title: SCA8_Met3

city: Gainesvillle

first: Lisa

last: Romano

state: Florida

address: 2033 Mowry Road

department: Molecular genetics and microbiology

institute: University of Florida

description: Library name: SCA8_Met3

data_processing:
FASTQ file quality and total number of reads were assessed using FASTQC (version 0.11.9) and datasets with an average read depth >35 million paired-end reads were accepted for this study. FASTQ files were aligned to the GRCm39/mm39 reference genome, which was modified to include the human ATXN8OS coding sequence, using STAR. To compare expression levels of ATXN8 and ATXN8OS, a human reference genome containing ATXN8OS and 10 kb upstream and downstream sequence was indexed using HiSat2 as described before5 and raw RNA-Seq reads were aligned to this custom reference genome. Fragment per kilobase million (FPKM) of ATXN8 and ATXN8OS was calculated by normalizing the read count mapped to gene‐specific regions of ATXN8 and ATXN8OS to the length. The difference was calculated by dividing both FPKM values by ATXN8OS FPKM value. This analysis was done on four biological replicates. Using BAM files as input, PSI values were quantitated using rMATS-turbo (version 4.2.0)29 to identify dysregulated exons. AS events were considered to be dysregulated according to the FDR (≤0.05) and absolute value of the inclusion level difference (|Δ PSI| ≥ 0.1) when comparing SCA8 mice to NT mice. rMATS raw files are provided in Supp. Table 1 and Supp. Table 2. Heatmaps were generated using the ComplexHeatmap (2.10.0) R package. Gene Ontology analysis was performed using Metascape (version v3.5.20230101)30 with default express analysis.
Assembly: mm39
Supplementary files format and content: tsv file include TPM values for each sample

source_name: Cerebellum,brainstem

extract_protocol:
Mouse tissue from cerebellum and brainstem was lysed and homogenized with 800 μL TRIzol reagent (Thermo Fisher Scientific, 15596018) in 2-mL tubes pre-filled with 1.5-mm high-impact zirconium beads (Benchmark Scientific, D1032-15). Tubes were agitated at 10,000 × g for 1 min using a Bead Ruptor 12 (OMNI International, 19-050A). Then, they were placed on ice for 1 min, for a total of four repetitions for complete tissue lysis. RNA was then extracted following the Direct-zol RNA Miniprep kit protocol, with DNase I treatment (Zymo Research, R2070). RNA concentration was measured using a Nanodrop One spectrophotometer (Thermo Fisher Scientific, ND-ONE-W). RNA integrity was assessed by measuring the RNA integrity number using capillary electrophoresis (Agilent, M5310AA) paired with the RNA kit (Agilent, DNF-471-0500). Samples with an RQN > 8 were further processed.
RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA library prep kit for Illumina, using ribosomal RNA depletion followed by strand-specific RNA-seq preparation. Samples were amplified with PCR for 9–11 cycles and sequenced using the Illumina NextSeq 2000. A total of 300 ng RNA was used as input for library preparation. rRNA was depleted from samples (NEB, E7405), and libraries were prepared for paired-end Illumina sequencing (NEB, E7760L) with the following adjustments to the manufacturer’s protocol: 1:40 adaptor dilution, universal and indexing primers at 1 μM final concentration, and 10 cycles for PCR enrichment of adaptor-ligated DNA. Library quality was assessed via capillary gel electrophoresis (Agilent, M5310AA) paired with the High Sensitivity Next Generation Sequencing Fragment Kit (Agilent, DNF-474-0500). Library concentrations were determined using a Library Quant Kit for Illumina (NEB, E7630L) following the manufacturer’s protocol. Sequencing was performed on the Illumina NextSeq 2000 platform (Illumina, 20038897) using the onboard denature and dilute protocol, paired with P3 reagents for 200 cycles (Illumina, 20040560). Sequencing output was demultiplexed and converted to FASTQ format via Basespace BCL Convert (version 2.3.0).

value: Cerebellum,brainstem

value: Metformin


title: SCA8_Met4

status: Public on Feb 24 2026

type: SRA

country: USA

description: Library name: SCA8_Met4

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: SCA8_Met2

description: Library name: SCA8_Met2


title: J1PN_4

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

data_processing:
RNA-seq: fastq files were aligned to mouse reference genome GRCm38 using the Hisat2 v2.0.5
RNA-seq: BAM files resulting from the alignments were summarized to genes using the featureCounts v2.0.0 with the parameters ' -p -O --fraction’
mouse reference genome GRCm38
tab-delimited text files include raw counts values for each sample

source_name: a single two cell embryo

extract_protocol:
C57BL/6 × JF1/Ms zygotes were selected 10 h after fertilization (late G2 or PN5 stage) and the second polar body was removed using a micromanipulator. Two-cell embryos were corrected 34 h after fertilization. Single 2-cell embryo were lysed using cell lysis buffer  [cantained in SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio)] in 0.2 mL single tube.
libraries were prepared with SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) and Nextera XT DNA Library Preparation Kit (illumina).

tag: methods

value: RNA-seq

tag: strain

tag: embryo type

tag: embryo type in silico


title: J2PN_10


title: WT, 6C10, 5535

city: Omaha

first: Justin

last: Rudd

address: 2500 California Plaza

institute: Creighton University

description: Library name: 10_S10

data_processing:
Analysis of bulk RNA-seq data was performed in PartekFlow. Adapter-trimmed reads were aligned to hg38 using STAR (Dobin et al., 2013) and quantified to ‘hg38-Ensembl Transcripts release 105’ using PartekE/M. Gene counts were normalized by median ratio, and normalized counts were used for differential expression analysis using DESeq2 (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: Text file includes normalized counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: xenograft tumor

growth_protocol: For subcutaneous xenografts of hFWE WT or KO cells, 1*106 SCC13 cells were resuspended in 100µl of cold 1:1 sterile PBS:Matrigel (Corning 356237) and subsequently injected into the subcutaneous space on the dorsal flank of a NOD-Prkdcem26Cd52Il2rgem26Cd22/NjuCrl (NCG) mouse (Charles River 572). Tumors were harvested at 26d post injection for transcriptomic analysis.

extract_protocol:
At necropsy, tumors were weighed before partitioning for RNA isolation or histological processing. RNA was isolated from flash frozen samples using Qiagen RNeasy Mini Kit (Qiagen 74104).
For preparation of sequencing libraries, 500ng of RNA isolated from flash frozen tumors was used with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina along with NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturers instructions. Library quality and quantity were assessed using RNA ScreenTape Assay (Agilent) and Agilent 4200 TapeStation System following the manufacturers protocol. 3 nM equimolar pooled libraries were sequence on the Illumina NextSeq 2000 system (Illumina) using NextSeq 1000/2000 P2 Reagent Cartridge 100 cycles and P2 Flow Cell (Illumina).

value: xenograft tumor

tag: cell line

tag: cell type

value: Cutaneous Squamous Cell Carcinoma

value: hFWE WT


title: J1PN_3

value: Parthenote


title: WT, 6C10, 5537

description: Library name: 12_S12


title: J1PN_2


title: SCA8_Water1

description: Library name: SCA8_Water1

value: Water


title: SCA8_Water3

description: Library name: SCA8_Water3


title: SCA8_Met1

description: Library name: SCA8_Met1


title: WT, 6C9, 5533

description: Library name: 8_S8


title: J1PN_1


title: B2PN_9

value: C57BL/6 xJF1/Ms


title: WT, 6C9, 5532

description: Library name: 7_S7


title: SCA8_Water4

description: Library name: SCA8_Water4


title: NT_Water1

description: Library name: NT_Water1

value: Non transgenic


title: B2PN_8


title: NT_Water3

description: Library name: NT_Water3


title: WT, 6C9, 5531

description: Library name: 6_S6


title: CATCH_H3K27me3_P1PN_rep2

description: Library name: Sample24

library_source: genomic

data_processing:
The reads were filtered using fastp with the ‘-3 -q 15 -l 15’ options.
The filtered reads were mapped to the mouse genome (mm10) using Bowtie2 v2.3 with ‘-N 1 -L 25’ options.
To distinguish the parental alleles of the read sequences of BDF1 × JF1/Ms embryos, diagnostic single nucleotide polymorphisms (dSNPs) were developed using the deposited deep sequence data obtained from JF1/Ms. After mapping the JF1/Ms reads to the mouse genome (mm10) using BWA-MEM v0.7 with the default parameters, SNPs were called using HaplotypeCaller implemented in GATK v4.1.4.1. After filtering out low-confidence SNPs with ‘QD < 2.0, QUAL < 30.0, SOR > 3.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, and ReadPosRankSum < -8.0’, differently fixed 20,885,964 sites were used as dSNPs. For the reference of allele-specific analysis, dSNP sites on the mouse genome (mm10) were masked as N. Each aligned read (see single-embryo RNA-seq and ChIL-seq above) was subjected to assign its parental origin using the dSNPs with SNPsplit v0.3.4.
Assembly: mm10
Supplementary files format and content: .bigwig

molecule: genomic DNA

source_name: embryo

growth_protocol: Embryos were cultured in Chatot, Ziomek, and Bavister medium (CZB).

extract_protocol:
BDF1(C57BL/6×DBA2) ×JF1/Ms zygotes were selected 10 h after fertilization (late G2 or PN5 stage). Zygotes were collected in 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with a complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride.
CATCH-seq libraries were prepared as previously described (Zhu, Y et al.,).

value: embryo

tag: developmental stage

value: Zygote

tag: cell no.

tag: antibody


title: WT, 6C10, 5534

description: Library name: 9_S9


title: NT_Water2

description: Library name: NT_Water2


title: CATCH_H3K27me3_PG_rep2

description: Library name: Sample20

value: PG


title: B2PN_5


title: B2PN_7


title: B2PN_6


title: CATCH_H3K27me3_AG_rep1

description: Library name: Sample21

value: AG


title: CATCH_H3K27me3_2PN_rep4

description: Library name: Sample18


title: WT, 6C9, 5530

description: Library name: 5_S5


title: WT, 5B2, 5529

description: Library name: 4_S4


title: CATCH_H3K27me3_2PN_rep3

description: Library name: Sample17


title: SCA8_Water2

description: Library name: SCA8_Water2


title: NT_Water4

description: Library name: NT_Water4


title: WT, 5B2, 5528

description: Library name: 3_S3


title: CATCH_H3K9me3_P1PN_rep2

description: Library name: Sample16


title: CATCH_H3K27me3_AG_rep2

description: Library name: Sample22


title: CATCH_H3K27me3_P1PN_rep1

description: Library name: Sample23


title: siFOXO1_LSS_3

city: New Haven

first: Hanqiang

last: Deng

state: CT

address: 116 Court Street

department: Yale Cardiovascular Research Center

institute: Yale University

description: Library name: DENG_FOXO1_LSS_S12

data_processing:
Samples were subjected to RNA-sequencing using Illumina NovaSeq 6000 sequencer (100bp paired end reads).
The base calling data from sequencing were transferred into FASTQ files using bcl2fastq2 conversion software (version 2.20, Illumina).
The raw reads were aligned to the human reference genome Hg19 using HISAT2 (version 2.1.0) alignment software and processed using HTSeq (version 0.11.1) to generate read counts for every gene.
DESeq2 (version 1.24, using default parameter) was used to pre-process raw data to remove the noise, normalize each sample to correct the batch effect, perform principal component analysis (PCA) for observing the similarity of replicates, and identify differential expression genes.
Assembly: human reference genome GRCh38 hg19.
Supplementary files format and content: Excel includes raw counts for each sample.

source_name: HUVEC

growth_protocol: HUVECs were maintained in EGM2 Endothelial Cells Growth Media (Lonza) and used for experiments between passage 2 and passage 5.

extract_protocol:
Total RNA was extracted from cells with RNeasy Plus Mini Kit (QIAGEN) according to the Manufacturer’s instructions.
RNA isolation and quality assessment, mRNA enrichment, cDNA synthesis, end repair, PCR amplification and library quantification.

treatment_protocol: HUVECs were transfected with Ctrl (siCtrl) or FOXO1 (siFOXO1) siRNA for 3 days, then subjected to low shear stress (LSS; 3 dynes/cm2) for 24 hours.

value: HUVEC

value: primary endothelial cell

value: FOXO1 knockdown

value: LSS (low shear stress)


title: B2PN_4


title: WT, 5B2, 5526

description: Library name: 1_S1


title: CATCH_H3K9me3_PG_rep2

description: Library name: Sample12


title: CATCH_H3K9me3_P1PN_rep1

description: Library name: Sample15


title: WT, 5B2, 5527

description: Library name: 2_S2


title: siFOXO1_LSS_1

description: Library name: DENG_FOXO1_LSS_S10


title: CATCH_H3K27me3_PG_rep1

description: Library name: Sample19


title: B2PN_3


title: CATCH_H3K9me3_AG_rep2

description: Library name: Sample14


title: siFOXO1_LSS_2

description: Library name: DENG_FOXO1_LSS_S11


title: KneeJoint-PD03-3

city: Shanghai

first: Chunmeng

last: Huang

address: Changjiang Rd

country: China

institute: The Second Rehabilitation Hospital of Shanghai

description: Library name: Sample 9

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly mRatBN7.2 (https://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz.
Assembly: mRatBN7.2
Supplementary files format and content: File include Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: knee

growth_protocol: Primary osteoblasts were isolated from the calvaria of 24-hourold male Sprague–Dawley rats, which were provided by Shanghai Xipur-Biak Experimental Animal Co., Ltd. (Shanghai, China). Calvarial bones were digested in 0.1% collagenase type I (BS163, Biosharp, China) at 37 °C for 60 minutes in a shaking water bath. Isolated osteoblasts were maintained in high-glucose Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (10270-106, Thermo Fisher, USA) and penicillin–streptomycin (ST488, Beyotime, China).

extract_protocol:
Remove the medium and directly add 1000μL Trizol into the each hydrogel group to harvest samples. Total RNA was extracted using Trizol reagent (Sigma-Aldrich, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: To evaluate the levels of phosphorylated proteins after intervention with thrombin and inhibitors, osteoblasts were cultured in serum-free DMEM for five hours prior to treatment. Subsequently, serum-free DMEM supplemented with 20U/mL thrombin (ST1699, Beyotime, China), thrombin + 0.1 mM PD03 (20–22) (S1036, Selleck, China) were administered for 5, 15, and 30 minutes to detect the expression levels of p-Stat3 and p-Erk1/2, and for 15, 30, and 60 minutes to detect the expression level of p-NF-kB; thrombin + 5 mM C188-9 (S8605, Selleck, China) for 5, 15, and 30 minutes to detect p-Stat3 and p-Erk1/2; thrombin + 0.1 mM QNZ (S4902, Selleck, China) for 15, 30, and 60 minutes to detect p-Erk1/2; 20ng/mL IL-1b (501-RL, Bio-Techne, USA) + 0.1 mM PD03 were administered for 15, 30, and 60 minutes to detect p-NF-kB; IL-1b + 0.1 mM QNZ were administered for 15, 30, and 60 minutes to detect p-Erk1/2.

value: knee

value: Primary osteoblasts


title: KneeJoint-PD03-2

description: Library name: Sample 8


title: CATCH_H3K9me3_2PN_rep4

description: Library name: Sample10


title: KneeJoint-Thrombin-2

description: Library name: Sample 5

value: thrombin


title: B2PN_28

value: RNA-seq


title: CATCH_H3K9me3_2PN_rep3

description: Library name: Sample9


title: siCtrl_LSS_3

description: Library name: DENG_FOXO1_LSS_S6

value: WT


title: KneeJoint-Thrombin-1

description: Library name: Sample 4


title: KneeJoint-PD03-1

description: Library name: Sample 7


title: CATCH_H3K9me3_AG_rep1

description: Library name: Sample13


title: B2PN_2


title: B2PN_29


title: siFOXO1_Static_3

description: Library name: DENG_FOXO1_LSS_S9

value: Static


title: siFOXO1_Static_2

description: Library name: DENG_FOXO1_LSS_S8


title: KneeJoint-Thrombin-3

description: Library name: Sample 6


title: B2PN_27


title: CATCH_H3K9me3_PG_rep1

description: Library name: Sample11


title: B2PN_26


title: siCtrl_LSS_2

description: Library name: DENG_FOXO1_LSS_S5


title: siFOXO1_Static_1

description: Library name: DENG_FOXO1_LSS_S7


title: B2PN_25


title: B2PN_24


title: KneeJoint-Control-2

description: Library name: Sample 2

value: NC


title: B2PN_23

value: C57BL/6 xJF1/Ms


title: CATCH_H3K4me3_P1PN_rep2

description: Library name: Sample8


title: KneeJoint-Control-3

description: Library name: Sample 3


title: CATCH_H3K4me3_P1PN_rep1

description: Library name: Sample7


title: siCtrl_LSS_1

description: Library name: DENG_FOXO1_LSS_S4


title: CATCH_H3K4me3_AG_rep2

description: Library name: Sample6


title: B2PN_20


title: siCtrl_Static_3

description: Library name: DENG_FOXO1_LSS_S3


title: siCtrl_Static_2

description: Library name: DENG_FOXO1_LSS_S2


title: B2PN_21


title: siCtrl_Static_1

description: Library name: DENG_FOXO1_LSS_S1


title: KneeJoint-Control-1

description: Library name: Sample 1


title: CATCH_H3K4me3_2PN_rep5

description: Library name: Sample2


title: siFOXO1_OSS-3

description: Library name: DENG_FOXO1_OSS_S12

source_name: HAEC

growth_protocol: HAECs were maintained in EGM2 Endothelial Cells Growth Media (Lonza) and used for experiments between passage 2 and passage 5.

treatment_protocol: HAECs were transfected with Ctrl (siCtrl) or FOXO1 (siFOXO1) siRNA for 3 days, then subjected to oscillatory shear stress (OSS; 0.5±4 dynes/cm2) for 24 hours.

value: HAEC

value: OSS (oscillatory shear stress)


title: midAna SHFSCs in October, female (bio rep 1)

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

description: Library name: Sample 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to goat (Capra hircus) transcriptomes (GCF_001704415.1_ARS1) using Kallisto (v.0.46.1) with parameters -b 100. The gene abundances were obtained by kallisto-sleuth (v.0.30.0) pipeline in TPM (transcripts per million) (Bray NL et al. 2016).
Assembly: GCF_001704415.1_ARS1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

organism: Capra hircus

source_name: Secondary hair follicle stem cells from goat skin

extract_protocol:
Total RNA was extracted from the secondary hair follicle stem cells using RNAiso Plus (TRIzol method, TaKaRa Bio, Dalian, China).
cDNA library construction of RNA-seq was performed according to the operating instructions for the NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

value: Secondary hair follicle stem cells

tag: Sex

value: female


title: CATCH_H3K4me3_AG_rep1

description: Library name: Sample5

value: embryo

value: Zygote

value: AG


title: CNE2-EBV_LMP2A-IT1_2

city: Guangzhou

first: Zhengzhou

last: Lu

state: Guangdong province

address: 74 Zhongshan Second Road

institute: Sun Yat-Sen University

description: Library name: Sample 4

data_processing:
Raw sequencing data were evaluated using fastp to assess sequence quality metrics. Adapters and low-quality bases were removed to generate clean reads for downstream analysis. We annotated the location of LMP2A-IT1 in the EBV genome (Akata strian, accession no. KC207813.1) and integrated the modified EBV genome with the human hg38 genome to generate a combined reference genome for read alignment. Clean reads were aligned to the reference genome using HISAT2 v2.2.1 with the parameter --rna-strandness RF to preserve strand-specific information. Aligned reads were assigned to genes using featureCounts v2.0.1 with the parameter -s 2 (specific to RF-stranded libraries). We only counted uniquely mapped reads. Raw count data were imported into the R environment and normalized using DESeq2 v1.34.0. Transcripts Per Million (TPM) values were calculated to estimate gene expression levels.
Assembly: Human genome (hg38); EBV genome (Akata strian, accession no. KC207813.1)
Supplementary files format and content: excel files include TPM values for each Sample

extract_protocol:
Total RNA was extracted with Trizol reagent and qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 300~350 bp fragments, and first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP). RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template without U was enriched by PCR, and the PCR product was purified to obtain the final library

treatment_protocol: Doxycycline 1ug/ml treatment for 48h

value: Epithelial cell

value: Doxycycline 1ug/ml


title: CATCH_H3K4me3_PG_rep2

description: Library name: Sample4

value: PG


title: siFOXO1_OSS-2

description: Library name: DENG_FOXO1_OSS_S11

value: primary endothelial cell

value: FOXO1 knockdown


title: midAna SHFSCs in October, male (bio rep 2)

description: Library name: Sample 4

value: Secondary hair follicle stem cells from goat skin

value: male


title: siFOXO1_OSS-1

description: Library name: DENG_FOXO1_OSS_S10


title: B2PN_22

value: RNA-seq


title: CATCH_H3K27me3_2PN_rep2

data_processing:
The reads were filtered using fastp with the ‘-3 -q 15 -l 15’ options.
The filtered reads were mapped to the mouse genome (mm10) using Bowtie2 v2.3 with ‘-N 1 -L 25’ options.
To distinguish the parental alleles of the read sequences of BDF1 × JF1/Ms embryos, diagnostic single nucleotide polymorphisms (dSNPs) were developed using the deposited deep sequence data obtained from JF1/Ms. After mapping the JF1/Ms reads to the mouse genome (mm10) using BWA-MEM v0.7 with the default parameters, SNPs were called using HaplotypeCaller implemented in GATK v4.1.4.1. After filtering out low-confidence SNPs with ‘QD < 2.0, QUAL < 30.0, SOR > 3.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, and ReadPosRankSum < -8.0’, differently fixed 20,885,964 sites were used as dSNPs. For the reference of allele-specific analysis, dSNP sites on the mouse genome (mm10) were masked as N. Each aligned read (see single-embryo RNA-seq and ChIL-seq above) was subjected to assign its parental origin using the dSNPs with SNPsplit v0.3.4.
Assembly: mm10
Supplementary files format and content: .bigwig
Library strategy: CATCH-seq

value: BDF1(C57BL/6xDBA2) xJF1/Ms


title: B2PN_19

value: C57BL/6 xJF1/Ms


title: B2PN_17


title: siFOXO1_Static-3

description: Library name: DENG_FOXO1_OSS_S9

value: HAEC

value: Static


title: B2PN_1


title: CATCH_H3K27me3_2PN_rep1


title: CATCH_H3K4me3_2PN_rep4

description: Library name: Sample1


title: CNE2-EBV_vector_2

description: Library name: Sample 2

value: WT

value: vector


title: CATCH_H3K4me3_PG_rep1

description: Library name: Sample3

value: embryo


title: earlyAna SHFSCs in April, male (bio rep 2)

description: Library name: Sample 2

value: Secondary hair follicle stem cells


title: CNE2-EBV_LMP2A-IT1_1

description: Library name: Sample 3


title: earlyAna SHFSCs in April, female (bio rep 1)

description: Library name: Sample 1

value: female


title: B2PN_16


title: B2PN_18


title: CATCH_H3K27me3_1PN_rep2

value: Zygote


title: siFOXO1_Static-2

description: Library name: DENG_FOXO1_OSS_S8


title: CATCH_H3K27me3_1PN_rep1


title: B2PN_14


title: siFOXO1_Static-1

description: Library name: DENG_FOXO1_OSS_S7


title: B2PN_15


title: siCtrl_OSS-3

description: Library name: DENG_FOXO1_OSS_S6

value: OSS (oscillatory shear stress)


title: CNE2-EBV_vector_1

description: Library name: Sample 1

value: Epithelial cell

value: Doxycycline 1ug/ml


title: HUVEC vehicle

city: Taipei

first: Yi-Lin

last: Chiu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Department of Biochemistry, College of Biomedical Sciences

country: Taiwan

institute: National Defense Medical University

description:
Library name: S1
S1

data_processing:
HISAT2 v2.2.1
Assembly: GRCh38.p14
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: HUVECs were obtained from Lonza (Walkersville, MD, USA). The cells were cultured using a sterile endothelial growth medium (EGM-2, Lonza, Walkersville, MD, USA) and maintained at 37°C in a 5% CO2 environment throughout the experiment.

extract_protocol:
Total RNA was extracted from HUVECs using TRIzol reagent according to the manufacturer’s instructions.
Poly(A)-selected mRNA was fragmented and used for cDNA synthesis with ProtoScript II. Second-strand synthesis followed, then end repair, A-tailing, adapter ligation, and size selection (~420 bp) via magnetic beads. Libraries were amplified (13 PCR cycles), quantified by Qubit 3.0, and sequenced using the Illumina HiSeq 4000 platform.

treatment_protocol: HUVECs were used upon reaching 80-90% confluence. Tetrahydrocurcumin (THC, over 98.0% purity by HPLC) was purchased from Wuhan ChemFaces Biochemical Co., Ltd. (Hubei, China). For treatments, cells were incubated for 24 hours with either a vehicle control (dimethyl sulfoxide; DMSO; Sigma-Aldrich, St. Louis, MO, USA) or varying concentrations of THC (2.5 and 5 µM)

value: HUVEC


title: B2PN_12


title: HUVEC + 5 µM THC

description:
Library name: S3
S3


title: siCtrl_OSS-2

description: Library name: DENG_FOXO1_OSS_S5

value: primary endothelial cell


title: HUVEC + 2.5 µM THC

description:
Library name: S2
S2


title: CATCH_H3K9me3_1PN_rep2


title: siCtrl_Static-3

description: Library name: DENG_FOXO1_OSS_S3


title: CATCH_H3K9me3_1PN_rep1


title: CATCH_H3K9me3_2PN_rep2


title: CATCH_H3K9me3_2PN_rep1


title: B1PN_9


title: siCtrl_OSS-1

description: Library name: DENG_FOXO1_OSS_S4


title: siCtrl_Static-1

description: Library name: DENG_FOXO1_OSS_S1


title: B2PN_13


title: kp3

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic (v0.39)
Trimmed sequences were aligned to the mm10 mouse genome and reads per gene was counted using STAR (v2.7.10b)
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

source_name: small intestine

extract_protocol:
RNA from small intestine tissue was extracted using the RNeasy Mini Kit (Qiagen).
The RNA library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: small intestine

value: Kazachstania pintolopesii


title: CATCH_H3K4me3_2PN_rep3

value: BDF1(C57BL/6xDBA2) xJF1/Ms


title: kp4


title: B2PN_11

value: RNA-seq

value: C57BL/6 xJF1/Ms


title: B2PN_10


title: siCtrl_Static-2

description: Library name: DENG_FOXO1_OSS_S2

value: HAEC

value: Static


title: kp1

value: WT


title: kp2


title: CATCH_H3K4me3_2PN_rep2

value: embryo


title: B1PN_8

value: Low quality


title: C9-ALS, iMNs, replicate2

city: Baltimore

first: Mingming

last: Liu

state: MD

address: 615 N. Wolfe Street

department: BMB, BSPH

institute: Johns Hopkins University

description:
Library name: C9ALS1_iMN_r2
column in iMN_RNA-seq_raw_counts.xlsx: C9ALS1_iMN_r2

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The trimmed reads were aligned to the human genome (hg19) and GENCODE v19 annotated transcripts using Hisat2 v2.2.1 and quantiﬁed with featureCounts v2.0.1
The R package edgeR was used to identify differentially expressed genes with an absolute log2 (fold change) >1, FPKM > 1 and P-value < 0.05.
Assembly: hg19
Supplementary files format and content: RNA-seq raw counts matrix for each sample

source_name: iMNs

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen).
cDNA libraries for sequencing were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) coupled with NEBNext rRNA Depletion Kit v2 (NEB, E7400)

value: iMNs

value: Motor Neuron


title: B1PN_7

value: Parthenote


title: CATCH_H3K4me3_2PN_rep1

value: Zygote


title: Isogenic, iMNs, replicate1

description:
Library name: Isogenic_CTRL1_iMN_r1
column in iMN_RNA-seq_raw_counts.xlsx: Isogenic_CTRL1_iMN_r1

value: Isogenic control


title: CATCH_H3K4me3_1PN_rep3


title: C9-ALS, iMNs, replicate1

description:
Library name: C9ALS1_iMN_r1
column in iMN_RNA-seq_raw_counts.xlsx: C9ALS1_iMN_r1


title: Isogenic, iMNs, replicate2

description:
Library name: Isogenic_CTRL1_iMN_r2
column in iMN_RNA-seq_raw_counts.xlsx: Isogenic_CTRL1_iMN_r2


title: ctr2

value: control


title: B1PN_6


title: ctr3


title: CTRL, B-lymphocyte, replicate1

description:
Library name: CTRL1_B_lymphocyte_r1
column in Blymphocyte_RNA-seq_raw_counts.xlsx: CTRL1_B_lymphocyte_r1

source_name: Lymphoblastoid

value: Lymphoblastoid

value: B-Lymphocyte

value: CTRL


title: DB23_P-SF3B1_T235_OTS964_REP4

city: Pamplona

first: Igor

last: Ruiz de los Mozos

state: Nyp

address: C. del Sadar s/n

department: Department of Personalized Medicine

country: Spain

institute: NASERTIC

description:
Library name: DB23_P-SF3B1_T235_OTS964_REP4
P-SF3B1_T235_OTS964
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr.bed.gz
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr_norm.bigWig

data_processing:
iCLIP sequencing data, including total, P-Thr211- and P-Thr235 SF3B1 samples, were analyzed on the flow.bio platform (https://app.flow.bio/ ) using the nf-core/clipseq pipeline (West, C. et al. 2023) (v1.0; https://github.com/nf-core/clipseq/tree/1.0.0 ).
Initial processing involved removing experimental barcodes (iCount version 2.0.0, de-multiplex function https://github.com/tomazc/iCount ),  followed by read alignment with STAR (Dobin, A. et al. 2013) against the human reference genome (hg38, GRCh38.p13 primary assembly, GENCODE version 39), allowing up to two mismatches. Unique molecular identifiers (UMIs) were applied to identify and eliminate PCR duplicates.
Cross-linking events were determined by identifying the nucleotide immediately preceding each uniquely mapped sequencing read.
Genome-wide coverage tracks for combined iCLIP replicates were generated using deepTools (Ramirez, F. et al. 2014) , normalized by sequencing depth and total read count, and binned per nucleotide.
Assembly: GRCh38.p13 primary assembly, GENCODE version 39
Supplementary files format and content: iCLIP individual sample crosslink site (bed.gz)
Supplementary files format and content: iCLIP individual sample crosslink site normalized by sequencing depth and total read count, and binned per nucleotide (bigWig)
Supplementary files format and content: iCLIP group merge sample crosslink site (bed.gz)
Supplementary files format and content: iCLIP group merge crosslink site normalized by sequencing depth and total read count, and binned per nucleotide (bigWig)

growth_protocol: Human colorectal HCT116 cell line was maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
Described in detail in library construction protocol
iCLIP was performed as previously described (Huppertz et al., 2014) with only minor modifications described below. Each cell pellet (originally from one 150 cm2 plate) was lysed in 1 ml of lysis buffer and the lysate was homogenized by passing three-times through an insulin syringe. Lysate was treated with 4 U/ml Turbo DNase (Thermo Fisher, AM2238), 12 U/ml RNase I (Thermo Fisher, AM2295) shaking at 1100 rpm and 37°C for 3 min. Clarified extracts (21000g for 30 min) were incubated for 2 h with appropriate antibody pre-bound to 50 µl of protein G Dynabeads. After series of stringent washes, adenylated L3 RNA adapter was ligated to the 3’end of crosslinked RNAs. Proteins and crosslinked RNAs were resolved by SDS-PAGE (NuPAGE 4-12% Bis-Tris Protein Gel, Thermo Fisher Scientific, NP0322) and transferred to nitrocellulose membrane. The region of the membrane containing the radioactively labeled crosslinked protein–RNA complexes was excised, RNA was isolated and reverse transcribed to cDNA. cDNA was fractionated using urea denaturing gel electrophoresis and three fractions running between 70-85 nt (L-low), 85-120 nt (M-medium) and 120-200 nt (H-high) were isolated. Each fraction was independently circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. After final PCR amplification using P3 and P5 Solexa primers all three fractions were pooled together in ratio 1:5:5 (L:M:H). Multiplexed libraries were sequenced as 75 bp single-end reads on Illumina sequencer (HiSeq 2500 or NextSeq 500)

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 50 nM OTS964 for 1 h. The cells were than crosslinked by UV-C (254 nm, 200 mJ/cm2).

tag: batch

value: biol. rep 3


title: B1PN_3

value: RNA-seq


title: B1PN_5

value: C57BL/6 xJF1/Ms


title: CATCH_H3K4me3_1PN_rep2

value: BDF1(C57BL/6xDBA2) xJF1/Ms


title: ctr4

value: small intestine


title: C9-ALS, B-lymphocyte, replicate2

description:
Library name: C9ALS1_B_lymphocyte_r2
column in Blymphocyte_RNA-seq_raw_counts.xlsx: C9ALS1_B_lymphocyte_r2


title: B1PN_4


title: ctr1

value: WT


title: CATCH_H3K4me3_1PN_rep1

value: embryo


title: CTRL, B-lymphocyte, replicate2

description:
Library name: CTRL1_B_lymphocyte_r2
column in Blymphocyte_RNA-seq_raw_counts.xlsx: CTRL1_B_lymphocyte_r2


title: B1PN_2


title: GC-AS-10308-27R,Recovery,27,male

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

description: Library name: GC-AS-10308-27R

data_processing:
Reduced representation bisulfite sequencing (RRBS) libraries were processed using a standard workflow. Raw base-call files were demultiplexed using Illumina bcl2fastq /2.19.1, and unique molecular identifiers (UMIs) were extracted using umi_tools 81. Reads were adapter and quality-trimmed (minimum phred score 30) with trim_galore (https://doi.org/10.5281/zenodo.5127898). in RRBS mode, reads less than 15 bp after trimming were discarded. Trimmed reads were aligned to the human reference genome (hg38) using bismark/0.22.1 82 with bowtie2, with the PBAT option enabled. PCR duplicates were removed with deduplicate_bismark in a UMI-aware manner. CpG methylation calls were obtained using bismark_methylation_extractor.
Assembly: hg38 Homo sapiens (TxDb.Hsapiens.UCSC.hg38.knownGene)
Supplementary files format and content: .bismark.cov.gz (Bismark coverage files)

source_name: Skeletal Muscle

extract_protocol:
Skeletal muscle tissue derived from humans (21 ± 3 mg) was added to 2 mL homogenizing mix tubes (Fisherbrand™, Fisher Scientific) containing 180 μl Buffer ATL (Qiagen, Hilden, Germany) before transferring to a tissue homogenizing instrument (MagNA Lyser; Roche, Basel, Switzerland) for subsequent homogenization (3 × 45 s at 6000 rpm, placing samples on ice for 5 mins between each disruption). Following homogenization, 20 μl proteinase K (Qiagen) was added and samples were incubated at 56°C until complete lysis (≈ 30-60 mins) before continuing with DNA purification using a DNeasy® Blood & Tissue kit (Qiagen) as per the manufacturer’s instructions. DNA quantity and quality for both human (251 ± 47 ng/mg tissue, 2 ± 0 A260/A280 and 2.1 ± 0.1 A260/A230) samples were quantified using spectrophotometry (NanoDrop™ 2000; Thermo Fisher Scientific) and concentrations confirmed via fluorometry (Qubit®, Qiagen). DNA integrity was confirmed prior to sequencing via Agilent Bioanalsyer 2100 with DIN scores 7.11 ± 0.17.
RRBS libraries were prepared from 100ng of genomic DNA using the Diagenode Premium RRBS v2 library preparation kit, as per the manufacturer's protocol. Two pools of 8 samples, and three pools of 7 samples were prepared after qPCR quantification of adapter-ligated sample and prior to bisulphite conversion. 14 cycles of final library amplification were performed after assessment of bisulphite converted library pool by qPCR. Libraries were sequenced using the Illumina NextSeq 2000 with P3 SBS 100-cycle sequencing kit, generating 50bp paired-end reads.

value: Skeletal Muscle

tag: condition/time

value: Recovery

tag: participant

tag: gender

value: male


title: GC-AS-10308-27A2,Repeated Atrophy,27,male

description: Library name: GC-AS-10308-27A2

tag: tissue

value: Repeated Atrophy


title: GC-AS-10308-27B,Baseline,27,male

description: Library name: GC-AS-10308-27B

value: Baseline


title: DB23_P-SF3B1_T235_OTS964_REP3

description:
Library name: DB23_P-SF3B1_T235_OTS964_REP3
P-SF3B1_T235_OTS964
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr.bed.gz
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr_norm.bigWig

value: biol. rep 2


title: B1PN_1


title: DB23_P-SF3B1_T235_DMSO_REP3

description:
Library name: DB23_P-SF3B1_T235_DMSO_REP3
P-SF3B1_T235_DMS
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr.bed.gz
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr_norm.bigWig

value: DMSO


title: GC-AS-10308-27A1-1,Atrophy,27,male

description: Library name: GC-AS-10308-27A1-1

value: Atrophy


title: DB23_P-SF3B1_T235_DMSO_REP4

description:
Library name: DB23_P-SF3B1_T235_DMSO_REP4
P-SF3B1_T235_DMS
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr.bed.gz
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr_norm.bigWig


title: C9-ALS, B-lymphocyte, replicate1

description:
Library name: C9ALS1_B_lymphocyte_r1
column in Blymphocyte_RNA-seq_raw_counts.xlsx: C9ALS1_B_lymphocyte_r1

value: Lymphoblastoid

value: B-Lymphocyte

tag: genotype


title: B1PN_19

value: Parthenote


title: Isogenic control iMNs, IgG, bioreplicate 1

description: Library name: ChIP_Isogenic_CTRL1_IgG

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The processed reads were mapped to the human genome (hg19) using Bowtie2. Duplicated reads and reads aligned to mitochondrial genome were discarded. The retained BAM files were then sorted, indexed, and used to generate bigWig files
BigWig files were generated using deepTools.
Assembly: hg19
Supplementary files format and content: bigwig files for each sample

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Diagenode) until the chromatin DNA was 100–500 bp in size.
The libraries were constrcuted  using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual.

value: iMNs

value: Motor Neuron

value: Isogenic control


title: B1PN_17

value: RNA-seq

value: C57BL/6 xJF1/Ms


title: iSLK_219_Latent

city: Boston

first: Soo Mi

last: Lee

state: MA

address: 3 BLACKFAN CIRCLE, CLS 417

department: Pathology

institute: BIDMC/Harvard Medical School

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase v22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80). Differential expression analysis was performed using DESeq2 v1.26.0.
Assembly: GRCh38; EMBL:U75698.1
Supplementary files format and content: excel,expression profiles

growth_protocol: iSLK.219 and iSLK cells were cultured in complete DMEM (Gibco) and stimulated with 0.5 µg/mL doxycycline (Sigma-Aldrich) for 72 hours to induce lytic reactivation. For all inducible cell lines, the Tet System approved FBS (Takara Bio) was used.

extract_protocol:
Total RNA was isolated using mirVana miRNA isolation Kit following the manufacturer's protocol.
Approximately 1 μg of total RNA were used to prepare small RNA library according to Illumina’s TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA, USA). Then the libraries were sequenced by Illumina’s HiSeq 2500 following the vector’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: KSHV-infected epithelial cells

value: WT

tag: treatment


title: B1PN_18

tag: methods


title: GC-AS-10308-15R,Recovery,15,male

description: Library name: GC-AS-10308-15R

value: Skeletal Muscle

value: Recovery


title: C9-ALS iMNs, PolII antibody IP

description: Library name: ChIP_iMN_C9ALS1_PolII


title: Isogenic control iMNs, Input, bioreplicate 1

description: Library name: ChIP_Isogenic_CTRL1_Input


title: iSLK_Dox_induced_rep1

source_name: iSLK

value: iSLK

value: Uninfected epithelial cells

value: Treated with 0.5 µg/mL Doxycycline for 72 h


title: Isogenic control iMNs, PolII antibody IP

description: Library name: ChIP_Isogenic_CTRL1_PolII


title: iSLK_219_Lytic


title: GC-AS-10308-15A1,Atrophy,15,male

description: Library name: GC-AS-10308-15A1

value: male


title: B1PN_16

tag: strain

value: dead


title: iSLK_Dox_induced_rep2


title: GC-AS-10308-15B,Baseline,15,male

description: Library name: GC-AS-10308-15B

value: Baseline


title: B1PN_15

tag: embryo type


title: GC-AS-10308-15A2,Repeated Atrophy,15,male

description: Library name: GC-AS-10308-15A2

value: Repeated Atrophy


title: C9-ALS iMNs, Input, bioreplicate 1

description: Library name: ChIP_iMN_C9ALS1_Input


title: GC-AS-10308-12A2,Repeated Atrophy,12,male

description: Library name: GC-AS-10308-12A2


title: GC-AS-10308-12R,Recovery,12,male

description: Library name: GC-AS-10308-12R


title: B1PN_14

tag: embryo type in silico

value: Parthenote


title: B1PN_12


title: GC-AS-10308-12B,Baseline,12,male

description: Library name: GC-AS-10308-12B


title: iSLK_Uninduced_rep2

tag: cell line


title: C9-ALS iMNs, IgG, bioreplicate 1

description: Library name: ChIP_iMN_C9ALS1_IgG

value: iMNs

tag: cell type


title: K562 cells, LDB1 shRNA, rep 1

city: Charlottesville

first: Francine

middle: E.

last: Garrett-Bakelman

state: VA

address: 1340 Jefferson park Ave.

department: Medicine and BMG

institute: University of Virginia

description: Library name: A3

data_processing:
Qualtiy was assessed using FastQC and aligned to the hg19 human genome using STAR. Differential expression analysis was conducted using MultiRankSeq.
Assembly: hg19
Supplementary files format and content: HEL siTAL1 FeatureCounts with reads aligned to each annotated gene in the hg19 genome. K562 LMO2-degron FRKM aligned to hg19. K562 shLDB1 TPM aligned to hg19.

extract_protocol:
RNA was extracted using phenol-chloroform/Trizol
HEL libraries were prepared using Fast RNA-seq Lib Prep Kit V2(Abclonal RK20306) by Novogene and K562 libraries were prepared for Illumina preparation by Azenta.

tag: group

value: LDB1 shRNA 1


title: K562 cells, LDB1 control shRNA

description: Library name: A1

value: control shRNA


title: B1PN_13

value: RNA-seq


title: iSLK_Uninduced_rep1


title: GC-AS-10308-12A1,Atrophy,12,male

description: Library name: GC-AS-10308-12A1

value: Atrophy


title: B1PN_11

value: C57BL/6 xJF1/Ms


title: GC-AS-10308-9B,Baseline,9,female

description: Library name: GC-AS-10308-9B

value: female


title: B1PN_10


title: iSLK_219_Dox_induced_rep2

value: KSHV-infected epithelial cells

value: WT


title: K562 cells, day 4, LMO2 degron rep 2, 750 uM dTAGv1, bio rep 2

description: Library name: JH24

value: LMO2 degron

tag: agent

value: 750 uM dTAGv1

tag: time point

value: day 4


title: iSLK_219_Uninduced_rep1


title: iSLK_219_Dox_induced_rep1

value: Treated with 0.5 µg/mL Doxycycline for 72 h


title: K562 cells, LDB1 shRNA, rep 2

description: Library name: A5

value: LDB1 shRNA 2


title: K562 cells, day 4, LMO2 degron rep 1, 750 uM dTAGv1, bio rep 2

description: Library name: JH23


title: w1_noHS_72hour_AgeMatchControl_rep1_LongRNA

city: Worcester

first: Samantha

last: Ho

address: 373 Plantation St.

department: Department of Molecular Medicine

institute: University of Massachusetts Chan Medical School

data_processing:
piSet_rnaseq pipeline from GitHub was used to analyze long RNA sequences reads. Steps were: Bowtie2 (Version 2.2.5) was used to map raw sequencing reads to rRNA sequence. Remaining reads were mapped to dm6 and transposon consensus using using STAR (Version 2.5.2b) and Hisat2. Transcript abundance for each gene, transposon, and piRNA cluster (rpkm) was counted using BEDTools (Version 2.27.1).
piSet_srnaseq was used to analyze small RNA sequencing reads. Steps were: the 3ʹ end adaptor (TGGAATTCTCGGG) was removed via cutadapt (Version 1.15) and the raw small RNA-seq reads were mapped to rRNA, miRNA hairpin, snoRNA, snRNA, and tRNA sequence allowing for no mismatches using Bowtie (Version 1.1.0). The remaining reads were mapped to the Drosophila genome (dm6) and transposon consensus sequences. Small RNA abundance was normalized to unique mapping reads.
Assembly: dm6
Supplementary files format and content: tab deliniated txt files containing RMPM values

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Total RNA was extracted from 2-4 day old female ovaries using the MirVana kit (Ambion).
For Long RNA-seq, rRNA was depleted using antisense rRNA oligo hybridization followed by RNase H digestion, RNA Fragmentation, Reverse Transcription, dUTP incorporation, end Repair, size selection using Ampure XP beads, A-tailing, Adaptor ligation, UDG treatment and PCR amplification.
For Small RNA-seq, small RNAs 18-29 nucleotide long were isolated using polyacrylamide gel purification followed by 2S rRNA depletion, 3’ adaptor ligation, 5’ adaptor ligation, reverse transcription, and PCR amplification.

treatment_protocol: Heat shock was carried on 2-4 day old flies with yeast for 1 hour in a water bath kept at 37oC. Flies were allowed to recover at room temp for designated times before proceeding with extraction and library construction.  No Shock control flies were kept at room temp as controls.

value: Ovary

tag: age

value: 5-7 day old

value: No heat shock 72 hour age match

tag: recovory time_after_heat_stress


title: w1_noHS_72hour_AgeMatchControl_rep2_LongRNA


title: iSLK_219_Dox_induced

description: RNA-seq

data_processing:
Single-end reads were mapped to the human genome (Ensembl GRCh37) or the KSHV reference genome (NC_009333) using Bowtie2 v2.2.9. The abundance of gene expression was estimated using RSEM v1.3.0 and the differential expression analysis was performed using edgeR v3.12.1.
Assembly: GRCh37
Supplementary files format and content: excel,expression profiles

growth_protocol: iSLK.219 cells were cultured in complete DMEM (Gibco) and stimulated with 0.5 µg/mL doxycycline (Sigma-Aldrich) for 72 hours to induce lytic reactivation. For all inducible cell lines, the Tet System approved FBS (Takara Bio) was used.

extract_protocol:
Total RNA was extracted using mirVana miRNA isolation Kit following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared according to the Illumina's TruSeq stranded mRNA sample preparation protocol or Illumina's TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA, USA).


title: GC-AS-10308-9R,Recovery,9,female

description: Library name: GC-AS-10308-9R

value: Skeletal Muscle

tag: condition/time

value: Recovery


title: K562 cells, day 4, LMO2 control, 750 uM dTAGv1, bio rep 2

description: Library name: JH22

value: LMO2 control


title: iSLK_219_Uninduced

description: RNA-seq


title: GC-AS-10308-9A1,Atrophy,9,female

description: Library name: GC-AS-10308-9A1

tag: participant


title: GC-AS-10308-8A2,Repeated Atrophy,8,male

description: Library name: GC-AS-10308-8A2

value: Repeated Atrophy

tag: gender

value: male


title: w1_noHS_48hour_AgeMatchControl_rep1_LongRNA

tag: tissue

value: 4-6 day old

value: No heat shock 48 hour age match


title: K562 cells, day 1, LMO2 degron rep 2, 750 uM dTAGv1, bio rep 2

description: Library name: JH20

value: day 1


title: GC-AS-10308-9A2,Repeated Atrophy,9,female

description: Library name: GC-AS-10308-9A2

value: female


title: GC-AS-10308-8A1,Atrophy,8,male

description: Library name: GC-AS-10308-8A1

value: Atrophy


title: w1_noHS_48hour_AgeMatchControl_rep2_LongRNA

tag: genotype


title: K562 cells, day 4, parental, 750 uM dTAGv1, bio rep 2

description: Library name: JH21

value: parental cells

value: 750 uM dTAGv1


title: w1_HS1hr37C_72hRec_rep2_LongRNA

tag: treatment

value: Heat Shock for 1 hour at 37oC

value: 72 hour recovoery after heat stress


title: GC-AS-10308-8B,Baseline,8,male

description: Library name: GC-AS-10308-8B

value: Baseline


title: K562 cells, day 1, LMO2 control, 750 uM dTAGv1, bio rep 2

description: Library name: JH18


title: GC-AS-10308-8R,Recovery,8,male

description: Library name: GC-AS-10308-8R


title: ERG245 "24h on-48h off", Donor 18

city: Washington

first: Adonia

middle: Evangelos

last: Papathanassiu

state: DC

address: 416 Marietta PL, NW

institute: Ergon Pharmaceuticals LLC

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
Differentially expressed genes were identified using the edgeR program.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: T cell

growth_protocol: CD8+ T cells were grown in RPMI containing 10%FBS, rhIL-2, and antibiotics (5% CO2, 37°C)

extract_protocol:
RNA was obtained using RNeasy Plus Mini kit (Qiagen). 250 ng of total RNA was used for library construction.
RNA-Seq library was prepared according to KAPA mRNA HyperPrep kit with 200-300 bp insert size (Roche, Wilmington, MA)

treatment_protocol: CD8+ T cells were activated in RPMI containing 10%FBS and antibiotics for the first 24h. Vehicle-treated cells received 10 mL PBS. ERG245-treated cells received 100 mM ERG245. After 24h at 37°C, media were replenished without addition of ERG245 and the cells were cultured in RPMI containing 10%FBS, rhIL-2 (30U/mL, PeproTech), and antibiotics (complete RPMI) for another 48h.

value: T cell

value: primary

value: WT

value: Activated and ERG245-treated for 24h-Additional culture for 48h


title: Vehicle "24h on- 48h off", Donor 18

value: Activated and  Vehicle-treated for 24h-Additional culture for 48h


title: K562 cells, day 1, LMO2 degron rep 1, 750 uM dTAGv1, bio rep 2

description: Library name: JH19

value: LMO2 degron


title: ERG245 "24h on-48h off", Donor 17

value: male


title: GC-AS-10308-7A1-1,Atrophy,7,male

description: Library name: GC-AS-10308-7A1-1

value: Skeletal Muscle


title: K562 cells, day 1, parental, 750 uM dTAGv1, bio rep 2

description: Library name: JH17


title: iSLK_219_Uninduced_rep2

value: KSHV-infected epithelial cells


title: ERG245 "24h on-48h off", Donor 16


title: w1_HS1hr37C_48hRec_rep2_LongRNA

value: Ovary

value: 4-6 day old

value: 48 hour recovoery after heat stress


title: w1_HS1hr37C_72hRec_rep1_LongRNA

value: 5-7 day old


title: K562 cells, day 0, LMO2 degron rep 1, no dTAGv1, bio rep 2

description: Library name: JH15

value: no dTAGv1

value: day 0


title: K562 cells, day 0, LMO2 degron rep 2, no dTAGv1, bio rep 2

description: Library name: JH16


title: Vehicle "24h on- 48h off", Donor 16


title: GC-AS-10308-7R,Recovery,7,male

description: Library name: GC-AS-10308-7R

value: Recovery


title: w1_HS1hr37C_24hRec_antiH3K9me3_rep2

data_processing:
Cut and Run analysis was performed using piSet_chipseq pipeline on GitHub. Briefly, Bowtie2 (Version 2.2.5) was used to map sequencing reads to the Drosophila genome (dm6) and transposon consensus sequence, signal mapping to transposons were normalized to total number of genome mapping Cut and Run reads.
Assembly: dm6
Supplementary files format and content: bigWig files
Library strategy: CUT and RUN

extract_protocol:
Ovaries were dissected from 2-4 day flies and bound to ConA beads, incubated with primary antibody, DNA digested with pAMA and DNA was recovered.
Recovered DNA undergone library construction with the following steps: end repair, A-tailing, adaptor ligation, and PCR amplification.

value: 2-4 day old

value: Heat Shock for 1 hour at 37oC

value: 24 hour recovoery after heat stress

tag: cut-and-run antibody


title: w1_HS1hr37C_24hRec_antiH3K9me3_rep1


title: GC-AS-10308-7B,Baseline,7,male

description: Library name: GC-AS-10308-7B

value: Baseline


title: Vehicle "24h on- 48h off", Donor 17

value: T cell

value: primary

value: WT


title: w1_HS1hr37C_48hRec_rep1_LongRNA


title: GC-AS-10308-7A2,Repeated Atrophy,7,male

description: Library name: GC-AS-10308-7A2

value: Repeated Atrophy

value: male


title: w1_HS1hr37C_24hRec_antiH3K27me3_rep2


title: K562 cells, day 0, LMO2 control, no dTAGv1, bio rep 2

description: Library name: JH14

value: LMO2 control


title: K562 cells, day 0, parental, no dTAGv1, bio rep 2

description: Library name: JH13

value: parental cells


title: Expt1_Confetti_mesenchyme

city: New York City

first: Joo-Hyeon

state: NY

address: 430 East 67th Street

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample 1
10x Genomics

data_processing:
Alignment performed using 10x cellranger (v8.0.0).
Assembly: GRCm38
Supplementary files format and content: mtx, tsv, csv files: raw count, barcodes and genes

source_name: Distal lung

extract_protocol:
For isolation of lung cell, mice were culled by cervical dislocation and lungs cleared of blood via perfusion with 10ml of PBS. Lungs were inflated with 2-3ml of a Dispase solution via intratracheal injection. When isolating mesenchymal cells, Collagenase I was added to the Dispase solution at 350U/ml before inflation. Lungs were carefully dissected out of the thoracic cavity and placed on a petri dish on ice. Individual lobes were separated from each lung, placed in a 50ml falcon and minced into small pieces. Cells were washes down with 3ml of PBS to the bottom of the falcon tube. When isolating epithelial cells only, 60ul of 100mg/ml Collagenase/Dispase solution was added per tube. Samples were places in a shaking incubator at 37ºC, 190 rpm, for 45 min. 7.5ul of 1% DNase I was added to each sample in the final 10 min of incubation. The resulting cell suspensions were filtered sequentially through 100 µm and 40 µm cell strainers and washed with 2 ml of 10% foetal bovine serum (FBS) in PBS (PF10) to collect remaining cells. Samples were centrifuged at 800 rpm for 5 min at 4ºC. Supernatant was removed and pellets were resuspended in 1 ml of red blood cell lysis buffer (RBC buffer, made inhouse: 150 mM NH4Cl and 10 mM KHCO3 in distilled H2O) for 60 seconds at RT. After lysis, 6 ml of Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 820 (DMEM/F-12) was added to the tube to neutralize the RBC buffer. 500µL of filtered FBS was added slowly to the bottom of each tube to collect live cells. Tubes were centrifuged again at 800rpm for 5 min at 4ºC. Cell pellets were resuspended in PF10 and placed into separate 1.5 ml tubes for antibody staining. CD45–CD31–EpCAM– cells were isolated and submitted for library preparation.
Cell suspensions were spun down, counted, and resuspended in 0.04% bovine serum albumin (BSA) in PBS to achieve a cell concentration of ~345 cells/µL. Single-cell 3′ RNA-seq libraries were generated according to manufacturer’s instructions (Chromium Single Cell 3′ Reagent v3 Chemistry Kit, 10X Genomics) and cDNA quality was assessed.

value: Distal lung

value: Mesenchymal cells

value: Sftpc-CreERT2; R26R-Confetti


title: GC-AS-10308-5A1,Atrophy,5,male

description: Library name: GC-AS-10308-5A1

value: Skeletal Muscle

value: Atrophy


title: w1_HS1hr37C_24hRec_antiH3K27me3_rep1

value: Ovary


title: K562 cells, day 4, LMO2 degron rep 2, 750 uM dTAGv1, bio rep 1

description: Library name: JH12

value: LMO2 degron

value: 750 uM dTAGv1

value: day 4


title: K562 cells, day 4, LMO2 degron rep 1, 750 uM dTAGv1, bio rep 1

description: Library name: JH11


title: Expt1_Red2Kras_mesenchyme

description:
Library name: Sample 2
10x Genomics

value: Sftpc-CreERT2; Red2Kras


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 6

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description: Library name: 23248XR-03-61

data_processing:
FastQC was employed to check the quality of raw reads.Sequences of poor quality were removed.
HiSAT2 was used for alignment of trimmed reads using mm39 build and GRCm39 GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Assembly: mm39
Supplementary files format and content: Raw_counts.txt (raw counts from Featurecounts for all samples compiled in a table with library name as headers), Normalized_counts.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers),

source_name: Hippocampus

extract_protocol:
RNA was isolated from samples using Qiazol phase separation followed by cleanup with RNeasy 96 Kit per manufacturer’s instruction. Isolated RNA sample quality was assessed by both RNA Tapestation assay and High Sensitivity RNA Tapestation assay (Agilent Technologies Inc., California, USA and quantified by Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland)
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 450bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus (Illumina, California, USA) with a read length configuration of 150 PE for 60M PE reads per sample (30M in each direction).

value: Hippocampus

tag: Sex

value: Male

tag: animal id


title: w1_HS1hr37C_24hRec_antiRbIgG_rep3

value: 2-4 day old

value: Heat Shock for 1 hour at 37oC

value: 24 hour recovoery after heat stress

value: Rabbit IgG


title: GC-AS-10308-5R,Recovery,5,male

description: Library name: GC-AS-10308-5R

value: Recovery

value: male


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 7

description: Library name: 23248XR-03-62


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 5

description: Library name: 23248XR-03-60


title: GC-AS-10308-5B,Baseline,5,male

description: Library name: GC-AS-10308-5B

value: Baseline


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 4

description: Library name: 23248XR-03-59


title: K562 cells, day 4, LMO2 control, 750 uM dTAGv1, bio rep 1

description: Library name: JH10

value: LMO2 control


title: w1_HS1hr37C_24hRec_antiRbIgG_rep2


title: K562 cells, day 4, parental, 750 uM dTAGv1, bio rep 1

description: Library name: JH9

value: parental cells


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 3

description: Library name: 23248XR-03-58


title: GC-AS-10308-4A2,Repeated Atrophy,4,male

description: Library name: GC-AS-10308-4A2

value: Skeletal Muscle

value: Repeated Atrophy


title: w1_HS1hr37C_1hRec_antiH3K9me3_rep2

value: Ovary

value: 1 hour recovoery after heat stress


title: K562 cells, day 1, LMO2 degron rep 2, 750 uM dTAGv1, bio rep 1

description: Library name: JH8

value: LMO2 degron

value: 750 uM dTAGv1

value: day 1


title: K562 cells, day 1, LMO2 degron rep 1, 750 uM dTAGv1, bio rep 1

description: Library name: JH7


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 2

description: Library name: 23248XR-03-57

value: Hippocampus

value: Male


title: w1_HS1hr37C_24hRec_antiRbIgG_rep1

value: 2-4 day old

value: Heat Shock for 1 hour at 37oC


title: GC-AS-10308-4R,Recovery,4,male

description: Library name: GC-AS-10308-4R


title: GC-AS-10308-4A1,Atrophy,4,male

description: Library name: GC-AS-10308-4A1

value: Atrophy


title: GC-AS-10308-5A2,Repeated Atrophy,5,male

description: Library name: GC-AS-10308-5A2


title: w1_HS1hr37C_1hRec_antiH3K27me3_rep2


title: K562 cells, day 1, LMO2 control, 750 uM dTAGv1, bio rep 1

description: Library name: JH6


title: GC-AS-10308-4B,Baseline,4,male

description: Library name: GC-AS-10308-4B


title: w1_HS1hr37C_1hRec_antiH3K27me3_rep1


title: w1_HS1hr37C_1hRec_antiH3K9me3_rep1


title: Hippocampus of Mrpl40 -/+,Slc25a1 -/+, biol rep 1

description: Library name: 23248XR-03-56


title: w1_HS1hr37C_1hRec_antiRbIgG_rep3

value: Rabbit IgG


title: K562 cells, day 1, parental, 750 uM dTAGv1, bio rep 1

description: Library name: JH5


title: GC-AS-10308-3R,Recovery,3,female

description: Library name: GC-AS-10308-3R

value: Recovery

value: female


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 6

description: Library name: 23248XR-03-54


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 7

description: Library name: 23248XR-03-55


title: K562 cells, day 0, LMO2 degron rep 2, no dTAGv1, bio rep 1

description: Library name: JH4

value: no dTAGv1

value: day 0


title: GC-AS-10308-3B,Baseline,3,female

description: Library name: GC-AS-10308-3B

value: Skeletal Muscle

value: Baseline


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 5

description: Library name: 23248XR-03-53


title: GC-AS-10308-3A1,Atrophy,3,female

description: Library name: GC-AS-10308-3A1


title: w1_HS1hr37C_1hRec_antiRbIgG_rep1

value: Ovary


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 4

description: Library name: 23248XR-03-52


title: GC-AS-10308-3A2,Repeated Atrophy,3,female

description: Library name: GC-AS-10308-3A2

value: Repeated Atrophy


title: K562 cells, day 0, LMO2 degron rep 1, no dTAGv1, bio rep 1

description: Library name: JH3

value: LMO2 degron


title: K562 cells, day 0, LMO2 control, no dTAGv1, bio rep 1

description: Library name: JH2

value: LMO2 control


title: w1_noHS_control_antiH3K9me3_rep2

value: No heat shock


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 2

description: Library name: 23248XR-03-50

value: Hippocampus


title: GC-AS-10307-7A1-1,Atrophy,7,male

description: Library name: GC-AS-10307-7A1-1

data_processing:
Resulting FastQ files were imported and processed in Partek Flow® software (version 12.4.0; Partek, Inc. Missouri, USA) to filter contaminants (rDNA/tRNA/mtrDNA) using Bowtie 2 (version 2.2.5) and align reads to the hg38 Homo sapiens (release 39) genome assembly using Spliced Transcripts Alignment to a Reference (STAR) alignment tool (version 2.7.3a). Total number of pre/post-aligned reads was 35/34 million (65 bp average read length). Phred scores were >33, thus trimming and filtering of reads was not required. Normalized differential gene expression analysis was performed using DESeq2 median of ratios.
Assembly: hg38 Homo sapiens (release 39)
Supplementary files format and content: .txt file contains normalised counts (CPM)

extract_protocol:
Skeletal muscle tissue derived from the human vastus lateralis (33 ± 6 mg) was added to 2 ml homogenizing mix tubes (Fisherbrand™, Fisher Scientific) containing 600 μl Buffer RLT (Qiagen) with added 1% β-Mercaptoethanol (β-ME) before transferring to a tissue homogenizing instrument (MagNA Lyser; Roche) for subsequent homogenization (3 × 45 s at 6000 rpm, placing samples on ice for 5 mins between each disruption). Following homogenization, RNA was purified using a RNeasy® Mini kit (Qiagen) and treated with DNase (RNAse-Free DNase Set, Qiagen) as per the manufacturer’s instructions. RNA quantity and purity for human samples (128 ± 175 ng/mg tissue, 1.9 ± 0.1 A260/A280 and 2.1 ± 0.2 A260/A230) samples were quantified via spectrophotometry (QIAxpert®, software version 2.4, Qiagen) and concentrations confirmed via fluorometry (Qubit®, Qiagen). RNA integrity prior to sequencing was confirmed via Agilent Bioanalsyer 2100 with RIN scores 7.22 + 0.36.
100 ng of total RNA from each sample was used to prepare mRNA libraries using the NEBNext mRNA isolation kit in conjunction with the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs, Massachusetts, USA), and samples were randomised before preparation. Fragmentation of isolated mRNA prior to first strand cDNA synthesis was carried out using incubation conditions recommended by the manufacturer for an insert size of 300 bp (94°C for 10 minutes). 13 cycles of PCR were performed for final library amplification. Resulting libraries were quantified using the Qubit 4.0 spectrophotometer (Life Technologies, California, USA) and average fragment size assessed using the Agilent 4200 Tapestation with D1000 screentape (Agilent Technologies, Waldbronn, Germany). A final sequencing pool was created for each project using equimolar quantities of each sample with compatible indexes. 59 bp paired-end reads were generated for each library using the Illumina NextSeq 2000 in conjunction with the NextSeq 2000 P3 100 cycle kit (Illumina Inc., Cambridge, UK).

value: male


title: w1_HS1hr37C_1hRec_antiRbIgG_rep2

value: 2-4 day old

value: 1 hour recovoery after heat stress


title: GC-AS-10307-3R,Recovery,3,female

description: Library name: GC-AS-10307-3R


title: w1_noHS_control_antiH3K27me3_rep2


title: K562 cells, day 0, parental, no dTAGv1, bio rep 1

description: Library name: JH1

value: parental cells


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 3

description: Library name: 23248XR-03-51

value: Male


title: w1_noHS_control_antiH3K27me3_rep1


title: w1_noHS_control_antiH3K9me3_rep1


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 7

description: Library name: 23248XR-03-47


title: Hippocampus of Mrpl40 -/+,Slc25a1 +/+, biol rep 1

description: Library name: 23248XR-03-49


title: GC-AS-10307-27R,Recovery,27,male

description: Library name: GC-AS-10307-27R

value: Recovery


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with rabbit IgG 2

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Library name: siVDRIgG2

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore!  Version 0.6.10 with default settings except for specifying Illumina adapter sequences and paired-end validation.
Alignment files were processed using Picard (http://broadinstitute.github.io/picard; Version 3.2.0) for duplicate removal and samtools (Version 1.18) to filter for reads with MAPQ 5
MACS2 and HOMER (Version 5.1) were used to call peaks for each sample with default parameters, except mode of operation set to factor and single-end reads. Peak calls for all samples were collapsed to a set of combined peaks. Each peak signal was normalized corresponding to control cells (pLenti-GFP vector) and IgG.
Assembly: hg38 genome
Supplementary files format and content: bed
Library strategy: CUT&Run

source_name: T-HESC

growth_protocol: The lentiviral plasmid-transduced cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum and 10 μg/mL puromycin. The regular endometrial stromal cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum, 100 units/mL penicillin, and 100 μg/mL streptomycin. All the cells were cultured and grown in a 5% CO2 and 37°C incubator. Cell media was changed every three days, and cells were passaged before reaching 90% confluency.

extract_protocol:
Targeted DNA amplicons were isolated using the Epicypher CUTANA Cut&Run Kit Version 3.
A total of 550,000 cells per sample were collected in DNA LoBind 1.5mL tubes containing wash buffer. Cells were captured with BioMag Plus Concanavalin A beads and incubated with corresponding antibodies overnight at 4°C in antibody incubation buffer. After washing away antibodies, pAG-MNase generated by the NIEHS proteomics core was added and incubated for 30 minutes at room temperature. After washing, CaCl2 was added and incubated for 30 minutes in an aluminum cold block placed in ice. The protein-DNA complexes were released by incubating at 37°C for 10 minutes. DNA was purified using the Qiagen MiniElute PCR Purification Kit. Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina according to the manufacturer’s instructions, with 12-14 cycles of PCR amplification. The PCR products were quantified using the Qubit dsDNA HS Assay Kit, and quality control was performed with Tapestation Analysis. The libraries were sequenced by the NIEHS sequencing core.

treatment_protocol: The cells were transfected with each siRNA in OPTI-MEM containing 2% v/v charcoal-stripped fetal bovine serum. 1,25(OH)2D3 treatment was conducted by dilution in OPTI-MEM containing 2% v/v charcoal-stripped fetal bovine serum.

value: T-HESC

value: Endometrial Stromal Cells

value: VDR knockdown


title: w1_noHS_control_antiRbIgG_rep3

value: Rabbit IgG


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with rabbit IgG 1

description: Library name: siVDRIgG1


title: GC-AS-10307-15A1,Atrophy,15,male

description: Library name: GC-AS-10307-15A1

value: Skeletal Muscle

value: Atrophy


title: GC-AS-10307-15R,Recovery,15,male

description: Library name: GC-AS-10307-15R


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with rabbit IgG 3

description: Library name: siVDRIgG3


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 6

description: Library name: 23248XR-03-46


title: GC-AS-10307-9B,Baseline,9,female

description: Library name: GC-AS-10307-9B

value: Baseline

value: female


title: w1_HS1hr37C_72hRec_antiRhi_rep2

value: Ovary

value: 5-7 day old

value: Heat Shock for 1 hour at 37oC

value: 72 hour recovoery after heat stress

value: Rhino


title: w1_noHS_control_antiRbIgG_rep2

value: 2-4 day old

value: No heat shock


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27me3 2

description: Library name: siVDR27me32


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 4

description: Library name: 23248XR-03-44

value: Hippocampus

value: Male


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27me3 3

description: Library name: siVDR27me33

value: T-HESC


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27ac 3

description: Library name: siVDR27ac3

value: Endometrial Stromal Cells


title: GC-AS-10307-15B,Baseline,15,male

description: Library name: GC-AS-10307-15B

value: male


title: w1_HS1hr37C_72hRec_antiRhi_rep1


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 2

description: Library name: 23248XR-03-42


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 5

description: Library name: 23248XR-03-45


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27me3 1

description: Library name: siVDR27me31

value: VDR knockdown


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27ac 2

description: Library name: siVDR27ac2


title: GC-AS-10307-27A1-1,Atrophy,27,male

description: Library name: GC-AS-10307-27A1-1

value: Skeletal Muscle


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K27ac 1

description: Library name: siVDR27ac1


title: GC-AS-10307-5A1,Atrophy,5,male

description: Library name: GC-AS-10307-5A1

value: Atrophy


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 9

description: Library name: 23248XR-03-40


title: w1_noHS_control_antiRbIgG_rep1

value: Rabbit IgG


title: GC-AS-10307-4B,Baseline,4,male

description: Library name: GC-AS-10307-4B

value: Baseline


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 8

description: Library name: 23248XR-03-39


title: w1_HS1hr37C_48hRec_antiRhi_rep2

value: Ovary

value: 4-6 day old

value: 48 hour recovoery after heat stress


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K4me3 3

description: Library name: siVDR4me33


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 3

description: Library name: 23248XR-03-43


title: w1_HS1hr37C_72hRec_antiIgG_rep1

value: 5-7 day old

value: Heat Shock for 1 hour at 37oC

value: 72 hour recovoery after heat stress

value: guinea pig IgG


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 7

description: Library name: 23248XR-03-38

value: Hippocampus


title: w1_HS1hr37C_48hRec_antiRhi_rep1

value: Rhino


title: GC-AS-10307-3B,Baseline,3,female

description: Library name: GC-AS-10307-3B

value: female


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K4me3 2

description: Library name: siVDR4me32

value: T-HESC

value: Endometrial Stromal Cells


title: w1_HS1hr37C_72hRec_antiIgG_rep2


title: Hippocampus of Mrpl40 +/+,Slc25a1 -/+, biol rep 1

description: Library name: 23248XR-03-41

value: Male


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with rabbit IgG 3

description: Library name: siNTIgG3

value: Non-target control


title: Immortalized endometrial stromal cells transfected with VDR siRNA and precipitated with H3K4me3 1

description: Library name: siVDR4me31

value: VDR knockdown


title: GC-AS-10307-5R,Recovery,5,male

description: Library name: GC-AS-10307-5R

value: Skeletal Muscle

value: Recovery

value: male


title: w1_HS1hr37C_48hRec_antiIgG_rep2

value: Ovary

value: 4-6 day old


title: GC-AS-10307-7B,Baseline,7,male

description: Library name: GC-AS-10307-7B

value: Baseline


title: w1_HS1hr37C_48hRec_antiIgG_rep1

value: Heat Shock for 1 hour at 37oC

value: 48 hour recovoery after heat stress


title: GC-AS-10307-3A1,Atrophy,3,female

description: Library name: GC-AS-10307-3A1

value: Atrophy


title: GC-AS-10307-4A2,Repeated Atrophy,4,male

description: Library name: GC-AS-10307-4A2

value: Repeated Atrophy


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 6

description: Library name: 23248XR-03-37

value: Hippocampus


title: w1_noHS_72hour_AgeMatchControl_antiRhi_rep2

value: 5-7 day old

value: No heat shock 72 hour age match

value: Rhino


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 5

description: Library name: 23248XR-03-36

value: Male


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 4

description: Library name: 23248XR-03-35


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with rabbit IgG 1

description: Library name: siNTIgG1

value: T-HESC

value: Endometrial Stromal Cells

value: Non-target control


title: GC-AS-10307-8A2,Repeated Atrophy,8,male

description: Library name: GC-AS-10307-8A2

value: Skeletal Muscle


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 3

description: Library name: 23248XR-03-34


title: GC-AS-10307-27B,Baseline,27,male

description: Library name: GC-AS-10307-27B

value: male


title: GC-AS-10307-15A2,Repeated Atrophy,15,male

description: Library name: GC-AS-10307-15A2


title: w1_noHS_72hour_AgeMatchControl_antiRhi_rep1

value: Ovary


title: w1_noHS_72hour_AgeMatchControl_antiIgG_rep2

value: guinea pig IgG


title: GC-AS-10307-12A2,Repeated Atrophy,12,male

description: Library name: GC-AS-10307-12A2


title: Hippocampus of Mrpl40 +/+,Slc25a1 +/+, biol rep 2

description: Library name: 23248XR-03-33


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27me3 2

description: Library name: siNT27me32


title: w1_noHS_48hour_AgeMatchControl_antiRhi_rep2

value: 4-6 day old

value: No heat shock 48 hour age match


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 6

description: Library name: 23248XR-03-30

source_name: Cortex

value: Cortex


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27me3 3

description: Library name: siNT27me33


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with rabbit IgG 2

description: Library name: siNTIgG2


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 5

description: Library name: 23248XR-03-29


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 4

description: Library name: 23248XR-03-28


title: GC-AS-10307-12R,Recovery,12,male

description: Library name: GC-AS-10307-12R

value: Recovery


title: w1_noHS_48hour_AgeMatchControl_antiRhi_rep1


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27me3 1

description: Library name: siNT27me31


title: w1_noHS_72hour_AgeMatchControl_antiIgG_rep1


title: GC-AS-10307-7R,Recovery,7,male

description: Library name: GC-AS-10307-7R


title: w1_noHS_48hour_AgeMatchControl_antiIgG_rep1


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27ac 3

description: Library name: siNT27ac3


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27ac 2

description: Library name: siNT27ac2


title: GC-AS-10307-4R,Recovery,4,male

description: Library name: GC-AS-10307-4R


title: 42ABDfxw1-F1s_antiRhi_rep2

value: 2-4 day old

value: No heat shock


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 7

description: Library name: 23248XR-03-31


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K4me3 3

description: Library name: siNT4me33


title: w1_noHS_48hour_AgeMatchControl_antiIgG_rep2


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 3

description: Library name: 23248XR-03-27


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K27ac 1

description: Library name: siNT27ac1


title: GC-AS-10307-3A2,Repeated Atrophy,3,female

description: Library name: GC-AS-10307-3A2

value: Repeated Atrophy

value: female


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 2

description: Library name: 23248XR-03-26


title: GC-AS-10307-9A1,Atrophy,9,female

description: Library name: GC-AS-10307-9A1

value: Atrophy


title: w1x42ABDf-F1s_antiRhi_rep2

value: Rhino


title: GC-AS-10307-8A1,Atrophy,8,male

description: Library name: GC-AS-10307-8A1


title: 42ABDfxw1-F1s_antiIgG_rep2


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with IgG 3

description: Library name: pLentiVDR125IgG3

value: T-HESC

value: Lentiviral-VDR plasmid

value: 1,25-dihydroxylated vitamin D3


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 7

description: Library name: 23248XR-03-24

value: Male


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K4me3 1

description: Library name: siNT4me31

value: Endometrial Stromal Cells

value: Non-target control


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA and precipitated with H3K4me3 2

description: Library name: siNT4me32


title: w1x42ABDf-F1s_antiIgG_rep2

value: Ovary

value: guinea pig IgG


title: GC-AS-10307-4A1,Atrophy,4,male

description: Library name: GC-AS-10307-4A1

value: Skeletal Muscle

value: male


title: Cortex of Mrpl40 -/+,Slc25a1 -/+, biol rep 1

description: Library name: 23248XR-03-25

value: Cortex


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with IgG 2

description: Library name: pLentiVDR125IgG2


title: GC-AS-10307-7A2,Repeated Atrophy,7,male

description: Library name: GC-AS-10307-7A2


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with IgG 1

description: Library name: pLentiVDR125IgG1


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 5

description: Library name: 23248XR-03-22


title: 42ABDfxOreR-F1s_antiIgG_rep2

value: 2-4 day old


title: GC-AS-10307-8R,Recovery,8,male

description: Library name: GC-AS-10307-8R

value: Recovery


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 4

description: Library name: 23248XR-03-21


title: GC-AS-10307-9R,Recovery,9,female

description: Library name: GC-AS-10307-9R


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 3

description: Library name: 23248XR-03-20


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 6

description: Library name: 23248XR-03-23


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with VDR 2

description: Library name: pLentiVDR125VDR2


title: OreRx42ABDf-F1s_antiRhi_rep2

value: No heat shock


title: GC-AS-10307-12B,Baseline,12,male

description: Library name: GC-AS-10307-12B

value: Baseline


title: OreRx42ABDf-F1s_antiIgG_rep2


title: GC-AS-10307-5B,Baseline,5,male

description: Library name: GC-AS-10307-5B


title: 42ABDfxOreR-F1s_antiRhi_rep2


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 1

description: Library name: 23248XR-03-18


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with VDR 3

description: Library name: pLentiVDR125VDR3


title: Cortex of Mrpl40 -/+,Slc25a1 +/+, biol rep 2

description: Library name: 23248XR-03-19


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with IgG 3

description: Library name: pLentiVDRVehIgG3

value: 0.01% v/v ethyl alcohol


title: GC-AS-10307-5A2,Repeated Atrophy,5,male

description: Library name: GC-AS-10307-5A2

value: Repeated Atrophy


title: LongRNA_mnk; armi 72.1/1_rep1

value: mnk; armi 72.1/1


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 7

description: Library name: 23248XR-03-16


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with IgG 2

description: Library name: pLentiVDRVehIgG2

value: T-HESC

value: Lentiviral-VDR plasmid


title: LongRNA_armi 72.1/1_rep2


title: GC-AS-10307-27A2,Repeated Atrophy,27,male

description: Library name: GC-AS-10307-27A2


title: Immortalized endometrial stromal cells transduced with lentiviral VDR, treated with ligand and precipitated with VDR 1

description: Library name: pLentiVDR125VDR1

value: 1,25-dihydroxylated vitamin D3


title: GC-AS-10307-12A1,Atrophy,12,male

description: Library name: GC-AS-10307-12A1

value: Atrophy


title: LongRNA_mnk; armi 72.1/1_rep2


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 5

description: Library name: 23248XR-03-14

value: Male


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 6

description: Library name: 23248XR-03-15


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 4

description: Library name: 23248XR-03-13


title: GC-AS-10307-9A2,Repeated Atrophy,9,female

description: Library name: GC-AS-10307-9A2

value: female


title: LongRNA_mnk; ago3 t2/t3_rep3

value: Ovary

value: mnk; ago3 t2/t3


title: LongRNA_armi 72.1/1_rep1


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 3

description: Library name: 23248XR-03-12


title: LongRNA_mnk; ago3 t2/t3_rep2


title: GC-AS-10307-8B,Baseline,8,male

description: Library name: GC-AS-10307-8B

value: Skeletal Muscle

value: male


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with IgG 1

description: Library name: pLentiVDRVehIgG1

value: Endometrial Stromal Cells


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with VDR 1

description: Library name: pLentiVDRVehVDR1


title: LongRNA_mnk; ago3 t2/t3_rep1

value: 2-4 day old


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with VDR 2

description: Library name: pLentiVDRVehVDR2


title: Immortalized endometrial stromal cells transduced with lentiviral VDR and precipitated with VDR 3

description: Library name: pLentiVDRVehVDR3


title: LongRNA_ago3 t2/t3_rep2

value: ago3 t2/t3


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 2

description: Library name: 23248XR-03-11

value: Cortex


title: HC3

city: Yokohama

first: Jonathan

last: Moody

address: 1-7-22 Suehiro-cho

institute: RIKEN Center for Integrative Medical Sciences

description:
Library name: Ileum6
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1.
Assembly: GRCh38-2020-A.
Supplementary files format and content: Tab-separated values and matrix files.

source_name: Ileum

extract_protocol:
Fresh-frozen human ileal biopsy sample were processed according to the manufacturer’s demonstrated protocol for tissue fixation and dissociation (CG000553, RevB). Briefly, tissues were weighed and minced on ice using a pre-chilled glass petri dish, followed by fixation in Fixation Buffer containing 4% formaldehyde for 16–24 hours at 4 °C without agitation. Fixed tissues were washed and resuspended in Quenching Buffer, then stored at –80 °C. Upon thawing, fixed tissues were enzymatically dissociated using pre-warmed Dissociation Solution containing Liberase TL and processed with a gentleMACS Octo Dissociator (Miltenyi Biotec). The resulting single-cell suspensions were filtered through a 30 µm strainer.
Fixed cells were then subjected to probe hybridization with the Chromium Human Transcriptome Probe Set v1.0.1, and barcoded using the Chromium X instrument. Libraries were generated with the Chromium Fixed RNA Profiling Reagent Kit and sequenced on an Illumina NovaSeq X Plus system.

value: Ileum

value: Immune cells, epithelial cells, mesenchymal cells


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with IgG 2

description: Library name: Ctrl125IgG2

value: Lentiviral-GFP plasmid


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with IgG 3

description: Library name: Ctrl125IgG3

value: T-HESC


title: LongRNA_ago3 t2/t3_rep1


title: HC2

description:
Library name: Ileum5
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 8

description: Library name: 23248XR-03-08


title: MS3

description:
Library name: Ileum4
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: MS4

description:
Library name: Ileum7
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: LongRNA_mnk, aub HN/QC_rep4

value: mnk, aub HN/QC


title: Cortex of Mrpl40 +/+,Slc25a1 -/+, biol rep 1

description: Library name: 23248XR-03-10


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 9

description: Library name: 23248XR-03-09


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with VDR 3

description: Library name: Ctrl125VDR3

value: 1,25-dihydroxylated vitamin D3


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with IgG 1

description: Library name: Ctrl125IgG1


title: LongRNA_mnk, aub HN/QC_rep2


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 7

description: Library name: 23248XR-03-07


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with VDR 2

description: Library name: Ctrl125VDR2


title: LongRNA_mnk, aub HN/QC_rep3


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 6

description: Library name: 23248XR-03-06


title: MS1

description:
Library name: Ileum2
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: Immortalized endometrial stromal cells transduced with lentiviral GFP, treated with ligand and precipitated with VDR 1

description: Library name: Ctrl125VDR1


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 4

description: Library name: 23248XR-03-04


title: MS2

description:
Library name: Ileum3
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: B lymhocyte, Control, line1, Sense probe, RNA

description: Library name: RNA_seq_B_CTRL1_S

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The trimmed reads were aligned to the human genome (hg19) using Bowtie v.2.3.5.1
Peaks were identified using the MACS2 v.2.1.1 software and filtered using a q-value cutoff of 0.01
BigWig files were generated using deepTools.
Assembly: hg19
Supplementary files format and content: BigWig files for each sample
Library strategy: ChIRP-seq

molecule: nuclear RNA

source_name: B lymphocyte

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Diagenode) until the chromatin DNA was 100–500 bp in size.
ChIRP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: B lymphocyte

value: Control


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 5

description: Library name: 23248XR-03-05

value: Male


title: LongRNA_aub HN/QC_rep2

value: Ovary

value: aub HN/QC


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with IgG 2

description: Library name: CtrlVehIgG2

value: 0.01% v/v ethyl alcohol


title: LongRNA_mnk, aub HN/QC_rep1


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with IgG 1

description: Library name: CtrlVehIgG1


title: HC1

description:
Library name: Ileum1
10x Chromium Single Cell Gene Expression Flex（probe-based whole transcriptome


title: LongRNA_aub HN/QC_rep3


title: B lymhocyte, Control, line1, G4C2 probe, RNA

description: Library name: RNA_seq_B_CTRL1_G4C2


title: LongRNA_aub HN/QC_rep1


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with IgG 3

description: Library name: CtrlVehIgG3


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 3

description: Library name: 23248XR-03-03


title: B lymhocyte, C9-ALS, line1, G4C2 probe, RNA

description: Library name: RNA_seq_B_C9ALS1_G4C2


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 1

description: Library name: 23248XR-03-01


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with VDR 3

description: Library name: CtrlVehVDR3


title: B lymhocyte, C9-ALS, line1, Sense probe, RNA

description: Library name: RNA_seq_B_C9ALS1_S


title: Cortex of Mrpl40 +/+,Slc25a1 +/+, biol rep 2

description: Library name: 23248XR-03-02


title: LongRNA_vas PD/PH_rep1

value: vas PD/PH


title: iMN, Isogenic control, line1, Sense probe

description: Library name: Isogenic_CTRL1_S

value: iMNs

value: Motor Neuron

value: Isogenic control


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with VDR 2

description: Library name: CtrlVehVDR2

value: Endometrial Stromal Cells


title: LongRNA_mnk, vas RG/PH_rep3

value: mnk, vas RG/PH

value: 2-4 day old


title: OT-II_TGM1-IL-2(DN)

city: Palo alto

first: Qinli

last: Sun

address: 279 Campus Drive

institute: Stanford University

description: Library name: Sample 6

data_processing:
Libraries were sequenced with Illumina NovaSeq X platform. Generated FASTQ files were processed with CellRanger v9.0.1 count pipeline using the GRCm39-2024-A transcriptome reference. Reads mapped to introns were included in the gene-expression calculation.
Assembly: Mouse GRCm39
Supplementary files format and content: Preprocessed Seurat object

source_name: Lymph node

extract_protocol:
One million sorted Thy1.1⁺ naïve OT-II cells were adoptively transferred into Thy1.2⁺ Foxp3-GFP recipient mice via retro-orbital intravenous injection. This was followed by six intraperitoneal injections of 100 μg OVA protein combined with 50 pmol of the indicated proteins, administered every other day. On day 11, donor OT-II cells and host Foxp3-GFP⁺ CD4⁺ T cells were sorted from the mLNs of the respective treatment groups and submitted to MedGenome, Inc. for library preparation and RNA sequencing.
The library was constructed using 10X Genomics Single Cell 3' v4 (polyA) chemistry according to the manufacturer's protocol.

value: Lymph node

value: CD4+ T cells

value: Donor OT-II cells


title: iMN, Isogenic control, line1, Scramble probe

description: Library name: Isogenic_CTRL1_Scramble


title: Immortalized endometrial stromal cells transduced with lentiviral GFP and precipitated with VDR 1

description: Library name: CtrlVehVDR1

value: T-HESC

value: Lentiviral-GFP plasmid


title: OT-II_TGM1-IL-2(WT)

description: Library name: Sample 5


title: iMN, Isogenic control, line1, Input probe

description: Library name: Isogenic_CTRL1_Input


title: OT-II_IL-2(WT)

description: Library name: Sample 4


title: LongRNA_vas RG/PH_rep3

value: vas RG/PH


title: iMN, Isogenic control, line1, HRE-M probe

description: Library name: Isogenic_CTRL1_HRE-M


title: LongRNA_mnk, vas RG/PH_rep1