title: Lu134A, IgG

data_processing:
After quality control, reads were aligned against hg38 by Bowtie2 (version 2.3.5.1). Peak calling was performed by SEACR (version 1.4) for ASCL1 and NEUROD1 with relaxed mode using non-normalized IgG control track.
Assembly: hg38
Supplementary files format and content: bigWig, peak(except for IgG)
Library strategy: CUT&Tag

extract_protocol:
Lu134A cells (1*10^5) were bound to concanavalin-coated magnetic beads (Bangs Laboratories). After permeabilization with digitonin, cells were incubated with primary antibody at room temperature for 2 h and subsequently incubated with secondary antibody for 1 h. Then, CUTANA pAG-Tn5 for CUT&Tag (EpiCypher) was bound to secondary antibody.
After incubation with Mg2+ containing solution to cleave the target DNA, the extracted DNA was amplified by PCR. The PCR product was purified using AMPureXP magnetic beads (Beckman Coulter). Sequence libraries were pooled at 5 nM. For non-specific IgG, the entire library was pooled. The pooled library was sequenced on HiSeqX (Illumina) using 150bp paired end reads.

value: Small cell lung cancer

tag: antibody

value: IgG


title: Mef_d0.3_Rep3_P2

status: Public on Jun 28 2025

type: SRA

city: Indianapolis

first: Andi

last: Dhroso

state: Indiana

address: 9330 Zionsville Rd

country: USA

institute: Corteva

library_source: transcriptomic

data_processing:
Adapter sequences remaining within the reads were trimmed (using parameters minlength=35 trimq=20 ktrim=r qtrim=rl k=23 mink=11 hdist=1) using the bbmap tool (v 38.18)
any reads aligning to Rattus norvegicus rRNA sequences were removed using the bbmap tool (v38.18) from the JGI bbtools software package.
Rattus norvegicus and Homo sapiens transcript abundances were calculated on a per sample basis using the Salmon software (v.1.2.0) 11 (with parameters “--seqBias --validateMappings --numBootstraps 100 --libType SR”) processed against the  Rattus norvegicus mRatBN7.2 and Homo sapiens GRCh38p13 reference genomes and annotation 4 downloaded from Ensembl
Following transcript level abundance estimation, gene level expression counts were summarized from the salmon output using the tximport package (v1.26) 12 in R
any protein coding gene with less than an abundance count of ten across all samples were removed from further analysis
Assembly: The DESeq2 analysis package (v1.34.0) in R 13 (version 4.1.3) was used for data normalization (using the variance stabilizing transformation (vst) method), and identification of differentially expressed genes between control groups and dose treatment groups for each molecule tested.
Supplementary files format and content: Rattus norvegicus mRatBN7.2 and Homo sapiens GRCh38p13 reference genomes
Supplementary files format and content: tab-delimited text file which includes raw gene count values for each Sample
Supplementary files format and content: tab-delimited text files include 1) raw gene count values for each Sample and 2) vst-normalized  (filtered for low expressing genes)

molecule: total RNA

organism: Homo sapiens

source_name: Human HepaRG

growth_protocol: Please refer to associated manuscript

extract_protocol: Total RNA was isolated from HepaRG and rat hepatocyte samples with the MagMax mirVana Total RNA isolation kit following the manufacturer’s protocol for cells using KingFisher™ flex magnetic particle processor (ThermoFisher, Waltham, MA). RNA samples had RNA Quality Scores ≥7 as determined with a 5200 Fragment Analyzer System (Agilent, Santa Clara, CA).

treatment_protocol: Please refer to associated manuscript

tag: tissue

value: Human HepaRG

tag: cell type

value: HepaRG

tag: treatment


title: Mef_d0.3_Rep1_P2


title: MDA-MB-231, RCOR2-KO1, Input for HDAC1, rep1

city: Dallas

first: Lei

last: Bao

state: TX

address: 5323 Harry Hines Blvd, NB6.126

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
FASTQ files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4). Low-quality reads and adapter were removed using fastq-mcf (v 1.05). The reads from FASTQ files were aligned to the human genome (hg19) using bowtie2 (v2.3.3.1). Picard-tool’s (v 2.10.10) MarkDuplicates module was then used to remove duplicate alignments
The duplicate removed alignment files were used to call peaks using MACS2 (v2.1.0), with a q-value threshold of 0.05 and using DNA input as background controls. The resulting peak summits (called peak sites with coordinate of single-nucleotide) and bed files from peak-calling were defined.
Assembly: hg19
Supplementary files format and content: bed (except for Input samples)

molecule: genomic DNA

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator (Brandson).
ChIP-seq libraries were prepared using the NEBNext UltraII DNA Library Prep Kit (NEB). 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified 13 cycles on the thermocycler. Post amplification libraries were gel-purified for size selection at 300-500bp. Libraries were validated using Tapestation (Agilent) and quantified using Qubit Fluorometer (Invitrogen).

tag: cell line

value: Breast cancer cells

tag: genotype

value: RCOR2 knockout

tag: chip-antibody


title: Ket_d10_Rep2_P2


title: Lu134A, NEUROD1

city: Bunkyo-ku, Hongo

first: Hiroshi

last: Takumida

state: Tokyo

department: Respiratory Medicine

country: Japan

institute: Graduate School of Medicine, The University of Tokyo


title: MDA-MB-231, parental, Input for HDAC1, rep2

value: Parental


title: Ethio_d100_Rep4_P2


title: MDA-MB-231, parental, Input for HDAC1, rep1


title: Ket_d100_Rep2_P2


title: Amit_d0.01_Rep03_P1

organism: Rattus norvegicus

source_name: Rat primary hepatocytes

value: Rat primary hepatocytes

value: hepatocytes


title: Gri_d1_Rep2_P2


title: Benz_d0.003_Rep03_P1


title: Buc_d10_Rep03_P1


title: Col_d0.03_Rep2_P1


title: MDA-MB-231, RCOR2-KO1, Input for HDAC1, rep2


title: Ket_d30_Rep2_P2


title: Amit_d0.1_Rep03_P1


title: Col_d10_Rep03_P1


title: Benz_d31.6_Rep04_P1


title: Eth_d100_Rep1_P1


title: MDA-MB-231, RCOR2-KO1, HDAC1, Bethyl, rep2

value: HDAC1 (Bethyl Laboratories, #A300-713A)


title: PHB_d500_Rep2_P2


title: Ket_d1_Rep2_P2


title: Lu134A, ASCL1


title: Eth_d0.1_Rep03_P1


title: Eth_d300_Rep4_P1


title: Amit_d100_Rep3_P1


title: Col_d0.1_Rep03_P1


title: Benz_d10_Rep1_P1


title: MDA-MB-231, RCOR2-KO1, HDAC1, Bethyl, rep1


title: MDA-MB-231, parental, HDAC1, Bethyl, rep1


title: Ethio_d10_Rep2_P2


title: Benz_d100_Rep4_P1


title: MDA-MB-231, Input for HA-RCOR2, rep1

value: HA-tagged RCOR2 overexpressing


title: MDA-MB-231, parental, HDAC1, Bethyl, rep2


title: PHB_d500_Rep1_P1


title: Amit_d100_Rep4_P1


title: Buc_d300_Rep3_P1


title: Eth_d3.16_Rep3_P1


title: Amit_d1_Rep2_P1


title: DMSO_d0_Rep5_P1


title: Col_d10_Rep02_P1


title: MDA-MB-231, Input for HA-RCOR2, rep2


title: PHB_d500_Rep2_P1


title: DMSO_Rep05_P1


title: Buc_d1_Rep03_P1


title: 3MC_d0.3_Rep04_P1


title: Col_d0.1_Rep2_P1


title: Benz_d3.16_Rep03_P1


title: Eth_d300_Rep1_P1


title: MDA-MB-231-HA-RCOR2, HA, CST, rep2


title: Eth_d0.3_Rep3_P1


title: Amit_d10_Rep04_P1


title: MDA-MB-231-HA-RCOR2, HA, CST, rep1


title: Benz_d0.1_Rep2_P1


title: Buc_d100_Rep3_P1


title: MDA-MB-231 cells, RCOR2-KO2, rep2

data_processing:
The Fastq files were subjected to quality check using fastqc (version 0.11.2) and fastq_screen (version 0.4.4), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806).
Trimmed fastq files were mapped to hg19 using Tophat.
Read counts were generated using featureCounts.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include RPKM values for all samples

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyper Prep kit following manufacturer's protocols.

value: No treatment


title: Buc_d300_Rep4_P1


title: Benz_d0.1_Rep1_P1


title: Buc_d0.3_Rep3_P1


title: Amit_d0.1_Rep02_P1


title: DMSO_Rep04_P1


title: Eth_d0.3_Rep2_P1


title: MDA-MB-231 cells, RCOR2-KO2, rep1


title: DMSO_d0_Rep7_P1


title: MDA-MB-231 cells, RCOR2-KO1, rep1


title: MDA-MB-231 cells, parental, rep2


title: Eth_d0.01_Rep03_P1


title: Col_d0.01_Rep03_P1


title: Buc_d0.1_Rep03_P1


title: MDA-MB-231 cells, parental, rep1


title: Col_d0.1_Rep1_P1


title: Amit_d10_Rep3_P1


title: MDA-MB-231, RCOR2-KO1, IgG, CST, rep2

data_processing:
FASTQ files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4). Low-quality reads and adapter were removed using fastq-mcf (v 1.05). The reads from FASTQ files were aligned to the human genome (hg19) using bowtie2 (v2.3.3.1). Picard-tool’s (v 2.10.10) MarkDuplicates module was then used to remove duplicate alignments
The duplicate removed alignment files were used to call peaks using MACS2 (v2.1.0), with a q-value threshold of 0.05 and using DNA input (IgG samples) as background controls. The resulting peak summits (called peak sites with coordinate of single-nucleotide) and bed files from peak-calling were defined.
Assembly: hg19
Supplementary files format and content: bed (except for IgG samples)

extract_protocol:
Cells were binded to Concanavalin A coated beads, permeabilized and incubated with anti-LSD1 antibody or Normal Rabbit IgG. pAG-Mnase binded to antibodies and digested targeted chromatin.
CUT&RUN libraries were prepared using the NEBNext UltraII DNA Library Prep Kit (NEB). 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified 11 cycles on the thermocycler. Post amplification libraries were gel-purified for size selection at 300-500bp. Libraries were validated using Tapestation (Agilent) and quantified using Qubit Fluorometer (Invitrogen).

tag: cut&run-antibody

value: Normal Rabbit IgG (CST, #2729)


title: Benz_d31.6_Rep03_P1


title: Buc_d300_Rep1_P1


title: Col_d0.001_Rep3_P1


title: Benz_d0.03_Rep03_P1


title: Col_d0.01_Rep1_P1


title: MDA-MB-231 cells, RCOR2-KO1, rep2


title: PHB_50_Rep04_P1


title: MDA-MB-231, parental, IgG, CST, rep2


title: Amit_d100_Rep1_P1


title: Col_d100_Rep02_P1


title: Col_d0.03_Rep3_P1


title: Amit_d0.1_Rep1_P1


title: MDA-MB-231, RCOR2-KO1, IgG, CST, rep1


title: Col_d0.01_Rep3_P1


title: Benz_d10_Rep3_P1


title: Benz_d31.6_Rep3_P1


title: Buc_d100_Rep03_P1


title: Col_d0.001_Rep1_P1


title: MDA-MB-231, RCOR2-KO1, LSD1, CST, rep2


title: MDA-MB-231, parental, IgG, CST, rep1


title: MDA-MB-231, RCOR2-KO1, LSD1, CST, rep1


title: Eth_d0.3_Rep1_P1


title: Eth_d100_Rep2_P1


title: Amit_d0.1_Rep2_P1


title: DMSO_d0_Rep3_P1


title: Buc_d0.01_Rep02_P1


title: DMSO_Rep03_P1


title: DMSO_d0_Rep1_P1


title: Benz_d0.03_Rep02_P1


title: Amit_d31.6_Rep1_P1


title: MDA-MB-231, parental, LSD1, CST, rep2


title: Benz_d1_Rep1_P1


title: MDA-MB-231, parental, LSD1, CST, rep1


title: Benz_d100_Rep3_P1


title: Eth_d100_Rep3_P1


title: Col_d0.0001_Rep1_P1


title: Amit_d1_Rep02_P1


title: DMSO_d0_Rep2_P1


title: Eth_d31.6_Rep1_P1


title: DMSO_Rep02_P1


title: SL0297_CEv3_afatinib_48_3

city: Birmingham

first: Benjamin

last: Lin

state: AL

address: 401F Wallace Tumor Institute

department: Pathology

institute: The University of Alabama at Birmingham

description: Library name: SL0297

data_processing:
Aligned with STAR aligner and transcripts quantified with SALMON
Assembly: Gencode vM32 genome with vH43 EGFR
Supplementary files format and content: Transcripts quantified by SALMON

organism: Mus musculus

extract_protocol:
RNeasy kit (Qiagen, Hilden, Germany)
KAPA Stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA)

value: starve serum culture


title: Eth_d10_Rep03_P1


title: Benz_d1_Rep2_P1


title: SL0296_CEv3_afatinib_24_3

description: Library name: SL0296


title: Benz_d31.6_Rep1_P1


title: Buc_d0.3_Rep1_P1


title: SL0293_CEv3_afatinib_48_2

description: Library name: SL0293


title: Eth_d1_Rep02_P1


title: SL0295_CEv3_afatinib_4_3

description: Library name: SL0295


title: PHB_d500_Rep4_P1


title: Col_d1_Rep02_P1


title: 3MC_d1_Rep3_P1


title: Col_d0.0001_Rep2_P1


title: Buc_d10_Rep02_P1


title: Amit_d31.6_Rep3_P1


title: Benz_d1_Rep3_P1


title: Amit_d1_Rep3_P1


title: Benz_d3.16_Rep02_P1


title: Eth_d300_Rep3_P1


title: SL0291_CEv3_afatinib_4_2

description: Library name: SL0291


title: SL0287_CEv3_afatinib_4_1

description: Library name: SL0287


title: DMSO_d0_Rep6_P1


title: SL0292_CEv3_afatinib_24_2

description: Library name: SL0292


title: Col_d0.1_Rep3_P1


title: Col_d0.1_Rep4_P1


title: Benz_d31.6_Rep2_P1


title: Buc_d100_Rep2_P1


title: SL0289_CEv3_afatinib_48_1

description: Library name: SL0289


title: Col_d0.001_Rep2_P1


title: Amit_d100_Rep2_P1


title: Col_d0.1_Rep02_P1


title: DMSO_Rep07_P1


title: SL0508_CEv3_starve_3

description: Library name: SL0508


title: Col_d0.01_Rep2_P1


title: Amit_d1_Rep1_P1


title: Col_d0.0001_Rep3_P1


title: Eth_d3.16_Rep1_P1


title: SL0509_CEv3_starve_2

description: Library name: SL0509


title: Benz_d10_Rep2_P1


title: Eth_d100_Rep03_P1


title: SL0507_E5_starve_2

description: Library name: SL0507


title: Eth_d0.1_Rep02_P1


title: 3MC_d0.3_Rep03_P1


title: Buc_d300_Rep2_P1


title: SL0504_G12_starve_1

description: Library name: SL0504


title: Amit_d0.1_Rep3_P1


title: Col_d0.03_Rep1_P1


title: SL0502_E5_starve_1

description: Library name: SL0502


title: SL0506_E4_starve_3

description: Library name: SL0506


title: Eth_d300_Rep2_P1


title: Buc_d1_Rep02_P1


title: Col_d0.01_Rep02_P1


title: PHB_d500_Rep3_P1


title: 3MC_d1_Rep1_P1


title: SL0310_G5_starve_2

description: Library name: SL0310


title: SL0511_G1_starve_2

description: Library name: SL0511


title: Buc_d0.1_Rep02_P1


title: Buc_d31.6_Rep3_P1


title: Sin3B_KO-1

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

description: Library name: HSC-KO-1

data_processing:
Fastq files were run through FastQC and trimmed using Trimmomatic. Reads were then aligned to the mouse genome using bowtie2 and duplicate reads were removed using sambamba. Bigwig files were generated using the deeptools package and peaks were called using MACS2.
The bed files containing peaks were read into R and the DiffBind package was used for further downstream analysis. Peaksets were read in and normalized before DESeq2 was used for differential peak analysis.
The HOMER package was used to analyze differential peaks to calcualte enrichment for DNA binding motifs, and the bedtoosl suite was used to overlap/subtract/compare peaksets between each other.
Peaks were also analyzed using the GREAT tool to determine local genes that were putatitvely regulated by regulatory regions, and those identified genes were fed into Enrichr for Gene Ontology and pathway enrichment.
Assembly: mm9
Supplementary files format and content: Procced data contains output from

source_name: Hematopoietic

growth_protocol: Cells were freshly isolated from C57BL/6 mice housed in a pathogen-free barrier facility with a 12h light/dark cycle and given food and water ad libitum.

extract_protocol:
Mice were humanely euthanized via CO2 inhalation followed by a secondary cervical dislocation. The femurs, tibiae, pelvis, spine, humerus, and sternum were all taken and crushed to release bone marrow. After red blood cell lysis with ACK buffer, cells were magnetically enriched for cKit+ cells and then stained with Lineage. cKit, Sca-1, Flk2, CD48, and CD150  antibodies to sort on LT-HSCs (L-S+K+Flk2-CD48-CD150+) cells. Cells were combined from 2 mice for each genotype. Cells were then pelleted and then subjected to the ATAC-Seq kit from ActiveMotif with the following modification: the amount of assemlbed transposomes were scaled based on the number of cells we were able to isolate. Then the rest of the directions were followed per the manufacturer's instructions.
Illumina Nexteria i7 and i5 primers were used to generate libraries and distinguish between samples. Samples were PCR amplified using Q5 polymerase for a total of 12 cycles and Solid Phase Reversible Immobilization (SPRI) beads were used for clean up. Libraries were analyzed on a tapestation and Bioanalyzer for fragment distribution and concentration respectively. Samples were sequenced on an Illumina NovaSeq with paired end reads.

value: Hematopoietic

value: LT-HSC


title: Benz_d0.316_Rep02_P1


title: Eth_d3.16_Rep2_P1


title: Sin3B_WT-2

description: Library name: HSC-WT-2

value: WT


title: SL0288_CEv3_afatinib_24_1

description: Library name: SL0288


title: Buc_d0.3_Rep2_P1


title: Amit_d10_Rep03_P1


title: Buc_d100_Rep1_P1


title: SL0179_E4_starve_2

description: Library name: SL0179


title: Col_d100_Rep01_P1


title: Benz_d0.1_Rep3_P1


title: DMSO_Rep01_P1


title: NIH3T3_KO_H7_passage8

city: South San Francisco

first: Heyuan

last: Li

state: California

address: 213 E Grand Ave

institute: Merck Research Laboratories

description:
Library name: sample_11
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

data_processing:
Omicsoft Aligner (Qiagen, v11). Gene-level raw counts and transcript per million (TPM) were determined by the OSA algorithm as implemented in Omicsoft Array Studio (v11) and using Ensembl.R86 gene models.
Assembly: GRCm38
Supplementary files format and content: tab-delimitated text file includes raw counts for each sample
Supplementary files format and content: tab-delimitated text file includes TPM values of each sample

source_name: fibroblast

growth_protocol: NIH3T3 cells are cultured with DMEM/F12(1:1) (Gibco,11320-0 33) containing 10% FBS

extract_protocol:
Total RNA Isolation Kit (Applied Biosystems, A27828) according to the manufacturer’s protocol. Purified total RNA was quantified and validated with nanodrop and fragment analyzer (Agilent, DNF 471 Standard Sensitivity RNA Analysis Kit, 15 nt).
cDNA was synthesized using 100 ng of total RNA. cDNA library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit. Quality control and quantification for amplified cDNA libraries and final sequencing libraries were performed using a Qubit High Sensitivity ds DNA and Agilent Bioanalyzer DNA High Sensitivity Chip analysis. Libraries were normalized to 4 nM concentration and pooled. The pooled libraries were paired end sequenced on NovaSeq SP platform.

value: fibroblast

value: AEBP1 KO

tag: clone

tag: passage

value: passage 8


title: NIH3T3_KO_H7_passage9

description:
Library name: sample_12
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

value: passage 9


title: NIH3T3_KO_H7_passage7

description:
Library name: sample_10
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

value: passage 7


title: PHB_50_Rep03_P1


title: Buc_d31.6_Rep1_P1

value: Human HepaRG

value: HepaRG


title: SL0312_G8_starve_1

description: Library name: SL0312


title: SL0306_G1_starve_1

description: Library name: SL0306


title: Sin3B_KO-2

description: Library name: HSC-KO-2


title: Eth_d0.01_Rep02_P1

value: Rat primary hepatocytes


title: Amit_d10_Rep2_P1


title: SL0387_CEv3_full_1

description: Library name: SL0387

value: full serum culture


title: Benz_d0.003_Rep02_P1

value: hepatocytes


title: Benz_d0.03_Rep01_P1


title: DMSO_d0_Rep4_P1


title: SL0308_G1_starve_3

description: Library name: SL0308


title: SL0316_G12_starve_2

description: Library name: SL0316


title: Sin3B_WT-1

description: Library name: HSC-WT-1


title: Amit_d10_Rep1_P1


title: Eth_d10_Rep02_P1


title: Amit_d1_Rep01_P1


title: Eth_d31.6_Rep3_P1


title: SL0142_CEv3_starve_1

description: Library name: SL0142


title: NIH3T3_KO_F5_passage9

description:
Library name: sample_6
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: PHB_50_Rep02_P1


title: SL0311_G5_starve_3

description: Library name: SL0311


title: Buc_d100_Rep02_P1


title: Amit_d0.01_Rep02_P1


title: Buc_d0.01_Rep01_P1


title: Buc_d3.16_Rep1_P1


title: NIH3T3_KO_G5_passage9

description:
Library name: sample_9
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: NIH3T3_KO_G5_passage7

description:
Library name: sample_7
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: NIH3T3_KO_G5_passage8

description:
Library name: sample_8
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: SL0384_CEv3_full_1

description: Library name: SL0384


title: SL0388_CEv3_full_2

description: Library name: SL0388


title: Eth_d31.6_Rep2_P1


title: SL0385_CEv3_full_2

description: Library name: SL0385


title: Benz_d100_Rep2_P1


title: SL0317_G12_starve_3

description: Library name: SL0317


title: Buc_d31.6_Rep2_P1


title: NIH3T3_KO_F5_passage8

description:
Library name: sample_5
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: 3MC_d1_Rep2_P1


title: NIH3T3_WT_Par_passage8

description:
Library name: sample_3
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

value: Parental


title: Eth_d1_Rep01_P1


title: SL0107_C_starve_2

description: Library name: SL0107

source_name: C

value: C


title: SL0178_E4_starve_1

description: Library name: SL0178


title: Col_d0.1_Rep01_P1


title: SL0108_C_starve_3

description: Library name: SL0108


title: Benz_d100_Rep1_P1


title: NIH3T3_WT_Par_passage6

description:
Library name: sample_1
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

value: passage 6


title: Buc_d10_Rep01_P1


title: NIH3T3_KO_F5_passage7

description:
Library name: sample_4
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables


title: decitabine-resistant THP-1 cells, decitabine, biol rep 2

city: Shanghai

first: Xueqin

last: Chen

address: No. 197 Ruijin 2nd Road

department: Ruijin Hospital

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Cutadapt (v1.9.1)
Clean data were aligned to reference human genome (hg38, downloaded from Ensembl browser) via software Hisat2 (v2.1.0) and ordered by samtools (v1.6)
Read count were calculated by using HTSeq (v0.13.5)
Assembly: hg38
Supplementary files format and content: A tab-delimited text file including FPKM values for each sample

growth_protocol: THP-1 or decitabine-resistant THP-1 cells were maintained in RPMI 1640 Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using a total RNA Purification Kit (B518651, Sangon Biotech). RNA was assessed for quantity and quality using Agilent Bioanalyzer 2100 for a minimum RIN score of 7 or higher.
The sequencing libraries were prepared using RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification using KAPA mRNA HyperPrep Kit (KK8581).

treatment_protocol: THP-1 or decitabine-resistant THP-1 cells were treated with or without 1μM decitabine for 6 days.

value: leukemia cell line

value: DAC

tag: time

value: 6 days


title: 3MC_d0.3_Rep02_P1


title: decitabine-resistant THP-1 cells, decitabine, biol rep 1

value: WT


title: Benz_d3.16_Rep01_P1


title: mod4

city: 天津市 / 市辖区 / 津南区

first: jin

last: yan

state: Not US or Canada

address: 天津市海河教育园区同砚路38号南开大学药学院

institute: nankai university

description:
Library name: library12
FPKM_mod4

data_processing:
Raw Data QC: Conduct adapter trimming and low-quality/base filtering using fastp v0.23.4. Set the minimum read length at 75 bp.
Alignment: Perform reference genome alignment with HISAT2 v2.2.1.
Quantification and Differential Analysis: First, calculate FPKM using featureCounts v2.0.6 and apply TMM/TPM normalization. Then, carry out differential analysis via DESeq2 v1.34.0 (for samples with replicates) and edgeR v3.36.0 (for samples without replicates), with thresholds of |log2FC|>1 and padj<0.05.
Functional Enrichment: Conduct GO/KEGG enrichment analysis using clusterProfiler v4.2.2 and perform GSEA with msigdbr v7.5.1.
Splicing and Variant Analysis: Detect alternative splicing with rMATS v4.2.0 (FDR<0.05) and perform SNV/InDel detection using VarScan2 v2.4.6. Annotate the results with snpEff v5.2.
Assembly: Species: Mus musculus Assembly: GRCm39.110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
After treatment, the cells were washed twice with PBS, lysed with TRIzol Reagent, and transferred to cryovials. The samples were then sent to Heyuan Biotechnology (Shanghai) Co., Ltd. for transcriptome analysis. Method: Total RNA extraction QC: RNA integrity (Agilent 2100), RNA concentration (NanoDrop)
Steps: 1. mRNA isolation (oligo-dT magnetic beads) 2. mRNA fragmentation 3. cDNA synthesis (1st/2nd strand) 4. End repair & 3'-end adenylation 5. Adapter ligation 6. PCR amplification 7. Purification (magnetic beads) QC: Library concentration (Qubit), Fragment length (Agilent Fragment Analyzer)

treatment_protocol: The RAW264.7 macrophages were divided into three experimental groups: the control group (Con), the model group (Mod), and the FA group. The Mod group was exposed to 1 μg/mL of LPS for 24 h to establish the inflammatory model. The FA group was pretreated with 10 μM of FA for 12 h, followed by LPS treatment for 24 h.

value: Macrophage


title: mod3

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library11
FPKM_mod3


title: mod2

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library10
FPKM_mod2


title: Amit_d10_Rep02_P1


title: NIH3T3_WT_Par_passage7

description:
Library name: sample_2
s3://ngs-bulk-rnaseq-pre-clinical/Analysis/OmicSoft/Pipeline_Results/22876/PID22876_AID5738_BATCH1_Mrk_RNA_Seq_24Jul2023_1690212267410/ExportedViewsAndTables

value: fibroblast


title: Amit_d31.6_Rep2_P1


title: SL0313_G8_starve_2

description: Library name: SL0313

value: starve serum culture


title: SL0195_E5_starve_3

description: Library name: SL0195


title: Col_d10_Rep01_P1


title: Eth_d100_Rep02_P1


title: mod1

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library9
FPKM_mod1


title: 3MC_d1_Rep4_P1


title: SL0106_C_starve_1

description: Library name: SL0106


title: decitabine-resistant THP-1 cells, control, biol rep 1

value: DMSO


title: SL0309_G5_starve_1

description: Library name: SL0309


title: FA4

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library8
FPKM_FA4


title: THP-1 cells, decitabine, biol rep 2


title: Amit_d0.001_Rep01_P1


title: THP-1 cells, decitabine, biol rep 1


title: FA3

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library7
FPKM_FA3


title: SL0123_C_full_3

description: Library name: SL0123


title: SL0386_CEv3_full_3

description: Library name: SL0386


title: Eth_d0.1_Rep01_P1


title: SL0314_G8_starve_3

description: Library name: SL0314


title: SL0122_C_full_2

description: Library name: SL0122


title: Col_d0.01_Rep01_P1


title: FA2

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library6
FPKM_FA2


title: THP-1 cells, control, biol rep 2


title: Buc_d1_Rep01_P1


title: SL0121_C_full_1

description: Library name: SL0121


title: decitabine-resistant THP-1 cells, control, biol rep 2


title: FA1

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library5
FPKM_FA1


title: THP-1 cells, control, biol rep 1


title: con4

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library4
FPKM_con4


title: Benz_d0.316_Rep01_P1


title: BICC1 S240P #2

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

data_processing:
Sequence reads were aligned to the human genome (GRCh38) using STAR in Galaxy (Galaxy Version 2.7.10B+galaxy4)  using the default parameters
Read count extraction using FeatureCounts in Galaxy (Galaxy Version 2.0.3+galaxy2) using the default parameters
Read count were normalized using DESeq2 in Galaxy (Galaxy Version 2.11.40.8+galaxy0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

source_name: Kidney

extract_protocol:
mRNA was extracted using triazole followed by DNAse treatment
Library generation was performed using TruSeq RNA Library Prep Kits (Illumina, San Diego, CA, USA)

value: Kidney

value: Human embryonic kidney


title: BICC1 S240P #1


title: con3

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library3
FPKM_con3


title: SL0157_CEv3_full_1

description: Library name: SL0157


title: con2

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library2
FPKM_con2


title: PHB_50_Rep01_P1


title: Amit_d10_Rep01_P1


title: BICC1 KO #2


title: SL0158_CEv3_full_2

description: Library name: SL0158


title: BICC1 WT #2

value: Wild-type


title: Buc_d3.16_Rep3_P1

value: Human HepaRG

value: HepaRG


title: BICC1 KO #1


title: Raw264.7 cells, cGAMP (20 uM) + 7a (20 uM) [36]

city: Seoul

first: Seung Bum

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Chemistry

country: South Korea

institute: Seoul National University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (0.38), (parameter - window size:4, mean quality:15, min length:36)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (v.2.1.0) and Bowtie2 (2.3.4.1)
Read count extraction and normalization were performed using StringTie (v2.1.3b)
Assembly: mm10
Supplementary files format and content: excel file (.xlsx) include read counts, FPKM, TPM for each sample
Supplementary files format and content: excel file (.xlsx) after Quantile Normalization with FPKM value of all samples

growth_protocol: Raw264.7 macrophage-like cells were maintaned in DMEM, supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic (anti-anti) solution. Cells were maintained in 37'C, 5% CO2, humidified chamber.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (QIAGEN).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina),  following the manufacturer’s protocol (TruSeq Stranded mRNA Reference Guide #  1000000040498v00).

treatment_protocol: Cells were treated with DMSO, cGAMP, SB24011, or in combination of cGAMP and SB24011 or 7a, respectively, for 6 h in serum-free DMEM.

value: macrophage-like

value: cGAMP (20 uM) + 7a (20 uM)


title: con1

city: 天津市 / 市辖区 / 津南区

address: 天津市海河教育园区同砚路38号南开大学药学院

description:
Library name: library1
FPKM_con1


title: Eth_d10_Rep01_P1

value: Rat primary hepatocytes

value: hepatocytes


title: Amit_d0.01_Rep01_P1


title: SL0159_CEv3_full_3

description: Library name: SL0159

value: full serum culture


title: SL0100_G5_full_1

description: Library name: SL0100


title: Eth_d0.01_Rep01_P1


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (20 uM) [35]


title: Eth_d100_Rep01_P1


title: SL0101_G5_full_2

description: Library name: SL0101


title: Amit_d0.1_Rep01_P1


title: Raw264.7 cells, cGAMP (20 uM) + 7a (20 uM) [26]


title: SL0102_G5_full_3

description: Library name: SL0102


title: BICC1 WT #1


title: Human RPE cells, donor3_ADT

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

description: CITE-Seq with ICELL8 platform

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cogent software v1.0 (https://www.takarabio.com/products/next-generation-sequencing/bioinformatics-tools/cogent-ngs-analysis-pipeline)
Seurat package was used to make and integrate seurat objects for RNA-seq libraries. CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) Was used for demultiplexing and counting ADT libraries.
Assembly: hg38
Supplementary files format and content: rds, includes Seurat objects containing read counts and clustering results

source_name: RPE

growth_protocol: RPE cells were isolated from human donor eyes and CITE-Seq was performed on acutely isolated and cultured cells at passage 2. Cultured cells were maintained in RPE medium: DMEM F12 50/50 medium (Corning), MEM alpha modification medium (Sigma-Aldrich), 1.25 mL Glutamax (Gibco), 2.5 mL Sodium Pyruvate (Gibco), 2.5 mL Niacinamide (1M; Spectrum Chemical Inc., CA), 2.5 mL MEM NEAA (Gibco), 2% or 10% or 2% heat inactivated fetal bovine serum (FBS), supplemented with THT (Taurine, Hydrocortisone, Triiodo-thyronin), and 1.25 mL N1 medium supplement (Sigma-Aldrich). Cells were incubated in a humidified incubator at 37 oC and 5% CO2. RPE medium with 10% FBS was used until the cultures were confluent and 2% FBS was used after confluency. The medium was replaced every 3 days.

extract_protocol:
RNA isolation and cDNA sythesis were performed using the SMART-Seq ICELL8 Application Kit. ADTs were separated from the cDNA after RT-PCR using Ampure beads (1.8X), from which a separate ADT library was prepared.
Single cell library preparation was performed using the SMART-Seq ICELL8 Application Kit. ADT library prepration was performed with ADTs isolated from the cDNA and sparq hifi master mix (Quantbio)

value: RPE

tag: donor gender

value: male

tag: donor age

tag: donor race

value: caucasian

tag: time in_culture


title: SL0103_E5_full_1

description: Library name: SL0103


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (20 uM) [5]

value: WT


title: Human RPE cells, donor4_ADT

description: CITE-Seq with ICELL8 platform

value: female


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (10 uM) [34]


title: Human RPE cells, donor3_RNA-seq

description: CITE-Seq with ICELL8 platform


title: Human RPE cells, donor2_ADT

description: CITE-Seq with ICELL8 platform


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (10 uM) [24]


title: SL0392_CEv3_full_3

description: Library name: SL0392


title: Raw264.7 cells, cGAMP (20 uM) + 7a (20 uM) [6]


title: SL0105_E5_full_3

description: Library name: SL0105


title: Col_d1_Rep01_P1


title: Buc_d100_Rep01_P1


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (10 uM) [4]


title: SL0390_CEv3_full_1

description: Library name: SL0390


title: Benz_d31.6_Rep01_P1


title: Human RPE cells, donor2_RNA-seq

description: CITE-Seq with ICELL8 platform


title: 3MC_d0.3_Rep01_P1


title: P2 RPE cells, lines 318 and 319, 10-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform

value: black / caucasian

value: 10 weeks


title: Benz_d0.003_Rep01_P1


title: Human RPE cells, donor1_RNA-seq

description: CITE-Seq with ICELL8 platform


title: Raw264.7 cells, SB24011 (20 uM) [33]


title: Raw264.7 cells, SB24011 (20 uM) [23]


title: SL0104_E5_full_2

description: Library name: SL0104


title: Buc_d0.1_Rep01_P1


title: P2 RPE cells, lines 318 and 319, 2-week-old_ADT

description: CITE-Seq with ICELL8 platform

value: 2 weeks


title: Raw264.7 cells, cGAMP (20 uM) + SB24011 (20 uM) [25]


title: SL0391_CEv3_full_2

description: Library name: SL0391


title: S30_Xenium

type: RNA

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

hyb_protocol: After inserting slides into Xenium cassettes, samples were decross-linked and incubated overnight (22 hours) with padlock probes, followed by a post-hybridization wash. Subsequently, padlock probes were ligated, followed by rolling circle amplification, autofluorescence quenching, and nuclear staining (DAPI).

scan_protocol: Slides were loaded on a 10X Xenium Analyzer (software v. 1.6.1.0), for region selection, with each region corresponding to one entire nerve bundle.

data_processing: Primary analysis, image processing and decoding, and secondary analysis, cell segmentation and transcript mapping, were performed on-instrument with the analysis software Xenium-1.6.0.8 resulting in a cell-feature matrix and an initial clustering. For cell segmentation, a custom neural network on DAPI images was initially used for nucleus segmentation. Then nucleus boundaries are expanded by 15 µm or until they encounter another cell boundary in X-Y to define cell boundaries. Transcripts were mapped to these 2D shapes according to their X and Y coordinates. Gene expression mapping was visualized using the Xenium Explorer software v.1.3. The post Xenium H&E staining was processed according to the manufacturer protocol, including quencher removal in advance (see 10x Genomics protocol CG000613/A).

label: Xenium Human Probe Set

source_name: sural nerve

label_protocol: For each patient, approximately 10 mg pieces (median of 13.9 mg) were cut on dry ice as starting material from the original samples. Nerve pieces were cut into smaller pieces and processed using the Miltenyi Biotec nuclei extraction protocol. In summary, samples were transferred to a gentleMACS C-tube (Cat.no. 130-093-237) containing 2 ml lysis buffer (nuclei extraction buffer (Cat. no. 130-128-024) + 0.2 U/µl RNase inhibitor (EO0381) and processed on a gentleMACS dissociator with program 4C_nuclei_1. After dissociation, the nuclei suspension was filtered through a pluriStrainer Mini 70-µm cell strainer (pluriSelect®) and washed in 200-400 µl resuspension buffer (PBS with 0.1% BSA and 0.2 U/μL RNase inhibitor (EO0381) depending on sample size and expected nuclei count. Nuclei suspension was then filtered through a pluriStrainer Mini 40-μm cell strainer (pluriSelect®), placed on a 1.5 ml DNA-LoBind tube (Merck). The nuclei suspension was stained with Trypan Blue to manually assess nuclei viability and count using a Fuchs-Rosenthal chamber. Equal volumes between samples were used for downstream application of single nucleus RNA seq.

extract_protocol: Residual material from the sural nerve grafts were used for control samples in this study. In PNP patients, sural nerve biopsy was performed as part of the clinical diagnostic workup. In total, 8 sural nerve formalin-fixed paraffin-embedded (FFPE) samples were included for Xenium spatial transcriptomics: 2 CTRL (S22, S24), 2 CIDP (S01, S11), 2 CIAP (S04, S14) and 2 VN (S29, S30) samples

tag: disease

value: Vn

tag: material

value: FFPE

tag: center

value: Würzburg


title: SL0056_G1_full_2

description: Library name: SL0056


title: SL0050_G8_full_2

description: Library name: SL0050


title: SL0049_G8_full_1

description: Library name: SL0049


title: P2 RPE cells, lines 318 and 319, 2-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform

tag: tissue


title: S29_Xenium

value: VN


title: P2 RPE cells, lines 319 and 322, 4-week-old_ADT

description: CITE-Seq with ICELL8 platform

tag: cell type

value: 4 weeks


title: SL0052_G12_full_1

description: Library name: SL0052

tag: treatment


title: S24_Xenium

value: CTRL

value: Essen


title: Raw264.7 cells, SB24011 (20 uM) [3]

tag: cell line

value: macrophage-like


title: Raw264.7 cells, cGAMP (20 uM) [22]

tag: genotype

value: cGAMP (20 uM)


title: P2 RPE cells, lines 319 and 322, 4-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform

value: RPE


title: S22_Xenium


title: SL0053_G12_full_2

description: Library name: SL0053

value: full serum culture


title: Raw264.7 cells, cGAMP (20 uM) [2]


title: S14_Xenium

value: CIAP


title: P2 RPE cells, line 322, 2- and 10-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform

value: caucasian

value: 2 or 10 weeks


title: SL0055_G1_full_1

description: Library name: SL0055


title: P2 RPE cells, line 318, 4-week-old_ADT

description: CITE-Seq with ICELL8 platform

value: female

value: black


title: P2 RPE cells, line 318, 4-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform


title: Raw264.7 cells, DMSO control [31]

value: WT

value: DMSO


title: SL0057_G1_full_3

description: Library name: SL0057


title: S11_Xenium

value: CIDP

value: FFPE


title: Raw264.7 cells, DMSO control [21]


title: SL0054_G12_full_3

description: Library name: SL0054


title: SL0051_G8_full_3

description: Library name: SL0051


title: S01_Xenium

value: Münster


title: S04_Xenium


title: Raw264.7 cells, cGAMP (20 uM) [32]


title: C57BL/6, 4 weeks, male, BAT, KO5

city: Los Angles

first: Kristina

last: Boström

address: 630 Charles E Young Dr S

department: Medicine Cardiology

institute: UCLA

data_processing:
Fastq files were aligned to reference genome using Spliced Transcripts Alignment to a Reference (STAR)
Gene counts were generated along the STAR alignment.
R package DESeq2 was used to normalize the data and perform differential gene expression analysis.
Differentially expressed genes (DEGs) were identified using cutoff of FDR 0.05.
Assembly: mm10
Supplementary files format and content: comma-separated values files include normalized gene counts for each sample

source_name: Mouse brown adipose tissue

growth_protocol: All mice were exposed to a standard 12h:12h light/dark cycles and fed a standard chow diet (Diet 8604; HarlanTeklad Laboratory).

extract_protocol:
RNA was harvested using RNeasy plus mini kit (Qiagen). 1.5 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.Libraries were sequenced using Hiseq3000 platform to a depth of approximately 20 million reads per library with single-end read 50 base pairs read length.

tag: strain

value: Mouse brown adipose tissue

value: Mgp KO

tag: gender

value: male

tag: age

value: 4 weeks


title: C57BL/6, 4 weeks, male, BAT, KO4


title: SL0043_E4_full_1

description: Library name: SL0043


title: Raw264.7 cells, DMSO control [1]

value: macrophage-like


title: C57BL/6, 4 weeks, male, BAT, KO2


title: SL0045_E4_full_3

description: Library name: SL0045


title: SL0044_E4_full_2

description: Library name: SL0044


title: WT Mice, No Transplant

city: Bronx

first: Rohan

last: Hofland

address: 1945 Eastchester Rd, Apt 17D

institute: Albert Einstein College of Medicine

description:
Library name: WT
10x Genomics

library_source: transcriptomic single cell

data_processing:
All processing on raw data files was performed with CellRanger software v 8.0.1
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files and matrix files - barcodes, features, and count matrix

source_name: Brain

extract_protocol:
Mice were provided a lethal dose of anesthesia, then decapitated on ice. Brains were dissociated using MACS Neural Dissociation Kit (P) (MACS 130-092-628). Cells were fixed using 10X GEM-X Flex Sample Preparation v2 Kit according to manufacturer's instructions
Library was generated with Chromium Fixed RNA Kit, Mouse Transcriptome for all samples according to manufacturer instructions. Briefly, the four treatment and four WT cells were labelled, then pooled into two groups of four. They were then hybridized with probes and barcodes to predefined RNA sequences, then pooled and partitioned into GEMs prior to creating a gene expression library

treatment_protocol: Mice for transplantation were anesthetized via isoflurane then injected with 200k cells suspended in 2uL of unsupplemented cell culture media (Sciencell 1901). Mice were maintained on tamoxifen (1mg/kg of AIN76A food) in chow ad libitum to prevent host repopulation of microglia and allow for spread of transplanted cells. One month after transplantation, mice were started on doxycycline (1.2 mg/mL in 1% sucrose water) for one month, then tissue was collected for sequencing. WT samples are age matched animals with the background of transplanted cells (Cx3Cr1-GFP).

value: Brain

value: Unsorted - Brain

value: No Treatment


title: T. rubrum STRB12, control, biological replicates 3

city: Nanchang

first: Suqing

last: Yang

address: Nanchang

institute: Jiangxi Provincial People's Hospital (the First Affiliated Hospital of Nanchang Medical College)

description: Library name: STRB12-KB-3A

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by StringTie (v2.1.2).
Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCF_000151425.1_ASM15142v1
Supplementary files format and content: tab-delimited txt file includes fpkm values for each sample
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

organism: Trichophyton rubrum

source_name: T. rubrum STRB12

growth_protocol: Before the experiments, the fungal strains were reactivated and subcultured twice on the Sabouraud Dextrose Agar (SDA: 15 g/L agar, 40 g/L glucose, 10 g/L peptone, 0.125 g/L chloromycetin) to purify the colony and enhance its vitality. Thereafter, T. rubrum was inoculated into SDA and grown at 28°C for 7-14 days, and spores were harvested from sporulating colonies and suspended in a sterile 0.85% NaCl solution containing 1% Tween-20. The spore concentrations were determined and adjusted to the inoculum of 5.0×10^5 CFU/mL using a hemocytometer. The working suspension with a final inoculum of 5.0×10^3 CFU/mL was obtained by 100× dilution of the inoculum suspension with Sabouraud dextrose broth (SDB: 40 g/L glucose, 10 g/L peptone, 0.125 g/L chloromycetin).

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
After the total RNA passed quality inspection, the magnetic beads connected to Oligo (dT) were used to enrich the eukaryotic messenger RNA (mRNA). The extracted mRNA was randomly interrupted into short fragments by RNA fragmentation buffer. Using fragmented mRNA as a template, a single-stranded complementary DNA (cDNA) was synthesized using random hexamers with 6 bases. Then buffer, dNTPs, RNaseH, and DNA polymerase I (Pol I) were added for double-strand cDNA synthesis. Hieff NGS®DNA Selection Beads were used to purify double-strand products and perform fragment selection. Finally, PCR amplification was performed to obtain the final sequencing library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-T7 platform at Tsingke Biotechnology Co., Ltd..

treatment_protocol: The experimental strain samples were divided into two groups: (1) the HQD-treated group (three biological replicates: STRB12-HQD1, STRB12-HQD2, STRB12-HQD3) fed with HQD at a final concentration of MIC (i.e., 3.13 mg/mL) which is a stress concentration for T. rubrum that can reflect the antifungal mechanism of HQD; (2) the control group (three biological replicates: STRB12-KB1, STRB12-KB2, STRB12-KB3) treated with identical volume of SDB as HQD. After 5 days of incubation at 28°C, the mycelium was filtered with sterile Whatman paper, washed twice with sterile distilled water, and dried on filter paper for RNA extraction.

value: T. rubrum STRB12

value: blank SDB without drugs


title: C57BL/6, 4 weeks, male, BAT, KO3


title: HNSCC, Ctrl

city: Guangzhou

first: Cheng

last: Wang

address: 56 Lingyuan Road West

institute: Sun Yat-sen University

data_processing:
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline
Gene expression matrix was created by using Seurat (V4.0.0) pipeline.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: tongue

extract_protocol:
HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol
MGI2000

treatment_protocol: Mice were induced with 4NQO to establish murine HNSCC model and then treated with JQ1 or control for 10 days.

value: tongue

value: wild type

tag: disease state

value: murine HNSCC model (induced with 4NQO)

value: control


title: HNSCC, JQ1


title: MEF_iPLU (scRNA-seq)

city: Shinjyuku-ku

first: Makoto

last: Ishii

address: 35, Shinanomachi

institute: Keio University

data_processing:
I1 read: contains the sample index.
R1 read: : contains the cell barcode (first 16 nt) and UMI (next 10 nt)
R2 read: contains the RNA sequence.
We converted BCLs to FASTQs using Cell Ranger mkfastq v3.0.2 (10X Genomics, Pleasanton, CA).
We aligned reads to mm10 and generated gene level counts using Cell Ranger count v3.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: pulmonary epithelial-like cells

extract_protocol:
For single cell preparation of iPUL cells, matrigel blocks containing the cells were digested using dispase at 37°C for 120 minutes. The clusters of the cells were separated using 70 μm cell strainer. Subsequently, the cell clusters were trypsinized with 0.05% trypsin/EDTA, and the cells were dissociated into single cells via pipetting and repeated filtering through a 70-μm cell strainer.
We loaded the dissociated cells onto the 10X Chromium system for barcoding and library preparation following the user guide for Single Cell 3’ Reagent Kits v3 (10X Genomics, Pleasanton, CA).

value: CBA/Ca x C57BL/6J

value: mouse embryonic fibroblast

tag: transduction

value: 4 factors (Nkx2-1, Foxa1, Foxa2, Gata6)


title: Transplanted Mice, No Virus and BDNF Virus

description:
Library name: MRL
10x Genomics

value: Microglial Transplant, No Virus or BDNF Infected


title: SL0001_C_full_1

description: Library name: SL0001

value: C

value: full serum culture


title: C57BL/6, 4 weeks, male, BAT, KO1

value: Mouse brown adipose tissue

value: Mgp KO

value: male

value: 4 weeks


title: rpl-36A(P55Q)/mIn1 hets, +CHX, 3-day, 23˚C, L4, Rep1 (+RNase H)

city: Austin

first: Qiuxia

last: Zhao

state: Texas

address: 2415 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: ESC_HSL_672

data_processing:
Adapter removal (Truseq HT adapters) and genome mapping (WBcel235) and assignment to protein coding genes were accomplished by using NextFlow preprocessing pipeline, Riboflow.
The raw reads per gene were extracted from the output ribo file using RiboR.
These reads were then analyzed for significant differences with and without auxin using Deseq2 analysis.
Assembly: WBcel235
Supplementary files format and content: CSV file includes transcript counts for each Sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Animals were grew at 23˚C

extract_protocol:
RNA was extracted using Trizol. rRNA depetion was performed with Rnase H.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Put synchronized eggs on without or with CHX (500 µg/ml) NGM plates.

value: whole worm

tag: developmental stage

tag: Sex

value: hermaphrodite

value: rpl-36A(P55Q)/mIn1 heterozygotes

value: embryos, +CHX, 3 days


title: SL0011_CEv3_full_2

description: Library name: SL0011


title: rpl-36A(P55Q)/mIn1 hets, +CHX, 3-day, 23˚C, L4, Rep3 (+RNase H)

description: Library name: ESC_HSL_674


title: SL0003_C_full_3

description: Library name: SL0003


title: T. rubrum STRB12, control, biological replicates 2

description: Library name: STRB12-KB-2A

value: T. rubrum STRB12

value: blank SDB without drugs


title: C57BL/6, 4 weeks, male, BAT, WT5

value: WT


title: SL0010_CEv3_full_1

description: Library name: SL0010


title: T. rubrum STRB12, control, biological replicates 1

description: Library name: STRB12-KB-1A


title: C57BL/6, 4 weeks, male, BAT, WT1


title: SL0012_CEv3_full_3

description: Library name: SL0012


title: rpl-36A(P55Q)/mIn1 hets, +CHX, 3-day, 23˚C, L4, Rep2 (+RNase H)

description: Library name: ESC_HSL_673


title: rpl-36A(P55Q)/mIn1 hets, -CHX, 2-day, 23˚C, L4, Rep3 (+RNase H)

description: Library name: ESC_HSL_671

value: embryos, no CHX, 2 days


title: scRNAseq for Day 4, replicate 2

status: Public on Jun 27 2025

city: Stanford

first: Jingxue

last: Xin

address: JAMES CLARK CENTER E100A

institute: Stanford University

description: 10x Genomics

data_processing:
For scRNA-seq data, we input the raw fastq files into 10x Genomics Cell Ranger 6.1.2 and the reference transcriptome for alignment and annotation was version mm10-2020-A. To combine all filtered count matrices for different replicates, the “cellranger aggr” command was applied with the default depth normalization method. For scATAC-seq data, we input the raw fastq files into 10x Genomics Cell Ranger ATAC 2.0.0 software and the reads were aligned to the reference genome version mm10-2020-A. The data for different replicates for each time point were aggregated with the “cellranger-atac aggr” function by specifying depth normalization.
Assembly: mm10
Supplementary files format and content: Feature barcode matrix HDF5 files, and ATAC Per fragment information file, index, and count matrix

source_name: Mouse embryonic stem cell line

extract_protocol:
mESCs were differentiated using the hanging drop method. Trypsinized cells were suspended in differentiation medium (mESC medium without LIF) to a concentration of 50,000 cells/ml. 20 μl drops (~1000 cells) were then placed on the lid of a bacterial plate and the lid was upside down. After 48 h incubation, Embryoid bodies (EBs) formed at the bottom of the drops were collected and placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 μM retinoic acid (RA) for up to 10 days, with the medium being changed daily. The EBs were collected at Day 0, 2, 4, and 10 after retinoic acid treatment. For each time point,the cells were first treated with StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) at 37◦C for 10-15 min with pipetting. Single cell suspension was obtained by passing through 37 μM cell strainer (STEMCELL Technologies) twice. After measuring cell concentration, approximately 1 million of cells were centrifuged at 300 rcf for 5 min. Nuclei were isolated by following the protocol provided by 10x Genomics (Nuclei isolation for single cell multiome ATAC + Gene expression sequencing, CG00365, Rev A). The final nuclei concentration was adjusted to 3000 cell/μL in 1X Nuclei Buffer (10x Genomics). The sample was immediately submitted to Stanford Genomics Service Center (SGSC) for single cell sorting using 10x Chromium Controller (target cells: 5000 per replicate, total 2-3 replicates per time point).
For scRNA-seq, we followed 10X Genomics library preparation protocol. The EBs were collected at Day 0, Day 2, Day 4, and Day 10. They were first treated with StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) at 37oC for 10-15 min with pipetting. Single cell suspension was obtained by passing through 37 μM cell strainer (STEMCELL Technologies) twice.  After measuring cell concentration, approximately 1 million cells were centrifuged at 300 rcf for 5 min. The cell pellet was washed once with PBS + 0.04% BSA. The final cell concentration was adjusted to 1000 cell/μL in PBS + 0.04% BSA. The sample was then submitted to Stanford Genomics Service Center (SGSC) for single cell sorting using 10X Chromium Controller (target cells: 5000 per replicate, total 2 replicates per time point). The scRNA-seq library was generated using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000268).  For scATAC-seq, we followed 10X Genomics library preparation protocol. The EBs were collected at Day 0, Day 2, Day 4, and Day 10. Single cell suspension was first obtained using the same procedure shown above. After measuring cell concentration, approximately 1 million cells were centrifuged at 300 rcf for 5 min at 4oC. Cells were lysed by incubating in 100 μL chilled Lysis Buffer for 5 min on ice. After wash with 1 mL chilled Wash Buffer, the nuclei were isolate by centrifuged at 500 rcf for 5 min at 4oC. The final nuclei concentration was adjusted to 3000 cell/μL in 1X Nuclei Buffer (10X Genomics). The sample was then submitted to Stanford Genomics Service Center (SGSC) for single cell sorting using 10X Chromium Controller (target cells: 5000 per replicate, total 2 replicates per time point). The scATAC-seq library was generated using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000175).
10X Genomics scRNA-seq and scATAC-seq

value: Mouse embryonic stem cell line


title: scRNAseq for Day 10, replicate 1

description: 10x Genomics


title: T. rubrum STRB12, HQD-treatment, biological replicates 2

description: Library name: STRB12-HQD-2A

value: HQD


title: C57BL/6, 4 weeks, male, BAT, WT4


title: T. rubrum STRB12, HQD-treatment, biological replicates 3

description: Library name: STRB12-HQD-3A


title: scRNAseq for Day 4, replicate 1

description: 10x Genomics


title: C57BL/6, 4 weeks, male, BAT, WT3


title: T. rubrum STRB12, HQD-treatment, biological replicates 1

description: Library name: STRB12-HQD-1A


title: C57BL/6, 4 weeks, male, BAT, WT2


title: scRNAseq for Day 0, replicate 2

description: 10x Genomics


title: SL0002_C_full_2

description: Library name: SL0002


title: scATACseq for Day 10, replicate 2

description: 10x Genomics


title: scRNAseq for Day 10, replicate 3

description: 10x Genomics


title: scATACseq for Day 4, replicate 2

description: 10x Genomics


title: scRNAseq for Day 2, replicate 1

description: 10x Genomics


title: rpl-36A(P55Q)/mIn1 hets, -CHX, 2-day, 23˚C, L4, Rep1 (+RNase H)

description: Library name: ESC_HSL_669


title: scRNAseq for Day 10, replicate 2

description: 10x Genomics


title: scATACseq for Day 0, replicate 1

description: 10x Genomics


title: scRNAseq for Day 0, replicate 1

description: 10x Genomics


title: scATACseq for Day 10, replicate 3

description: 10x Genomics


title: three week old, rosette, ZT0, jaz4-1_2

city: Davis

first: Maeli

last: Melotto

state: CA

address: 549 Kleiber Hall Dr

department: Plant Sciences

institute: University of California - Davis

description:
Library name: jaz4_0_2
jaz4-1 ZT0 bio rep 2

data_processing:
High quality reads were mapped to the Arabidopsis reference genome (TAIR10) using HISAT2 software.
FeatureCounts function was used to count the read numbers mapped of each gene, including known and novel genes.
Assembly: TAIR10
Supplementary files format and content: jaz4-1_Col-0_Transcriptomic Dataset.xlsx displays all RPKM (reads per kilobase of exon model per million mapped reads) for each gene for all samples.

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: Arabidopsis thaliana (L. Heyhn.) seeds were sown directly onto soil (SunGro Horticulture Sunshine Mix #1) in tray plugs (3.5 x 3.5 x 5.5 cm) or pots (5 cm3). Plants were kept in growth chamber maintained at 22⁰C, with a 12-hour photoperiod, light intensity of 100 ± 20 µmol/m2/sec, and 60 ± 5% relative humidity.

extract_protocol:
RNA was extracted from Col-0 and jaz4-1 plants using RNeasy plant mini kit (Qiagen, Valencia, CA)
For library preparation and transcriptome sequencing, 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Illumina sequencing and quality control were performed at Novogene Corporation Inc. (Sacramento, CA, USA).

treatment_protocol: Rosette shoots were collected at six-hour increments starting at dawn and spanning 18 hours (ZT 0, 6, 12, and 18). Three biological replicates were sampled, each containing six rosettes that were cut at the hypocotyl region, immediately frozen in liquid nitrogen, and stored at -80oC until the time for tissue processing.

value: rosette

value: Collected at ZT0


title: three week old, rosette, ZT6, jaz4-1_3

description:
Library name: jaz4_6_3
jaz4-1 ZT6 bio rep 3

value: Collected at ZT6


title: three week old, rosette, ZT12, jaz4-1_2

description:
Library name: jaz412_2
jaz4-1 ZT12 bio rep 2

value: Collected at ZT12


title: rpl-36A(P55Q)/mIn1 hets, -CHX, 2-day, 23˚C, L4, Rep2 (+RNase H)

description: Library name: ESC_HSL_670


title: scATACseq for Day 4, replicate 1

description: 10x Genomics


title: scATACseq for Day 10, replicate 1

description: 10x Genomics


title: scATACseq for Day 2, replicate 1

description: 10x Genomics


title: three week old, rosette, ZT12,Col-0_2

description:
Library name: WT_12_2
Col-0 ZT12 bio rep 2


title: three week old, rosette, ZT12,Col-0_1

description:
Library name: WT_12_1
Col-0 ZT12 bio rep 1


title: three week old, rosette, ZT18, jaz4-1_3

description:
Library name: jaz418_3
jaz4-1 ZT18 bio rep 3

value: Collected at ZT18


title: three week old, rosette, ZT18, jaz4-1_2

description:
Library name: jaz418_2
jaz4-1 ZT18 bio rep 2


title: three week old, rosette, ZT6,Col-0_2

description:
Library name: WT_6_2
Col-0 ZT6 bio rep 2


title: three week old, rosette, ZT12, jaz4-1_3

description:
Library name: jaz412_3
jaz4-1 ZT12 bio rep 3


title: three week old, rosette, ZT18, jaz4-1_1

description:
Library name: jaz418_1
jaz4-1 ZT18 bio rep 1


title: three week old, rosette, ZT6,_Col-0_1

description:
Library name: WT_6_1
Col-0 ZT6 bio rep 1


title: three week old, rosette, ZT0, Col-0_2

description:
Library name: WT_0_2
Col-0 ZT0 bio rep 2


title: three week old, rosette, ZT0, Col-0 _3

description:
Library name: WT_0_3
Col-0 ZT0 bio rep 3


title: three week old, rosette, ZT6, jaz4-1_2

description:
Library name: jaz4_6_2
jaz4-1 ZT6 bio rep 2


title: three week old, rosette, ZT0, jaz4-1_1

description:
Library name: jaz4_0_1
jaz4-1 ZT0 bio rep 1


title: three week old, rosette, ZT0, jaz4-1_3

description:
Library name: jaz4_0_3
jaz4-1 ZT0 bio rep 3


title: three week old, rosette, ZT18, Col-0_3

description:
Library name: WT_18_3
Col-0 ZT18 bio rep 3


title: LV_ExT_r27

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

data_processing:
Sequencing and base-calling was performed on the NovaSeq 6000 platform.
Reads underwent initial quality check with FastQC v0.74, then quality filtering and adapter trimming was conducted with Cutadapt v4.6.
Filtered reads were aligned using STAR v2.7.11a in 2-pass mode.
Gene expression was quantified at the gene level using HTseq-counts v2.0.5 and collated into a counts matrix
Assembly: Ensembl mRatBN7.2 v106
Supplementary files format and content: tab-delimited counts matrix text file includes raw counts for each sample

source_name: left ventricle (LV)

growth_protocol: Wistar Kyoto 4-5 week old male rats (n=32) were obtained from the Animal Resource Centre, Perth, Western Australia. Rats were housed in pairs and maintained for a 1-week familiarisation period with a 12-hour light/dark cycle, constant temperature of 21 ± 2°C, and humidity levels between 40 and 70%. Rats had ad libitum access to standard chow diet and tap watersupplemented with deuterium oxide (8% v/v).

extract_protocol:
Whole tissues (SM & LV) were mechanically disrupted with 2 cycles at 4m/s for 10 s (MP Biomedical FastPrep) in a cryotube with with a 5 mm stainless steel bead, and homogenised in TRI-reagent. SM & LV total RNA was extracted using spin-columns with on-column DNase-I digest as per the manufacturer’s instructions (Zymo DirectZol RNA Miniprep kit #R2050, Zymo Research). Purified isolated mitochondria (MT) samples were homogenised in 5 volumes of TRI-reagent, then RNA was extracted using spin-columns with on-column DNase-I digest as per the manufacturer’s instructions (Zymo Direct-Zol Micro Prep kit #R2060, Zymo Research).
Skeletal muscle tissue total RNA (50 ng) and isolated mitochondria total RNA (10 ng) was converted to cDNA libraries (Zymo-SeqRiboFreeTotal RNA kit #R300, Zymo Research). Left ventricle tissue total RNA (100 ng) was converted to cDNA libraries (Illumina TruSeq Stranded Total RNA Ribo-Zero H/M/R)

treatment_protocol: At 5-weeks of age, animals began the exercise training protocol which consisted of running on a motorized treadmill 5 days per week. Running duration was progressively increased in 10-minute increments each day during week 1 of training, from 20 to 60 minutes, with speed set at 15 m/min for the first week and 20 m/min thereafter. The training protocol remained the same (60 minutes of treadmill running at a speed of 20 m/min) between weeks 2 and 4 of training. Sedentary control group rats were placed on a stationary treadmill for the same duration while the exercise training group rats were running. At 9-weeks of age and 24 hours following the competition of the 4-week training protocol, animals were heavily anaesthetised with 5% isoflurane gas then humanely killed via exsanguination following removal of the heart. The left ventricle wall was dissected and snap frozen for subsequent whole tissue RNA extraction. In addition, the inner red portion of the gastrocnemius skeletal muscle was dissected and one portion was snap frozen for subsequent whole tissue RNA extraction, and a fresh portion of tissue was taken for mitochondrial isolation via immunoprecipitation (#130-096-946, Miltenyi Biotek, Australia) followed by RNase-A and proteinase-K purification steps.

value: left ventricle (LV)

value: Wistar Kyoto

value: Male

value: wild-type

tag: age (weeks)

value: Exercise-trained (ExT)


title: LV_ExT_r18


title: LV_ExT_r17


title: three week old, rosette, ZT18, Col-0_2

description:
Library name: WT_18_2
Col-0 ZT18 bio rep 2


title: three week old, rosette, ZT18, Col-0_1

description:
Library name: WT_18_1
Col-0 ZT18 bio rep 1


title: three week old, rosette, ZT6,Col-0_3

description:
Library name: WT_6_3
Col-0 ZT6 bio rep 3


title: three week old, rosette, ZT12, jaz4-1_1

description:
Library name: jaz412_1
jaz4-1 ZT12 bio rep 1


title: LV_Sed_r30

value: Sedentary-control (Sed)


title: three week old, rosette, ZT6, jaz4-1_1

description:
Library name: jaz4_6_1
jaz4-1 ZT6 bio rep 1


title: LV_Sed_r29


title: LV_ExT_r25


title: LV_Sed_r20


title: LV_Sed_r19


title: MT_ExT_r28

source_name: isolated mitochondria (MT) from skeletal muscle, gastrocnemius


title: scATACseq for Day 0, replicate 2

description: 10x Genomics


title: LV_ExT_r28


title: three week old, rosette, ZT0, Col-0_1

description:
Library name: WT_0_1
Col-0 ZT0 bio rep 1


title: LV_ExT_r26


title: three week old, rosette, ZT12, Col-0_3

description:
Library name: WT_12_3
Col-0 ZT12 bio rep 3


title: MT_ExT_r22

value: isolated mitochondria (MT) from skeletal muscle, gastrocnemius


title: LV_ExT_r14


title: MT_ExT_r18


title: MT_ExT_r21


title: LV_Sed_r32


title: LV_Sed_r31


title: MT_ExT_r14


title: MT_ExT_r10


title: MT_ExT_r26


title: MT_ExT_r27


title: MT_ExT_r25


title: MT_ExT_r17


title: MT_ExT_r06


title: MT_ExT_r13


title: MT_ExT_r09


title: MT_Sed_r31


title: MT_Sed_r30


title: MT_Sed_r19


title: MT_ExT_r02


title: MT_Sed_r20


title: MT_Sed_r12


title: MT_Sed_r24


title: MT_Sed_r32


title: SM_ExT_r28

source_name: skeletal muscle (SM), gastrocnemius

value: skeletal muscle (SM), gastrocnemius


title: MT_Sed_r29


title: LV_Sed_r16


title: MT_Sed_r16


title: MT_Sed_r08


title: MT_Sed_r07


title: SM_ExT_r21


title: SM_ExT_r17


title: SM_ExT_r14


title: MT_Sed_r23


title: MT_Sed_r04


title: SM_ExT_r27


title: MT_Sed_r11


title: SM_ExT_r10


title: MT_Sed_r15


title: SM_ExT_r26


title: SM_ExT_r25


title: SM_ExT_r05


title: MT_ExT_r05


title: SM_ExT_r06


title: SM_ExT_r09


title: SM_ExT_r02


title: SM_ExT_r18


title: SM_ExT_r13


title: SM_Sed_r30


title: SM_Sed_r31


title: SM_Sed_r29


title: SM_Sed_r24


title: SM_Sed_r23


title: SM_ExT_r22


title: SM_Sed_r19


title: SM_Sed_r20


title: SM_Sed_r16


title: SM_Sed_r15


title: SM_Sed_r12


title: SM_Sed_r08


title: SM_Sed_r07


title: SM_Sed_r32


title: SM_Sed_r11


title: SM_Sed_r04


title: WT, 2 dpf, biol rep 1

city: Ghent

first: Karo

last: De Rycke

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

description:
Library name: RNA021956
Column name in merged_gene_counts_SMAPLE.txt: RNA021956

data_processing:
Read quality was verified using FastQC v0.11.9, followed by adapter trimming with Trim Galore v0.6.6. Trimmed reads were mapped to Danio rerio GRCz11 genome using STAR v2.7.6a. FeatureCounts package from SubRead v2.0.0 was used for count estimation per gene. Count estimates were analyzed in R.
Data normalization and filtering were conducted using standard workflows in R. Differential expression analysis was performed with edgeR, applying corrections for multiple testing. Differentially expressed genes (DEGs) were defined using a false discovery rate (FDR)-adjusted p-value threshold of 0.05 and a minimum fold change of 1.
Assembly: GRCz11
Supplementary files format and content: Tab delimited text file includes raw counts for each sample.

organism: Danio rerio

source_name: Whole-embryo's

extract_protocol:
Total RNA of 10 pooled WT, and fbn2b homozygous mutant zebrafish, collected at 1 and 2 dpf were extracted using Trizol. Subsequently, RNA was purified using the RNeasy Mini Kit in combination with on-column DNAse I treatment according to the manufacturer’.
Total RNA kit from Illumina, following the manufacturer's recommended procedures.

value: Whole-embryo's

value: fbn2b +/+

value: 2 dpf


title: WT, 2 dpf, biol rep 3

description:
Library name: RNA021964
Column name in merged_gene_counts_SMAPLE.txt: RNA021964


title: WT, 1 dpf, biol rep 4

description:
Library name: RNA021958
Column name in merged_gene_counts_SMAPLE.txt: RNA021958

value: 1 dpf


title: MT, 1 dpf, biol rep 3

description:
Library name: RNA021957
Column name in merged_gene_counts_SMAPLE.txt: RNA021957

value: fbn2b -/-


title: MT, 2 dpf, biol rep 2

description:
Library name: RNA021953
Column name in merged_gene_counts_SMAPLE.txt: RNA021953


title: WT, 2 dpf, biol rep 2

description:
Library name: RNA021959
Column name in merged_gene_counts_SMAPLE.txt: RNA021959


title: MT, 2 dpf, biol rep 5

description:
Library name: RNA021967
Column name in merged_gene_counts_SMAPLE.txt: RNA021967


title: MT, 1 dpf, biol rep 2

description:
Library name: RNA021952
Column name in merged_gene_counts_SMAPLE.txt: RNA021952


title: MT, 2 dpf, biol rep 1

description:
Library name: RNA021949
Column name in merged_gene_counts_SMAPLE.txt: RNA021949


title: WT, 1 dpf, biol rep 2

description:
Library name: RNA021950
Column name in merged_gene_counts_SMAPLE.txt: RNA021950


title: MT, 2 dpf, biol rep 4

description:
Library name: RNA021966
Column name in merged_gene_counts_SMAPLE.txt: RNA021966


title: WT, 1 dpf, biol rep 3

description:
Library name: RNA021955
Column name in merged_gene_counts_SMAPLE.txt: RNA021955


title: MT, 1 dpf, biol rep 1

description:
Library name: RNA021947
Column name in merged_gene_counts_SMAPLE.txt: RNA021947


title: WT, 1 dpf, biol rep 5

description:
Library name: RNA021963
Column name in merged_gene_counts_SMAPLE.txt: RNA021963


title: MT, 2 dpf, biol rep 3

description:
Library name: RNA021954
Column name in merged_gene_counts_SMAPLE.txt: RNA021954


title: WT, 1 dpf, biol rep 1

description:
Library name: RNA021945
Column name in merged_gene_counts_SMAPLE.txt: RNA021945


title: zebrafish 5dpf larvae exposured to 4 mg/L Lurasidone 3

city: hangzhou

first: Hongjian

last: Gong

state: zhejiang

address: yuhang street 866

institute: zhejiang university

description:
Library name: sample 6
Lurasidone exposured for 5days

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped  to GRCz11/danRer11 using CLC genomic benchwork (parameters-mismatch cost: 2  insertion cost: 3   deletion cost: 3  length fraction:0.8  similarity fracation:0.8 )
Read count extraction and normalization were performed  using CLC genomic benchwork
Assembly: danRer11
Supplementary files format and content: tab-delimited text files inclued RPKM values for each Sample

source_name: zebrafish larvae

growth_protocol: zebrafish embroys were  cultivated in refreshed fish water with standardized physiochemical parameters: conductivity of 600 ± 55 µS/cm and pH 7.8 ± 0.2 at 28.5°C.

extract_protocol:
RNA was  harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used  for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-SeqLibrary Prep Kit  following manufacturer's protocols.

treatment_protocol: 4 mg/L Lurasidone exposured at the 3hpf of zebrafish embroys until 5dpf zerbrafish larvare.

value: zebrafish larvae

value: tissue

value: AB wilde type

value: Lurasidone exposured for 5days


title: zebrafish 5dpf larvae exposured to 4 mg/L Lurasidone 2

description:
Library name: sample 5
Lurasidone exposured for 5days


title: zebrafish 5dpf larvae  2

description:
Library name: sample 2
control

value: control


title: zebrafish 5dpf larvae  3

description:
Library name: sample 3
control


title: zebrafish 5dpf larvae 1

description:
Library name: sample 1
control


title: zebrafish 5dpf larvae exposured to 4 mg/L Lurasidone 1

description:
Library name: sample 4
Lurasidone exposured for 5days


title: LHCN-M2 cells, wildtype, Dam,control for CBX1 and MBD3

city: Grand Rapids

first: Gerd

last: Pfeifer

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

description: Library name: Dam_control

data_processing:
Sequencing was performed with an Illumina HiSeq with 150-bp paired-end read runs.
paired-end  reads were trimmed using TrimGalore with defaut parameters.
the aligned reads were binned into GATC fragments according to GATC sites, then were normalized  to Dam-only control, using damidseq_pipeline (Marshall and Brand, 2015), the log2(Dam-fusion/Dam alone) values of each GATC fragments were then calculated.
Assembly: hg19
Supplementary files format and content: bigWig,  log2(Dam-fusion/Dam)
Library strategy: DamID-Seq

growth_protocol: LHCN-M2 cells were cultured on 0.1% gelatin-coated tissue culture plates in DMEM / medium 199 (4:1) supplemented with 15% fetal bovine serum, 0.02 M HEPES, 0.03 μg/ml zinc sulfate, 1.4 μg/ml vitamin B12, 0.055 μg/ml dexamethasone, 2.5 ng/ml hepatocyte growth factor, 10 ng/ml basic FGF, 60 units/ml penicillin and 60 μg/ml streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA of stable lines was purified Quick-DNA Miniprep Plus kit (Zymo Research, D4070, with the RNase A digested step included. The Rnase treated thee Genomic DNA then were digested with DpnI overnight (at least 12 h) at 37 °C
Ligate the DamID adaptors to 750ng(up to 15ul) DpnI-digested DNA for 2h at 16 °C, followed by DpnII Enzyme into the mixture, digest the mixture at 37 for 3 h. Perform DamID PCR with the programs as followed: 68 °C, 10 min, 1 cycle of 94 °C for 30 s,  65 °C for 5 min,  68 °C, 15 min. 3 cycle of 94 °C, 30 s, 65 °C, 1 min , 68 °C, 10 min, 17 cycle of 94 °C, 30 s 65 °C, 1 min 68 °C, 2 min, followed final extension step with 68 °C for 5 mins. Purified DNA was sonicated with Covaris E220 Evo sonicator to shear DNA from 300 to 500 bp size fragments. Incubated 1 μL of AlwI and sheared mixtures at 37°C for overnight to remove the DamID adaptors. Cleanup the mixtures with AMPure Beads according to the manufacturer’s instructions. 500ng of cleanup DNA  were treated with end-repair, A-tailing and adaptor ligation. AMPupre beads cleanup then were performed according to manufacturer’s instructions. The purified DNA then were amplified by PCR condition:   98 °C, 30 s. 6 cycles of 98 °C, 10 s 60 °C, 30 s 72 °C, 30 s, then final extension at 72 °C for  5mins.

value: human myoblast

value: WT

value: control for CBX1 and MBD3


title: LHCN-M2 cells, wildtype, MBD3,clone2

description: Library name: Dam_MBD3_WT2


title: LHCN-M2 cells, wildtype, MBD3,clone1

description: Library name: Dam_MBD3_WT1


title: LHCN-M2 cells, wildtype, CBX1,clone2

description: Library name: Dam_CBX1_WT2


title: LHCN-M2 cells, wildtype, CBX1,clone1

description: Library name: Dam_CBX1_WT1


title: LHCN-M2 cells,SMCHD1KO, clone2,H2AK119ub1

description: Library name: H2AK119ub1_SMCHD1KO2

data_processing:
The paried-end reads were trimmed with Trim Galore (version 0.4.0) with default parameters, then the trimmed reads were mapped to human genome hg19 with Bowtie2(version 2.3.5)
The aligned reads were deduplicated with the software picard(version 2.19.0)
Then the deduplicated reads were used for peak calling by MACS2. All ChIP data was normalized against the corresponding input control using the ‘-c’ option of MACS2. For H3K27me3 and H2AK119ub1,  the ‘–broad’ option of MACS2 was used to identify broad peaks
Bigwig tracks of ChIP-seq were generated using bamCoverage of deeptools (version 3.5.5) to compute coverage across the entire genome.
Assembly: hg19
Supplementary files format and content: bigWig,  counts coverage

extract_protocol:
For H2AK119ub1 and H3K27me3, cells were crosslinked with 1% formaldehyde only for 8 minutes,after quenching and cell lysis, chromatin was sonicated using a Covaris E220 Evo sonicator.
TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1012, IP-202-1024) was used according to the manufacturer’s instructions to perform ChIP-seq library preparation.  5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 14 cycles on the thermocycler.  Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: SMCHD1 knockout

tag: antibody


title: LHCN-M2 cells, wildtype, clone2,H2AK119ub1

description: Library name: H2AK119ub1_WT2


title: LHCN-M2 cells, wildtype, clone2,H3K27me3

description: Library name: H3K27me3_WT2


title: LHCN-M2 cells, wildtype, clone1,H3K27me3

description: Library name: H3K27me3_WT1


title: LHCN-M2 cells, wildtype, WGBS, clone3

data_processing:
Paired-end reads were trimmed using TrimGalore(version 0.5.0) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.
Trimmed reads were aligned to the hg19 using Bismark version 0.19.0
Duplication were  removed using the deduplicate_bismark script provided with Bismark
CpG methylation values were called  by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Assembly: hg19
Supplementary files format and content: bigWig, methylation coverage with cutoff 3

extract_protocol:
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.


title: UV-crosslinked replicate 3

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

data_processing:
Demultiplexed FASTQ files were processed with goodwright/clipseq pipeline (https://github.com/goodwright/clipseq). To align the reads to tRNA and rRNA, the trimmed fastq files generated in the pipline were used as input for bowtie aligner. Bowtie index was generated with fasta tRNA and rRNA sequences from gtrnadb(hg38-tRNAs.fa) and NCBI (all sequences of 5S, 5.8S, 18S and 28S were considered, including the predicted ones). respectively.
Assembly: hg38
Supplementary files format and content: tab separated file with peaks identified for each sample. This is the output of clippy peak caller.

growth_protocol: cells were cultured in DMEM-Glutamax media (Gibco 31966021) supplemented with 10% FBS (Gibco 10270106) and 1% penicillin-streptomycin (Gibco 15070063) at 37°C and 5% CO2 and grown upon 80% confluency

extract_protocol:
Cells were lysed in iCLIP lysis buffer (50 mM Tris-HCl, 100 mM NaCl, 1% Igepal, 0.1% SDS, 0.5% sodium deoxycholate and complete protease inhibitor cocktail), sonicated using a bioruptor (Digenode) for 3 cycles with alternating 30 sec on/off at high intensity, and cleared by centrifugation (10 min, 15000 rpm, 4ºC).
eIF2A was immunoprecipitated by incubation with a-eIF2A coupled to Dynabeads A for 2h at 4ºC. Beads were washed twice with High Salt wash buffer (50 mM Tris-HCl, 1M NaCl, 1 mM EDTA, 1% Igepal, 0.1% SDS and 0.5% sodium deoxycholate), once with PNK wash buffer (20 mM Tris-HCl, 10 mM MgCl2, 0.2% Tween-20) and resuspended in PNK buffer pH 6.5 (350 mM Tris-HCl pH 6.5, 40 mM MgCl2, 4 mM DTT) containing 10 U PNK enzyme (NEB, #M0201L), 0.5 µl RNasin (Promega, #N2111) and 0.5 µl of FastAP alkaline phosphatase (ThermoFisher, #EF0654), and subsequently incubated for 40 min at 37ºC with shaking (1100 rpm) to phosphorylate the 3’end. After washing with ligation buffer (50 mM Tris-HCl, 10 mM MgCl2) 3'-end adaptor ligation was performed by resuspending the beads in 25 µl of ligation mix (50 mM Tris-HCl, 10 mM MgCl2, 0.8 µl DMSO, 2.5 µl T4 RNA ligase I – high concentration (NEB, #M0437M), 0.4 µl RNasin, 0.5 µl PNK (NEB, #M0201L), 9 µl 50% PEG800) containing 2.5 µl of 1 µM preadenylated adaptor L3-App (/5Phos/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA/iAzideN/AA AAA AAA AAA A/3Bio/) which had been previously conjugated to an infra-red-dye (IRdye-800CW-DBCO (Licor)). This mixture was incubated for 75 min at RT with flickering every 10 min. Beads were washed twice with High Salt buffer and once with PNK buffer prior to adding loading buffer and being resolved on a NuPage 4-12% BisTris Gel, from which they were transferred to a nitrocellulose membrane. Protein-infrared-RNA complexes were visualized using an Odyssey machine, isolated, and RNA was extracted with phenol-chloroform and precipitated in ethanol. The RNA pellet was resuspended in 7 µl RNA/primer mix (5.5 µl water, 0.5 µl 10 mM dNTP mix, 1 µl of irCLIP_ddRT primer) (table S8). RNA was reverse-transcribed, cDNA gel-size selected, isolated, circularized and amplified
iCLIP

treatment_protocol: crosslinked on ice at 0.15 J/cm2 with UV light at 254 nm in ice-cold PBS. Non-crosslinked controls were kept on ice and no UV light was applied.

value: Metastatic melanoma cells

value: UV-crosslinked


title: Non-crosslinked replicate 3

value: Non-crosslinked


title: LHCN-M2 cells, wildtype, clone1,H2AK119ub1

description: Library name: H2AK119ub1_WT1


title: Non-crosslinked replicate 2


title: LHCN-M2 cells, wildtype, WGBS, clone5


title: LHCN-M2 cells, wildtype, WGBS, clone4


title: LHCN-M2 cells, wildtype, WGBS, clone2


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K27me3

description: Library name: H3K27me3_SMCHD1KO2


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K27me3

description: Library name: H3K27me3_SMCHD1KO1


title: UV-crosslinked replicate 1


title: LHCN-M2 cells, wildtype, WGBS, clone1


title: LHCN-M2 cells, wildtype, DamID, clone5

data_processing:
Sequencing was performed with an Illumina HiSeq with 150-bp paired-end read runs.
paired-end  reads were trimmed using TrimGalore with defaut parameters.
the aligned reads were binned into GATC fragments according to GATC sites, then were normalized  to Dam-only control, using damidseq_pipeline (Marshall and Brand, 2015), the log2(Dam-fusion/Dam alone) values of each GATC fragments were then calculated.
Assembly: hg19
Supplementary files format and content: bigWig,  log2(Dam-fusion/Dam)


title: Non-crosslinked replicate 1


title: LHCN-M2 cells, wildtype, WGBS, clone6


title: UV-crosslinked replicate 2


title: LHCN-M2 cells, wildtype, DamID, clone2


title: LHCN-M2 cells, wildtype, DamID, clone1


title: LHCN-M2 cells, wildtype, DamID, clone4


title: LHCN-M2 cells, wildtype, input2

data_processing:
75-bp single-end reads were trimmed with Trim Galore (version 0.4.0) with default parameters, then the trimmed reads were mapped to human genome hg19 with Bowtie2(version 2.3.5)
The aligned reads were deduplicated with the software picard(version 2.19.0)
Then the deduplicated reads were used for peak calling by MACS2. All ChIP data was normalized against the corresponding input control using the ‘-c’ option of MACS2. For CTCF, Rad21, H3K4me3 and H3K27ac, ChIP-Seq peaks were called using the ‘callpeak’ function of MACS2 with default parameters. For H3K9me3, H3K36me2, H3K36me3,  H3K4me1 and Pol II,  the ‘–broad’ option of MACS2 was used to identify broad peaks
Bigwig tracks of ChIP-seq were generated using bamCoverage of deeptools (version 3.5.5) to compute coverage across the entire genome.
Assembly: hg19
Supplementary files format and content: bigWig,  counts coverage

extract_protocol:
Total RNA was isolated with PureLink RNA Mini Kit (Invitrogen).
TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1012, IP-202-1024) was used according to the manufacturer’s instructions to perform ChIP-seq library preparation.  5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 14 cycles on the thermocycler.  Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: LHCN-M2 cells,SMCHD1KO, clone1,H2AK119ub1

description: Library name: H2AK119ub1_SMCHD1KO1


title: LHCN-M2 cells,SMCHD1KO, clone2,RAD21

tag: chip antibody

value: RAD21(Abcam, ab992)


title: LHCN-M2 cells,SMCHD1KO, clone1,RAD21


title: LHCN-M2 cells, wildtype, clone2,RAD21


title: LHCN-M2 cells, wildtype, clone1,RAD21


title: LHCN-M2 cells, wildtype, Dam_control


title: LHCN-M2 cells,SMCHD1KO, clone2,Pol2

value: Pol2(Millipore, 05-623)


title: LHCN-M2 cells, wildtype, clone2,Pol2


title: LHCN-M2 cells, wildtype, clone1,Pol2


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K9me3

value: H3K9me3(Abcam, ab8898)


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K4me3

value: H3K4me3(Millipore, 07-473)


title: LHCN-M2 cells, wildtype, clone2,H3K4me3


title: LHCN-M2 cells, wildtype, clone2,H3K4me1


title: LHCN-M2 cells, wildtype, clone1,H3K4me3


title: LHCN-M2 cells, wildtype, clone2,H3K9me3


title: LHCN-M2 cells, wildtype, input3


title: LHCN-M2 cells, wildtype, clone1,H3K9me3


title: LHCN-M2 cells, wildtype, input1


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K4me3


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K4me1


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K36me2


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K36me3


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K36me3


title: LHCN-M2 cells, wildtype, clone1,H3K4me1


title: LHCN-M2 cells, wildtype, clone1,H3K36me3


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K36me2


title: LHCN-M2 cells, wildtype, clone2,H3K36me2


title: LHCN-M2 cells, wildtype, clone1,H3K36me2


title: LHCN-M2 cells, wildtype, clone2,H3K27ac

value: H3K27ac(Abcam, ab4729)


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K27ac


title: LHCN-M2 cells,SMCHD1KO, clone1,Pol2


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K9me3


title: LHCN-M2 cells, wildtype, clone1,H3K27ac


title: LHCN-M2 cells,SMCHD1KO, clone1,H3K4me1


title: LHCN-M2 cells, wildtype, clone2,H3K36me3


title: LHCN-M2 cells, wildtype, clone2,CTCF

value: CTCF(Active motif,61311)


title: LHCN-M2 cells,SMCHD1KO, clone1,CTCF


title: Raji, Input

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
ChIP-seq reads were trimmed using Trimmomatic-0.39, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg38 using Bowtie2 with parameter: --mp 2
peaks were called using MACS2 with following parameters “-q 0.05 -B --nomodel --extsize 200”
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

source_name: Raji

extract_protocol:
CCL86 Raji and HTB96 U2OS cells were cultured for 80% confluency for ChIP-seq assay. Half of the cell cultures were treatment with doxorubicin and the other half remained untreated. We used 150 ng/ml concentration of doxorubicin for U2OS cells and 200 ng/ml for Raji cells. The multiple culture plates were pooled and then divided into six separate Petri dishes for determining cMYC and P53 genomic binding. Cells were fixed with 1% formaldehyde for 10 minutes, then quenched and washed two times before lysis. Chromatin was fragmented by sonication using ultrasonicator for 1.5 hours.
Illumina HiSeq2500 platform in a 2x100bp paired-end configuration was used to obtain 35 million reads on average for each library sample

value: Raji

value: Burkitt lymphoma

value: Input


title: Raji, cMYC untreated control

value: untreated control

value: Monoclonal anti-cMYC (sc-40)


title: LHCN-M2 cells, wildtype, clone1,CTCF

value: human myoblast

value: WT


title: Raji, cMYC treated with doxorubicin

value: doxorubicin


title: LHCN-M2 cells,SMCHD1KO, clone2,H3K27ac

value: SMCHD1 knockout


title: Raji, treated with doxorubicin, rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR (parameters: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Read counts were obtained from STAR output
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

extract_protocol:
CCL86 Raji and HTB96 U2OS cells were cultured for 80% confluency for RNA-seq assay. Half of the cell cultures were treatment with doxorubicin and the other half remained untreated. We used 150 ng/ml concentration of doxorubicin for U2OS cells and 200 ng/ml for Raji cells. The multiple culture plates were pooled and then divided into six separate Petri dishes for determining transcriptional profil in each cell line. Total RNA was extracted using min-plus kit from Qiagen. Around 10ug total RNA was used for the sequencing libraries.
Illumina HiSeq2500 platform in a 2x100bp paired-end configuration was used to obtain 35 million reads on average for each library sample


title: Raji, P53 treated with doxorubicin

value: monoclonal anti-P53 (sc-126)


title: Raji, untreated, rep1


title: U2OS, P53 untreated control

value: osteosarcoma


title: U2OS, cMYC treated with doxorubicin


title: U2OS, Input


title: U2OS, cMYC untreated control


title: Raji, untreated, rep2


title: Raji, P53 untreated control


title: Raji, untreated, rep3


title: Raji, treated with doxorubicin, rep2


title: Raji, treated with doxorubicin, rep1


title: U2OS, treated with doxorubicin, rep3


title: U2OS, treated with doxorubicin, rep1


title: U2OS, untreated control, rep3


title: U2OS, treated with doxorubicin, rep2


title: U2OS, untreated control, rep2


title: U2OS, untreated control, rep1


title: LHCN-M2 cells,SMCHD1KO, clone2,CTCF


title: LL-Plateau-2

city: Ningbo

first: Bin

last: Hu

address: No.169 Qixing South Road, Meishan Street, Beilun District, Ningbo City, Zhejiang Province, China

institute: Ningbo university

description:
Library name: Sample 95
L_10_B_2

data_processing:
Fastp Software for Quality Control with Default Parameters
Alignment to the Reference Genome Using HISAT2 v2.2.1
The alignment results were sorted and converted to BAM format using SAMtools
FeatureCounts was used for gene quantification(TPM)
Assembly: Strain: NIES-144GenBank accession: GCA_011766145.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: The table file includes TPM values for all samples combined into one

organism: Haematococcus lacustris

source_name: Unicellular Alga

extract_protocol:
Total RNA of each sample was extracted using Trizol (Sangon Biotech, China) in accordance with the manufacturer’s instructions. RNA concentration and quality were assessed using a NanoDrop ND1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). RNA samples meeting the following criteria were used for library preparation and sequencing: concentration > 200 ng/μL, OD260/OD280 > 1.8, OD260/OD230 > 1.8, RIN > 6.5, and 28S/18S ratio > 1.0.
After passing quality control, RNA sequencing libraries were constructed using the MGIEasy™ mRNA Library Preparation Kit (MGI, Shenzhen, China). mRNA was enriched using oligo(dT) magnetic beads, which bind to the polyA tail of mRNA through A-T base pairing. The enriched mRNA was fragmented and reverse transcribed into second-strand cDNA using N6 random primers. The cDNA was then purified using DNA magnetic beads and subjected to PCR amplification. After amplification, the library was purified again using DNA magnetic beads. The quality and size of the libraries were evaluated using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and an Agilent 2100 system (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed by Wuhan BGI (Wuhan, China) on the MGISEQ-2000 platform, generating approximately 20 million clean reads per sample using single-end sequencing.

value: Unicellular Alga

value: Green Motile Cells,Red Non-Motile Cells

tag: light intensity

value: Low light

tag: sampling time

value: Plateau phase

tag: exogenous treatment


title: LL-Plateau-3

description:
Library name: Sample 96
L_10_B_3

tag: tissue

tag: cell type


title: U2OS, P53 treated with doxorubicin

tag: cell line

tag: treatment


title: LL-Plateau-1

description:
Library name: Sample 94
L_10_B_1

tag: genotype


title: LL-Exponential-NaAc-2

description:
Library name: Sample 92
L_5_C_2

value: Exponential phase

value: 1.8 g/L Sodium acetate


title: LL-Exponential-3

description:
Library name: Sample 90
L_5_B_3


title: LL-Exponential-NaAc-1

description:
Library name: Sample 91
L_5_C_1


title: LL-Exponential-NaAc-3

description:
Library name: Sample 93
L_5_C_3


title: LL-Exponential-2

description:
Library name: Sample 89
L_5_B_2


title: LL-Exponential-1

description:
Library name: Sample 88
L_5_B_1


title: HL-Day5-Uri-3

description:
Library name: Sample 87
H_5_U_3

value: High light

value: Day 5

value: 1 mM Uridine


title: HL-Day5-NR-3

description:
Library name: Sample 84
H_5_IN_3

value: Nitrogen-repletion


title: HL-Day5-NR-2

description:
Library name: Sample 83
H_5_IN_2


title: HL-Day5-ND-3

description:
Library name: Sample 81
H_5_DN_3

value: Nitrogen-deprivation


title: HL-Day5-NR-1

description:
Library name: Sample 82
H_5_IN_1


title: HL-Day5-ND-2

description:
Library name: Sample 80
H_5_DN_2


title: HL-Day5-ND-1

description:
Library name: Sample 79
H_5_DN_1


title: HL-Day5-Gua-2

description:
Library name: Sample 77
H_5_G_2

value: 1 mM Guanine


title: HL-Day5-8

description:
Library name: Sample 74
H_5_B_8

value: WT


title: HL-Day5-7

description:
Library name: Sample 73
H_5_B_7


title: HL-Day5-9

description:
Library name: Sample 75
H_5_B_9


title: HL-Day5-Uri-2

description:
Library name: Sample 86
H_5_U_2


title: HL-Day5-6

description:
Library name: Sample 72
H_5_B_6


title: HL-Day5-5mM-FDP-3

description:
Library name: Sample 71
H_5_5mFDP_3

value: 5 mM Fructose diphosphate


title: HL-Day5-Gua-1

description:
Library name: Sample 76
H_5_G_1


title: HL-Day5-5mM-FDP-2

description:
Library name: Sample 70
H_5_5mFDP_2


title: HL-Day5-5

description:
Library name: Sample 68
H_5_B_5


title: HL-Day5-5mM-FDP-1

description:
Library name: Sample 69
H_5_5mFDP_1


title: HL-Day5-3

description:
Library name: Sample 66
H_5_B_3


title: HL-Day5-2

description:
Library name: Sample 65
H_5_B_2


title: HL-Day5-4

description:
Library name: Sample 67
H_5_B_4


title: HL-Day5-Uri-1

description:
Library name: Sample 85
H_5_U_1


title: HL-Day5-1mM-KI-3

description:
Library name: Sample 64
H_5_KI_3

value: 1 mM Potassium iodide


title: HL-Day5-Gua-3

description:
Library name: Sample 78
H_5_G_3


title: HL-Day5-1mM-FDP-3

description:
Library name: Sample 61
H_5_1mFDP_3

value: 1 mM Fructose diphosphate


title: HL-Day5-1mM-KI-2

description:
Library name: Sample 63
H_5_KI_2


title: HL-Day5-1mM-KI-1

description:
Library name: Sample 62
H_5_KI_1


title: HL-Day5-1

description:
Library name: Sample 58
H_5_B_1


title: HL-Day3-Xan-4

description:
Library name: Sample 55
H_3_H_4

value: Day 3

value: 1 mM Xanthosine


title: HL-Day3-Xan-6

description:
Library name: Sample 57
H_3_H_6

value: Unicellular Alga

value: Green Motile Cells,Red Non-Motile Cells


title: HL-Day3-Xan-3

description:
Library name: Sample 54
H_3_H_3


title: HL-Day3-Xan-1

description:
Library name: Sample 52
H_3_H_1


title: HL-Day3-Xan-2

description:
Library name: Sample 53
H_3_H_2


title: HL-Day3-9

description:
Library name: Sample 48
H_3_B_9


title: HL-Day3-6

description:
Library name: Sample 45
H_3_B_6


title: HL-Day3-7

description:
Library name: Sample 46
H_3_B_7


title: HL-Day3-Tau-2

description:
Library name: Sample 50
H_3_N_2

value: 1 Mm Taurine


title: HL-Day3-8

description:
Library name: Sample 47
H_3_B_8


title: HL-Day3-4

description:
Library name: Sample 43
H_3_B_4


title: HL-Day3-5

description:
Library name: Sample 44
H_3_B_5


title: HL-Day3-Tau-1

description:
Library name: Sample 49
H_3_N_1


title: HL-Day3-3

description:
Library name: Sample 42
H_3_B_3