title: YA_Ex, Animal A84, Colon

city: Hong Kong

middle: J.

last: Kwok

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Medicine and Therapeutics

country: Hong Kong

institute: Chinese University of Hong Kong

description:
RNAseq batch6
A84_colon

data_processing:
Raw sequencing FASTQ files were mapped with STAR98 (v2.7.10b) with default parameters using the Mus musculus genome assembly GRCm39.
Quality control was carried out with the FastQC (v0.11.9) and MultiQC99 (v1.13a) packages.
HTSeq100 (v2.0.2) was used to obtain read counts with default options except ‘mode’ being set to ‘intersection-strict’, and ‘nonunique’ being set to ‘fraction’ for ambiguous reads. Gene counts were filtered for a minimum of at least 10 reads in a minimum number of samples, with the minimum number based on the number of animals constituting the smallest comparator group size in the experiment.
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts
Supplementary files format and content: CSV metadata file

source_name: Colon

extract_protocol:
The tissues were retrieved from RNAlater (AM7021, Thermo Fisher Scientific, US), combined with the TRIzol reagent (15596018, Thermo Fisher Scientific, US) or the lysis buffer of the RNAqueous kit (AM1912, Thermo Fisher Scientific, US), homogenized using the TissueLyser II system (Qiagen, US), and total RNA extraction was performed following the instructions in the vendor’s manuals.
Total RNA samples were sent for library preparation and sequencing by Novogene (Novogene Biology Information Technology Co., Ltd., Beijing, China). Libraries were prepared with a poly(A) selection strategy using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770, New England Biolabs, US).

value: Colon


title: YA_Ex, Animal A88, Colon

status: Public on Nov 20 2025

type: SRA

first: Andrew

description:
RNAseq batch6
A88_colon

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue


title: IL-15SA+IL-21Fc

city: Lausanne

first: Yi

last: Wang

address: Rte Csntonale, Station9, MED1 2926

country: Switzerland

institute: EPFL

library_source: transcriptomic single cell

data_processing:
Reads were demultiplexed according to cell barcodes and unique molecular identifiers (UMI), and poly-A tails and adaptor sequences were removed by Cutadapt using CeleScope v1.13.0. After quality control, reads were mapped to the reference genome (Mus_musculus_ensembl_92). Gene counts and UMI counts were acquired via feature Counts software. Gene expression matrix files for subsequent analyses were generated based on gene counts and UMI counts. Downstream data analysis was performed with the Seurat v4 pipeline and Scanpy pipeline78. Cells were first filtered based on three metrics: 1) the number of detected genes per cell between 500 to 5000; 2) the proportion of mitochondrial gene counts (UMIs from mitochondrial genes / total UMIs) must be less than 10 %; 3) the total counts of cells must between 1000 to 10000.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: CT26_b2m-/- colon carcionma

extract_protocol:
Tumors were dissected and dissected tumors were mechanically minced and digested through stirring in RPMI 1640 medium that contained collagenases Type IV (1 mg/mL, Thermo Fisher Scientific), dispase II (100 μg/mL, Sigma-Aldrich), hyaluronidase (100 μg/mL, Sigma-Aldrich), and DNase I (100 μg/mL, Sigma-Aldrich) at 37 °C for 60 min. Red blood cells were removed with ACK lysing buffer after digestion. TILs were enriched by density gradient centrifugation against Percoll (GE Healthcare) and resuspended in FACS buffer (1 × PBS containing 0.2 % BSA (wt / v), Sigma-Aldrich), then sorted by MACS (Miltenyi) and FACS (Sony).
CD45.2+CD3-NKp46+ NK cells were sorted as described above, cells from the same treatment group were pooled together and resuspended at 3 × 105 cells/mL in PBS. Next, 100 µL cell resuspension was loaded onto a standard GEXSCOPE® microwell chip. scRNA-seq library was constructed using the GEXSCOPE® Single-Cell RNA Library Kit according to the manufacturer’s instructions (Singleron Biotechnologies GmbH). Individual libraries were diluted to equimolar and pooled for sequencing. Pools were sequenced on a lane of an S4 flow cell on an Illumina NovaSeq 6000 with 150 bp paired-end reads to a total depth of 90 GB per sample and an average read depth per cell of 50,000 reads. Raw reads were processed with FastQC to evaluate the quality of raw data.

value: CT26_b2m-/- colon carcionma

tag: cell type

value: NK cell


title: HEK293 WT sorbitol replicate 1 Hi-C

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

country: USA

institute: UNC Chapel Hill

description:
Library name: HEK293_WT_sorbitol_rep1
Hi-C of HEK293 cells at 1h

library_source: genomic

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Hi-C contact matrices in .hic format (hg38 reference genome). Files include both individual biological replicates and merged replicates (megaMap) for each condition. Datasets include HCT116 wild-type cells (control and 1h sorbitol treatment), HEK293 wild-type cells from the Phanstiel lab (control and sorbitol treatment), HEK293 eGFP-YAP cells from the Cai lab (control and sorbitol treatment), HEK293 wild-type sorbitol timecourse (10m, 30m, 1h, 3h, 6h, 12h, 24h), and HEK293 eGFP-YAPdTAD cells from the Cai lab (control and sorbitol treatment). MegaMap files represent merged replicates for increased sequencing depth. Spike-in normalized loop calls at 5kb resolution are provided for eGFP-YAP and WT Phanstiel conditions. Differential loop analysis (diffLoops_WT_noDroso_10kb.rds) comparing control vs sorbitol treatment is provided for WT Phanstiel samples.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T and HCT116 cells were cultured at 37 °C in a humidified incubator with 5% CO₂. HEK293T cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin. HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and penicillin/streptomycin. Cells were routinely monitored for mycoplasma contamination and maintained at ~70–80% confluence to ensure log-phase growth. Cells were harvested for experiments only when healthy and within 5–15 passages from thaw.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
In situ Hi-C libraries were prepared using MboI restriction digestion, fill-in with biotinylated nucleotides, proximity ligation, reverse crosslinking, and DNA purification. Libraries were size-selected and PCR-amplified prior to sequencing.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

tag: cell line

tag: genotype

value: wild type

tag: treatment

value: 0.2M sorbitol for 1h


title: YA_Ex, Animal A82, Colon

description:
RNAseq batch6
A82_colon


title: YA_Ex, Animal A80, Colon

description:
RNAseq batch6
A80_colon


title: HEK293 WT control replicate 3 Hi-C

description:
Library name: HEK293_WT_control_rep3
Hi-C of HEK293 cells at 0h

value: untreated


title: HEK293 WT control replicate 2 Hi-C

description:
Library name: HEK293_WT_control_rep2
Hi-C of HEK293 cells at 0h


title: HCT116 sorbitol replicate 4 Hi-C

description:
Library name: HCT116_sorbitol_rep4
Hi-C of HCT116 cells at 1h


title: YA_Ex, Animal A79, Colon

description:
RNAseq batch6
A79_colon


title: YA_Ex, Animal A34, Colon

description:
RNAseq batch6
A34_colon


title: HCT116 sorbitol replicate 3 Hi-C

description:
Library name: HCT116_sorbitol_rep3
Hi-C of HCT116 cells at 1h


title: HCT116 sorbitol replicate 2 Hi-C

description:
Library name: HCT116_sorbitol_rep2
Hi-C of HCT116 cells at 1h


title: HCT116 control replicate 4 Hi-C

description:
Library name: HCT116_control_rep4
Hi-C of HCT116 cells at 0h


title: YA_ctrl, Animal A81, Colon

description:
RNAseq batch6
A81_colon


title: YA_ctrl, Animal A41, Colon

description:
RNAseq batch6
A41_colon


title: YA_ctrl, Animal A83, Colon

description:
RNAseq batch6
A83_colon


title: HCT116 control replicate 3 Hi-C

description:
Library name: HCT116_control_rep3
Hi-C of HCT116 cells at 0h


title: YA_ctrl, Animal A36, Colon

description:
RNAseq batch6
A36_colon


title: HCT116 control replicate 2 Hi-C

description:
Library name: HCT116_control_rep2
Hi-C of HCT116 cells at 0h


title: HCT116 control replicate 1 Hi-C

description:
Library name: HCT116_control_rep1
Hi-C of HCT116 cells at 0h


title: YA_ctrl, Animal A33, Colon

description:
RNAseq batch6
A33_colon


title: YA_ctrl, Animal A38, Colon

description:
RNAseq batch6
A38_colon


title: YA_ctrl, Animal A32, Colon

description:
RNAseq batch6
A32_colon


title: HEK293 sorbitol 9h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-9h-1
RNA-seq of HEK293 cells treated with sorbitol at 9h

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Strand-specific bigWig files containing normalized RNA-seq signal tracks for each replicate and timepoint. This includes merged untreated and sorbitol replicate bigWig files. Files are provided separately for forward and reverse strands across the sorbitol timecourse (0h control, 3h, 6h, 9h, 12h, and 24h treatment).

growth_protocol: Cells were cultured in standard conditions (37 °C, 5% CO₂) in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
mRNA or total RNA input was subjected to library preparation compatible with strand-specific sequencing. Libraries were constructed using manufacturer protocols, indexed, pooled, and sequenced.

value: wildtype

value: 0.2M sorbitol


title: HEK293 sorbitol 6h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-6h-2
RNA-seq of HEK293 cells treated with sorbitol at 6h


title: HEK293 sorbitol 9h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-9h-2
RNA-seq of HEK293 cells treated with sorbitol at 9h


title: HEK293 sorbitol 6h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-6h-1
RNA-seq of HEK293 cells treated with sorbitol at 6h


title: YA_Ex, Animal A37, Colon

description:
RNAseq batch6
A37_colon


title: YA_Ex, Animal A31, Colon

description:
RNAseq batch6
A31_colon


title: ST_A_ctrl_KD, Animal E9, Skeletal_muscle

description:
RNAseq batch5
E9_ SkeletalMuscle


title: HEK293 sorbitol 3h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-3h-2
RNA-seq of HEK293 cells treated with sorbitol at 3h


title: HEK293 WT control replicate 1 Hi-C

description:
Library name: HEK293_WT_control_rep1
Hi-C of HEK293 cells at 0h


title: YA_ctrl, Animal A87, Colon

description:
RNAseq batch6
A87_colon


title: ST_A_ctrl_KD, Animal E9, Hippocampus

description:
RNAseq batch5
E9_HIPPO

source_name: Hippocampus

value: Hippocampus


title: HCT116 sorbitol replicate 1 Hi-C

description:
Library name: HCT116_sorbitol_rep1
Hi-C of HCT116 cells at 1h


title: ST_A_ctrl_KD, Animal E9, Colon

description:
RNAseq batch5
E9_Colon


title: ST_A_ctrl_KD, Animal E9, Frontal_cortex

description:
RNAseq batch5
E9_FCTX


title: HEK293 sorbitol 24h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-24h-1
RNA-seq of HEK293 cells treated with sorbitol at 24h


title: ST_A_ctrl_KD, Animal E9, Adipose_tissue

description:
RNAseq batch5
E9_Adipose


title: HEK293 sorbitol 3h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-3h-1
RNA-seq of HEK293 cells treated with sorbitol at 3h


title: HEK293 sorbitol 1h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-1h-1
RNA-seq of HEK293 cells treated with sorbitol at 1h


title: HEK293 sorbitol 1h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-1h-2
RNA-seq of HEK293 cells treated with sorbitol at 1h


title: ST_A_ctrl_KD, Animal E8, Circulating_WBCs

description:
RNAseq batch5
E8_WBC


title: HEK293 sorbitol 24h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-24h-2
RNA-seq of HEK293 cells treated with sorbitol at 24h


title: ST_A_ctrl_KD, Animal E9, Circulating_WBCs

description:
RNAseq batch5
E9_WBC


title: HEK293 sorbitol 12h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-12h-1
RNA-seq of HEK293 cells treated with sorbitol at 12h


title: ST_A_ctrl_KD, Animal E8, Hippocampus

description:
RNAseq batch5
E8_HIPPO


title: HEK293 sorbitol 12h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-sorbitol-12h-2
RNA-seq of HEK293 cells treated with sorbitol at 12h


title: HEK293 control 0h replicate 2 RNA-seq

description:
Library name: STRS-HEK293-WT-control-0h-2
RNA-seq of HEK293 cells without treatment at 0h


title: ST_A_ctrl_KD, Animal E8, Heart

description:
RNAseq batch5
E8_Heart

source_name: Heart

value: Heart


title: HEK293 control 0h replicate 1 RNA-seq

description:
Library name: STRS-HEK293-WT-control-0h-1
RNA-seq of HEK293 cells without treatment at 0h


title: HEK293 sorbitol YAP1 replicate 1 CUT&Tag

description:
Library name: HEK293_sorbitol_YAP1_1_S3
CUT&Tag for YAP1 in HEK293 cells treated with sorbitol for 1h

data_processing:
CUT&Tag reads were trimmed using Trim Galore, quality checked with FastQC, and aligned to the hg38 reference genome using bwa mem v0.7.17. Alignments were sorted and indexed with samtools, PCR duplicates were removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true), and reads overlapping ENCODE hg38 blacklist regions were removed using bedtools v2.31.1. Peaks were called using MACS2 v2.2.6 (callpeak -f BAMPE -g hs --keep-dup 1 -q 0.01), and a unified peak set was generated by merging peaks across samples. Fragment counts per peak were quantified using bedtools multicov. The following primary antibodies were used: GFP (Abcam #ab290), CTCF (Cell Signaling Technology #3418S), RAD21 (Abcam #ab217678), and H3K27ac (Abcam #ab4729). NIH3T3 spike-in fragments were used to confirm normalization consistency; no spike-in scaling factor was applied. This GEO submission includes raw FASTQ files, peak BED files, and peak-by-sample count matrices.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: bigWig files contain CUT&Tag signal tracks for each replicate and condition (0h control, 1h and 2h sorbitol treatment) across different protein targets (CTCF, RAD21, YAP1, H3K27ac) and GFP (eGFP-YAP). This includes merged untreated and sorbitol replicate files. TSV files contain count matrices for called peaks across all samples, used for differential analysis.
Library strategy: CUT&Tag

growth_protocol: HEK293 cells were cultured in standard conditions (37 °C, 5% CO₂) in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
CUT&Tag was performed on concanavalin-A bead–bound nuclei incubated with primary antibody (CTCF, CST #3418S; RAD21, Abcam #ab217678; GFP for eGFP-YAP, Abcam #ab290; H3K27ac, Abcam #ab4729), followed by secondary antibody and pA-Tn5 transposome. Tagmented DNA was released, purified, PCR-amplified with indexed adapters, size-selected, and sequenced.

value: eGFP-YAP

tag: chip antibody

value: GFP (Abcam, #ab290)


title: ST_A_Ex, Animal E7, Skeletal_muscle

description:
RNAseq batch5
E7_SkeletalMuscle


title: ST_A_ctrl_KD, Animal E9, Heart

description:
RNAseq batch5
E9_Heart


title: ST_A_Ex, Animal E7, Hippocampus

description:
RNAseq batch5
E7_HIPPO


title: ST_A_ctrl_KD, Animal E8, Adipose_tissue

description:
RNAseq batch5
E8_ADIPOSE


title: ST_A_Ex, Animal E7, Circulating_WBCs

description:
RNAseq batch5
E7_WBC


title: HEK293 sorbitol YAP1 replicate 2 CUT&Tag

description:
Library name: HEK293_sorbitol_YAP1_2_S4
CUT&Tag for YAP1 in HEK293 cells treated with sorbitol for 1h


title: ST_A_ctrl_KD, Animal E8, Frontal_cortex

description:
RNAseq batch5
E8_FCTX


title: HEK293 vehicle H3K27ac replicate 1 CUT&Tag

description:
Library name: HEK293_Veh_H3K27ac_1_S9
CUT&Tag for H3K27ac in HEK293 cells with vehicle treatment

value: vehicle

value: H3K27ac (Abcam, #ab4729)


title: ST_A_ctrl_KD, Animal E8, Colon

description:
RNAseq batch5
E8_COLON


title: HEK293 vehicle YAP1 replicate 2 CUT&Tag

description:
Library name: HEK293_Veh_YAP1_2_S2
CUT&Tag for YAP1 in HEK293 cells with vehicle treatment


title: HEK293 sorbitol RAD21 replicate 2 CUT&Tag

description:
Library name: HEK293_sorbitol_RAD21_2_S8
CUT&Tag for RAD21 in HEK293 cells treated with sorbitol for 1h


title: HEK293 vehicle H3K27ac replicate 2 CUT&Tag

description:
Library name: HEK293_Veh_H3K27ac_2_S10
CUT&Tag for H3K27ac in HEK293 cells with vehicle treatment


title: HEK293 sorbitol H3K27ac replicate 2 CUT&Tag

description:
Library name: HEK293_sorbitol_H3K27ac_2_S12
CUT&Tag for H3K27ac in HEK293 cells treated with sorbitol for 1h


title: HEK293 vehicle YAP1 replicate 1 CUT&Tag

description:
Library name: HEK293_Veh_YAP1_1_S1
CUT&Tag for YAP1 in HEK293 cells with vehicle treatment


title: HEK293 sorbitol H3K27ac replicate 1 CUT&Tag

description:
Library name: HEK293_sorbitol_H3K27ac_1_S11
CUT&Tag for H3K27ac in HEK293 cells treated with sorbitol for 1h


title: ST_A_Ex, Animal E7, Colon

description:
RNAseq batch5
E7_Colon


title: HEK293 sorbitol CTCF replicate 1 CUT&Tag

description:
Library name: HEK293_sorbitol_CTCF_1_S15
CUT&Tag for CTCF in HEK293 cells treated with sorbitol for 1h

value: CTCF (Cell Signaling Technology, #3418S)


title: ST_A_ctrl_KD, Animal E8, Skeletal_muscle

description:
RNAseq batch5
E8_SkeletalMuscle


title: HEK293 vehicle RAD21 replicate 2 CUT&Tag

description:
Library name: HEK293_Veh_RAD21_2_S6
CUT&Tag for RAD21 in HEK293 cells with vehicle treatment


title: HEK293 sorbitol RAD21 replicate 1 CUT&Tag

description:
Library name: HEK293_sorbitol_RAD21_1_S7
CUT&Tag for RAD21 in HEK293 cells treated with sorbitol for 1h


title: ST_A_Ex, Animal E7, Frontal_cortex

description:
RNAseq batch5
E7_FCTX


title: HEK293 sorbitol CTCF replicate 2 CUT&Tag

description:
Library name: HEK293_sorbitol_CTCF_2_S16
CUT&Tag for CTCF in HEK293 cells treated with sorbitol for 1h


title: ST_A_rapa, Animal E6, Hippocampus

description:
RNAseq batch5
E6_HIPPO


title: ST_A_rapa, Animal E6, Circulating_WBCs

description:
RNAseq batch5
E6_WBC


title: ST_A_rapa, Animal E6, Skeletal_muscle

description:
RNAseq batch5
E6_SkeletalMuscle


title: ST_A_rapa, Animal E6, Heart

description:
RNAseq batch5
E6_Heart


title: ST_A_Ex, Animal E7, Heart

description:
RNAseq batch5
E7_Heart


title: ST_A_Ex, Animal E7, Adipose_tissue

description:
RNAseq batch5
E7_Adipose


title: HEK293 vehicle RAD21 replicate 1 CUT&Tag

description:
Library name: HEK293_Veh_RAD21_1_S5
CUT&Tag for RAD21 in HEK293 cells with vehicle treatment


title: ST_A_rapa, Animal E6, Colon

description:
RNAseq batch5
E6_Colon


title: ST_A_Ex, Animal E5, Skeletal_muscle

description:
RNAseq batch5
E5_SkeletalMuscle


title: ST_A_rapa, Animal E6, Adipose_tissue

description:
RNAseq batch5
E6_Adipose


title: ST_A_rapa, Animal E6, Frontal_cortex

description:
RNAseq batch5
E6_FCTX


title: HEK293 vehicle CTCF replicate 2 CUT&Tag

description:
Library name: HEK293_Veh_CTCF_2_S14
CUT&Tag for CTCF in HEK293 cells with vehicle treatment


title: ST_A_Ex, Animal E5, Hippocampus

description:
RNAseq batch5
E5_HIPPO


title: Early latent phase_1

city: Bengaluru

first: Ranga

last: Udaykumar

state: Karnataka

address: Jakkur post

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

description:
Library name: P3_1
SP1

data_processing:
FastQC to remove reads below Q30, analysis performed on ubuntu system.
Trimmomatic used to remove low qaulity reads. Hisat2 used to align against GRCh38 genome, Picard to remove PCR duplicates,  Feature count to count Raw reads
Assembly: GRch38
Supplementary files format and content: tab-delimited file with Gene counts, csv file,  Geneexpression_NGS3

source_name: Jurkat

extract_protocol:
RNA extraction was performed with monophasic Trizol reagent.
NEBNext RNA Ultra RNA library with 1 µg of RNA

value: Jurkat

value: CD4+ T-cells


title: Active phase_2

description:
Library name: P2_2
DP2


title: Early latent phase_3

description:
Library name: P3_3
SP3


title: ST_A_rapa, Animal E36, Skeletal_muscle

description:
RNAseq batch5
E36_SkeletalMuscle


title: Active phase_1

description:
Library name: P2_1
DP1


title: ST_A_Ex, Animal E5, Colon

description:
RNAseq batch5
E5_Colon

value: Colon


title: Latent phase_2

description:
Library name: P1_2
dn2


title: Early latent phase_2

description:
Library name: P3_2
sp2


title: ST_A_rapa, Animal E36, Circulating_WBCs

description:
RNAseq batch5
E36_WBC


title: ST_A_rapa, Animal E36, Heart

description:
RNAseq batch5
E36_Heart


title: Latent phase_1

description:
Library name: P1_1
DN1


title: ST_A_Ex, Animal E5, Adipose_tissue

description:
RNAseq batch5
E5_Adipose


title: Control (Jurkat cells expressing Tet-ON-Tat)_2

description:
Library name: diTat_2
C2


title: ST_A_rapa, Animal E36, Hippocampus

description:
RNAseq batch5
E36_HIPPO


title: HEK293 vehicle CTCF replicate 1 CUT&Tag

description:
Library name: HEK293_Veh_CTCF_1_S13
CUT&Tag for CTCF in HEK293 cells with vehicle treatment


title: Control (Jurkat cells expressing Tet-ON-Tat)_3

description:
Library name: diTat_3
C3


title: Latent phase_3

description:
Library name: P1_3
DN3


title: ST_A_rapa, Animal E36, Frontal_cortex

description:
RNAseq batch5
E36_FCTX


title: ST_A_Ex, Animal E5, Frontal_cortex

description:
RNAseq batch5
E5_FCTX


title: Control (Jurkat cells expressing Tet-ON-Tat)_1

description:
Library name: diTat_1
C1


title: ST_A_Ex, Animal E5, Heart

description:
RNAseq batch5
E5_Heart


title: Active phase_3

description:
Library name: P2_3
DP3


title: ST_A_rapa, Animal E36, Colon

description:
RNAseq batch5
E36_Colon


title: ST_A_rapa, Animal E36, Adipose_tissue

description:
RNAseq batch5
E36_Adipose


title: Control (Jurkat cells expressing rtTA3)_3

description:
Library name: rtTA3_3
P3


title: Control (Jurkat cells expressing rtTA3)_2

description:
Library name: rtTA3_2
P2


title: Control (Jurkat cells expressing rtTA3)_1

description:
Library name: rtTA3_1
P1


title: ST_A_ctrl_KD, Animal E35, Skeletal_muscle

description:
RNAseq batch5
E35_SkeletalMuscle


title: ST_A_ctrl_KD, Animal E35, Circulating_WBCs

description:
RNAseq batch5
E35_WBC


title: Bulk_HCF3_DTP827_CAF3

city: Nanjing

first: Siwei

state: Jiangsu

address: No. 42, Baiziting

department: Thoracic Surgery

country: China

institute: Jiangsu Cancer Hospital

description:
Library name: Bulk_HCF3_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF3

data_processing:
scRNA-seq:Cell Ranger software v3.1.0 was used for data demultiplexing, barcode processing, gene counting, and data aggregation.bulk RNA-seq:Fastp was used to remove adapter sequences and low-quality bases (Q<20).
The Seurat package was used for data normalization, dimensionality reduction, and clustering analysis;Trimmed reads were aligned to the human reference genome (hg38) using STAR aligner v2.7.3a.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung cancer cell line

extract_protocol:
scRNA-seq:An appropriate amount of lung cancer tissue was digested with a digestion solution containing collagenase and DNase I at 37°C for about 30 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution . Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue to check the viability .       bulk RNA-seq: Total RNA was extracted from 827 lung adenocarcinoma cell lines using the RNeasy Mini Plus Kit (Qiagen) according to the manufacturer's instructions. 1.3 ug of total RNA was used for the construction of sequencing libraries.
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.RNA libraries for bulk RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

value: lung cancer cell line

value: 827 cell line

value: bulk population

value: EGFR-mutant

value: DTP + CAF3

tag: batch


title: Bulk_HCF2_DTP827_CAF2

description:
Library name: Bulk_HCF2_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF2

value: DTP + CAF2


title: ST_A_ctrl_KD, Animal E35, Colon

description:
RNAseq batch5
E35_COLON


title: ST_A_ctrl_KD, Animal E35, Frontal_cortex

description:
RNAseq batch5
E35_FCTX


title: Bulk_HNF2_DTP827_CAF2

description:
Library name: Bulk_HNF2_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF2


title: Bulk_HNF1_DTP827_CAF1

description:
Library name: Bulk_HNF1_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF1

value: DTP + CAF1


title: ST_A_ctrl_KD, Animal E35, Heart

description:
RNAseq batch5
E35_HEART


title: ST_A_Ex_KD, Animal E34, Circulating_WBCs

description:
RNAseq batch5
E34_WBC


title: Bulk_HCF1_DTP827_CAF1

description:
Library name: Bulk_HCF1_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF1


title: Bulk_H3_DTP827

description:
Library name: Bulk_H3_Lib
Bulk RNA-seq of DTP 827 sample H3

value: TKI-induced DTP


title: ST_A_Ex_KD, Animal E34, Skeletal_muscle

description:
RNAseq batch5
E34_SkeletalMuscle


title: Bulk_H1_DTP827

description:
Library name: Bulk_H1_Lib
Bulk RNA-seq of DTP 827 sample H1


title: ST_A_Ex_KD, Animal E34, Hippocampus

description:
RNAseq batch5
E34_HIPPO

value: Hippocampus


title: Bulk_P3_Parental827

description:
Library name: Bulk_P3_Lib
Bulk RNA-seq of Parental 827 sample P3

value: Parental


title: Bulk_H2_DTP827

description:
Library name: Bulk_H2_Lib
Bulk RNA-seq of DTP 827 sample H2


title: ST_A_Ex_KD, Animal E34, Heart

description:
RNAseq batch5
E34_HEART

value: Heart


title: ST_A_Ex_KD, Animal E34, Frontal_cortex

description:
RNAseq batch5
E34_FCTX


title: Bulk_P2_Parental827

description:
Library name: Bulk_P2_Lib
Bulk RNA-seq of Parental 827 sample P2


title: ST_A_Ex_KD, Animal E34, Colon

description:
RNAseq batch5
E34_COLON


title: Bulk_P1_Parental827

description:
Library name: Bulk_P1_Lib
Bulk RNA-seq of Parental 827 sample P1


title: ST_A_Ex_KD, Animal E34, Adipose_tissue

description:
RNAseq batch5
E34_ADIPOSE


title: ST_A_Ex_KD, Animal E33, Circulating_WBCs

description:
RNAseq batch5
E33_WBC


title: Lin230412

description:
Library name: Lin230412_Lib
Lung cancer tissue surgically resected from Lin230412 for single cell sequencing analysis

source_name: lung cancer tissue

value: lung cancer tissue

value: mixed cell types

value: No specific mutation

value: No additional treatment


title: ST_A_ctrl_KD, Animal E35, Hippocampus

description:
RNAseq batch5
E35_HIPPO


title: Han230412

description:
Library name: Han230412_Lib
Lung cancer tissue surgically resected from Han230412 for single cell sequencing analysis


title: Bulk_HNF3_DTP827_CAF3

description:
Library name: Bulk_HNF3_Lib
Bulk RNA-seq of DTP827 co-cultured with CAF3


title: ST_A_ctrl_KD, Animal E35, Adipose_tissue

description:
RNAseq batch5
E35_ADIPOSE


title: ST_A_Ex_KD, Animal E33, Skeletal_muscle

description:
RNAseq batch5
E33_SkeletalMuscle


title: Cheng230329

description:
Library name: Cheng230329_Lib
Lung cancer tissue surgically resected from Cheng230329 for single cell sequencing analysis


title: Wang221128

description:
Library name: Wang221128_Lib
Lung cancer tissue surgically resected from Wang221128 for single cell sequencing analysis


title: ST_A_Ex_KD, Animal E33, Hippocampus

description:
RNAseq batch5
E33_HIPPO


title: ST_A_Ex_KD, Animal E33, Heart

description:
RNAseq batch5
E33_HEART


title: X10.19

description:
Library name: X10.19_Lib
Lung cancer tissue surgically resected from X10.19 for single cell sequencing analysis


title: Ning221109

description:
Library name: Ning221109_Lib
Lung cancer tissue surgically resected from Ning221109 for single cell sequencing analysis


title: ST_A_Ex_KD, Animal E33, Frontal_cortex

description:
RNAseq batch5
E33_FCTX


title: ST_A_Ex_KD, Animal E33, Colon

description:
RNAseq batch5
E33_COLON


title: -Ab-2，replicate2

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Library name: Sample 11

data_processing:
RNA-seq: fastp (version 0.18.0); ChIP-seq: Clean Reads Filtering.
RNA-seq: short reads alignment tool Bowtie2 (version 2.2.8); ChIP-seq: BWA (version 0.7.12).
RNA-seq: HISAT2. 2.4; ChIP-seq: MACS[2] (version: macs14).
RNA-seq: StringTie v1.3.1; ChIP-seq: Peak Related Genes Annotation.
RNA-seq: RSEM software.
Assembly: RNA-seq: GRCH38 ensemble release100; ChIP-seq: GRCH38 ensemble release100.
Supplementary files format and content: RNA-seq: Excel files include raw counts and  FPKM values for each Sample; ChIP-seq: Excel files include raw counts and  RPKM values for each Sample;
Supplementary files format and content: RNA-seq: GRCH38 ensemble release100; ChIP-seq: GRCH38 ensemble release100.

source_name: retinal organoids

extract_protocol:
RNA-seq: Total RNA was extracted by Trizol reagent (Sigma), mRNA was enriched by Oligo(dT) beads. ChIP-seq: CRX-bound regions of genomic DNA were enriched with CRX antibody or not.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols, then transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB, #7530,New England Biolabs, Ipswich, MA, USA). ChIP-seq libraries were constructed using the Hyperactive® Universal ChIP Assay Kit (Vazyme, TD903) according to the manufacturer's instructions.

value: retinal organoids

value: CRX-mCherry hiSPCs

value: differentiated retinal cells

value: CRX-mCherry

value: without CRX antibody


title: ST_A_ctrl, Animal E32, Skeletal_muscle

description:
RNAseq batch5
E32_SkeletalMuscle


title: +Ab-2，replicate2

description: Library name: Sample 8

value: with CRX antibody


title: ST_A_Ex_KD, Animal E33, Adipose_tissue

description:
RNAseq batch5
E33_ADIPOSE


title: ST_A_ctrl, Animal E32, Hippocampus

description:
RNAseq batch5
E32_HIPPO


title: -Ab-1，replicate1

description: Library name: Sample 10


title: mP-3, replicate3

description: Library name: Sample 6

value: FACS, mCherry+


title: +Ab-1，replicate1

description: Library name: Sample 7


title: +Ab-3，replicate3

description: Library name: Sample 9


title: ST_A_ctrl, Animal E32, Heart

description:
RNAseq batch5
E32_HEART


title: ST_A_ctrl, Animal E32, Frontal_cortex

description:
RNAseq batch5
E32_FCTX


title: ST_A_ctrl, Animal E32, Colon

description:
RNAseq batch5
E32_COLON

value: Colon


title: mP-2, replicate2

description: Library name: Sample 5


title: mP-1, replicate1

description: Library name: Sample 4


title: ST_A_ctrl, Animal E32, Adipose_tissue

description:
RNAseq batch5
E32_ADIPOSE


title: ST_A_Ex, Animal E31, Circulating_WBCs

description:
RNAseq batch5
E31_WBC


title: mN-3, replicate3

description: Library name: Sample 3

value: FACS, mCherry-


title: ST_A_Ex, Animal E31, Skeletal_muscle

description:
RNAseq batch5
E31_SkeletalMuscle


title: mN-1, replicate1

description: Library name: Sample 1


title: ST_A_Ex, Animal E31, Hippocampus

description:
RNAseq batch5
E31_HIPPO


title: HiC shMTR4 Rep2, lane 1

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

description: Library name: Sample 3

data_processing:
Software versions and workflow details:  Juicer version: 1.6 Juicer Tools version: 1.19.02 BWA version: 0.7.17-r1188 Java version: OpenJDK 1.8.0_312 Data processing: Biological replicates ("rep1" and "rep2") were processed from sequencing data obtained across two lanes per replicate. For alignment on hg19 genome, four FASTQ files were provided as input to Juicer (script juicer.sh v1.6): paired-end reads (R1 and R2) from both lanes of the same replicate were aligned simultaneously using Juicer Tools pre v1.19.02. The resulting alignments for the replicates were then merged using Juicer Tools mega v1.19.02.
Assembly: genome_version : GRCh37
Supplementary files format and content: HiC contact matrix (.hic format)

source_name: HeLa Cells

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium containing high glucose supplémed with GlutaMAXmedium complemented with 10% heat-inactivated FBS and 1% pen-strep

extract_protocol:
ARIMA HiC Kit
KAPA hyperprep

treatment_protocol: For experiments using RNAi, 3 × 10 6 cells were seeded in 100 mm culture dishes at the day of siRNA transfection. Double-stranded RNA oligonucleotides used for RNAi were purchased from Eurofins MWG.Sequences of siRNAs used in this study re shown in Additional file. HeLa cells were transfected with siRNA (10 nM final concentration) using INTERFERin® siRNA transfection reagent (PolyPlus Transfection) according to the manufacturer’s instructions. Cells were collected approximately 65 h after transfection.

value: HeLa Cells

value: epithelial cell

value: MTR4 KD


title: ST_A_ctrl, Animal E32, Circulating_WBCs

description:
RNAseq batch5
E32_WBC


title: ST_A_Ex, Animal E31, Frontal_cortex

description:
RNAseq batch5
E31_FCTX


title: HiC shMTR4 Rep1, lane 2

description: Library name: Sample 2


title: ST_A_Ex, Animal E31, Colon

description:
RNAseq batch5
E31_COLON


title: ST_A_Ex, Animal E31, Adipose_tissue

description:
RNAseq batch5
E31_ADIPOSE


title: ST_A_ctrl, Animal E30, Circulating_WBCs

description:
RNAseq batch5
E30_WBC


title: oe_circ2

city: Nanchang

first: Boxuan

last: Zhou

state: Jiangxi

address: 17th Yongwai Street, Donghu District

department: Department of Breast Disease Center

institute: Nanchang University

data_processing:
Software Tools: Used Fastp v0.18.0 for quality control of circRNA-seq, Bowtie2 v2.3.0 for rRNA and genome alignment, TopHat2 v2.1.1 for reference genome alignment in circRNA-seq and RNA-seq, find_circ v1.2 for circRNA identification, RSEM v1.2.19 for RNA-seq quantification, and DESeq2 for DEG analysis.
Processing Pipeline: CircRNA-seq reads were trimmed with fastp, aligned to rRNA with Bowtie2 (removing mapped reads), then aligned to hg38 genome with TopHat2 (unmapped reads used for circRNA detection with find_circ); circRNAs were annotated using circBase, and unannotated ones were considered novel; RNA-seq reads were mapped with TopHat2, quantified by RSEM, normalized as FPKM, and DE analysis was performed with fold change ≥1.5 and P < 0.05.
Reference Genome: Used human (hg38) for circRNA-seq and RNA-seq.
Assembly: mm10
Supplementary files format and content: CircRNA-seq: Tab-delimited text file containing RPM values and DE analysis results.
Supplementary files format and content: RNA-seq: Tab-delimited text file containing raw counts, FPKM values, and DE results.

extract_protocol:
Total RNA was extracted using the TRIzol reagent kit (Invitrogen) according to the manufacturer's instructions. RNA quality was evaluated with an Agilent 2100 Bioanalyzer and confirmed by RNase-free agarose gel electrophoresis.
RNA libraries were prepared by removing rRNA to enrich for mRNA and ncRNA, followed by fragmentation, cDNA synthesis, and library preparation using the Illumina platform with adapter ligation, size selection, and PCR amplification according to the standard protocol.

value: ER positive Breast cancer cell


title: ST_A_ctrl, Animal E30, Skeletal_muscle

description:
RNAseq batch5
E30_SkeletalMuscle


title: oe_circIRESmut2


title: S3

source_name: Breast Cancer tumor

value: Breast Cancer tumor


title: oe_circIRESmut1


title: ST_A_ctrl, Animal E30, Heart

description:
RNAseq batch5
E30_HEART

value: Heart


title: ST_A_ctrl, Animal E30, Hippocampus

description:
RNAseq batch5
E30_HIPPO

value: Hippocampus


title: S2


title: ST_A_ctrl, Animal E30, Frontal_cortex

description:
RNAseq batch5
E30_FCTX


title: ST_A_ctrl, Animal E30, Colon

description:
RNAseq batch5
E30_COLON


title: mN-2, replicate2

description: Library name: Sample 2


title: ST_A_ctrl, Animal E30, Adipose_tissue

description:
RNAseq batch5
E30_ADIPOSE


title: R3


title: ST_A_ctrl, Animal E29, Circulating_WBCs

description:
RNAseq batch5
E29_WBC


title: S1


title: R2


title: ST_A_Ex, Animal E31, Heart

description:
RNAseq batch5
E31_HEART


title: HiC shMTR4 Rep2, lane 2

description: Library name: Sample 4


title: ST_A_ctrl, Animal E29, Skeletal_muscle

description:
RNAseq batch5
E29_SkeletalMuscle


title: R1


title: HiC shMTR4 Rep1, lane 1

description: Library name: Sample 1


title: ST_A_ctrl, Animal E29, Hippocampus

description:
RNAseq batch5
E29_HIPPO


title: ST_A_ctrl, Animal E29, Heart

description:
RNAseq batch5
E29_HEART


title: KO,IFN,77d

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020). The pipeline was executed with Nextflow v23.04.1 (Di Tommaso et al., 2017).
Reads were aligned with STAR (version 2.7.9a) against an index of the GRCh38 human reference genome, built using Gencode v42 gene annotations, with the following command: --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA
Gene-level expression was quantified based on the STAR output using salmon (version 1.10.1) and transcript models from Gencode v42, with the following non-default settings: --noLengthCorrection.
Gene quantitation results were imported into R (version 4.1.1) with the tximeta Bioconductor package (version 1.12.0) and combined with sample and gene metadata.
To obtain normalized counts per million (CPM), raw counts were library-size normalized with the calcNormFactors function from the edgeR Bioconductor package (version 4.0.12), using the TMM method.
Assembly: GRCh38
Supplementary files format and content: The processed_counts.xlsx file is a Microscoft excel file with three worksheets: 1) sample_annotations, 2) raw_counts and 3) normalized cpm, providing sample metadata, gene-level raw counts or normalized CPMs for all samples, respectively.

source_name: iPSC-derived microglia

growth_protocol: Human iPSCs (Thermo Fisher Scientific, A1894) were maintained in mTESR-Plus (STEMCELL Technologies, 100-0276) media until seeding for differentiation. At ~80% confluence hematopoietic differentiation was initiated following the protocol published by Guttikonda et al, Nat Neurosci, 2021. On Day 4 cells CD235a-positive cells were identified using FACS and replated on matrigel coated plates into Hematopoietic Kit Medium B (STEMCELL Technologies, 05310) containing 10µM ROCK inhibitor (ATCC, Y27632) at a density of 500,000 cells per well of a 6-well plate. Hematopoetic precursor cells (HPCs) were confirmed to be >90% CD43-positive by FACS, and seeded directly onto astrocyte feeder layers to generate microglia as previously described in van Lengerich et al, Nat Neurosci, 2023. Cells were differentiated using STEMCELL Technolgies STEMDiff Microglia Differentiation (100-0019) and STEMDiff Microglia Maturation (100-0020) protocols.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) and resuspended in nuclease-free water. RNA quality was assessed with the Bioanalyzer RNA Pico kit (Agilent, 5067-1513).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with Qubit™ 1X dsDNA HS Assay Kits (Invitrogen Q33231) and Bioanalyzer High Sense DNA chip (Agilent 5067-4626). Libraries were pooled in equimolar ratios for sequencing.

treatment_protocol: 25,000-30,000 wild type (WT) or PILRA knock-out (KO) iPSC-derived microglia were seeded and were dosed with LPS (100ng/ml, Sigma-Aldrich, 055-B5,) or IFNg (1ng/ml, Peprotech, AF-300-02) for 24 hours. Treatments were replicated independently on five different days.

value: iPSC-derived microglia

value: PILRA knockout

value: IFNg

tag: treatment dose

value: 1 ng/ml

tag: treatment duration

value: 24 hours

tag: rin

value: 77 days in vitro


title: oe_circ1


title: KO,Untreated,77d

value: vehicle

value: 0 ng/ml


title: KO,LPS,77d

value: LPS

value: 10 ng/ml


title: ST_A_ctrl, Animal E29, Frontal_cortex

description:
RNAseq batch5
E29_FCTX


title: ST_A_ctrl, Animal E29, Colon

description:
RNAseq batch5
E29_COLON

value: Colon


title: WT,IFN,77d

value: WT


title: ST_A_ctrl, Animal E29, Adipose_tissue

description:
RNAseq batch5
E29_ADIPOSE


title: ST_A_rapa, Animal E28, Skeletal_muscle

description:
RNAseq batch5
E28_SkeletalMuscle


title: KO,IFN,73d

value: 73 days in vitro


title: WT,LPS,77d


title: ST_A_rapa, Animal E28, Hippocampus

description:
RNAseq batch5
E28_HIPPO


title: ST_A_rapa, Animal E28, Heart

description:
RNAseq batch5
E28_HEART


title: WT,Untreated,77d


title: ST_A_rapa, Animal E28, Circulating_WBCs

description:
RNAseq batch5
E28_WBC


title: WT,LPS,73d


title: ST_A_rapa, Animal E28, Adipose_tissue

description:
RNAseq batch5
E28_ADIPOSE


title: KO,Untreated,73d


title: WT,IFN,73d


title: ST_A_Ex, Animal E25, Circulating_WBCs

description:
RNAseq batch5
E25_WBC


title: ST_A_rapa, Animal E28, Frontal_cortex

description:
RNAseq batch5
E28_FCTX


title: WT,Untreated,73d


title: ST_A_Ex, Animal E25, Skeletal_muscle

description:
RNAseq batch5
E25_SkeletalMuscle


title: KO,LPS,73d


title: ST_A_rapa, Animal E28, Colon

description:
RNAseq batch5
E28_COLON


title: KO,IFN,70d

value: 70 days in vitro


title: KO,LPS,70d


title: ST_A_Ex, Animal E25, Hippocampus

description:
RNAseq batch5
E25_HIPPO


title: ST_A_Ex, Animal E25, Heart

description:
RNAseq batch5
E25_HEART


title: KO,Untreated,70d


title: WT,IFN,70d


title: ST_A_Ex, Animal E25, Frontal_cortex

description:
RNAseq batch5
E25_FCTX


title: WT,LPS,70d


title: WT,Untreated,70d


title: ST_A_Ex, Animal E25, Adipose_tissue

description:
RNAseq batch5
E25_ADIPOSE


title: KO,IFN,63d

value: 63 days in vitro


title: KO,LPS,63d


title: KO,Untreated,63d


title: ST_A_ctrl, Animal E23, Circulating_WBCs

description:
RNAseq batch5
E23_WBC


title: WT,IFN,63d


title: ST_A_ctrl, Animal E23, Skeletal_muscle

description:
RNAseq batch5
E23_SkeletalMuscle


title: ST_A_ctrl, Animal E23, Hippocampus

description:
RNAseq batch5
E23_HIPPO


title: ST_A_ctrl, Animal E23, Colon

description:
RNAseq batch5
E23_COLON


title: WT,Untreated,63d


title: KO,IFN,59d

value: 59 days in vitro


title: ST_A_ctrl, Animal E23, Adipose_tissue

description:
RNAseq batch5
E23_ADIPOSE


title: ST_A_rapa, Animal E22, Circulating_WBCs

description:
RNAseq batch5
E22_WBC


title: KO,LPS,59d


title: ST_A_ctrl, Animal E23, Heart

description:
RNAseq batch5
E23_HEART

value: Heart


title: ST_A_ctrl, Animal E23, Frontal_cortex

description:
RNAseq batch5
E23_FCTX


title: KO,Untreated,59d

value: iPSC-derived microglia


title: ST_A_rapa, Animal E22, Skeletal_muscle

description:
RNAseq batch5
E22_SkeletalMuscle


title: ST_A_rapa, Animal E22, Hippocampus

description:
RNAseq batch5
E22_HIPPO

value: Hippocampus


title: ST_A_rapa, Animal E22, Heart

description:
RNAseq batch5
E22_HEART


title: ST_A_Ex, Animal E25, Colon

description:
RNAseq batch5
E25_COLON


title: ST_A_rapa, Animal E22, Frontal_cortex

description:
RNAseq batch5
E22_FCTX


title: ST_A_rapa, Animal E22, Colon

description:
RNAseq batch5
E22_COLON


title: GEO_120DIV_ARX_3

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: One UTSA Circle

department: Department of Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

description:
10X Genomics
GEO_120DIV_ARX_3

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) . All further analysis was done by Suerat v.3.2 or v.4.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values, files and matrix files

source_name: Ganglionic Eminence Organoid

extract_protocol:
For single cell dissociation and RNA seq, cortical and ganglionic eminence organoid were dissociated using Worthington papain dissociation kit (Cat. No. LK003150) as per instruction manual. Each developmental timepoint (30 DIV and 120 DIV) and each subtype of spheroid (cortical and ganglionic eminence) was processed separately. A total of 3 lines, and one clone per line, were used for each condition. Briefly, 3-4 organoids for each timepoint and subtype were collected in a small petri dish with 5 ml of prewarmed Worthington papain solution and 250 µl of Worthington DNase solution. The spheroids were chopped into small pieces using sterile blades and the dishes were placed on a digital rocker in a cell culture incubator for 60 minutes at 37 °C. Digested tissue was collected in a 15-ml tube and 5 ml of room temperature (RT) Earle's Balanced Salt Solution (EBSS) was added. The mixture was then triturated by gently pipetting up and down 10 times with 10-ml plastic pipette followed by 1-ml and 200-µl pipettes. Any undissociated tissue was allowed to settle at the bottom of the tube and the cloudy suspension was carefully aspirated in a clean 15-ml tube. Next, 3.15 ml of inhibitor solution (2.7 ml of EBSS, 300 µl of reconstituted Worthington albumin-ovomucoid solution and 150 µl of DNase solution) was carefully layered over the cloudy suspension and tubes were centrifuged at 300 g for 5 minutes at RT. The supernatant was carefully discarded, and cell pellet was gently suspended in 500 µl of cold neurobasal A media. Cell viability was determined using trypan blue.
10x Genomics single cell libraries were generated by the University of Texas at San Antonio (UTSA) Genomics Core. Cell suspensions were loaded into 10x Genomics microfluidics chips from Chip B Single Cell kit (Cat. No. 1000153) and onto the 10x Chromium controller to capture single cells in Gel Beads-in-emulsion (GEMs). 7,000 cells/sample were targeted for capture in GEMs preceding library prep following manufacturer’s recommendations for 10x Genomics 3’ Gene Expression Reagent kit (Cat. No. 1000269) with v3 chemistry. Sequencing was performed on either NextSeq 500 at University of Texas Health Science Center (UTHSC) at San Antonio or NovaSeq 6000 at North Texas Genome Center (NTGC) to generate 50,000 reads/cell in each sample.

value: Ganglionic Eminence Organoid

tag: age


title: GEO_120DIV_ARX_2

description:
10X Genomics
GEO_120DIV_ARX_2


title: ST_A_rapa, Animal E22, Adipose_tissue

description:
RNAseq batch5
E22_ADIPOSE


title: GEO_120DIV_Control_3

description:
10X Genomics
GEO_120DIV_Control_3


title: ST_A_ctrl_KD, Animal E21, Circulating_WBCs

description:
RNAseq batch5
E21_WBC


title: ST_A_ctrl_KD, Animal E21, Skeletal_muscle

description:
RNAseq batch5
E21_SkeletalMuscle


title: GEO_120DIV_Control_2

description:
10X Genomics
GEO_120DIV_Control_2


title: GEO_30DIV_ARX_3

description:
10X Genomics
GEO_30DIV_ARX_3


title: WT,LPS,63d


title: WT,IFN,59d

value: IFNg

value: 1 ng/ml


title: GEO_30DIV_ARX_2

description:
10X Genomics
GEO_30DIV_ARX_2


title: ST_A_ctrl_KD, Animal E21, Heart

description:
RNAseq batch5
E21_HEART


title: ST_A_ctrl_KD, Animal E21, Colon

description:
RNAseq batch5
E21_COLON


title: GEO_30DIV_Control_2

description:
10X Genomics
GEO_30DIV_Control_2


title: ST_A_ctrl_KD, Animal E21, Frontal_cortex

description:
RNAseq batch5
E21_FCTX


title: GEO_30DIV_Control_3

description:
10X Genomics
GEO_30DIV_Control_3


title: CO_120DIV_ARX_3

description:
10X Genomics
CO_120DIV_ARX_3

source_name: Cortical Organoid

value: Cortical Organoid


title: ST_A_ctrl_KD, Animal E21, Adipose_tissue

description:
RNAseq batch5
E21_ADIPOSE


title: WT,LPS,59d

value: 24 hours


title: ST_A_ctrl_KD, Animal E20, Circulating_WBCs

description:
RNAseq batch5
E20_WBC


title: ST_A_ctrl_KD, Animal E20, Skeletal_muscle

description:
RNAseq batch5
E20_SkeletalMuscle


title: CO_120DIV_ARX_2

description:
10X Genomics
CO_120DIV_ARX_2


title: CO_120DIV_Control_3

description:
10X Genomics
CO_120DIV_Control_3


title: ST_A_ctrl_KD, Animal E20, Hippocampus

description:
RNAseq batch5
E20_HIPPO


title: ST_A_ctrl_KD, Animal E20, Heart

description:
RNAseq batch5
E20_HEART


title: WT,Untreated,59d

value: vehicle

value: 0 ng/ml


title: CO_30DIV_ARX_3

description:
10X Genomics
CO_30DIV_ARX_3


title: CO_120DIV_Control_2

description:
10X Genomics
CO_120DIV_Control_2


title: ST_A_ctrl_KD, Animal E20, Frontal_cortex

description:
RNAseq batch5
E20_FCTX


title: CO_30DIV_Control_3

description:
10X Genomics
CO_30DIV_Control_3


title: ST_A_ctrl_KD, Animal E21, Hippocampus

description:
RNAseq batch5
E21_HIPPO


title: ST_A_ctrl_KD, Animal E20, Colon

description:
RNAseq batch5
E20_COLON


title: ST_A_ctrl_KD, Animal E20, Adipose_tissue

description:
RNAseq batch5
E20_ADIPOSE


title: CO_30DIV_Control_2

description:
10X Genomics
CO_30DIV_Control_2


title: ST_A_Ex, Animal E19, Circulating_WBCs

description:
RNAseq batch5
E19_WBC


title: ST_A_Ex, Animal E19, Skeletal_muscle

description:
RNAseq batch5
E19_SkeletalMuscle


title: K562 cells, CBD-treated sample 12h rep 2

city: Sofia

first: Petar

middle: Petrov

last: Donchev

address: "Akademic Georgi Bonchev" building 26

department: Immunology

country: Bulgaria

institute: Stephan Angeloff Institute of Microbiology

description: Library name: CBD_12h_2

data_processing:
Sequencing reads were filtered using SOAPnuke to remove low-quality reads and adaptor sequences
Clean reads were mapped to the reference genome using HISAT2. Gene and splicing analysis were performed using Eriscript and rMATS
RNA identification was conducted using Bowtie2. Gene expression levels were quantified using RSEM
Differential expression analysis was conducted using DESeq2. DEGs were selected with thresholds of fold change ≥ 2 and p ≤ 0.05 (adjusted p ≤ 0.05); a secondary threshold of fold change ≥ 1.5 was applied.
Gene Ontology enrichment analysis was performed using Phyper via hypergeometric testing. Pathway significance was defined as Q ≤ 0.05
Assembly: All statistical analyses were conducted in R using paired Student's t-test and Benjamini-Hochberg correction for FDR. Visualizations and tables were generated using Dr. Tom
Supplementary files format and content: NCBI_GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt files contain TPM and FPKM data for each sample

source_name: K562 cells treated with CBD for 12 hours, rep 2

growth_protocol: K562 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum. Cells were maintained at 37°C in a humidified incubator with 5% CO₂. Cultures were kept in suspension and passaged every 2–3 days to maintain a density between 2 × 10⁵ and 1 × 10⁶ cells/mL. Cells were harvested at mid-log phase for RNA extraction

extract_protocol:
The mRNA isolation from K562 cells was performed with Aurum™ Total RNA Mini Kit (#7326820)
RNA was extracted and converted to cDNA. Libraries were prepared using BGI’s standard protocol, including fragmentation, adaptor ligation, and PCR amplification. The libraries were circularized and sequenced on the DNBSEQ-G400 platform.

value: bone marrow

value: erythroleukemia cell

value: wild-type

value: CBD


title: K562 cells, CBD-treated sample 12h rep 1

description: Library name: CBD_12h_1

source_name: K562 cells treated with CBD for 12 hours, rep 1


title: ST_A_Ex, Animal E19, Hippocampus

description:
RNAseq batch5
E19_HIPPO


title: ST_A_Ex, Animal E19, Heart

description:
RNAseq batch5
E19_HEART


title: K562 cells, CBD-treated sample 4h rep 2

description: Library name: CBD_4h_2

source_name: K562 cells treated with CBD for 4 hours, rep 2


title: ST_A_Ex, Animal E19, Frontal_cortex

description:
RNAseq batch5
E19_FCTX


title: K562 cells, CBD-treated sample 4h rep 3

description: Library name: CBD_4h_3

source_name: K562 cells treated with CBD for 4 hours, rep 3


title: K562 cells, CBD-treated sample 4h rep 1

description: Library name: CBD_4h_1

source_name: K562 cells treated with CBD for 4 hours, rep 1


title: ST_A_Ex, Animal E19, Colon

description:
RNAseq batch5
E19_COLON

source_name: Colon

value: Colon


title: K562 cells, Control sample replicate 2

description: Library name: Control_2

source_name: K562 cells untreated, 0h, replicate 2

value: control


title: ST_A_Ex, Animal E19, Adipose_tissue

description:
RNAseq batch5
E19_ADIPOSE


title: CO_30DIV_ARX_2

description:
10X Genomics
CO_30DIV_ARX_2


title: K562 cells, Control sample replicate 3

description: Library name: Control_3

source_name: K562 cells untreated, 0h, replicate 3


title: K562 cells, Control sample replicate 1

description: Library name: Control_1

source_name: K562 cells untreated, 0h, replicate 1


title: ST_A_Ex_KD, Animal E16, Skeletal_muscle

description:
RNAseq batch5
E16_SkeletalMuscle


title: ST_A_Ex_KD, Animal E16, Circulating_WBCs

description:
RNAseq batch5
E16_WBC


title: HiC control Rep2, lane 2

description: Library name: Sample 8

value: HeLa Cells

value: epithelial cell

value: Control KD


title: HiC control Rep2, lane 1

description: Library name: Sample 7


title: ST_A_Ex_KD, Animal E16, Frontal_cortex

description:
RNAseq batch5
E16_FCTX


title: ST_A_Ex_KD, Animal E16, Heart

description:
RNAseq batch5
E16_HEART

source_name: Heart

value: Heart


title: ST_A_Ex_KD, Animal E16, Hippocampus

description:
RNAseq batch5
E16_HIPPO

source_name: Hippocampus

value: Hippocampus


title: K562 cells, CBD-treated sample 12h rep 3

description: Library name: CBD_12h_3

source_name: K562 cells treated with CBD for 12 hours, rep 3


title: HiC control Rep1, lane 1

description: Library name: Sample 5

source_name: HeLa Cells


title: A46_CardiacMuscle

type: genomic

description:
A46
208114950002_R01C02

hyb_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

data_processing:
Raw data were processed with SeSaMe (v1.16.1)
Processed data are presented in the form of beta values.

label: Cy3 and Cy5

source_name: CardiacMuscle

extract_protocol: Genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (D4069, Zymo Research) for blood or EZNA Tissue DNA Kit (D3396-02, Omega Bio-Tek) for solid tissue)

value: CardiacMuscle


title: ST_A_Ex_KD, Animal E16, Colon

description:
RNAseq batch5
E16_COLON


title: A88_HTH

description:
A88
208114950002_R06C01

scan_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array

source_name: HTH

value: HTH


title: ST_A_Ex_KD, Animal E16, Adipose_tissue

description:
RNAseq batch5
E16_ADIPOSE


title: A88_CardiacMuscle

description:
A88
208114950002_R05C01

label_protocol: Methylation assays were carried out by the Clock Foundation custom BeadChip array


title: ST_A_Ex_KD, Animal E15, Circulating_WBCs

description:
RNAseq batch5
E15_WBC


title: E28_CardiacMuscle

description:
E28
208114950002_R04C01


title: A87_HTH

description:
A87
208114950002_R03C01


title: ST_A_Ex_KD, Animal E15, Heart

description:
RNAseq batch5
E15_HEART


title: ST_A_Ex_KD, Animal E15, Frontal_cortex

description:
RNAseq batch5
E15_FCTX


title: A47_CardiacMuscle

description:
A47
208114950060_R06C02


title: HiC control Rep1, lane 2

description: Library name: Sample 6


title: A84_CardiacMuscle

description:
A84
208114950060_R04C02


title: E33_CardiacMuscle

description:
E33
208114950002_R01C01


title: ST_A_Ex_KD, Animal E15, Colon

description:
RNAseq batch5
E15_COLON


title: ST_A_Ex_KD, Animal E15, Adipose_tissue

description:
RNAseq batch5
E15_ADIPOSE


title: A84_HTH

description:
A84
208114950060_R05C02


title: ST_A_ctrl, Animal E13, Skeletal_muscle

description:
RNAseq batch5
E13_SkeletalMuscle


title: ST_A_ctrl, Animal E13, Circulating_WBCs

description:
RNAseq batch5
E13_WBC


title: ST_A_ctrl, Animal E13, Hippocampus

description:
RNAseq batch5
E13_HIPPO


title: ST_A_ctrl, Animal E13, Heart

description:
RNAseq batch5
E13_HEART


title: ST_A_ctrl, Animal E13, Frontal_cortex

description:
RNAseq batch5
E13_FCTX


title: A83_CardiacMuscle

description:
A83
208114950060_R06C01


title: A83_HTH

description:
A83
208114950060_R01C02


title: ST_A_Ex_KD, Animal E15, Skeletal_muscle

description:
RNAseq batch5
E15_SkeletalMuscle


title: E34_CardiacMuscle

description:
E34
208114950060_R04C01


title: ST_A_ctrl, Animal E13, Adipose_tissue

description:
RNAseq batch5
E13_ADIPOSE


title: ST_A_ctrl, Animal E13, Colon

description:
RNAseq batch5
E13_COLON


title: ST_A_Ex_KD, Animal E15, Hippocampus

description:
RNAseq batch5
E15_HIPPO


title: ST_A_Ex_KD, Animal E12, Circulating_WBCs

description:
RNAseq batch5
E12_WBC


title: A88_Hippo

description:
A88
208114950060_R03C01

source_name: Hippo

value: Hippo


title: A87_CardiacMuscle

description:
A87
208114950002_R02C01


title: ST_A_Ex_KD, Animal E12, Hippocampus

description:
RNAseq batch5
E12_HIPPO


title: E31_CardiacMuscle

description:
E31
208114950045_R06C02


title: A87_SkeletalMuscle

description:
A87
208114950045_R04C02

source_name: SkeletalMuscle

value: SkeletalMuscle


title: A88_SkeletalMuscle

description:
A88
208114950060_R02C01


title: E30_CardiacMuscle

description:
E30
208114950060_R01C01


title: A87_Hippo

description:
A87
208114950045_R05C02


title: ST_A_Ex_KD, Animal E12, Frontal_cortex

description:
RNAseq batch5
E12_FCTX


title: ST_A_Ex_KD, Animal E12, Heart

description:
RNAseq batch5
E12_HEART


title: ST_A_Ex_KD, Animal E12, Colon

description:
RNAseq batch5
E12_COLON


title: A45_CardiacMuscle

description:
A45
208114950045_R03C02


title: E36_CardiacMuscle

description:
E36
208114950060_R02C02


title: ST_A_rapa, Animal E10, Skeletal_muscle

description:
RNAseq batch5
E10_SkeletalMuscle


title: ST_A_Ex_KD, Animal E12, Adipose_tissue

description:
RNAseq batch5
E12_ADIPOSE


title: E25_CardiacMuscle

description:
E25
208114950060_R03C02


title: E21_CardiacMuscle

description:
E21
208114950060_R05C01


title: A84_Hippo

description:
A84
208114950045_R01C02


title: E35_CardiacMuscle

description:
E35
208114950045_R02C02


title: A84_SkeletalMuscle

description:
A84
208114950045_R06C01


title: ST_A_rapa, Animal E10, Hippocampus

description:
RNAseq batch5
E10_HIPPO


title: E22_CardiacMuscle

description:
E22
208114950045_R05C01


title: ST_A_Ex_KD, Animal E12, Skeletal_muscle

description:
RNAseq batch5
E12_SkeletalMuscle


title: ST_A_rapa, Animal E10, Heart

description:
RNAseq batch5
E10_HEART


title: ST_A_rapa, Animal E10, Frontal_cortex

description:
RNAseq batch5
E10_FCTX


title: A83_Hippo

description:
A83
208114950045_R03C01


title: A83_SkeletalMuscle

description:
A83
208114950045_R02C01


title: ST_Y_ctrl, Animal A47, Circulating_WBCs

description:
RNAseq batch5
A47_WBC


title: ST_A_rapa, Animal E10, Adipose_tissue

description:
RNAseq batch5
E10_ADIPOSE


title: ST_Y_ctrl, Animal A47, Skeletal_muscle

description:
RNAseq batch5
A47_SkeletalMuscle


title: E16_CardiacMuscle

description:
E16
208114950045_R01C01


title: A88_Colon

description:
A88
208114950042_R06C02


title: ST_Y_ctrl, Animal A47, Hippocampus

description:
RNAseq batch5
A47_HIPPO


title: E19_CardiacMuscle

description:
E19
208114950042_R03C02


title: ST_Y_ctrl, Animal A47, Heart

description:
RNAseq batch5
A47_HEART


title: A88_Adipose

description:
A88
208114950042_R04C02

source_name: Adipose

value: Adipose


title: ST_Y_ctrl, Animal A47, Frontal_cortex

description:
RNAseq batch5
A47_FCTX


title: ST_Y_ctrl, Animal A47, Colon

description:
RNAseq batch5
A47_COLON


title: A87_Colon

description:
A87
208114950042_R02C02


title: A87_Adipose

description:
A87
208114950042_R06C01


title: ST_Y_ctrl, Animal A46, Skeletal_muscle

description:
RNAseq batch5
A46_SkeletalMuscle


title: E20_CardiacMuscle

description:
E20
208114950042_R05C01


title: A87_FCTX

description:
A87
208114950042_R01C02

source_name: FCTX

value: FCTX


title: E32_CardiacMuscle

description:
E32
208114950045_R04C01


title: ST_Y_ctrl, Animal A47, Adipose_tissue

description:
RNAseq batch5
A47_ADIPOSE


title: ST_Y_ctrl, Animal A46, Hippocampus

description:
RNAseq batch5
A46_HIPPO


title: A84_FCTX

description:
A84
208114950042_R03C01


title: ST_Y_ctrl, Animal A46, Colon

description:
RNAseq batch5
A46_COLON


title: ST_Y_ctrl, Animal A46, Heart

description:
RNAseq batch5
A46_HEART


title: ST_A_rapa, Animal E10, Colon

description:
RNAseq batch5
E10_COLON


title: A84_Adipose

description:
A84
208114950042_R02C01


title: ST_Y_ctrl, Animal A46, Adipose_tissue

description:
RNAseq batch5
A46_ADIPOSE


title: E29_CardiacMuscle

description:
E29
208114950042_R01C01


title: ST_Y_ctrl, Animal A46, Frontal_cortex

description:
RNAseq batch5
A46_FCTX


title: ST_Y_ctrl, Animal A45, Circulating_WBCs

description:
RNAseq batch5
A45_WBC


title: A83_Colon

description:
A83
208114950036_R06C02


title: A88_FCTX

description:
A88
208114950042_R05C02


title: ST_Y_ctrl, Animal A45, Skeletal_muscle

description:
RNAseq batch5
A45_SkeletalMuscle


title: A83_FCTX

description:
A83
208114950036_R05C02


title: ST_Y_ctrl, Animal A45, Hippocampus

description:
RNAseq batch5
A45_HIPPO


title: A83_Adipose

description:
A83
208114950036_R04C02


title: ST_Y_ctrl, Animal A45, Heart

description:
RNAseq batch5
A45_HEART


title: B26_WBC

description:
B26
208114950036_R02C02

source_name: WBC

value: WBC


title: ST_Y_ctrl, Animal A45, Frontal_cortex

description:
RNAseq batch5
A45_FCTX


title: ST_Y_ctrl, Animal A45, Adipose_tissue

description:
RNAseq batch5
A45_ADIPOSE


title: B40_Liver

description:
B40
208114950036_R01C02

source_name: Liver

value: Liver


title: B26_Liver

description:
B26
208114950036_R06C01


title: ST_Y_ctrl, Animal A44, Skeletal_muscle

description:
RNAseq batch5
A44_SkeletalMuscle


title: B37_HTH

description:
B37
208114950036_R05C01


title: A84_Colon

description:
A84
208114950042_R04C01


title: ST_Y_ctrl, Animal A44, Colon

description:
RNAseq batch5
A44_COLON


title: ST_Y_ctrl, Animal A44, Circulating_WBCs

description:
RNAseq batch5
A44_WBC


title: B41_Liver

description:
B41
208114950036_R03C01


title: ST_Y_ctrl, Animal A44, Heart

description:
RNAseq batch5
A44_HEART


title: ST_Y_ctrl, Animal A43, Circulating_WBCs

description:
RNAseq batch5
A43_WBC


title: B27_WBC

description:
B27
208114950036_R04C01


title: ST_Y_ctrl, Animal A44, Adipose_tissue

description:
RNAseq batch5
A44_ADIPOSE


title: ST_Y_ctrl, Animal A43, Frontal_cortex

description:
RNAseq batch5
A43_FCTX


title: B24_Liver

description:
B24
208114950036_R02C01


title: ST_Y_ctrl, Animal A43, Colon

description:
RNAseq batch5
A43_COLON


title: ST_Y_ctrl, Animal A43, Hippocampus

description:
RNAseq batch5
A43_HIPPO


title: A56_HTH

description:
A56
208114950036_R01C01


title: A58_Liver

description:
A58
208114950032_R05C02


title: A58_WBC

description:
A58
208114950032_R06C02


title: ST_Y_ctrl, Animal A43, Adipose_tissue

description:
RNAseq batch5
A43_ADIPOSE


title: B26_HTH

description:
B26
208114950036_R03C02


title: ST_Y_ctrl, Animal A42, Circulating_WBCs

description:
RNAseq batch5
A42_WBC


title: A54_Liver

description:
A54
208114950032_R04C02


title: B28_HTH

description:
B28
208114950032_R02C02


title: ST_Y_ctrl, Animal A42, Hippocampus

description:
RNAseq batch5
A42_HIPPO


title: B25_HTH

description:
B25
208114950032_R03C02


title: B25_WBC

description:
B25
208114950032_R01C02


title: ST_Y_ctrl, Animal A42, Heart

description:
RNAseq batch5
A42_HEART


title: ST_Y_ctrl, Animal A42, Frontal_cortex

description:
RNAseq batch5
A42_FCTX


title: B25_Liver

description:
B25
208114950032_R05C01


title: B36_Liver

description:
B36
208114950032_R06C01


title: B27_HTH

description:
B27
208114950032_R04C01


title: ST_Y_ctrl, Animal A42, Colon

description:
RNAseq batch5
A42_COLON


title: YA_ctrl, Animal A36, Hypothalamus

description:
RNAseq batch4
A36_HTH

source_name: Hypothalamus

value: Hypothalamus


title: B24_WBC

description:
B24
208114950032_R02C01


title: B39_Liver

description:
B39
208114950032_R01C01


title: YA_ctrl, Animal A36, Frontal_cortex

description:
RNAseq batch4
A36_FCTX


title: B19_Liver

description:
B19
208114950030_R06C02


title: YA_Ex, Animal A34, Circulating_WBCs

description:
RNAseq batch4
A34_WBC


title: A55_HTH

description:
A55
208114950030_R05C02


title: B39_WBC

description:
B39
208114950030_R04C02


title: YA_Ex, Animal A34, Skeletal_muscle

description:
RNAseq batch4
A34_SkeletalMuscle


title: YA_Ex, Animal A34, Hippocampus

description:
RNAseq batch4
A34_Hippo


title: YA_Ex, Animal A34, Heart

description:
RNAseq batch4
A34_Heart


title: YA_ctrl, Animal A36, Adipose_tissue

description:
RNAseq batch4
A36_Adipose


title: A53_WBC

description:
A53
208114950030_R03C02


title: YA_Ex, Animal A34, Hypothalamus

description:
RNAseq batch4
A34_HTH


title: ST_Y_ctrl, Animal A42, Skeletal_muscle

description:
RNAseq batch5
A42_SkeletalMuscle


title: YA_Ex, Animal A34, Frontal_cortex

description:
RNAseq batch4
A34_FCTX


title: A53_Liver

description:
A53
208114950030_R01C02


title: A57_Liver

description:
A57
208114950030_R02C02


title: YA_ctrl, Animal A33, Circulating_WBCs

description:
RNAseq batch4
A33_WBC


title: B14_HTH

description:
B14
208114950030_R06C01


title: B41_WBC

description:
B41
208114950032_R03C01


title: B14_WBC

description:
B14
208114950030_R04C01


title: YA_Ex, Animal A34, Adipose_tissue

description:
RNAseq batch4
A34_Adipose


title: YA_ctrl, Animal A33, Hippocampus

description:
RNAseq batch4
A33_Hippo


title: B30_Liver

description:
B30
208114950030_R03C01


title: YA_ctrl, Animal A33, Skeletal_muscle

description:
RNAseq batch4
A33_SkeletalMuscle


title: YA_ctrl, Animal A33, Heart

description:
RNAseq batch4
A33_Heart


title: B14_Liver

description:
B14
208114950030_R02C01


title: YA_ctrl, Animal A33, Hypothalamus

description:
RNAseq batch4
A33_HTH


title: B24_HTH

description:
B24
208114950030_R01C01


title: B37_WBC

description:
B37
208114950029_R06C02


title: YA_ctrl, Animal A33, Frontal_cortex

description:
RNAseq batch4
A33_FCTX


title: B19_WBC

description:
B19
208114950029_R05C02


title: B30_WBC

description:
B30
208114950030_R05C01


title: YA_ctrl, Animal A32, Circulating_WBCs

description:
RNAseq batch4
A32_WBC


title: B16_Liver

description:
B16
208114950029_R03C02


title: YA_ctrl, Animal A32, Skeletal_muscle

description:
RNAseq batch4
A32_SkeletalMuscle


title: B34_Liver

description:
B34
208114950029_R04C02


title: YA_ctrl, Animal A33, Adipose_tissue

description:
RNAseq batch4
A33_Adipose


title: A52_HTH

description:
A52
208114950029_R02C02


title: A57_WBC

description:
A57
208114950029_R01C02


title: YA_ctrl, Animal A32, Hypothalamus

description:
RNAseq batch4
A32_HTH


title: A56_Liver

description:
A56
208114950029_R05C01


title: YA_ctrl, Animal A32, Frontal_cortex

description:
RNAseq batch4
A32_FCTX


title: YA_ctrl, Animal A32, Adipose_tissue

description:
RNAseq batch4
A32_Adipose


title: B28_WBC

description:
B28
208114950029_R02C01


title: YA_Ex, Animal A31, Circulating_WBCs

description:
RNAseq batch4
A31_WBC


title: B13_HTH

description:
B13
208114950029_R03C01


title: YA_Ex, Animal A31, Hippocampus

description:
RNAseq batch4
A31_Hippo


title: YA_Ex, Animal A31, Skeletal_muscle

description:
RNAseq batch4
A31_SkeletalMuscle


title: B13_WBC

description:
B13
208114950029_R01C01


title: YA_Ex, Animal A31, Heart

description:
RNAseq batch4
A31_Heart


title: B28_Liver

description:
B28
208114950020_R06C02


title: YA_Ex, Animal A31, Hypothalamus

description:
RNAseq batch4
A31_HTH


title: B19_HTH

description:
B19
208114950020_R04C02


title: B13_Liver

description:
B13
208114950020_R05C02


title: YA_Ex, Animal A31, Frontal_cortex

description:
RNAseq batch4
A31_FCTX


title: YA_ctrl, Animal A32, Hippocampus

description:
RNAseq batch4
A32_Hippo


title: YA_Ex, Animal A31, Adipose_tissue

description:
RNAseq batch4
A31_Adipose


title: YA_Ex, Animal A84, Frontal_cortex

description:
RNAseq batch4
A84_FCTX


title: B15_WBC

description:
B15
208114950020_R02C02


title: B27_Liver

description:
B27
208114950020_R01C02


title: YA_ctrl, Animal A32, Heart

description:
RNAseq batch4
A32_Heart


title: YA_ctrl, Animal A83, Circulating_WBCs

description:
RNAseq batch4
A83_WBC


title: YA_Ex, Animal A84, Adipose_tissue

description:
RNAseq batch4
A84_Adipose


title: A52_WBC

description:
A52
208114950029_R06C01


title: A56_WBC

description:
A56
208114950020_R04C01


title: YA_ctrl, Animal A83, Skeletal_muscle

description:
RNAseq batch4
A83_SkeletalMuscle


title: A51_HTH

description:
A51
208114950020_R05C01


title: A52_Liver

description:
A52
208114950029_R04C01


title: YA_ctrl, Animal A83, Hippocampus

description:
RNAseq batch4
A83_Hippo


title: YA_ctrl, Animal A83, Heart

description:
RNAseq batch4
A83_Heart


title: A55_Liver

description:
A55
208114950020_R02C01


title: B16_WBC

description:
B16
208114950020_R03C01


title: A51_Liver

description:
A51
208114950020_R01C01


title: YA_ctrl, Animal A83, Adipose_tissue

description:
RNAseq batch4
A83_Adipose


title: YA_ctrl, Animal A83, Hypothalamus

description:
RNAseq batch4
A83_HTH


title: YA_ctrl, Animal A83, Frontal_cortex

description:
RNAseq batch4
A83_FCTX


title: YA_Ex, Animal A82, Circulating_WBCs

description:
RNAseq batch4
A82_WBC


title: B40_Kidney

description:
B40
208114950067_R06C02

source_name: Kidney

value: Kidney


title: B34_WBC

description:
B34
208114950020_R03C02


title: B15_Liver

description:
B15
208114950020_R06C01


title: YA_Ex, Animal A82, Skeletal_muscle

description:
RNAseq batch4
A82_SkeletalMuscle


title: B26_Kidney

description:
B26
208114950067_R05C02


title: B40_Spleen

description:
B40
208114950067_R04C02

source_name: Spleen

value: Spleen


title: YA_Ex, Animal A82, Hippocampus

description:
RNAseq batch4
A82_Hippo


title: YA_Ex, Animal A82, Heart

description:
RNAseq batch4
A82_Heart


title: YA_Ex, Animal A82, Hypothalamus

description:
RNAseq batch4
A82_HTH


title: B26_Spleen

description:
B26
208114950067_R03C02


title: B26_CardiacMuscle

description:
B26
208114950067_R01C02


title: YA_Ex, Animal A82, Frontal_cortex

description:
RNAseq batch4
A82_FCTX


title: B40_SkeletalMuscle

description:
B40
208114950067_R06C01


title: B40_CardiacMuscle

description:
B40
208114950067_R02C02


title: YA_ctrl, Animal A81, Circulating_WBCs

description:
RNAseq batch4
A81_WBC


title: YA_ctrl, Animal A81, Skeletal_muscle

description:
RNAseq batch4
A81_SkeletalMuscle


title: YA_Ex, Animal A82, Adipose_tissue

description:
RNAseq batch4
A82_Adipose


title: YA_ctrl, Animal A81, Hippocampus

description:
RNAseq batch4
A81_Hippo


title: B41_Kidney

description:
B41
208114950067_R04C01


title: B27_Kidney

description:
B27
208114950067_R03C01


title: B41_Spleen

description:
B41
208114950067_R02C01


title: B26_SkeletalMuscle

description:
B26
208114950067_R05C01


title: YA_ctrl, Animal A81, Heart

description:
RNAseq batch4
A81_Heart


title: B27_Spleen

description:
B27
208114950067_R01C01


title: YA_ctrl, Animal A81, Hypothalamus

description:
RNAseq batch4
A81_HTH


title: YA_ctrl, Animal A81, Frontal_cortex

description:
RNAseq batch4
A81_FCTX


title: YA_ctrl, Animal A81, Adipose_tissue

description:
RNAseq batch4
A81_Adipose


title: B27_CardiacMuscle

description:
B27
208114950051_R05C02


title: B27_SkeletalMuscle

description:
B27
208114950051_R03C02


title: B41_SkeletalMuscle

description:
B41
208114950051_R04C02


title: YA_Ex, Animal A80, Circulating_WBCs

description:
RNAseq batch4
A80_WBC


title: YA_Ex, Animal A80, Skeletal_muscle

description:
RNAseq batch4
A80_SkeletalMuscle


title: A54_Kidney

description:
A54
208114950051_R01C02


title: YA_Ex, Animal A80, Hypothalamus

description:
RNAseq batch4
A80_HTH


title: YA_Ex, Animal A80, Hippocampus

description:
RNAseq batch4
A80_Hippo


title: A58_Kidney

description:
A58
208114950051_R02C02


title: YA_Ex, Animal A80, Heart

description:
RNAseq batch4
A80_Heart


title: A54_Spleen

description:
A54
208114950051_R05C01


title: A54_CardiacMuscle

description:
A54
208114950051_R03C01


title: A58_SkeletalMuscle

description:
A58
208114950051_R02C01


title: YA_Ex, Animal A80, Adipose_tissue

description:
RNAseq batch4
A80_Adipose


title: YA_Ex, Animal A80, Frontal_cortex

description:
RNAseq batch4
A80_FCTX


title: YA_Ex, Animal A79, Circulating_WBCs

description:
RNAseq batch4
A79_WBC


title: YA_Ex, Animal A79, Skeletal_muscle

description:
RNAseq batch4
A79_SkeletalMuscle


title: A54_SkeletalMuscle

description:
A54
208114950051_R01C01


title: B36_Kidney

description:
B36
208114950049_R06C02


title: YA_Ex, Animal A79, Hippocampus

description:
RNAseq batch4
A79_Hippo


title: B41_CardiacMuscle

description:
B41
208114950051_R06C02


title: YA_Ex, Animal A79, Heart

description:
RNAseq batch4
A79_Heart


title: B36_Spleen

description:
B36
208114950049_R04C02


title: YA_Ex, Animal A79, Frontal_cortex

description:
RNAseq batch4
A79_FCTX


title: B25_Spleen

description:
B25
208114950049_R03C02


title: B36_CardiacMuscle

description:
B36
208114950049_R02C02


title: YA_ctrl, Animal A41, Circulating_WBCs

description:
RNAseq batch4
A41_WBC


title: YA_Ex, Animal A79, Adipose_tissue

description:
RNAseq batch4
A79_Adipose


title: A58_Spleen

description:
A58
208114950051_R06C01


title: B25_CardiacMuscle

description:
B25
208114950049_R01C02


title: A58_CardiacMuscle

description:
A58
208114950051_R04C01


title: YA_ctrl, Animal A41, Skeletal_muscle

description:
RNAseq batch4
A41_SkeletalMuscle


title: B36_SkeletalMuscle

description:
B36
208114950049_R06C01


title: B25_SkeletalMuscle

description:
B25
208114950049_R05C01


title: YA_ctrl, Animal A41, Heart

description:
RNAseq batch4
A41_Heart


title: YA_ctrl, Animal A41, Hippocampus

description:
RNAseq batch4
A41_Hippo


title: B24_Kidney

description:
B24
208114950049_R03C01


title: YA_ctrl, Animal A41, Hypothalamus

description:
RNAseq batch4
A41_HTH


title: B39_Spleen

description:
B39
208114950049_R02C01


title: YA_ctrl, Animal A41, Frontal_cortex

description:
RNAseq batch4
A41_FCTX


title: B25_Kidney

description:
B25
208114950049_R05C02


title: B39_CardiacMuscle

description:
B39
208114950037_R06C02


title: B24_Spleen

description:
B24
208114950049_R01C01


title: YA_ctrl, Animal A38, Skeletal_muscle

description:
RNAseq batch4
A38_SkeletalMuscle


title: YA_ctrl, Animal A38, Hippocampus

description:
RNAseq batch4
A38_Hippo


title: YA_Ex, Animal A79, Hypothalamus

description:
RNAseq batch4
A79_HTH


title: YA_ctrl, Animal A38, Circulating_WBCs

description:
RNAseq batch4
A38_WBC


title: B16_Kidney

description:
B16
208114950037_R02C02


title: YA_ctrl, Animal A38, Frontal_cortex

description:
RNAseq batch4
A38_FCTX


title: YA_ctrl, Animal A38, Hypothalamus

description:
RNAseq batch4
A38_HTH


title: A57_Spleen

description:
A57
208114950037_R06C01


title: YA_ctrl, Animal A38, Adipose_tissue

description:
RNAseq batch4
A38_Adipose


title: YA_ctrl, Animal A41, Adipose_tissue

description:
RNAseq batch4
A41_Adipose


title: YA_Ex, Animal A37, Circulating_WBCs

description:
RNAseq batch4
A37_WBC


title: B39_SkeletalMuscle

description:
B39
208114950037_R04C02


title: B24_CardiacMuscle

description:
B24
208114950037_R05C02


title: B39_Kidney

description:
B39
208114950049_R04C01


title: B24_SkeletalMuscle

description:
B24
208114950037_R03C02


title: YA_Ex, Animal A37, Skeletal_muscle

description:
RNAseq batch4
A37_SkeletalMuscle


title: A53_Spleen

description:
A53
208114950037_R05C01


title: A57_CardiacMuscle

description:
A57
208114950037_R04C01


title: YA_Ex, Animal A37, Hippocampus

description:
RNAseq batch4
A37_Hippo


title: YA_Ex, Animal A37, Hypothalamus

description:
RNAseq batch4
A37_HTH


title: A53_CardiacMuscle

description:
A53
208114950037_R03C01


title: A57_SkeletalMuscle

description:
A57
208114950037_R02C01


title: YA_Ex, Animal A37, Heart

description:
RNAseq batch4
A37_Heart


title: A53_SkeletalMuscle

description:
A53
208114950037_R01C01


title: B30_Kidney

description:
B30
208114950024_R06C02


title: YA_ctrl, Animal A38, Heart

description:
RNAseq batch4
A38_Heart


title: YA_Ex, Animal A37, Adipose_tissue

description:
RNAseq batch4
A37_Adipose


title: YA_Ex, Animal A37, Frontal_cortex

description:
RNAseq batch4
A37_FCTX


title: B30_Spleen

description:
B30
208114950024_R04C02


title: A53_Kidney

description:
A53
208114950037_R01C02


title: YA_ctrl, Animal A36, Circulating_WBCs

description:
RNAseq batch4
A36_WBC


title: YA_ctrl, Animal A36, Skeletal_muscle

description:
RNAseq batch4
A36_SkeletalMuscle


title: B14_Spleen

description:
B14
208114950024_R03C02


title: YA_Ex, Animal A88, Circulating_WBCs

description:
RNAseq batch4
A88_WBC


title: B14_CardiacMuscle

description:
B14
208114950024_R01C02


title: YA_ctrl, Animal A36, Hippocampus

description:
RNAseq batch4
A36_Hippo


title: B14_SkeletalMuscle

description:
B14
208114950024_R05C01


title: YA_ctrl, Animal A36, Heart

description:
RNAseq batch4
A36_Heart


title: B30_SkeletalMuscle

description:
B30
208114950024_R06C01


title: B37_Kidney

description:
B37
208114950024_R04C01


title: B30_CardiacMuscle

description:
B30
208114950024_R02C02


title: YA_Ex, Animal A88, Skeletal_muscle

description:
RNAseq batch4
A88_SkeletalMuscle


title: YA_Ex, Animal A88, Hippocampus

description:
RNAseq batch4
A88_Hippo


title: B37_Spleen

description:
B37
208114950024_R02C01


title: B19_Kidney

description:
B19
208114950024_R03C01


title: YA_Ex, Animal A88, Hypothalamus

description:
RNAseq batch4
A88_HTH


title: B14_Kidney

description:
B14
208114950024_R05C02


title: YA_Ex, Animal A88, Heart

description:
RNAseq batch4
A88_Heart


title: B19_Spleen

description:
B19
208114950024_R01C01


title: B19_CardiacMuscle

description:
B19
208114950010_R05C02


title: YA_ctrl, Animal A87, Circulating_WBCs

description:
RNAseq batch4
A87_WBC


title: B37_SkeletalMuscle

description:
B37
208114950010_R04C02


title: B19_SkeletalMuscle

description:
B19
208114950010_R03C02


title: YA_ctrl, Animal A87, Skeletal_muscle

description:
RNAseq batch4
A87_SkeletalMuscle


title: YA_ctrl, Animal A87, Hippocampus

description:
RNAseq batch4
A87_Hippo


title: YA_ctrl, Animal A87, Heart

description:
RNAseq batch4
A87_Heart


title: YA_ctrl, Animal A87, Hypothalamus

description:
RNAseq batch4
A87_HTH


title: A52_Kidney

description:
A52
208114950010_R01C02


title: A56_Kidney

description:
A56
208114950010_R02C02


title: A56_Spleen

description:
A56
208114950010_R06C01


title: YA_ctrl, Animal A87, Frontal_cortex

description:
RNAseq batch4
A87_FCTX


title: YA_ctrl, Animal A87, Adipose_tissue

description:
RNAseq batch4
A87_Adipose


title: A52_Spleen

description:
A52
208114950010_R05C01


title: A56_CardiacMuscle

description:
A56
208114950010_R04C01


title: YA_Ex, Animal A84, Skeletal_muscle

description:
RNAseq batch4
A84_SkeletalMuscle


title: YA_Ex, Animal A84, Hippocampus

description:
RNAseq batch4
A84_Hippo


title: YA_Ex, Animal A84, Circulating_WBCs

description:
RNAseq batch4
A84_WBC


title: A52_CardiacMuscle

description:
A52
208114950010_R03C01


title: A56_SkeletalMuscle

description:
A56
208114950010_R02C01


title: YA_Ex, Animal A88, Frontal_cortex

description:
RNAseq batch4
A88_FCTX


title: YA_Ex, Animal A88, Adipose_tissue

description:
RNAseq batch4
A88_Adipose


title: B28_Kidney

description:
B28
208114950008_R06C02


title: B13_Kidney

description:
B13
208114950008_R05C02


title: B37_CardiacMuscle

description:
B37
208114950010_R06C02


title: LT_A_ctrl, Animal B41, Spleen

description:
RNAseq batch3
B41_Spleen


title: B28_Spleen

description:
B28
208114950008_R04C02


title: B13_Spleen

description:
B13
208114950008_R03C02


title: B28_CardiacMuscle

description:
B28
208114950008_R02C02


title: LT_A_ctrl, Animal B41, Liver

description:
RNAseq batch3
B41_Liver


title: LT_A_ctrl, Animal B41, Lung

description:
RNAseq batch3
B41_Lung

source_name: Lung

value: Lung


title: LT_A_ctrl, Animal B41, Kidney

description:
RNAseq batch3
B41_Kid


title: B13_CardiacMuscle

description:
B13
208114950008_R01C02


title: LT_A_ctrl, Animal B41, Hippocampus

description:
RNAseq batch3
B41_Hipp


title: B28_SkeletalMuscle

description:
B28
208114950008_R06C01


title: B13_SkeletalMuscle

description:
B13
208114950008_R05C01


title: B34_Kidney

description:
B34
208114950008_R04C01


title: LT_A_ctrl, Animal B41, Heart

description:
RNAseq batch3
B41_Heart


title: A52_SkeletalMuscle

description:
A52
208114950010_R01C01


title: B15_Kidney

description:
B15
208114950008_R03C01


title: LT_A_ctrl, Animal B41, Hypothalamus

description:
RNAseq batch3
B41_HTH


title: LT_A_ctrl, Animal B41, Colon

description:
RNAseq batch3
B41_Colon

source_name: Colon

value: Colon


title: YA_Ex, Animal A84, Hypothalamus

description:
RNAseq batch4
A84_HTH


title: LT_A_ctrl, Animal B41, Adipose_tissue

description:
RNAseq batch3
B41_Adipose


title: YA_Ex, Animal A84, Heart

description:
RNAseq batch4
A84_Heart

source_name: Heart


title: B34_Spleen

description:
B34
208114950008_R02C01


title: LT_A_Ex, Animal B40, Spleen

description:
RNAseq batch3
B40_Spleen


title: B15_Spleen

description:
B15
208114950008_R01C01


title: LT_A_ctrl, Animal B41, Skeletal_muscle

description:
RNAseq batch3
B41_SkeletalMuscle


title: B15_CardiacMuscle

description:
B15
208114950003_R05C02


title: B34_CardiacMuscle

description:
B34
208114950003_R06C02


title: LT_A_Ex, Animal B40, Liver

description:
RNAseq batch3
B40_Liver


title: LT_A_Ex, Animal B40, Lung

description:
RNAseq batch3
B40_Lung


title: B15_SkeletalMuscle

description:
B15
208114950003_R03C02


title: A55_Kidney

description:
A55
208114950003_R02C02


title: LT_A_Ex, Animal B40, Heart

description:
RNAseq batch3
B40_Heart


title: LT_A_Ex, Animal B40, Hippocampus

description:
RNAseq batch3
B40_Hipp

source_name: Hippocampus


title: A51_Kidney

description:
A51
208114950003_R01C02


title: LT_A_Ex, Animal B40, Hypothalamus

description:
RNAseq batch3
B40_HTH


title: A55_Spleen

description:
A55
208114950003_R06C01


title: LT_A_Ex, Animal B40, Colon

description:
RNAseq batch3
B40_Colon


title: LT_A_Ex, Animal B40, Skeletal_muscle

description:
RNAseq batch3
B40_SkeletalMuscle


title: A51_Spleen

description:
A51
208114950003_R05C01


title: LT_A_Ex, Animal B40, Frontal_cortex

description:
RNAseq batch3
B40_FCTX


title: A55_CardiacMuscle

description:
A55
208114950003_R04C01


title: A51_CardiacMuscle

description:
A51
208114950003_R03C01


title: A55_SkeletalMuscle

description:
A55
208114950003_R02C01


title: LT_A_ctrl, Animal B37, Spleen

description:
RNAseq batch3
B37_Spleen


title: LT_A_Ex, Animal B40, Adipose_tissue

description:
RNAseq batch3
B40_Adipose


title: B40_Colon

description:
B40
208114950093_R06C02


title: A51_SkeletalMuscle

description:
A51
208114950003_R01C01


title: B26_Colon

description:
B26
208114950093_R05C02


title: LT_A_ctrl, Animal B37, Liver

description:
RNAseq batch3
B37_Liver


title: LT_A_ctrl, Animal B37, Hippocampus

description:
RNAseq batch3
B37_Hipp


title: B40_Adipose

description:
B40
208114950093_R04C02


title: LT_A_ctrl, Animal B37, Heart

description:
RNAseq batch3
B37_Heart


title: LT_A_Ex, Animal B40, Kidney

description:
RNAseq batch3
B40_Kid


title: B26_Adipose

description:
B26
208114950093_R03C02


title: B34_SkeletalMuscle

description:
B34
208114950003_R04C02


title: LT_A_ctrl, Animal B37, Kidney

description:
RNAseq batch3
B37_Kid


title: LT_A_ctrl, Animal B37, Hypothalamus

description:
RNAseq batch3
B37_HTH


title: B40_FCTX

description:
B40
208114950093_R02C02


title: LT_A_ctrl, Animal B37, Colon

description:
RNAseq batch3
B37_Colon


title: B26_FCTX

description:
B26
208114950093_R01C02


title: LT_A_Ex, Animal B30, Colon

description:
RNAseq batch3
B30_Colon


title: Complexity 10K replicate 1

city: Cambridge

first: Catherine

last: Wu

state: Massachusetts

address: 415 Main Street-Rm

institute: Broad Institute of MIT and Harvard - Cambridge, MA

description: Library name: Prosit-10K

library_source: other

data_processing:
Raw reads were trimmed of adapter contents utilizing fastp. Read were alligned to custome reference encompasing peptide coding sequences used for library construction using BWA. Samtools was used to count reads from reference.
Assembly: Custom
Supplementary files format and content: tab delimited file including the counts for each library prep.

molecule: other

organism: unidentified plasmid

source_name: plasmid

growth_protocol: Transformed e.coli grown in LB medium overnight

extract_protocol:
Zymo research Midi prep
Amplicon sequencing.

value: plasmid


title: Complexity 10K replicate 2

description: Library name: 0465424130_10K_lib


title: ES_In_PLKO_LmnaKO_rep2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: In_PLKO_LmnaKO_rep2

data_processing:
ChIP-Seq reads were mapped to the mouse mm10 reference genome using STAR.
The MarkDuplicates.jar from Picard 2.27.4 was used to remove PCR duplicates.
Bam files from each 2 replicates of conditions for comparison were merged
For generating bigWig files for visualization of ChIP-seq reads in genome browser IGV, BamCoverage (--normalizeUsing PKM  -bs 10) from deeTools was used. Scalefactors for each sample were obtained from Deseq2 for normalization.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Embryonic bodies Day4

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were differentiated with hanging drop to form EBs . Briefly, mESCs were dissociated by 0.05% trypsin-EDTA and were then aggregated on the lid of petri dish as 500 cells in 15ul drops in mESC medium without LIF. After 48 hours of culture, embryonic bodies (EBs) was collected in low attachment culture dishes with ES cell growth medium. Cells were then harvested at d4 for ChIP.

extract_protocol:
ESCs were dissociated by 0.05% trypsin-EDTA followed by pre-plating to remove feeders. 1 million ESCs were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) at room temperature for 10 minutes and fixation was quenched by addition of glycine to a final concentration of 125 mM for 10 minutes on ice. Cells were collected and washed three times with ice-cold PBS, and then resuspended in cell lysis buffer (50mmol/L Tris pH 8.0, 2 mM EDTA pH 8.0, 0.1% NP-40, 10% glycerol) supplemented with protease and phosphatase inhibitors (Merck, 535142 and 524632). After 10 minutes of incubation on ice, the nuclei were pelleted at 960xg for 5 minutes and lysed in nuclei lysis buffer (50mmol/L Tris pH 8.0, 1% SDS, 5mmol/L EDTA pH 8.0) supplemented with protease and phosphatase inhibitors for 10 minutes at room temperature. Lysates were then sonicated with Bioruptor® Plus (Diagenode) with high power mode for 45 cycles (sonication cycle: 30 sec ON, 30 sec OFF) to shear chromatin to 200–500 bp in nuclear lysis buffer. After centrifugation, the supernatant was diluted 1:10 with ChIP dilution buffer (50mmol/L Tris pH8.0, 200mmol/L NaCl, 5mmol/L EDTA pH 8.0, 0.5% NP40) with protease and phosphatase inhibitors and pre-cleaned with Protein G Sepharose beads (GE Healthcare, 17061801) for 1 hour at 4°C while rotating.  The diluted lysates were incubated with 1µg H3K9ac (Cell Signaling Technology, 9649S), H3K27ac (Active motif, 39135), H3K9me3 (Abcam, ab8898) antibodies overnight followed by incubation with BSA-coated protein G sepharose. The immunoprecipitate was washed three times for 5 minutes each with NaCl wash buffer (20mmol/L Tris pH 8.0, 500mmol/L NaCl, 2mmol/L EDTA pH 8.0, 0.1% SDS, 1% NP-40), LiCl wash buffer (20mmol/L Tris pH 8.0, 500mmol/L LiCl, 2mmol/L EDTA pH 8.0, 0.1% SDS, 1% NP40) and TE wash buffer (20mmol/L Tris pH 8.0, 2mmol/L EDTA pH 8.0). Elution buffer (20mmol/L Tris pH 8.0, 2mmol/L EDTA pH 8.0, and 2% SDS) was used to extract protein/DNA complexes from protein G Sepharose beads. After reverse crosslinking at 65 °C overnight, proteinase K digestion at 55 °C for 1h was performed and DNA was purified with the ChiP DNA Clean&Concentrator kit (D5205, Zymo Research). The size of sheared chromatin was assessed by Bioanalyzer 2100 (Agilent).
NGS libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit from Illumina (E7645s, New England BioLabs).

value: Embryonic bodies Day4

tag: chip antiboy

value: E14 Tg(Nkx2-5-EmGFP)

value: shPLKO viral transfection


title: B26_Hippo

description:
B26
208114950093_R05C01


title: LT_A_Ex, Animal B30, Frontal_cortex

description:
RNAseq batch3
B30_FCTX


title: LT_A_ctrl, Animal B37, Skeletal_muscle

description:
RNAseq batch3
B37_SkeletalMuscle


title: ES_In_PLKO_LmnaKO_rep1

description: Library name: In_PLKO_LmnaKO_rep1


title: LT_A_Ex, Animal B30, Adipose_tissue

description:
RNAseq batch3
B30_Adipose


title: ES_In_LmnaKO_shCth_rep2

description: Library name: In_LmnaKO_shCth_rep2

value: shCth viral transfection


title: B41_Colon

description:
B41
208114950093_R04C01


title: B27_Colon

description:
B27
208114950093_R03C01


title: ES_In_LmnaKO_shCth_rep1

description: Library name: In_LmnaKO_shCth_rep1


title: LT_A_ctrl, Animal B19, Skeletal_muscle

description:
RNAseq batch3
B19_SkeletalMuscle


title: ES_In_LmnaKO_shCbs_rep1

description: Library name: In_LmnaKO_shCbs_rep1

value: ShCbs viral transfection


title: LT_A_ctrl, Animal B19, Spleen

description:
RNAseq batch3
B19_Spleen


title: ES_LmnaKO_shCth_H3K9ac_rep2

description: Library name: 04ES_LmnaKO_shCth_H3K9ac_rep2

value: H3K9ac, Cell Signaling Technology, 9649S


title: B41_Adipose

description:
B41
208114950093_R02C01


title: ES_LmnaKO_shCth_H3K9ac_rep1

description: Library name: 04ES_LmnaKO_shCth_H3K9ac_rep1


title: B27_Adipose

description:
B27
208114950093_R01C01


title: ES_LmnaKO_shCbs_H3K9ac_rep2

description: Library name: 03ES_LmnaKO_shCbs_H3K9ac_rep2


title: ES_In_LmnaKO_shCbs_rep2

description: Library name: In_LmnaKO_shCbs_rep2


title: LT_A_ctrl, Animal B19, Liver

description:
RNAseq batch3
B19_Liver


title: ES_LmnaKO_shCbs_H3K9ac_rep1

description: Library name: 03ES_LmnaKO_shCbs_H3K9ac_rep1


title: LT_A_ctrl, Animal B19, Lung

description:
RNAseq batch3
B19_Lung


title: B41_FCTX

description:
B41
208114950077_R06C02


title: ES_PLKO_LmnaKO_H3K9ac_rep2

description: Library name: 02PLKO_LmnaKO_H3K9ac_rep2


title: B40_Hippo

description:
B40
208114950093_R06C01

value: Hippo


title: LT_A_ctrl, Animal B19, Kidney

description:
RNAseq batch3
B19_Kid


title: B27_FCTX

description:
B27
208114950077_R05C02


title: LT_A_ctrl, Animal B19, Hippocampus

description:
RNAseq batch3
B19_Hipp

value: Hippocampus


title: Whole Blood Transcriptome Baseline D33V1

city: Boston

first: Adriana

last: Tomic

address: 650 Albany St.

institute: Boston University

description: Library name: D33V1

data_processing:
Raw sequencing reads were quality controlled and then aligned and quantified using Salmon (v1.x) against the human reference transcriptome (hg38). Transcript-level counts were aggregated to gene-level counts for analysis.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Comma-separated values (CSV) matrix containing gene-level counts. Rows represent genes and columns represent samples. Counts were aggregated from transcript-level abundance estimates generated by Salmon.

source_name: whole blood

extract_protocol:
Total RNA was extracted from Paxgene-stabilized whole blood using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) to preserve strand information and deplete ribosomal RNA.

treatment_protocol: Samples were collected at Visit 1 (Baseline) immediately prior to vaccination.

value: whole blood

tag: Sex

value: female

tag: group

value: Baseline (Pre-vaccination)


title: B41_Hippo

description:
B41
208114950077_R04C02


title: Whole Blood Transcriptome Baseline D32V1

description: Library name: D32V1

value: male


title: Whole Blood Transcriptome Baseline D27V1

description: Library name: D27V1


title: Whole Blood Transcriptome Baseline D26V1

description: Library name: D26V1


title: LT_A_ctrl, Animal B19, Heart

description:
RNAseq batch3
B19_Heart

data_processing:
Raw sequencing FASTQ files were mapped with STAR98 (v2.7.10b) with default parameters using the Mus musculus genome assembly GRCm39.
Quality control was carried out with the FastQC (v0.11.9) and MultiQC99 (v1.13a) packages.
HTSeq100 (v2.0.2) was used to obtain read counts with default options except ‘mode’ being set to ‘intersection-strict’, and ‘nonunique’ being set to ‘fraction’ for ambiguous reads. Gene counts were filtered for a minimum of at least 10 reads in a minimum number of samples, with the minimum number based on the number of animals constituting the smallest comparator group size in the experiment.
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts
Supplementary files format and content: CSV metadata file

extract_protocol:
The tissues were retrieved from RNAlater (AM7021, Thermo Fisher Scientific, US), combined with the TRIzol reagent (15596018, Thermo Fisher Scientific, US) or the lysis buffer of the RNAqueous kit (AM1912, Thermo Fisher Scientific, US), homogenized using the TissueLyser II system (Qiagen, US), and total RNA extraction was performed following the instructions in the vendor’s manuals.
Total RNA samples were sent for library preparation and sequencing by Novogene (Novogene Biology Information Technology Co., Ltd., Beijing, China). Libraries were prepared with a poly(A) selection strategy using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770, New England Biolabs, US).

value: Heart


title: B27_Hippo

description:
B27
208114950077_R03C02


title: Whole Blood Transcriptome Baseline D24V1

description: Library name: D24V1


title: Whole Blood Transcriptome Baseline D25V1

description: Library name: D25V1


title: LT_A_ctrl, Animal B19, Hypothalamus

description:
RNAseq batch3
B19_HTH

value: Hypothalamus


title: A58_Colon

description:
A58
208114950077_R02C02


title: Whole Blood Transcriptome Baseline D22V1

description: Library name: D22V1


title: Whole Blood Transcriptome Baseline D20V1

description: Library name: D20V1


title: A58_Adipose

description:
A58
208114950077_R06C01

value: Adipose


title: A54_Colon

description:
A54
208114950077_R01C02

value: Colon


title: Whole Blood Transcriptome Baseline D18V1

description: Library name: D18V1


title: ES_PLKO_LmnaKO_H3K9ac_rep1

description: Library name: 02PLKO_LmnaKO_H3K9ac_rep1


title: LT_A_ctrl, Animal B19, Colon

description:
RNAseq batch3
B19_Colon