: SM31_S13: Skeletal muscle tongue

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
RNA-seqreads were aligned to the genome using STAR (v2.5.2b)
RNA-seq counts were obtained using featureCounts v1.6.1

organism: Eptatretus atami

source_name: Skeletal muscle tongue

extract_protocol:
RNA-seq: RNA was extracted using Trizol reagent (Invitrogen).
RNA-seq: Strand-specific RNA-seq libraries were prepared using the TruSeq RNA Library (Illumina) and sequenced in a 2x150bp layout.

value: Skeletal muscle tongue

value: Whole organism

value: Normal embryonic development


title: Marmoset_PRA_rep1

source_name: parent rearing, aged, replicate 1

value: hippocampus tissue

value: aged


title: dura, 14 dpi

source_name: meninges, dura mater

value: meninges, dura mater


title: Marmoset_HRY_rep2

source_name: hand rearing, young, replicate 2


title: Marmoset_HRA_rep2

source_name: hand rearing, aged, replicate 2


title: Marmoset_HRY_rep3

source_name: hand rearing, young, replicate 3


title: Marmoset_PRY_rep2

description: Gene expression in parent-reared marmoset at young stage

source_name: parent rearing, young, replicate 2

value: parent rearing


title: lepto, 7 dpi

value: EAE, 7 dpi


title: brain, 14 dpi

source_name: brain, cerebral cortex

value: brain, cerebral cortex


title: CpG treated 2

source_name: CD8 dendritic cells

value: CD103 high

value: CpG treated


title: KO_C3

value: dorsal skin

value: male

value: telogen

value: Tnfrsf1a/b KO

value: no UVB ctrl


title: CpG treated 1


title: SK1_S6: Skin

source_name: Skin

value: Skin

value: WT


title: KO_C2


title: dura, 7 dpi

value: PdgfrbCreERT2/+, Rosa-iDTR+/-

value: tamoxifen


title: KO_C1


title: OV11_S5: ovar

source_name: ovar

value: ovar

value: Whole organism

value: Normal embryonic development


title: brain, 7 dpi


title: LI1_S3: Liver

source_name: Liver

value: Liver


title: lepto, naïve

value: meninges, leptomeninges

value: naïve


title: dura, naïve

value: meninges, dura mater


title: WT_U4

source_name: dorsal skin


title: KO_U1


title: KO_C4


title: WT_U3


title: HE21_S4: Heart3


title: SG1_S9: Slime gland

source_name: Slime gland

value: Slime gland


title: adult cardiomyocyte, tarmoxifen treatment,3day

city: Beijing

first: li

last: wang

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital

data_processing:
The raw reads were processed by the Mappa (v1.0) pipeline supplied by the Takara Company.
The pipeline involved demultiplexing reads according to the barcode tag, filtering read pairs by cutadapt and aligning them to the mouse genome (mm10) with STAR, assigning them to Gencode genes (vM25) by featureCounts, and combining reads with the same UMIs.
Assembly: mm10
Supplementary files format and content: barcodes files
Supplementary files format and content: matrix files for each group

source_name: heart

extract_protocol:
Single-cell sequencing library was generated using the iCell8 platform. In brief, isolated cells were stained with a mixture of Hoechst 33342 and propidium iodide (Thermo Scientific, R37610) according to the manufacturer’s instruction. After staining, cells were washed with PBS, and counted on a Moxi TM Automated Cell Counter. Afterwards, a cell suspension of 20,000 cells/ml was submitted to the Multi Sample Nano Dispenser (MSND, Wafergen Biosystems) for single cell preparation. The dispensed cells were then imaged on the Imaging Station, and single live cells, defined by Hoechst-positive and propidium iodide-negative staining, were selected. Selected cells were subjected to reverse transcription and first-step amplification on a Chip Cycler (Bio-Rad), and the resulting cDNA was purified and size-selected with Agencourt AMPure XP beads (Beckman Coulter, A63880).
One nanogram of purified cDNA was applied to generate a sequencing library using Nextera XT DNA sample preparation Kit (Illumina, FC-131-1024). Libraries were sequenced on the NovaSeq 6000 (Illumina) using paired-end sequencing protocol.

value: heart

value: adult cardiomyocyte

value: D3_INO80_OE, D3_Ctrl

value: tarmoxifen


title: WT_U2

value: dorsal skin

value: male

value: telogen


title: WT_U1

value: WT


title: GI1_S7: Gills

source_name: Gills

value: Gills


title: adult cardiomyocyte, tarmoxifen treatment,2day


title: WT_C4

value: no UVB ctrl


title: GB1_S10: Gall bladder

source_name: Gall bladder

value: Gall bladder

value: Whole organism


title: WT_C3


title: adult cardiomyocyte, tarmoxifen treatment,1day


title: 11FEDHFD_PIT

source_name: Pituitary

value: Pituitary


title: BR1_S1: Brain

source_name: Brain

value: Brain

value: Normal embryonic development


title: Sham6W4

city: JiNan

first: Meirong

last: Zhu

address: NO. 105  Jiefang Road

institute: Jinan Central Hospital

description:
FPKM.Sham6W4
LR21F28FV8

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Aorta

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood vessel

value: APOE knockdown

value: Normal purified laboratory 6W


title: Sham6W3

description:
FPKM.Sham6W3
LR21F28FV7


title: WT_C2


title: BC1_S11: Blood cells

source_name: Blood cells

value: Blood cells


title: KI1_S8: Kidney

source_name: Kidney

value: Kidney


title: Sham6W2

description:
FPKM.Sham6W2
LR21F28FV6


title: 10FEDHFD_FAT

source_name: Epididymal white adipose tissue(eWAT)

value: Epididymal white adipose tissue(eWAT)


title: WT_C1

value: dorsal skin


title: AT1_S2: Adipose tissue

source_name: Adipose tissue

value: Adipose tissue


title: WT_M2.B2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.10; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 4 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Raw p values were adjusted to control the global FDR across all comparisons using the ‘global’ option in decideTests function in the limma package. Genes were called differentially expressed (DE) if they achieved a False Discovery Rate (FDR) of 10% or less.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.tsv, includes raw read counts for genes in all the libraries.

extract_protocol:
RNA extraction from total VAT tissue was performed following the manufacturer's instructions using the Rneasy Lipid Tissue Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: Foxp3cre (control)

value: visceral/perigonadal adipose tissue

value: 27-33 week old

value: Male


title: Sham6W1

description:
FPKM.Sham6W1
LR21F28FV5


title: brain, naïve

source_name: brain, cerebral cortex

value: brain, cerebral cortex

value: PdgfrbCreERT2/+, Rosa-iDTR+/-

value: tamoxifen

value: naïve


title: IN1_S12: Intestine

source_name: Intestine

value: Intestine

value: Whole organism

value: WT

value: Normal embryonic development


title: H33-g2 , Entorhinal cortex

city: San Francisco

first: Marcos

middle: Assis

last: Nascimento

state: CA

address: 35, Medical Center Way

institute: University of California, San Francisco

data_processing:
We used Cellranger to automatically detect barcodes that corresponded to high quality nuclei. Cellranger was set to detect 10,000 cells in samples from germinal zones.
Trimming extremes: Nuclei in the top or in the bottom 2% of number of transcripts.
Ambient RNA atenuation: We used SoupX to reduce the impact of ambient RNA
Doublet removal: in multiplexed batches, doublets were detected by freemuxlet. In non-multiplexed samples, potential doublets were eliminated using DoubletFinder
Nuclear fraction, the fraction of reads containing intronic regions, was used to filter out low-quality nuclei. We selected nuclei with a nuclear fraction > 0.5.
Assembly: Optimized reference based on human GRCh38, from Pool et al. 2023, Nature Methods.
Supplementary files format and content: count matrix (counts.mtx) , genes (genes.tsv), barcodes (barcodes.tsv) and metadata (metadata.csv)

molecule: nuclear RNA

source_name: Entorhinal cortex

extract_protocol:
Frozen sections were transferred from tubes in dry ice to ice cold lysis buffer (0.01M Tris-HCl, 0.14M NaCl, 1mM CaCl2, 0.02M MgCl2, 0.03% Tween-20, 0.01% BSA, 10% Nuclei Ez Lysis Buffer (Sigma), 0.2U/μL Protector RNAse inhibitor (Sigma) in DEPC-treated water) and the tissue was dissociated using a glass dounce homogenizer (Thomas Scientific, Cat # 3431D76). Tissue homogenates were transferred to a separate 30 mL thick wall polycarbonate ultracentrifuge tube (Beckman Coulter, Cat # 355631). Sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, 10 mM Tris-HCl in DEPC-treated water) was added at the bottom of the tube and homogenates were centrifuged at 107,000 x g for 2.5 hours at 4°C. The supernatant was discarded, and the nuclei pellet was incubated in 200 μL of  wash/resuspension buffer (WRB: 1% BSA, 0.2U/μL Protector RNAse inhibitor in DEPC-based PBS) for 20 min on ice before resuspending the pellet. For multiplexed runs: resuspended nuclei were filtered twice through a 30 μm strainer. Each one of the five nuclei suspensions was incubated with its own unique CellPlex Cell Multiplexing Oligo (CMO) barcode (10x Genomics) for 5 minutes followed by a 500 x g centrifugation at 4C for 10 minutes. After centrifugation, supernatant was discarded and nuclei were gently resuspended in WRB using a P200 pipette for a minimum of 2 mins, until a clean single-nuclei suspension was obtained. After two more centrifugations/WRB washes to remove unbound CMOs, 10 µL of each nuclei suspension was stained with DAPI and counted on a hemocytometer. Samples were pooled together and diluted to 2,000 nuclei/μL. A target capture of 30,000 nuclei/well in two wells of a G chip (10x Genomics) was used. Gene expression and barcode libraries were prepared in parallel using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to manufacturer's instructions. A detailed step-by-step protocol can be found on  dx.doi.org/10.17504/protocols.io.kqdg369keg25/v2. For non-multiplexed assays: After centrifugation, each tissue homogenate was gently resuspended in WRB, filtered twice, counted, centrifuged and resuspended at 1,000 nuclei/ µL. 16,500 nuclei were loaded in each of the 10x chip G wells, aiming for a 10,000 nuclei recovery/sample. A detailed protocol can be found at: dx.doi.org/10.17504/protocols.io.j8nlkk9ydl5r/v2. All libraries were sequenced in a Novaseq 6000 system (Illumina).
Gene expression libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1(10x Genomics)

value: Entorhinal cortex

tag: donor

value: 54 days

tag: assay type

value: multiplex


title: H33-g1 , Entorhinal cortex


title: AS6W4

description:
FPKM.AS6W3
LR21F28FV4

value: Blood vessel

value: APOE knockdown

value: Western Diet 6W


title: H29-g2 , Entorhinal cortex


title: WT_M1.B2

value: Foxp3cre (control)

value: visceral/perigonadal adipose tissue


title: WT_M1.B1

value: 27-33 week old

value: Male


title: H29-g1 , Entorhinal cortex


title: WT_F2.B2

value: Female


title: AS6W1

description:
FPKM.AS6W1
LR21F28FV1


title: H46-g2 , Entorhinal cortex

value: 33 days


title: WT_F2.B1


title: H46-g1 , Entorhinal cortex


title: Sham22W4

description:
FPKM.Sham22W4
LR21J13FV8

value: Normal purified laboratory 22W


title: H39-g2 , Entorhinal cortex

value: 3 years


title: Sham22W3

description:
FPKM.Sham22W3
LR21J13FV7


title: WT_F1.B2


title: WT_F1.B1


title: H39-g1 , Entorhinal cortex


title: Sham22W2

description:
FPKM.Sham22W2
LR21J13FV6


title: TbetFP3_M2.B2


title: TbetFP3_M2.B1


title: AS22W4

description:
FPKM.AS22W4
LR21J13FV4

value: Western Diet 22W


title: H48-g1 , Entorhinal cortex

value: 2 years


title: WT_M2.B1


title: TbetFP3_M1.B2


title: AS6W3

description:
FPKM.AS6W3
LR21F28FV3


title: AS6W2

description:
FPKM.AS6W2
LR21F28FV2


title: AS22W3

description:
FPKM.AS22W3
LR21J13FV3


title: TbetFP3_M1.B1


title: H31 , Entorhinal cortex

value: 13 years

value: singleplex


title: Muscle, exercised, WT, rep 4

source_name: skeletal muscles

value: skeletal muscles

value: WT

value: Treadmill training


title: H37 , Entorhinal cortex

value: Entorhinal cortex

value: 27 years


title: AS22W2

description:
FPKM.AS22W2
LR21J13FV2

value: Blood vessel

value: APOE knockdown


title: TbetFP3_F2.B2

value: visceral/perigonadal adipose tissue

value: 27-33 week old


title: H71 , Entorhinal cortex

value: 14 days


title: TbetFP3_F2.B1

value: Female


title: TbetFP3_F1.B2


title: hypothalamus, Saline, rep8

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ-file generation and demultiplexing using bcl2fastq 2.20.0
Add UMIs to header in FASTQ-files using bash script
Align to genome and determine transcript and gene counts with the nfcore-rnaseq pipeline v. 3.8.1 using the STAR->Salmon workflow.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated file containing the raw gene counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample
Supplementary files format and content: Tab-seperated file containing the raw transcript counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample

source_name: hypothalamus

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, #74106) according to the manufacturer’s protocol.
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Fragment Analyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.7 billion reads were generated.

treatment_protocol: DIO mice (average body weight 53g, double-housed) were injected with 56 mg/kg mPD5 (n=8), 25 mg/kg UCCB01-147 (n=8) or isotonic saline (n=6) daily, for 5 days. On experimental days 1 to 4, injections were performed 2 hours before the onset of the dark phase. Body weight and food intake were measured daily. On the morning of the 5th experimental day, mice were injected and sacrificed 2 hours later. Whole hypothalamus was flash frozen on dry ice in preparation for RNA isolation.

value: hypothalamus

value: Saline


title: AS22W1

description:
FPKM.AS22W1
LR21J13FV1

value: Western Diet 22W


title: H71 , EC stream region

source_name: EC stream region

value: EC stream region


title: Sham22W1

description:
FPKM.Sham22W1
LR21J13FV5

value: Normal purified laboratory 22W


title: H69 , Entorhinal cortex

value: 23 GW

value: singleplex


title: H69 , LGE region

source_name: LGE region

value: LGE region


title: H69 , MGE region

source_name: MGE region

value: MGE region


title: TbetFP3_F1.B1


title: hypothalamus, PSD-95i, rep8


title: H48-g2 , Entorhinal cortex

value: Entorhinal cortex

value: 2 years

value: multiplex


title: Pparg_M1.B2

value: Male


title: hypothalamus, PSD-95i, rep7


title: hypothalamus, PICK1i, rep7


title: Pparg_M2.B1

value: visceral/perigonadal adipose tissue


title: hypothalamus, PICK1i, rep8


title: Pparg_M1.B1

value: 27-33 week old


title: Pparg_F2.B2


title: MPM,029,Sup

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: MPM

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer's instructions.

value: MPM


title: MPM,029,Inf


title: H69 , CGE region

source_name: CGE region

value: CGE region


title: MPM,029,Lat


title: hypothalamus, PSD-95i, rep4

value: hypothalamus


title: MPM,028,Sup


title: Pparg_F1.B2

value: Female


title: hypothalamus, PSD-95i, rep3


title: Pparg_M2.B2


title: hypothalamus, PSD-95i, rep5


title: Pparg_F1.B1


title: hypothalamus, PICK1i, rep6


title: hypothalamus, PSD-95i, rep6


title: Pparg_F2.B1


title: MPM,028,Lat


title: MPM,028,Inf


title: cKO27 Input hypothalamus, knockout, week 5

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
The aligning of the raw fastq reads to the reference genome using Bowtie 2.0.
The Samtools collection used to sort, remove PCR duplicates (rmdup), index BAM files (index), and calculate library statistics.
SMC3 '‘peaks'’ determined by the MACS2 package (callpeak function, --broad peaks).
differential binding analysis was performed where immunoprecipitated over input scores were calculated using the Diffbind package.
Correlation analysis between differential SMC3 binding sites and DEGs was performed by GeneOverlap R package
Assembly: mouse mm9
Supplementary files format and content: BroadPeak

growth_protocol: 8 week old mice, treated by tamoxifen, waited for 5 weeks to harvest the hypothalamus

extract_protocol:
each cross-linked hypothalamic sample (1% formaldehyde) was sonicated in cell lysis buffer, resulting in chromatin fragments ranging from 200 to 1000 bp. These fragments incubated in ChIP dilution buffer with an αSMC3 antibody (5 μg/sample; Bethyl, Montgomery, Texas, USA, #A300-060A). Simultaneously, 5% input (without immunoprecipitation step) was utilized to normalize the amount of chromatin in each sample. Subsequently, DNA was isolated from each immunoprecipitated/input sample and subjected to genomic library preparation
20ul of DNA were used for libraries preperation using the NEBNext Ultra II DNA kit (NEB, #E7645). Quantification of the library was performed using dsDNA HS Assay Kit and Qubit 2.0 (Molecular Probes, Life Technologies) and qualification was done using the Agilent D1000 Tapestation Kit and Tapestation 4200.  25nM of each library was pooled together and was diluted to 4nM according to NextSeq manufacturer’s instructions. 1.5pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced on an Illumina NextSeq 500 instrument, 75 cycles single read sequencing.

treatment_protocol: Hypothalamus of wild type and Smc3 conditional knockout mice

value: Brain

value: Hypothalamus

value: cKO


title: hypothalamus, PICK1i, rep5


title: cKO21 Input hypothalamus, knockout, week 5


title: MPM,027,Sup


title: MPM,027,Lat


title: hypothalamus, PSD-95i, rep1


title: MPM,027,Inf


title: hypothalamus, PSD-95i, rep2


title: Marmoset_PRY_rep1

source_name: parent rearing, young, replicate 1

value: hippocampus tissue

value: young

value: parent rearing


title: MPM,026,Sup


title: hypothalamus, Saline, rep6

value: Saline


title: WT15 Input hypothalamus, knockout, week 5

source_name: Brain

value: WT


title: cKO01 Input hypothalamus, knockout, week 5


title: MPM,026,Lat


title: cKO09 Input hypothalamus, knockout, week 5


title: hypothalamus, Saline, rep5


title: MPM,025,Sup


title: MPM,026,Inf


title: hypothalamus, Saline, rep3


title: WT12 Input hypothalamus, knockout, week 5


title: WT11 Input hypothalamus, knockout, week 5


title: hypothalamus, PICK1i, rep3


title: hypothalamus, Saline, rep7


title: MPM,025,Lat


title: MPM,025,Inf


title: WT4 Input hypothalamus, knockout, week 5


title: WT2 Input hypothalamus, knockout, week 5


title: cKO15 Input hypothalamus, knockout, week 5


title: hypothalamus, Saline, rep2


title: hypothalamus, Saline, rep1


title: MPM,024,Sup


title: MPM,024,Inf


title: MPM,024,Lat


title: cKO27 hypothalamus, knockout, week 5

tag: chip antibody

value: Bethyl #A300-060A


title: cKO21 hypothalamus, knockout, week 5


title: hypothalamus, PICK1i, rep2


title: hypothalamus, Saline, rep4


title: cKO15 hypothalamus, knockout, week 5


title: hypothalamus, PICK1i, rep1


title: MPM,023,Sup


title: MPM,023,Lat


title: cKO01 hypothalamus, knockout, week 5


title: Spinal cord EAE + Bone marrow transplant Replicate 2

city: Stanford

first: Marius

middle: Marc-Daniel

last: Mader

address: 265 Campus Drive

institute: Stanford University

description:
single-nuclei RNA
10x Genomics

data_processing:
Raw reads were processed using the CellRanger software (v4.0.0) provided by 10x Genomics and counting reads mapping to introns.  The number of nuclei for each sample was determined using the cellranger count command.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spinal cord

extract_protocol:
Single-nuclei preparation was performed as previously described (Hahn et al., 2022) with the following modifications. The thoracolumbar section of spinal cords were first mechanically dissociated with an ice-cold razor blade in a petri dish with 1ml EZ Prep lysis buffer (Sigma, NUC-101) on ice. Transfer of tissue suspension into a 2ml glass dounce tissue grinder tube (Sigma, D8938). Petri dish was rinsed off with another 1ml EZ buffer, which was added to the grinder tube. Suspension was homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15ml tube on ice. The grinder tube was rinsed with 2 ml fresh lysis buffer, which was added to the 15ml tube for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant was removed, and the pellet resuspended with 4 ml EZ lysis buffer and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing the supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. The pellet was resuspended in 100µl FC block buffer (BD Biosciences, 553141, 1:50 in FACS buffer) and 1ul recombinant RNase inhibitor (Takara, 2313B) incubated on ice for 5min. FACS buffer consisted of PBS (Gibco, 10010049) containing 1% BSA (Thermo Fisher, BP9700100)). To 50µl of the cell suspension, we added 150µl FACS buffer with 2µl Olig2-Alexa Fluor488 (Sigma, MABN50A4), 1ul NeuN-AlexaFluor647 (Abcam, ab190565), and 1.5ul RNase inhibitor. After 30min incubation covered from light and shaking on ice, 3ml FACS buffer were added. Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out. The pellet was resuspended in 700µl FACS buffer with 3.5ul recombinant RNase inhibitor and Hoechst dye (Thermo Fisher, H3570, 1:2000) and incubated 4min on ice covered from light. Single nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology) gating for NeuN negative nuclei. 100,000 single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with 800ul PBS, 200ul UltraPure BSA (Thermo Fisher, AM2618), and 5ul RNase inhibitor. If libraries were representing two animals, samples were pooled by collecting identical numbers (2x 50,000) of nuclei into the same sample tube. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40µl suspended nuclei. Nuclei were counted using a hemacytometer (Sigma, Z359629-1EA) and assessed for concentration and quality.
Reagents of the Chromium Single Cell 3’ GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer’s protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3’ Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility.
10X Nuc-seq, v3.1 chemistry

value: Spinal cord

value: EAE + Bone marrow transplant

tag: clinical score


title: hypothalamus, PICK1i, rep4


title: MPM,023,Inf


title: WT15 hypothalamus, control, week 5


title: Spinal cord EAE Replicate 2

description:
single-nuclei RNA
10x Genomics

tag: strain

value: EAE


title: Spinal cord EAE + Bone marrow transplant + PLX Replicate 3

description:
single-nuclei RNA
10x Genomics

value: EAE + Bone marrow transplant + PLX


title: Spinal cord control Replicate 1

description:
single-nuclei RNA
10x Genomics

value: Control


title: MPM,022,Sup

value: MPM


title: WT12 hypothalamus, control, week 5


title: WT11 hypothalamus, control, week 5


title: MPM,022,Inf


title: Spinal cord EAE + Bone marrow transplant Replicate 1

description:
single-nuclei RNA
10x Genomics


title: WT4 hypothalamus, control, week 5


title: MPM,022,Lat


title: MPM,021,Sup


title: WT2 hypothalamus, control, week 5


title: Male High Fat Diet Pituitary 15 wk rep2

city: Little Rock

first: Allen

last: Gies

address: 4301 W. Markham

institute: University of Arkansas for Medical Sciences

description: 10X Genomics

data_processing:
Demultiplexed fastq files generated by the UAMS Genomics Core were analyzed with the 10x Genomics Cell Ranger 3.1.0 count function for sequence alignment and gene counting
The reads were aligned to the University of California, Santa Cruz (UCSC) mm10 reference transcriptome using STAR and transcript counts are generated (37,38).
The R package Seurat was used to further analyze the filtered, aggregated, and depth normalized counts generated by cellranger count and cellranger aggr (http://software.10xgenomics.com/single-cell/overview/welcome, Butler et al, 2018).
Cells with unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less 200 unique features, total gene counts more than more the 75th percentile plus 1.5 times the IQR or less than 1000 counts, and/or mitochondrial feature percentage more the 75th percentile plus 1.5 times the IQR or less than the 25th percentile minus 1.5 times the IQR were filtered out of the data. Next, the 2000 highest variable features are selected. The data is then scaled by a linear transformation and variation associated with cell death and cell cycling where regressed out of the scaled data using mitochondrial feature percentage and cell cycle scoring values. Counts were normalized using the SCTransform and PCA was performed on the scaled data. A Uniform Manifold Approximation and Projection (UMAP) was used to visualize and explore the clustering results. Seurat’s FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections. Seurat FindAllMarkers function was used to identify gene markers that define cluster cell types. These gene markers were compared to known markers of expected cell types in order to assign appropriate cell type labels (Frazén et al, 2019). Differential expression analysis was performed using the FindMarkers to compare similar cell types across diet and gender. The MAST test, a GLM-framework that treats cellular detection rate as a covariate, was used to determine statistically different transcription (Finak et al, 2015). Genes with an FDR adjusted p-values < 0.055 and a Log2FC ≥ 0.58 (fold increase 1.5) were considered significant.
Assembly: University of California, Santa Cruz (UCSC) mm10 reference transcriptome
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: Pituitary

extract_protocol:
Pituitaries were removed for dispersion/centrifugation, cells were washed gently, centrifuged, and resuspended in DMEM with no gentamicin.
individual pituitary cell suspensions were pooled within treatment groups (2-3 pituitaries/pool) and counted.  Concentration of the cells within each pool was adjusted to optimally target 10,000 cells according to 10X Genomics guidelines.   Samples were then submitted to the UAMS Cancer Institute Genomics Core facility, where cells were resuspended in PBS with 0.04% BSA, filtered, recounted, and assessed for viability.  Then, 10,000 cells from each pool were targeted for scRNA-seq according to the 10X Genomics protocol.

treatment_protocol: Each group was first acclimated to the thermoneutral environment for 1 week (beginning at 12 weeks of age) and then exposed to the HFD  or normal control diet (ND) for either 10 weeks or 15 weeks. For all groups, the HFD (fat, 60 kcal%; carbohydrate, 36 kcal%; protein, 19 kcal%) was supplied as palatable pellets. The sources of fat were lard and soybean oil (ENVIGO, TD.06414). Mice receiving the control, normal diet (ND) received ENVIGO Reduced Sucrose Control Diet (10% fat, TD.08806).

value: Pituitary

value: FVB.129P2-Pde6b + Tyr c-ch/AntJ

value: male

value: High Fat Diet


title: Spinal cord EAE + Bone marrow transplant + PLX Replicate 2

description:
single-nuclei RNA
10x Genomics

value: Female


title: MPM,021,Lat


title: MPM,021,Inf


title: Male High Fat Diet Pituitary 15 wk rep1

description: 10X Genomics


title: Spinal cord EAE + Bone marrow transplant + PLX Replicate 1

description:
single-nuclei RNA
10x Genomics


title: Spinal cord EAE Replicate 1

description:
single-nuclei RNA
10x Genomics

value: Spinal cord EAE


title: Twin22_TSH_low

type: genomic

city: Yamadaoka,Suitashi

first: Yuya

last: Arakawa

state: Osaka

department: Graduate school of Medicine

institute: Osaka university

description: peripheral blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Bead Chip

scan_protocol: Arrays were imaged using Illumina iScan System and iScan Control Software

data_processing: GenomeStudio

label: Cy5 and Cy3

label_protocol: standard illumina protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using NucleoSpin® Blood L Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: whole blood

tag: disease state

value: normal


title: MPM,020,Sup


title: Twin22_TSH_high

description: peripheral blood sample


title: Female High Fat Diet Pituitary 15 wk rep2

description: 10X Genomics


title: cKO09 hypothalamus, knockout, week 5

value: Brain

value: Hypothalamus

value: cKO


title: Twin21_TSH_low

description: peripheral blood sample


title: Female High Fat Diet Pituitary 15 wk rep1

description: 10X Genomics


title: MPM,020,Lat


title: MPM,020,Inf


title: Twin21_TSH_high

description: peripheral blood sample


title: Male Control Pituitary 15 wk rep2

description: 10X Genomics


title: MPM,019,Sup


title: Twin20_TSH_low

description: peripheral blood sample


title: Female Control Pituitary 15 wk rep2

description: 10X Genomics


title: Male Control Pituitary 15 wk rep1

description: 10X Genomics


title: Twin20_TSH_high

description: peripheral blood sample


title: Twin19_TSH_low

description: peripheral blood sample


title: Female Control Pituitary 15 wk rep1

description: 10X Genomics


title: MPM,018,Sup


title: Twin19_TSH_high

description: peripheral blood sample


title: Twin18_TSH_low

description: peripheral blood sample


title: Male High Fat Diet Pituitary 10 wk

description: 10X Genomics


title: MPM,018,Lat


title: Female High Fat Diet Pituitary 10 wk

description: 10X Genomics


title: Male Control Pituitary 10 wk

description: 10X Genomics


title: MPM,017,Sup


title: MPM,018,Inf


title: Twin18_TSH_high

description: peripheral blood sample


title: Twin17_TSH_high

description: peripheral blood sample


title: MPM,017,Lat


title: Twin16_TSH_low

description: peripheral blood sample


title: adult cardiomyocyte,D2_OE,rep2

data_processing:
Paired-end reads were mapped to the mm10 transcriptome and genome by STAR.
The featureCounts function of the Rsubread package was used to counts the reads for each gene.
The genes reads count table was normalized and the differentially expressed genes were identified by DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include genes reads count  for each Sample

source_name: heart

extract_protocol:
RNA was harvested 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kits following manufacturer's protocols.

value: heart

tag: time

value: adult cardiomyocyte

value: Tamoxifen


title: Twin17_TSH_low

description: peripheral blood sample


title: MPM,017,Inf


title: Female Control Pituitary 10 wk

description: 10X Genomics

tag: Sex

value: Control


title: adult cardiomyocyte,D2_OE,rep3


title: MPM,015,Sup

value: MPM


title: MPM,019,Lat


title: Twin16_TSH_high

description: peripheral blood sample


title: adult cardiomyocyte,D2_OE,rep1


title: MPM,019,Inf


title: adult cardiomyocyte,D2_Control,rep3

value: WT


title: Twin15_TSH_low

description: peripheral blood sample


title: Twin15_TSH_high

description: peripheral blood sample


title: MPM,015,Inf


title: adult cardiomyocyte,D2_Control,rep2


title: MPM,014,Sup


title: adult cardiomyocyte,D2_Control,rep1


title: MPM,014,Lat


title: Twin14_TSH_low

description: peripheral blood sample


title: Twin14_TSH_high

description: peripheral blood sample


title: adult cardiomyocyte,D4_OE,rep2


title: MPM,014,Inf


title: adult cardiomyocyte,D4_OE,rep3


title: adult cardiomyocyte,D4_OE,rep1


title: Twin13_TSH_low

description: peripheral blood sample


title: Twin13_TSH_high

description: peripheral blood sample


title: Twin12_TSH_low

description: peripheral blood sample


title: MPM,013,Sup


title: Twin12_TSH_high

description: peripheral blood sample


title: MPM,013,Lat


title: adult cardiomyocyte,D4_Control,rep1


title: adult cardiomyocyte,D4_Control,rep2


title: MPM,015,Lat


title: adult cardiomyocyte,D6_OE,rep3


title: adult cardiomyocyte,D6_OE,rep1


title: MPM,013,Inf


title: Twin11_TSH_high

description: peripheral blood sample


title: MPM,011,Lat


title: Twin11_TSH_low

description: peripheral blood sample


title: MPM,011,Inf


title: Twin10_TSH_high

description: peripheral blood sample


title: MPM,010,Sup


title: adult cardiomyocyte,D6_Control,rep3


title: adult cardiomyocyte,D6_Control,rep2


title: MPM,010,Lat


title: adult cardiomyocyte,D6_Control,rep1


title: MPM,011,Sup


title: MPM,010,Inf


title: Twin9_TSH_high

description: peripheral blood sample


title: Twin8_TSH_low

description: peripheral blood sample


title: TAC4W_Input_2

data_processing:
The reads were aligned to the mm10 genome using BWA, and the peaks were called with SICER.
For differential analysis of ChIP-seq data, the SICER-df.sh script of SICER package (V1.1) was used with the parameters: window size 200bp, gap size 600bp and FDR q value 0.01
ChIP-Seq peakswere evaluated and normalized by the function of annotatePeaks.pl in HOMER
For visualizing individual samples, the BAM file was converted to BIGWIG format using the bamCoverage function of deepTools.
Assembly: mm10
Supplementary files format and content: bigWig(except for Input sample)

source_name: Heart

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
DNA libraries for ChIP-seq were prepared using Nextera XT DNA Library Preparation Kit following manufacturer's protocols.

value: Heart

tag: group

value: TAC 4w

value: Adult cardiomyocyte

value: input


title: MPM,009,Lat


title: Twin8_TSH_high

description: peripheral blood sample

value: Female


title: Twin7_TSH_low

description: peripheral blood sample

value: Male


title: adult cardiomyocyte,D6_OE,rep2

tag: cell type


title: Twin10_TSH_low

description: peripheral blood sample

value: whole blood


title: TAC4W_Input_1


title: MPM,007,Sup


title: TAC4W_INO80_1

value: 18810-1-AP, Proteintech


title: Twin7_TSH_high

description: peripheral blood sample

value: normal


title: MPM,009,Inf


title: MPM,007,Inf


title: Twin6_TSH_high

description: peripheral blood sample


title: Sham_Input

value: sham


title: Twin6_TSH_low

description: peripheral blood sample


title: MPM,007,Lat


title: Twin9_TSH_low

description: peripheral blood sample


title: TAC4W_INO80_2


title: Twin5_TSH_low

description: peripheral blood sample


title: Sham_INO80


title: MPM,006,Lat


title: D2_OE_INO80_2

value: OE

value: tarmoxifen


title: MPM,009,Sup


title: D2_OE_Input_2


title: Twin5_TSH_high

description: peripheral blood sample


title: Twin4_TSH_low

description: peripheral blood sample


title: D2_Ctrl_Input_2

value: control


title: MPM,005,Sup


title: MPM,006,Inf


title: D2_Ctrl_INO80_2


title: Twin4_TSH_high

description: peripheral blood sample


title: MPM,005,Lat


title: Twin3_TSH_low

description: peripheral blood sample


title: Twin3_TSH_high

description: peripheral blood sample


title: D2_OE_INO80_1


title: MPM,005,Inf


title: D2_OE_Input_1


title: MPM,006,Sup


title: MPM,004,Lat


title: MPM,004,Sup


title: Twin2_TSH_low

description: peripheral blood sample


title: Twin1_TSH_low

description: peripheral blood sample


title: Twin1_TSH_high

description: peripheral blood sample


title: MPM,003,Sup


title: control adult cardiomyocyte, tamoxifen treatment 2 days, rep1

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie2 with default paired end settings.all non-nuclear and unmapped paired reads were discarded. Duplicated reads were removed with the picard MarkDuplicates function with default settings
Peak calling for differential accessibility analysis was carried out with Macs2 on the merged BAM file, Macs2 callpeak nomodel broad.
Blacklisted regions, identified by ENCODE, from mm10 were removed from the comprehensive peak file using the bedtools subtract module.
Assembly: mm10
Supplementary files format and content: bigWig(except for Input sample)

extract_protocol:
Aliquots of 50,000 cardiomyocytes were lysed with 3 ml chilled lysis buffer (3.75 mmol/L PIPES, 450 mmol/L KCl, 1% NP-40, 1% Tween-20, 1% Triton X-100 in water; pH 7.3) for 6 minutes, immediately spun down at 500 ´ g for 10 minutes at 4°C. Nuclear pellets were transposed with 25 µl Tagment DNA Buffer, 2.5 µl Tagment DNA Enzyme (Nextera Sample Prep Kit from Illumina, FC-121-1030), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, and 5 µl nuclease-free water. Samples were mixed and incubated at 37°C for 30 minutes in a thermomixer at 1000 rpm.
Transposed samples were purified with the QIAGEN MinElute Reaction Cleanup Kit (28204) and amplified with 25 µl NEB Next High-Fidelity 2× PCR Master Mix (M0541S), 1.25 mmol/L Nextera custom primers with unique barcodes, and nuclease-free water. Samples were amplified at the following PCR conditions: 72 °C for 5 min and 98 °C for 30 sec and cycled at 98 °C for 10 sec, 63 °C for 30 sec, and 72 °C for 1 min. Half of each sample was amplified for 12 cycles, purified, and assessed by Bioanalyzer (Agilent) for library quality. Sample concentration was quantified by Qubit (Invitrogen) before pooling. Pooled samples were sequenced with a PE75 run on a NextSeq500 instrument (Illumina).

value: adult cardiomyocyte

value: tamxifen


title: MPM,004,Inf

value: MPM


title: D2_Ctrl_Input_1


title: Twin22_FT4_low

description: peripheral blood sample

label_protocol: Standard Illumina Protocol


title: MPM,003,Lat


title: Twin22_FT4_high

description: peripheral blood sample


title: Twin21_FT4_low

description: peripheral blood sample


title: INO80-OE adult cardiomyocyte, tamoxifen treatment 2 days, rep2


title: Twin21_FT4_high

description: peripheral blood sample


title: MPM,002,Lat


title: EAEinput, 6

city: SASKATOON

first: Michael

middle: C

last: Levin

state: Saskatchewan

address: 701 Queen St, CMSNRC (Cameco Multiple Sclerosis Neuroscience Research Centre)

country: Canada

institute: University of Saskatchewan

data_processing:
Adapter Trimming: Sequencing reads were extracted from each run and adapter trimmed using bcl2fastq (version 2.19.0.316; Illumina) with the following settings: “--use-bases-mask Y*,I8Y*,Y* --minimum-trimmed-read-length 0 --mask-short-adapter reads 0”. Residual sequencing adapters and low-quality bases were trimmed using fastp with default settings except for “-f 5 -Y 0 -g” and the adapter sequences specified by PerkinElmer for use with the NEXTFlex v3 kit.
Contig Assembly: Adapter-trimmed reads were assembled into contigs using rnaSPAdes (from SPAdes, version 3.15.3) with default settings.
Alignment: Contigs were aligned to the GRCm38 mouse reference genome using minimap2 (version 2.17) in spliced alignment mode to identify regions corresponding to putative hnRNP A1 RNA binding sites.
Site Selection: Sites identified in the animal-matched input samples, or the treatment-matched pooled IgG sample, were considered to be background signal and were depleted from the set of sites for each immunoprecipitation sample using bedtools subtract (version 2.29.2) with default settings. Overlapping and book-ended sites were combined using bedtools merge with default settings for each sample to generate a total hnRNP A1 footprint at each site.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Files in .bed format indicating locations on GRCm36 genome. Output of Site Selection data processing step, indicating hnRNP A1 RNA binding footprint in that animal. Each file corresponds to a single animal.

source_name: spinal cord

growth_protocol: All animal experiments were performed in accordance with the University of Saskatchewan’s Animal Research Ethics Board under Animal Use Protocol AUP20170104. Mice were housed five to a cage under pathogen-free conditions on a 12h/12h light:dark cycle with ad libitum access to standard rodent chow and water. Adult female C57BL/6N mice (10 weeks) were purchased from Charles River Laboratories.

extract_protocol:
After dissecting the spinal column from the euthanized mouse, the spinal cord was hydraulically extruded through the cervical opening with sterile, RNase-free PBS. The cord was then diced into <1 cubic mm fragments in a petri dish with 5mL ice cold RNase-free PBS and UV crosslinked with two doses of 400mJ 254nm UV light, with swirling in between doses. Fragments were then collected into a 15mL conical tube in RNase-free PBS. Tissue was lysed in iCLIP lysis buffer [Van Nostrand et al (2016). Nature Methods, 13(6), 508–514. https://doi.org/10.1038/nmeth.3810] with protease and RNase inhibitors, then 2mg protein was immunoprecipitated with anti-hnRNP A1 antibody clone 9H10 in the presence of RNaseI overnight at 4degC,  using magnetic protein A/G beads. In parallel, equal amounts of naive samples were pooled to a total of 2mg, and equal amounts of EAE samples were pooled to a total of 2mg, and these pools were each immunoprecipitated in the presence of RNaseI with anti-IgG2a (clone GC198) as negative controls. Samples were washed after immunoprecipitation, RNA was end-healed (described below in library preparation), and then RNA was liberated from the crosslinked protein by treatment with Proteinase K. RNA was eluted using phenol-chloroform-isoamyl alcohol (25:24:1), then purified using the Zymo RNA Clean & Concentrator kit. Input samples were collected prior to immunoprecipitation, and RNA was extracted using the same Proteinase K,  phenol-chloroform-isoamyl alcohol, and Zymo kit process.
RNA was end-healed while still complexed with hnRNP A1/antibody/beads, but after immunoprecipitation and washing, using polynucleotide kinase (PNK) in two stages. First, at pH 6.5 in the absence of ATP to repair the 2’,3’-cyclic phosphate end of the RNA left by RNase I, and then at a pH of 7.6 supplemented with 1mM ATP to repair the 5’-hydroxyl end of the RNA left by RNaseI. Enzymes and buffers were washed away again prior to purification. Input samples were also end-healed as described. After purification, samples were prepared using the NEXTFlex Small RNA Sequencing Kit v3 according to the manufacturer’s protocol, with the recommended “No Size Selection Protocol” modification for bead cleanup, and using PAGE Size-selection and Cleanup to extract library DNA between 150-170nt in length. Sequencing libraries were quantified using a Qubit 4.0 fluorometer and Qubit 1x dsDNA HS assay. The library fragment length distributions were determined using a TapeStation 4150 instrument with High Sensitivity D1000 ScreenTape and reagents. The barcoded libraries were pooled equimolar and 76 bp paired-end reads generated on a NextSeq 550 instrument.

treatment_protocol: EAE was induced through active immunization with reagents purchased from Hooke Laboratories (cat. no. EK-2110). At 12 weeks of age, mice were subcutaneously immunized with 0.1 mL emulsion of MOG(35-55) in complete Freund’s adjuvant between both the shoulder blades and hind limbs. On days 0 and 1, mice also received 100 ng of pertussis toxin diluted in PBS intraperitoneally. Following induction, mice were evaluated daily for the appearance of clinical signs. Mice were assigned clinical scores based on disease severity according to the scoring scale established by Hooke Laboratories. Mice were sacrificed at 15 days post-clinical onset with an overdose of Euthanyl for spinal cord extraction.

tag: vendor

value: Charles River laboratories

value: wild-type

value: spinal cord

value: female

tag: rip antibody

value: EAE

tag: mouse identifier

tag: eae clinical_score


title: Twin20_FT4_low

description: peripheral blood sample


title: D2_Ctrl_INO80_1

tag: tissue

value: Heart

value: Adult cardiomyocyte

tag: treatment


title: MPM,002,Inf


title: EAEinput, 4

tag: genotype

value: input


title: Twin20_FT4_high

description: peripheral blood sample

value: Male

value: whole blood


title: control adult cardiomyocyte, tamoxifen treatment 2 days, rep2

value: Control


title: MPM,001,Main


title: MPM,001,Sup


title: EAEinput, 2


title: MPM,001,Lat


title: Naiveinput, 3

value: Naïve


title: Twin18_FT4_low

description: peripheral blood sample

value: Female

value: normal


title: EAEinput, 7


title: Twin19_FT4_low

description: peripheral blood sample


title: Twin2_TSH_high

description: peripheral blood sample


title: MPM,003,Inf


title: TCCSUPT_2CM1758

city: Madrid

first: Sandra

middle: Isabel

last: Nunes

state: Madrid

address: Av. Complutense, 40

country: Spain

institute: CIEMAT

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads' quality, total bases, total reads, GC (%) and basic statistics are calculated
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes total count values for each sample

source_name: TCCSUP

growth_protocol: 253J, J82 and RT112  were maintained in DMEM GlutaMAX™ medium (Thermo Fisher Scientific, Waltham, Massachusetts, USA), whereas TCCSUP cells were grown in EMEM medium (Lonza, Basel, Switzerland), all supplemented with 10% fetal bovine serum (FBS) and 1% of Antibiotic Antimycotic solution (Thermo Fisher Scientific), at 5% CO2 and 37°C in a humidifying chamber.

extract_protocol:
Total RNA was extracted using the miRNAeasy Mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. One µg of total RNA was sent for RNAseq analysis by Macrogen RNA-seq services (Seoul, South Korea).
Sequencing of the samples was performed by Macrogen.

treatment_protocol: The half maximal inhibitory concentration (IC50) of CM-1758 was calculated for all cell lines. All cell lines were seeded and, 24 h later, treated with CM-1758 for 48 h with the IC50 concentration calculated for each cell line, or with DMSO 0.01% for the  vehicle control.

tag: cell line

value: TCCSUP

value: bladder cancer

value: WT


title: INO80-OE adult cardiomyocyte, tamoxifen treatment 2 days, rep3

value: adult cardiomyocyte

value: tamxifen


title: Naiveinput, 2

value: Charles River laboratories

value: wild-type

value: spinal cord


title: EAEinput, 5

value: female

value: EAE


title: TCCSUPT_1CM1758


title: MPM,002,Sup

value: MPM


title: Naiveinput, 1

value: input


title: TCSUPNT_2CM1758

value: vehicle control


title: Twin17_FT4_low

description: peripheral blood sample

value: whole blood


title: INO80-OE adult cardiomyocyte, tamoxifen treatment 2 days, rep1

value: Heart


title: EAEinput, 3


title: Twin16_FT4_low

description: peripheral blood sample

value: Female


title: RT112T_2CM1758


title: Twin19_FT4_high

description: peripheral blood sample

value: normal


title: EAEinput, 1


title: NaiveIgG, 1

value: anti-IgG2a (clone GC198)

value: anti-IgG immunoprecipitation

value: Naïve (pooled)

value: Naïve pool


title: Twin16_FT4_high

description: peripheral blood sample


title: RT112T_1CM1758

value: bladder cancer

value: WT


title: Twin15_FT4_low

description: peripheral blood sample


title: EAEIgG, 1

value: Charles River laboratories

value: wild-type

value: EAE (pooled)

value: EAE pool


title: J82T_3CM1758


title: RT112NT_2CM1758


title: EAEIP, 4

value: spinal cord

value: female

value: anti-hnRNP A1 (clone 9H10)

value: anti-hnRNP A1 immunoprecipitation

value: EAE


title: J82T_1CM1758


title: EAEIP, 6


title: EAEIP, 2


title: Twin14_FT4_high

description: peripheral blood sample

value: Female

value: whole blood


title: RT112NT_1CM1758

value: vehicle control


title: J82NT_3CM1758


title: Twin18_FT4_high

description: peripheral blood sample

value: normal


title: Twin14_FT4_low

description: peripheral blood sample


title: NaiveIP, 3

value: Naïve


title: Twin15_FT4_high

description: peripheral blood sample


title: J82NT_1CM1758


title: Twin13_FT4_low

description: peripheral blood sample


title: EAEIP, 7


title: TCSUPNT_1CM1758

value: TCCSUP


title: 253JT_3CM1758

value: bladder cancer


title: NaiveIP, 2


title: Twin12_FT4_high

description: peripheral blood sample


title: Twin17_FT4_high

description: peripheral blood sample


title: 253JT_1CM1758

value: WT


title: EAEIP, 5

value: Charles River laboratories


title: Twin11_FT4_low

description: peripheral blood sample


title: 253JNT_3CM1758


title: 253JNT_2CM1758


title: NaiveIP, 1

value: wild-type


title: Twin11_FT4_high

description: peripheral blood sample


title: EAEIP, 1


title: FKH1

city: Nottingham

first: Sophie

middle: G

last: Kellaway

department: School of Medicine

institute: University of Nottingham

data_processing:
Raw paired-end sequencing reads were processed with Trimmomatic v0.32 to remove sequencing adaptors and low-quality sequences, then aligned to hg38 with Hisat2 2.1.0 with default parameters. Gene expression values were calculated as fragments per kilobase of transcript per million mapped reads (FPKM) using Stringtie 1.3.3.
Assembly: hg38
Supplementary files format and content: tsv Stringtie output containing FPKMs

source_name: Human AML cell line

growth_protocol: Cells were obtained from DSMZ and routinely cultured in RPMI 1640 with 10% FBS

extract_protocol:
RNA was extracted using Trizol.
Sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat

value: Human AML cell line