title: 129S1/SvlmJ kidney, KlothoCtrl, male, replicate 2

description: Library name: kid_FdK15_S13_R1_001 sample 2

data_processing:
Partek Flow
sequence reads were trimmed based on quality score Phred <20 (default)
trimmed sequence reads were aligned with StarAligner 2.78a and mapped to mm39
read counts and TPM normalization were done using Partek Flow
Assembly: mm39
Supplementary files format and content: txt file includes TPM normalization for each sample

extract_protocol:
miRNeasy Mini Kit (Qiagen Inc.)
New England Biolabs Ultra Directional RNA Library Prep Kit.
cDNA libraries purified with AmpureXP beads, quantified on the Agilent Bioanalyzer,  Qubit Fluorometric Quantification

value: kidney

value: male

value: healthy renal function

value: 45 days

value: +/Kl


title: tcx5/6, D13, FT, LD, RNA-seq, rep2

status: Public on Oct 01 2025

type: SRA

city: Berkeley

first: Dawei

last: Dai

address: 2151 Berkeley Way

country: USA

institute: University of California, Berkeley

description:
Library name: tcx5/6_D13_FT_LD_rep2
150x 150

library_source: transcriptomic

data_processing:
Adapters were trimmed using cutadapt and Trim Galore 0.6.6 (Babraham Bioinformatics) by trimming 9 bp from the 5’-end of reads and enforcing a 3’-end quality of > 25%
Reads were mapped to the Araport11 genome using STAR 2.7.1a, permitting 0.05 mismatches as a fraction of total read length and discarding reads that did not map uniquely
Normalization of reads count was performed by running htseq-count of HTSeq 2.0  and DESeq2 1.40.1.
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt file includes normalized reads count for all samples.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: First true leaves

extract_protocol:
Total RNA was isolated using a QIAGEN RNeasy plant mini kit.
Non-stranded libraries from poly-A-tailed RNA were generated according to the manufacturer’s instructions (Illumina).

tag: tissue

value: First true leaves

tag: background

tag: developmental stage

tag: genotype

tag: treatment

value: grown under long day conditions (16h light/ 8 h dark)


title: cortex_WT_seizure_rep2

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Paired end sequencing reads were processed using 10X Genomics Cellranger v5.0.1. Reads were aligned to the mm10 genome optimized for single cell sequencing through a hybrid intronic read recovery approach.
Raw matrices for each individual replicate per condition were converted to Seurat objects using Seurat 5.0.1 and filtered to remove UMIs with thresholds of > 200 minimum features, > 250 genes detected per nuclei, < 20% mitochondrial reads, and < 2% ribosomal reads.
Pseudobulk differentially expressed genes were identified using DElegate with a fold change threshold of 1.5 and Benjamini-Hochberg adjusted p value ≤ .05. Counts were aggregated by individual mice per condition under the orig.ident identity, then pairwise comparisons were computed using quasi-likelihood dispersion with glmQLFit through the findDE function.
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Cortical tissue was mechanically homogenized in a sucrose solution and nuclei were isolated through a sucrose gradient and ultracentrifugation
single-nucleus Drop-seq; Nuclei were captured and libraries were prepared for sequencing using the sNucDrop-seq protocol described in Hu et al. 2017

treatment_protocol: Seizures were induced via intraperitoneal injection of pentylenetetrazol.

value: cortex

value: WT

value: seizure


title: IL_control_wt1

city: Shanghai

first: Bing

last: Liu

address: No. 280, South Chongqing Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were aligned to the mouse reference genome (version mm10) using Bowtie2 RNASeq alignment software. HTSeq (version 2.0.2) was used to generate read counts of each gene. Normalized counts were obtained by normalizing raw counts with size factors using the median ratio method in DESeq2 1.36.0 package.
Assembly: mm10
Supplementary files format and content: Matrix of read counts, with each row representing a gene and each column representing a sample.

molecule: total RNA

source_name: pituitary intermediate lobe

extract_protocol:
The intermediate lobe tissue was obtained using laser capture microdissection (LCM) from frozen pituitary sections. LCM-collected tissues in 10 μL lysis buffer with RNase inhibitor were submitted for RNA isolation using TRIzol (Sigma).
Samples with appropriate size distribution were selected for sequencing library construction using TruePrep RNA Library Prep Kit V2 for illumina (Vazyme, China). The final library was sequenced using an Illumina Novaseq 6000 sequencer, generating an average of approximately 20 million 150-bp paired-end reads per sample.

value: pituitary intermediate lobe

value: wt

value: control


title: tcx5/6, D13, FT, LD, RNA-seq, rep1

description:
Library name: tcx5/6_D13_FT_LD_rep1
150x 150


title: IL_control_wt2


title: Col-0, D40, FT, SD, RNA-seq, rep3

description:
Library name: Col-0_D40_FT_SD_rep3
150x 150

value: grown under short day conditions (8 h light/ 16 h dark)


title: Pituitary, Phf6_restraint_P_2_IgG

library_source: genomic

data_processing:
The clean reads were then aligned to the mouse reference genome (mm10) using the BWA program.
MACS2 was used for peak calling with “-f BAMPE” option and default threshold of q-value (BH-adjusted p-value) cutoff at 0.05.
Annotation of peaks was conducted using the annotatePeaks.pl script from the HOMER software suite.
Peaks around transcription start sites were plotted using deeptools (version 1.5.3).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Pituitary

extract_protocol:
Each mouse's pituitary was dissected in ice-cold dissection solution (1× HBSS, 10 mM HEPES, 23 mM D-glucose). Pituitary tissue micro-dissected from 100 mice was pooled together for further CUT&Tag assays.
The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer. Sequencing was performed on the Illumina Novaseq 6000 platform with 150 bp paired-end reads.

value: Pituitary


title: SOX17+Achilles+_R1

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: DP_1
SOX17+Achilles+_R1

data_processing:
nf-core Nextflow RNAseq pipeline, revision 3.14.0 (https://github.com/nf-core/rnaseq), with STAR aligner and RSEM quantification - all other parameers as default
Assembly: Ensembl GRCh38 release-86
Supplementary files format and content: raw count matrix of sequencing reads

organism: Homo sapiens

source_name: H1 FOXC1-Achilles reporter

growth_protocol: H1 FOXC1-Achilles hESCs were maintained in mTeSR1 (Stem Cell Technologies, #85850) and on GFR Matrigel (Corning, #354230). Cells were passaged every 3 days with Gentle Cell Dissociation Reagent (Stem Cell Technologies, #100-0485).

extract_protocol:
Sorted samples were initially lysed by treatment with 100µL specified lysis buffer to cell pellets [10 mM Tris-HCl (pH 7.9), 50 mM EDTA (pH 7.9), 0.2 M NaCl, 2.2% SDS, +1:100 RNAsin Plus (Promega) and 1000 µg/ml proteinase K (NEB)] at 55°C for 1hour. 500µL TRI reagent (ThermoFisher, #AM9738) was added to each sample and RNA was extracted according to manufacturers protocol using Qiagen MaXtract tubes (Qiagen, #129056). Extracted RNA was resuspeneded in RNAse free water and quantified by Qubit.
Watchmaker RNA Ribo/Globin depletion

treatment_protocol: Control cells were maintained in mTeSR1. Differentiated cells were seeded (1:24) 24 hours prior to differentiation and treated with Activin A (Cambridge Biosciences, #GFH6-10) 100 ng/mL, BMP4 (LifeTechnologies, PHC9534) 10 ng/mL, FGF2 (LifeTechnologies, PHG0026) 20 ng/mL, LY29004 (Cambridge Biosciences, CAY70920) 1 µM and Insulin (Sigma, I1882) in TeSR-E5 (Stem Cell Technologies, #5916). After 72 hours cells were harvested with Accutase (Gibco, #A1110501) for 5 mins at 37oC. Dissociated cells were centrifuged at 1500g and resuspended in 4% PFA (ThermoFisher, #28908) for 15 minutes rocking on ice with 1:1000 RNAsin plus  (Promega, N2611). Cells were diluted in PBS+0.5%BSA, centrifuged at 1400g and cell pellets resuspended in PBS + 0.5% BSA and 0.1% Triton-X100 and 1:3000 dillution of anti-SOX17 (CST, 81778) primary antibody and incubated for 1.5 hours at room temperature. Cells were washed in PBS + 0.5% BSA and 0.1% Triton-X100 and centrifuged at 1500g and resuspended with Alexa-647 secondary antibody 1:1000 (LifeTechnologies #A31573) for 40 minutes. Stained samples were washed and resuspended in PBS + 0.5% BSA and RNAsin Plus for cell sorting. Samples were sorted on the BD Aria III FACS system into specified populations and collected in PBS + 0.5% BSA and RNAsin Plus.

tag: cell line

value: H1 FOXC1-Achilles reporter

tag: cell type

value: Embryonic stem cells

value: Activin 100 ng/mL BMP4 10 ng/mL

tag: repeat


title: SOX17-Achilles-_R2

description:
Library name: DN_2
SOX17-Achilles-_R2


title: mTeSR1_R1

description:
Library name: C_1
mTeSR1_R1


title: Col-0, D40, FT, SD, RNA-seq, rep2

description:
Library name: Col-0_D40_FT_SD_rep2
150x 150


title: tcx5/6, D18, FT, LD, RNA-seq, rep1

description:
Library name: tcx5/6_D18_FT_LD_rep1
150x 150


title: IL_control_wt3


title: Pituitary, Phf6_control_P_1_IgG


title: cortex_WT_control_rep1


title: Col-0, D40, FT, SD, RNA-seq, rep1

description:
Library name: Col-0_D40_FT_SD_rep1
150x 150


title: p53 activator-2

city: Cambridge

first: Ping-Cheih

last: Pao

state: MA

address: 43 Vassar St

department: Brain and Cognitive Sciences

institute: MIT

data_processing:
Tophat2, Cufflinks 2.0.0
Assembly: mm9
Supplementary files format and content: .csv, transcript abundance estimates

source_name: Mouse cotrical neurons

extract_protocol:
Total RNA was extracted from mouse cultured neuron using TRIzol reagent
NEB ribosomal depletion kit

value: Mouse cotrical neurons

value: wild-type

value: p53 activation


title: p53 activator-1


title: CLI, replicate 9, RRBS

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description: Library name: PK39

data_processing:
The Cutadapt tool was used to remove adapter sequences, primers, and poly-A tails from sequencing reads. Next, Bismark (v. 0.22.3) was used to map bisulfite converted sequence reads and determine cytosine methylation states.
Assembly: hg38
Supplementary files format and content: Methylation Bedgraph files

source_name: skeletal muscle

extract_protocol:
Genomic DNA was isolated using Quick-DNA Microprep kit (Zymo Research, Irvine, CA, Cat#: D3021) following the manufacturer’s instructions.
Starting input genomic DNA (~100 ng) was digested with 30 units of MspI (New England Biolabs, Ipswich, MA, Cat#: R0106S). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s guidelines (Illumina Inc., San Diego, CA, USA). Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator-5 (Zymo Research, Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research, Cat#: D5030).

value: skeletal muscle


title: SOX17-Achilles+_R1

description:
Library name: A_1
SOX17-Achilles+_R1


title: Pituitary, Phf6_control_P_1


title: Col-0, D30, FT, SD, RNA-seq, rep3

description:
Library name: Col-0_D30_FT_SD_rep3
150x 150

value: First true leaves


title: cortex_WT_control_rep2


title: tcx5/6, D18, FT, LD, RNA-seq, rep3

description:
Library name: tcx5/6_D18_FT_LD_rep3
150x 150

value: grown under long day conditions (16h light/ 8 h dark)


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_LPS_rep3

city: Beijing

first: ji

last: yiliang

address: No. 10 right outside the Western headlines

department: Department of Immunology

institute: Capital Medical University

data_processing:
RNA-seq : the RNA-seq  data were mapped to the Mus musculus (mm10) using hisat2 with the default parameters.
Assembly: mm10
Supplementary files format and content: txt

growth_protocol: MDA-MB-231 cells were infected with lentivirus, and stable cell lines were generated by puromycin (1 μg/mL) selection

extract_protocol:
The total RNA was extracted with RNA isolater Total RNA Extraction Reagent (Vazyme, R401-01) according to the manufacturer’s instruction
The poly(A) RNA-seq libraries were prepared according to the Illumina TruSeq protocol and sequenced using Illumina Novaseq6000

value: macrophage


title: ob/ob female 1

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description:
Parse Biosciences
These raw fastq files of sublibrary 2 and 6 contain uniquely barcoded cells from all four samples (15,16,20 and 23). The Wild type female data described in this study are available in GSM7733790 [Samples 6,12,18, and 24]. Samples details are provided in the sample manifest tab of this file.

data_processing:
Each sublibrary contains uniquely barcoded cells from all samples.  Raw sequencing data for sub library-2 and sub library-6 were preprocessed and combined using Parse Biosciences’ split-pipe pipeline (v0.9.6p). Expression matrices were imported into Seurat for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: text

source_name: left hippocampus

extract_protocol:
Wild type (C57BL/6J) and ob/ob female mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and fixed using Parse biosciences nuclei isolation and fixation protocol.
Barcoded single cell libraries were prepared from fixed single cell suspensions using Evercode Whole Transcriptome Mega kit (Parse Biosciences) following the manufacturer’s instructions.  Individual transcriptomes from all samples were uniquely labeled by passing fixed nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Using next-generation sequencing, cells from individual samples are identified using the first well (first barcode) placement. Each sublibrary contains uniquely barcoded cells from all samples.  At the end of library prep, cells are distributed into 16 different sublibraries. The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 and TapeStation, respectively. The libraries were quantified by fluorometry on a Qubit instrument and by qPCR with a Kapa Library Quant kit prior to sequencing. The libraries were sequenced with paired-end 100 bp reads.  The sequencing generated approximately 35,000 reads per cell.
single nuclei RNA sequencing

value: left hippocampus

tag: age

value: 4.5 months

value: All hippocampal cells

tag: Sex

value: female

value: ob/ob

tag: strain


title: CLI, replicate 8, RRBS

description: Library name: PK38


title: Col-0, D30, FT, SD, RNA-seq, rep1

description:
Library name: Col-0_D30_FT_SD_rep1
150x 150

value: grown under short day conditions (8 h light/ 16 h dark)


title: DMSO-2

value: no treatment


title: DMSO-1


title: CLI, replicate 7, RRBS

description: Library name: PK37


title: Col-0, D23, FT, SD, RNA-seq, rep3

description:
Library name: Col-0_D23_FT_SD_rep3
150x 150


title: cortex_WT_seizure_rep1

value: cortex

value: WT

value: seizure


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_LPS_rep2


title: SOX17-Achilles-_R1

description:
Library name: DN_1
SOX17-Achilles-_R1

value: H1 FOXC1-Achilles reporter

value: Embryonic stem cells

value: Activin 100 ng/mL BMP4 10 ng/mL


title: IL_control_cko2

value: pituitary intermediate lobe

value: cko

value: control


title: CLI, replicate 6, RRBS

description: Library name: PK36

value: skeletal muscle


title: RNA-seq_RAW264.7_macroH2A.siFACT_LPS_rep3

value: macrophage


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_LPS_rep1


title: Col-0, D23, FT, SD, RNA-seq, rep2

description:
Library name: Col-0_D23_FT_SD_rep2
150x 150

value: First true leaves


title: DKO

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description: Bone with WWOX and p53 deletion

data_processing:
Fastq files were filtered and trimmed using trim_galore V0.6.1, an adapter and base quality trimmer. Files were tested with fastqc quality control tool V0.11.8. Reads shorter than 20 bp were discarded.
Filtered Fastq files were mapped to murine genome mm39 with HISAT2 V2.2.1 alignment program, disallowing spliced alignments and creating BAM files.
Signal Bigwig files were generated with deepTools utility bamCompare V3.5.1 by calculating ratio between treated sample and input, scaling by read counts, skipping zero over zero sites all at bin size of 50.
Assembly: mm39
Supplementary files format and content: Bigwig formatted file of ratio between signal of treated sample and signal of input sample.

source_name: bone marrow

growth_protocol: After BM and tumor cells extraction from the mice, the cells were kept in in MEM-Alpha supplemented with 10%FBS and 1%glumatin with antibiotics in humidefied atomsphere with 5%CO2 at 37

extract_protocol:
cells were crosslinked with 1% formaldehyde  and quenched with glycine. Fixed cells were washed in lysis buffer. Cells were sonicated using bioruptor sonicator to produce chromatin fragments of ~200-300 bp. The chromatin was immunoprecipitated by incubation with 5 μl of anti-cMYC antibody (rabbit polyclonal c-Myc (9402)-Cell Signaling,). Immune complexes were captured with protein G Dynabeads. DNA was precipitated by phenol/chloroform/isoamylalcohol extraction.
library was prepaired using kappa hyperprep kit

value: bone marrow

value: WWOX and p53 deletion

tag: antibody

value: c-Myc


title: DKO_BMT_3

data_processing:
Fastq files were filtered and trimmed using trim_galore V0.6.1, an adapter and base quality trimmer. Files were tested with fastqc quality control tool V0.11.8. Reads shorter than 20 bp were discarded.
Filtered Fastq files were mapped to murine transcriptome mm39 with salmon quant  transcript quantification tool V1.10.0 creating count tables.
Differential genes analysis was performed with Deseq2 statistical package tool.
Assembly: mm39
Supplementary files format and content: tab separated text file with sample columns and gene rows.

source_name: Bone with WWOX and p53 deletion

extract_protocol:
Total RNA was extracted using TRI reagent (Biolab), as described by the manufacturer for the phenol/chloroform-based method.
RNA quality was checked using a tape station (Agilent Technologies), followed by poly-A cleanup and cDNA preparation. To prepare cDNA, 1 µg of RNA from each sample was processed using the KAPA Stranded mRNA-Seq Kit with mRNA Capture Beads (Kapa Biosystems). Sequencing was performed using NextSeq 500 (Illumina).

value: Bone marrow(BMT)

value: DKO


title: RNA-seq_RAW264.7_macroH2A.siFACT_LPS_rep2


title: Pituitary, Phf6_restraint_P_2

value: Pituitary


title: input

description: Bone with WWOX and p53 deletion

value: input


title: RNA-seq_RAW264.7_macroH2A.siFACT_LPS_rep1


title: Col-0, D18, FT, SD, RNA-seq, rep3

description:
Library name: Col-0_D18_FT_SD_rep3
150x 150

value: grown under short day conditions (8 h light/ 16 h dark)


title: CLI, replicate 3, RRBS

description: Library name: PK33


title: CLI, replicate 5, RRBS

description: Library name: PK35


title: Col-0, D18, FT, SD, RNA-seq, rep1

description:
Library name: Col-0_D18_FT_SD_rep1
150x 150


title: CLI, replicate 4, RRBS

description: Library name: PK34


title: CLI, replicate 1, RRBS

description: Library name: PK31


title: Col-0, D30, FT, SD, RNA-seq, rep2

description:
Library name: Col-0_D30_FT_SD_rep2
150x 150


title: Col-0, D23, FT, SD, RNA-seq, rep1

description:
Library name: Col-0_D23_FT_SD_rep1
150x 150


title: DKO_BMT_2


title: Col-0, D18, FT, SD, RNA-seq, rep2

description:
Library name: Col-0_D18_FT_SD_rep2
150x 150


title: CLI, replicate 2, RRBS

description: Library name: PK32


title: DKO_T_2

source_name: OS tumor WWOX and p53 deletion

value: Tumor-OS


title: RNA-seq_RAW264.7_macroH2A(S139A)_LPS_rep3


title: DKO_BMT_1


title: IC, replicate 10, RRBS

description: Library name: PK29


title: CLI, replicate 10, RRBS

description: Library name: PK40


title: DKO_T_3


title: IC-post, replicate 9, RRBS

description: Library name: PK28

value: revascularization


title: RNA-seq_RAW264.7_macroH2A(S139A)_LPS_rep2


title: Col-0, D13, FT, SD, RNA-seq, rep1

description:
Library name: Col-0_D13_FT_SD_rep1
150x 150


title: SKO_BMT_2

source_name: Bone withd p53 deletion

value: SKO


title: Col-0, D13, FT, SD, RNA-seq, rep3

description:
Library name: Col-0_D13_FT_SD_rep3
150x 150


title: RNA-seq_RAW264.7_macroH2A(S139A)_LPS_rep1


title: SKO_BMT_3


title: RNA-seq_RAW264.7_macroH2A_LPS_rep3


title: DKO_T_1


title: Col-0, D40, FT, LD, RNA-seq, rep3

description:
Library name: Col-0_D40_FT_LD_rep3
150x 150

value: grown under long day conditions (16h light/ 8 h dark)


title: RNA-seq_RAW264.7_macroH2A_LPS_rep2


title: IC, replicate 9, RRBS

description: Library name: PK27


title: Col-0, D13, FT, SD, RNA-seq, rep2

description:
Library name: Col-0_D13_FT_SD_rep2
150x 150


title: RNA-seq_RAW264.7_macroH2A_LPS_rep1


title: SKO_T_3

source_name: OS tumor  p53 deletion


title: SKO_BMT_1


title: IC-post, replicate 8, RRBS

description: Library name: PK26


title: Col-0, D40, FT, LD, RNA-seq, rep2

description:
Library name: Col-0_D40_FT_LD_rep2
150x 150


title: Col-0, D40, FT, LD, RNA-seq, rep1

description:
Library name: Col-0_D40_FT_LD_rep1
150x 150


title: SKO_T_2


title: RNA-seq_RAW264.7_macroH2A.KO_LPS_rep3


title: IC, replicate 8, RRBS

description: Library name: PK25


title: IC-post, replicate 10, RRBS

description: Library name: PK30


title: RNA-seq_RAW264.7_macroH2A.KO_LPS_rep1


title: RNA-seq_RAW264.7_macroH2A.KO_LPS_rep2


title: SKO_T_1


title: Col-0, D30, FT, LD, RNA-seq, rep1

description:
Library name: Col-0_D30_FT_LD_rep1
150x 150


title: RNA-seq_RAW264.7_WT_LPS_rep3

value: wild-type


title: Col-0, D30, FT, LD, RNA-seq, rep2

description:
Library name: Col-0_D30_FT_LD_rep2
150x 150


title: yBM_DKO_3

value: Bone marrow


title: IC-post, replicate 6, RRBS

description: Library name: PK22

value: skeletal muscle


title: Col-0, D30, FT, LD, RNA-seq, rep3

description:
Library name: Col-0_D30_FT_LD_rep3
150x 150


title: IC, replicate 6, RRBS

description: Library name: PK21


title: yBM_DKO_2


title: RNA-seq_RAW264.7_WT_LPS_rep2

value: macrophage


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_rep3


title: IC-post, replicate 5, RRBS

description: Library name: PK20


title: RNA-seq_RAW264.7_WT_LPS_rep1


title: yBM_DKO_1


title: Col-0, D23, FT, LD, RNA-seq, rep2

description:
Library name: Col-0_D23_FT_LD_rep2
150x 150

value: First true leaves


title: Col-0, D23, FT, LD, RNA-seq, rep1

description:
Library name: Col-0_D23_FT_LD_rep1
150x 150


title: yBM_SKO_3


title: IC-post, replicate 4, RRBS

description: Library name: PK18


title: yBM_SKO_2


title: Col-0, D18, FT, LD, RNA-seq, rep3

description:
Library name: Col-0_D18_FT_LD_rep3
150x 150


title: IC, replicate 7, RRBS

description: Library name: PK23


title: IC, replicate 5, RRBS

description: Library name: PK19


title: Col-0, D18, FT, LD, RNA-seq, rep2

description:
Library name: Col-0_D18_FT_LD_rep2
150x 150


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_rep2


title: IC, replicate 4, RRBS

description: Library name: PK17


title: IC-post, replicate 3, RRBS

description: Library name: PK16


title: Col-0, D18, FT, LD, RNA-seq, rep1

description:
Library name: Col-0_D18_FT_LD_rep1
150x 150


title: Control--2

source_name: WT bone marrow

value: Bone marrow (BM)

value: Control-WT


title: RNA-seq_RAW264.7_macroH2A.siFACT_rep3


title: Col-0, D13, FT, LD, RNA-seq, rep3

description:
Library name: Col-0_D13_FT_LD_rep3
150x 150


title: Col-0, D23, FT, LD, RNA-seq, rep3

description:
Library name: Col-0_D23_FT_LD_rep3
150x 150


title: RNA-seq_RAW264.7_macroH2A.siFACT_rep1


title: IC, replicate 3, RRBS

description: Library name: PK15


title: Col-0, D13, FT, LD, RNA-seq, rep1

description:
Library name: Col-0_D13_FT_LD_rep1
150x 150


title: IC, replicate 2, RRBS

description: Library name: PK13


title: RNA-seq_RAW264.7_macroH2A(S139A).siFACT_rep1


title: IC-post, replicate 2, RRBS

description: Library name: PK14


title: Control--1


title: Control_3


title: Control_4


title: Noise+fluoxetine2

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: cochlear nuclei

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: cochlear nuclei

value: Noise+fluoxetine


title: Control_2


title: RNA-seq_RAW264.7_macroH2A_rep3


title: RNA-seq_RAW264.7_macroH2A(S139A)_rep3


title: Col-0, D13, FT, LD, RNA-seq, rep2

description:
Library name: Col-0_D13_FT_LD_rep2
150x 150


title: Noise+fluoxetine1


title: IC, replicate 1, RRBS

description: Library name: PK11


title: RNA-seq_RAW264.7_macroH2A.siFACT_rep2


title: IC-post, replicate 1, RRBS

description: Library name: PK12


title: Control, replicate 10, RRBS

description: Library name: PK10


title: Control_1


title: Control--3


title: Noise+vehicle2

value: Noise+vehicle


title: RNA-seq_RAW264.7_macroH2A(S139A)_rep2


title: RNA-seq_RAW264.7_macroH2A_rep2


title: Control, replicate 9, RRBS

description: Library name: PK9


title: RNA-seq_RAW264.7_macroH2A_rep1


title: Fluoxetine

value: Fluoxetine


title: Control, replicate 8, RRBS

description: Library name: PK8


title: BMT_3

value: Bone marrow (BMT)

value: DKO


title: Noise+vehicle1


title: Tumor_3

value: Tumor-OS


title: RNA-seq_RAW264.7_macroH2A(S139A)_rep1


title: RNA-seq_RAW264.7_macroH2A.KO_rep3


title: Vehicle2

value: Vehicle


title: RNA-seq_RAW264.7_macroH2A.KO_rep2


title: Control, replicate 7, RRBS

description: Library name: PK7


title: Control, replicate 6, RRBS

description: Library name: PK6


title: Tumor_2


title: RNA-seq_RAW264.7_macroH2A.KO_rep1


title: Vehicle1


title: Sperm_MPs_PANDORA_3

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: School of Medicine

institute: University of California, Riverside

description:
Library name: CZ_MP_4_S45_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Sperm

growth_protocol: 8-week-old wild-type male mice were orally gavaged with MPs for 4 weeks.

extract_protocol:
Total RNAs were extracted by Trizol (Sigma). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: Mice were orally gavaged with either water or 10 mg/kg body weight/day of polystyrene microplastics (MPs, 1.1 μm mean particle size) for 4 weeks.

value: Sperm

value: wild type

value: Low cholesterol diet


title: BMT_1


title: Sperm_MPs_PANDORA_2

description:
Library name: CZ_MP_3_S44_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: 10 mg/kg body weight/day of polystyrene microplastics (MPs, 1.1 μm mean particle size)


title: Control, replicate 4, RRBS

description: Library name: PK4

value: skeletal muscle


title: yBM_SKO_1

value: Bone marrow

value: SKO


title: RNA-seq_RAW264.7_WT_rep2

value: macrophage

value: wild-type


title: Sperm_MPs_PANDORA_1

description:
Library name: CZ_MP_2_S41_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: RNA-seq_RAW264.7_WT_rep3


title: Control, replicate 5, RRBS

description: Library name: PK5


title: RNA-seq_RAW264.7_WT_rep1


title: Sperm_Control_PANDORA_3

description:
Library name: CZ_CON_3_S39_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.

value: control


title: yBM_5

value: Bone marrow (BM)-4 months


title: Sperm_Control_PANDORA_2

description:
Library name: CZ_CON_2_S38_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: BMT_2


title: kidney K_4

city: Guangzhou

first: Xiaolong

last: Li

address: 1838 North Guangzhou Ave

department: Nanfang Hospital

institute: Southern Medical University

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: kidney

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: kidney

value: FAM3D knockout

value: UUO


title: Control, replicate 1, RRBS

description: Library name: PK1


title: yBM_4

value: DKO


title: kidney K_3


title: Sperm_Control_PANDORA_1

description:
Library name: CZ_CON_1_S37_Sperm_PANDORA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: HCT116_WT_rep3

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

data_processing:
The paired-end reads from bulk RNA-seq datasets were processed to remove the Illumina universal adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”. The resulting filtered reads were aligned to their respective reference genome using STAR aligner (v2.7.10b) with default parameters. Coordinate-sorted alignment files were indexed using SAMtools (v1.17). Exon mapped reads were counted using featureCounts from the subread package (v2.0.6). ATAC-seq datasets were processed to remove the Nextera adapter (CTGTCTCTTATACACATCT) using Cutadapt (v4.4) with the parameters “-q 25 -m 25”115. The resulting filtered reads were aligned to reference human genome using bowtie2 aligner (v2.5.1) with the parameter “--very-sensitive” (Bowtie2122). The alignment file was sorted by coordinate, indexed and filtered for mitochondrial reads using SAMtools (v1.17). The filtered alignment file was further processed to keep only uniquely mapped, non-duplicated reads using sambamba (v1.0.1). Reads were further processed using alignmentSieve from deepTools (v3.5.5) to account for transposon dimerization before insertion. Positive and negative strand alignments were shifted by +4 bp and −5 bp, respectively. Additionally, fragments of 100 bp, corresponding to nucleosome-free regions (NFRs), were retained with the parameters “--minMappingQuality 25 --maxFragmentLength 100 --ATACshift --BED”. Peaks were called on the resulting BEDPE files using MACS3 (v3.0.1) MACS3 with the parameters “--call-summits --bdg --nomodel --nolambda --gsize hs --keep-dup all --format BEDPE --qvalue 0.05”. The predicted peaks were filtered for ENCODE project blacklisted regions using BEDTools (v2.31.0) intersect.
Assembly: The reference genomes for human (GRCh38; annotation version 108) and mouse (GRCm39; annotation version 112) were obtained from ENSEMBL
Supplementary files format and content: HCT116_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: HCT116_si11_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: HCT116_si11_nfr_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: HCT116_si11_rna_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_all_atac_raw_counts.tsv is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr and nucleosomes.
Supplementary files format and content: mESC_diff_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.
Supplementary files format and content: mESC_nfr_atac_raw_counts.tsv  is a tab-separated file. It contains raw counts for ATAC-seq samples taking into consideration Nfr only.
Supplementary files format and content: mESC_rna_seq_raw_counts.tsv is a tab-separated file. It contains raw counts for RNA-seq samples.

growth_protocol: HCT116 (CCL-247; ATCC), were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal calf serum (FCS; Eurobio Scientific) and 100 µg/mL penicillin/streptomycin (Corning) at 37°C, 5% CO2. ES-E14TG2a mESCs (CRL-1821; ATCC) were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Sigma) supplemented with 13% fetal calf serum (FCS; Sigma), 0.32% 2-mercaptoethanol (Gibco), and 100 µg/mL penicillin/streptomycin (Corning). Media was freshly supplemented with 1000 units/mL recombinant mouse LIF protein (ESGRO®), 1 µM of the MEK/ERK inhibitor PD0325901 (Sigma), and 3 µM of the GSK inhibitor CHIR99021 (Sigma) (2i). Cells were plated at a density of 2.65 x 105 cells per cm2 on plates coated with 0.2% gelatin from porcine skin (Sigma). Cells were grown at 37°C, 8% CO2, and passaged every 48 hours using 0.05% Trypsin-EDTA for detachment (Gibco). Cells were frozen in fetal calf serum (FCS; Sigma) supplemented with 10% DMSO (Gibco).

extract_protocol:
To prepare samples for RNA-seq, 3 individual batches of cells were plated on the same day and further processed in parallel. Freshly harvested cells were lysed with 500 µL of QIAzol lysis reagent (QIAGEN #79306) and mixed by gentle pipetting. Subsequently, 100 µL of chloroform (Sigma) was added, samples were vortexed for 10 s and spun at 12’000 x g for 15 s at 4°C. The upper phase was transferred into a new tube, 600 μL of isopropanol (Sigma) added and samples incubated O/N at -20°C. After centrifugation at 16’000 x g for 10 min at 4°C, the RNA pellet was washed in 75% ethanol and resuspended in RNase-free water (Invitrogen). DNase digestion of RNA was performed using RNase-Free DNase Set (QIAGEN) following the manufacturer’s instructions. RNA was then precipitated by adding sodium acetate (Sigma) to a final concentration of 0.3 M, and adding 3 volumes of 100% ethanol O/N at -20°C. RNA was recovered by centrifugation at 16’000 x g for 10 min and washed two times with 70% ethanol. RNA was dissolved in RNase-free water (Invitrogen). To prepare ATAC-seq samples, 3 individual batches of cells were plate on the same day in 6-wells (for si-11) or 10 cm plates (for KO cells). Cell batches were then further processed in parallel, during all subsequent steps. For harvest, cells were washed twice with 1x PBS and detached using 0.5 mM EDTA in 1x PBS. Cells were counted and 80’000 cells were pelleted. Pellets were resuspended in 200 µL of freezing medium (10% DMSO in FCS) and slowly frozen at -80°C. ATAC-seq was performed at QuickBiology (Monrovia, California). Here, cells were washed and lysed to generate a crude preparation of nuclei. This crude extract was then treated with Tn5 Transposase. Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR-amplified and subsequently purified using the MinElute PCR Purification Kit (Qiagen, Maryland, USA).
The ATAC-seq library was prepared as described in Corces, M.R. et al.Nat Methods, 2017. After quality control using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), the libraries were sequenced (150 bp paired-end reads) on an Illumina HiSeq Sequencer (Illumina Inc., San Diego, CA). For RNA-seq, the quality of the isolated RNA was determined using a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further used for library preparation. The Illumina Ribo Zero Plus (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (25-1000 ng) were depleted of ribosomal RNA and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before ligation of an anchor. Fragments containing the anchor on both ends were selectively enriched with PCR at the same time adding the index with unique dual indexes (UDI). The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA). The libraries were normalized to 10 nM in Tris-HCl 10 mM, pH8.5 with 0.1% Tween20.

value: Human colon cancer cell line


title: mESC_WT_rep3_atac

source_name: mESC

value: mESC


title: kidney K_2


title: HCT116_WT_rep2


title: Tumor_1

value: Tumor-OS


title: HCT116_WT_rep1


title: mESC_WT_rep2_atac


title: yBM_1

value: Bone marrow (BM)-1.5 months


title: kidney U_3

value: WT


title: Control, replicate 3, RRBS

description: Library name: PK3


title: mESC_WT_rep1_atac


title: HCT116_TMPO_KO_HT10_rep3


title: kidney K_1


title: yBM_6


title: yBM_2


title: Control, replicate 2, RRBS

description: Library name: PK2


title: MC38-Ctrl xenograft

first: Cong

state: None Selected

address: 160 Pujian Road, Pudong New Area, Shanghai, China,200127.

institute: Renji hospital

data_processing:
Sequencing data were processed with the Cell Ranger version 3.0.1 (10X Genomics, Pleasanton, CA).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: xenograft tissue

extract_protocol:
After the xenograft was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagent was added.
Single-cell suspensions were resuspended in 0.04% BSA in PBS after digestion, the concentration was at least 400 cells/μL. Single-cell RNA-sequencing libraries were prepared by the Chromium Single Cell 3′ reagent kit v2 (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. In brief, the cells were diluted into the Chromium Single Cell A Chip to yield a recovery of around 6000 single-cell transcriptomes with < 5% doublet rate, then the libraries were prepared. The libraries were sequenced in multiplex on the NextSeq 500 sequencer (Illumina, San Diego, CA). Sequencing data were processed with the Cell Ranger version 3.0.1 (10X Genomics, Pleasanton, CA).

value: xenograft tissue


title: mESC_LBR_TMPO_LMNA_KO_rep3_atac


title: MC38-RSPO3-OE xenograft


title: mESC_LBR_TMPO_LMNA_KO_rep2_atac


title: IC-post, replicate 7, RRBS

description: Library name: PK24

value: skeletal muscle

value: revascularization


title: yBM_3


title: HCT116_TMPO_KO_HT10_rep2


title: kidney C_3

value: Sham


title: HCT116_TMPO_KO_HT10_rep1


title: HCT116_LMNA_KO_H10_rep3


title: mESC_LBR_TMPO_LMNA_KO_rep1_atac


title: mESC_LBR_TMPO_KO_rep3_atac


title: mESC_LBR_TMPO_KO_rep2_atac


title: gene expression library_CD3+ T cells [D1GEX]

city: Dallas

first: Longchao

state: Texas

address: 6001 Forest Park Rd.

institute: UTSW

description: 10x Genomics

data_processing:
The Cell Ranger (3.0.1) Software Suite was used to process the raw sequence data into gene expression profiles. The fastq files for each sample were processed with Cell Ranger count, which was used to align to mm10 reference genome, filter and quantify.
The output files of Cell Ranger for each sample included gene expression (in UMI count). Gene expression data were obtained using the cellranger aggr, which performed an inter-sample normalization and merged the results of all samples into one file, to remove the potential technique variability of samples.
For scTCR-seq data, TCR reads were aligned to the vdj_GRCm38_alts_ensembl-3.1.0 reference genome and TCR annotation was performed using the 10x cellranger vdj pipeline.
The Cd3 expression was defined as the average UMI counts of Cd3d, Cd3e, Cd3g, and those cells with Cd3 expression > 0 were kept for subsequent analysis.
The Seurat pipeline was applied to the combined expression data. Principle component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP) were  was performed on the scaled data of all genes.
Clusters were identified using shared nearest neighbor (SNN)-based clustering based on the same principal components. We used the function FindClusters for clustering with resolution from 0.1 to 1.5. For each resolution, the silhouette values were calculated. Such value was used to determine the optimaloptional cluster number k.
Assembly: mm10
Supplementary files format and content: matrix.mtx file, features.tsv file, and a barcodes.tsv file with rawcounts from CellRanger Count

source_name: tumor

extract_protocol:
MC38 tumors harvested at day 1 post first treatment. Tumor tissues were cut into approximately 1 mm3 pieces in the RPMI-1640 medium (Invitrogen) with 2% fetal bovine serum (FBS), and enzymatically digested with MACS tumor Dissociation Kit (Miltenyi Biotec) for 40 min on gentleMACS™ Dissociator according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 70 μm cell strainer and centrifuged at 500 g for 10 min.
As described in Single Cell V(D)J Reagent Kits User maual.

treatment_protocol: A total of 1x10^6 MC38 tumor cells were inoculated subcutaneously into right dorsal flanks of the mice in 100 μl phosphate buffered saline (PBS). Tumor-bearing mice were randomly grouped into treatment groups when tumors grew to around 80-100mm3. For bispecific antibody treatment, two doses of 0.25mg/kg antibody was intraperitoneally given starting from day 8-10 with 3-4 days interval.

value: tumor

value: MC38 mouse tumor infiltrated CD3+ T cell


title: HCT116_LMNA_KO_H10_rep2


title: gene expression library_CD3+ T cells [D2GEX]

description: 10x Genomics

value: PBS


title: HCT116_LMNA_KO_H10_rep1


title: gene expression library_CD3+ T cells [C12GEX]

description: 10x Genomics


title: mESC_LBR_TMPO_KO_rep1_atac


title: kidney U_2


title: H_rep_2

city: Wuhan

first: yiqian

last: yu

state: Hubei

address: Luoyu Road 237#, 430079, Wuhan, Hubei

institute: wuhan university

data_processing:
Raw sequencing data processed by Trim_Galore (v.0.6.7) for removing adapters and low-quality base pairs.
Reads were aligned with hisat2 (v.2.1.0) to GRCm38 reference genome.
Read counts were generated by featureCounts (v.2.0.1)
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Parietal and interparietal bone of the calvaria

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

tag: time


title: H_rep_1

value: Parietal and interparietal bone of the calvaria


title: kidney C_1

value: kidney


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep2


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep3


title: kidney U_1


title: E7.75, FLAG-Lhx1, rep 2

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

description: 100 bp paired end reads

data_processing:
Alignment against mouse genome (GRCm38/mm10) using STAR in splice-aware, paired-end mode.
Duplicate alignments removed and alignments mapping to genes were counted using FeatureCounts in the R Subread package. ("The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote." Nucleic Acids Research, 41(10):e108)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: E7.75 chimeric mouse embryo

growth_protocol: FLAG-Lhx1 and FLAG-Lhx1-Δ (mt) ESCs were grown in 2i media, ESCs were injected into 8-cell embryos (ARC x RLZRFP cross) and transferred to pseudopregnant females. 24 hours before collection, pseudopregnant females were given 2mg/mL doxycycline (2.31mg/mL doxycycline hyclate) and 5% sucrose in autoclaved water. Embryos collected at E7.75 (collected them at E8.5, but they’re about a day delayed in development). Contribution was checked and embryos were snap frozen.

extract_protocol:
Geo-seq protocol was used to generated mRNA libraries (“Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq”, 2017, Nature Protocol, 12:3, 566-580).
10 cycles of cDNA preamplification used after optimisation. 0.65x AMPure XP beads used after cDNA pre-amplification. 0.5 ng cDNA used for library preparation with the Nextera XT DNA kit. After library preparation, 0.5x AMPure XP beads followed by 0.15x AMPure XP beads were used.

value: E7.75 chimeric mouse embryo

value: 24 hours doxycycline


title: gene expression library_CD3+ T cells [C11GEX]

description: 10x Genomics


title: E7.75, FLAG-Lhx1, rep 1

description: 100 bp paired end reads


title: gene expression library_CD3+ T cells [C10GEX]

description: 10x Genomics


title: TCR library_CD3+ T cells [C9TCR]

description: 10x Genomics


title: Q_rep_1

source_name: Frontal bone of the calvaria

value: Frontal bone of the calvaria


title: gene expression library_CD3+ T cells [D3GEX]

description: 10x Genomics


title: HCT116_LBR_TMPO_LMNA_KO_HLTLad5_rep1

value: Human colon cancer cell line


title: E7.75, FLAG-Lhx1-mt, rep 2

description: 100 bp paired end reads


title: kidney C_2


title: E14.5_rep_3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Reads were then aligned with hisat2 (v.2.0.1) to GRCm38 reference genome.
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: HCT116_LBR_TMPO_KO_HLTd3_rep3


title: TCR library_CD3+ T cells [C8TCR]

description: 10x Genomics


title: E7.75, FLAG-Lhx1-mt, rep 1

description: 100 bp paired end reads


title: TCR library_CD3+ T cells [C7TCR]

description: 10x Genomics


title: TCR library_CD3+ T cells [C6TCR]

description: 10x Genomics


title: E14.5_rep_2


title: donor 3, HDL, 3h

city: Cincinnati

first: Claire

last: Chougnet

state: OH

address: 240 Albert Sabin Way

department: Immunobiology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: Sample 9
HDL_rep3

data_processing:
nf-core RNA-seq pipeline (vv3.14.0)
Raw sequencing reads were assessed for quality using FastQC (v0.12.1) and low-quality reads were removed using Trim Galore (v0.6.7)
filtered reads were aligned to the reference genome using STAR (v2.6.1d) and transcript quantification was performed using Salmon (v1.10.1) in alignment-based mode
Post-alignment metrics, duplication rates and coverage statistics were generated using Qualimap (v2.3) and RSeQC (v5.0.2)
Assembly: hg38
Supplementary files format and content: tab separated values file containing raw read counts for all samples

source_name: blood

growth_protocol: Effector memory Treg were sorted from human total CD4+ T cells by FACS and culture in X-vivo 15 media in humidified atmosphere 5% CO2 at 37C for 3 h

extract_protocol:
Cells were gently resuspended in Trizol (Thermofisher). Samples were stored at -80°C until further analysis. RNA was isolated using RNeasy MinElute (Qiagen)
Full-length cDNA was generated by using non-directional NEBNext Single Cell/Low Input RNA Library Prep Kit

treatment_protocol: Effector memory Treg were treated with 700 ug/ml of linoleic acid or HDL (based on the protein concentration) for 3h

tag: donor

value: donor 3

value: blood

value: primary

value: CD4+ T cell (Treg)

value: HDL


title: EoE Esophageal tissue

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
Library name: Esophageal tissue
This sample represents a set of 2887 samples, each with transcriptome data. All sample metadata are included in the file "sample_metadata.xlsx".

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: GRCh37
Supplementary files format and content: csv file include read counts for each sample
Supplementary files format and content: csv file include TPM for each sample

source_name: Esophageal tissue

extract_protocol:
Esophageal tissue for RNA analysis was collected from pinch biopsies of proximal, mid, and distal regions of the esophagus and frozen in RNAlater (Thermo Fisher Scientific, Waltham, MA, United States).
Strand-specific RNA-seq libraries were prepared using a KAPA Stranded mRNA-Seq Kit with random priming (KAPA Biosystems, Roche Sequencing and Life Sciences, MA, United States). After amplification, sequencing was performed on Illumina HiSeq2500 (Illumina, CA, United States) by multiplexed single-read run (80 bp, 40M reads).

value: Esophageal tissue

tag: diagnosis

value: eosinophilic esophagitis (EoE)


title: Shogaol_3

city: wenzhou

first: xiandong

last: zhu

address: The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Ouhai

department: Department of Hepatobiliary Surgery

institute: The First Affiliated Hospital, Wenzhou Medical University,

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: glioma

growth_protocol: U251 cancer cells  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was extracted using Trizol reagent (Invitrogen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The U251 cancer cells were treated with or without 6-shogaol (60μm) for 24 h

value: glioma

value: WT

value: with 6-shogaol (60μm)

tag: time point


title: HCT116_LBR_LMNA_KO_HLLad7_rep2


title: HCT116_LBR_TMPO_KO_HLTd3_rep1


title: E13.5_rep_2


title: donor 3, LA, 3h

description:
Library name: Sample 8
LA_rep3

value: LA


title: HCT116_LBR_LMNA_KO_HLLad7_rep1


title: Q_rep_2


title: HCT116_LBR_LMNA_KO_HLLad7_rep3


title: E13.5_rep_1


title: Shogaol_1


title: E13.5_rep_3


title: Control_3

value: without 6-shogaol (60μm)


title: E12.5_rep_3


title: HCT116_LBR_KO_HL38_rep2


title: HCT116_LBR_TMPO_KO_HLTd3_rep2


title: HCT116_LBR_KO_HL38_rep1


title: Shogaol_2


title: Control_2


title: donor 2, LA, 3h

description:
Library name: Sample 5
LA_rep2

value: donor 2


title: donor 3, control, 3h

description:
Library name: Sample 7
Ctl_rep3

value: PBS


title: E12.5_rep_2


title: Control_1


title: donor 2, HDL, 3h

description:
Library name: Sample 6
HDL_rep2


title: E14.5_rep_1


title: NHA_Enh465_CNN1_RepB_150ng, Batch5_12

type: RNA

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

institute: The University of New South Wales

hyb_protocol: TagSet Hyb setup NanoString MAN-10057-03.  A normalisation plate was prepared for 150 ng input. Prepared working (30x) stock dilutions of Master stock probe pools for 12 reactions,  See table 4 of protocol TagSet Hyb setup MAN-10057-03.  Creating working pools is also in Manual LBL-10241-04 June 2018 nCounter Elements XT reagents user manual.  Hyb set up as per protocol page 5. Hyb for 20 hours at 67'C. Samples were cleaned up on a nanoString Max Flex PrepStation. See MAN-C0035, nCounter Analysis System User Manual for details

scan_protocol: NanoString cartridges were scanned on a nanoString Digital Analyser: nCounter Analysis System User Manual MAN-C0035-07 July 18.

data_processing: Raw RCCs were processed following the nSolver pipeline implemented in NanoTube (Class et al., Bioinformatics, 2023), which normalizes expression across samples by relative housekeeping gene (n=6) and positive control probe (n=6) expression scale. BEST1 was was filtered out during preprocessing, as it fell below the minimum expression threshold (2SD above the mean of negative control probes) in 57.4% of samples.

source_name: NHA, transduced with CRISPRi sgRNA targeting enhancer

growth_protocol: NHA cells stably expressing dCas9-KRAB were grown in DMEM media supplemented with 10% foetal bovine serum and 1% streptomycin/penicillin at 37°C, 5% CO2

extract_protocol: 7 days after transduction, RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004)

treatment_protocol: NHA-dCas9-KRAB cells were transduced with 1-3 sgRNA that target enhancers linked to one gene at an MOI of 1 per sgRNA. After 4 days, cells were selected with 3 µg/mL of puromycin and 10 µg/mL blasticidine S hydrochloride

value: Normal Human Astrocytes (Lonza, #CC-2565)

tag: enhancer crispri target

tag: gene regulated by targeted enhancer

tag: replicate

value: RepB

tag: amount of input rna


title: E12.5_rep_1

tag: tissue

value: Frontal bone of the calvaria

tag: developmental stage


title: E12_rep_3


title: donor 1, HDL, 3h

description:
Library name: Sample 3
HDL_rep1

value: donor 1

tag: cell line

tag: treatment


title: donor 2, control, 3h

description:
Library name: Sample 4
Ctl_rep2

value: blood

tag: cell type


city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: rad14_cdc13-1_cellular_48h_full_deamination
Replicate 1

data_processing:
Base calling by Azenta
Read1 Fastq files were trimmed using Trimmomatic v0.39 (BOLGER et al. 2014), with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences and the counts for the trinucleotide context of lesion sites associated with dCPD-seq reads are included. For the No UV sample, only the trinucleotide file is provided.
Library strategy: dCPD-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: rad14∆ cdc13-1 yeast were grown overnight in rich (YPD or YPDA) medium at a permissive temperature (~23C), diluted with pre-warmed (37C) fresh YPDA medium, and incubated with shaking at 37C for six hours to induce G2/M arrest.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for about 2 min each time. After adding TE (10mM Tris-HCl, pH 7.5-8.0, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 2.5-3 volumes of 100% ethanol and stored at -20C to allow DNA precipitiation to occur.  DNA pellets were washed with 75-80% ethanol, dissolved in mixture of 1xTE (pH7.5) and 0.2 μg/μl RNase A, and incubated at 37C for about 15 minutes. The purified genomic DNA was then used for each sequencing library preparation.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, genomic DNA isolated from irradiated and deaminated yeast was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a biotinylated dsS2 splint adaptor that was linked to biotin on the complementary 5’ end. Ligated DNA was fragmented via sonication and then purified with size selection beads (Cytiva). Adaptor-ligated DNA fragments were then captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ S2 adaptor was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with dsF1 adaptors was performed. The library was then amplified 10 cycles in a PCR reaction with a unique set of barcoded primers that were also complementary to the S2 and F1 adaptors. Following amplification and cleaning, libraries were submitted to Azenta (Genewiz) for Illumina sequencing.

treatment_protocol: Cells were washed with water and exposed to ~600 J/m^2 UVC radiation. Cells were then incubated in the dark at 37C for a designated deamination timepoint (0h, 6h, 24h, or 48h), before spinning down the cells to obtain cell pellets. For full deamination control, RNase A treated genomic DNA from 48 hr sample was further incubated 16 hr in a thermocycler set to 67C. Genomic DNA was either immediately extracted from cells following UV exposure, or cell pellets were frozen at -80C until all deamination timepoints were complete.

value: Yeast cells

tag: genotype

value: rad14 cdc13-1

value: UV irradiated 600 J/m2

tag: deamination time

value: 48 hr + 16hr at 67C


title: E12_rep_2


title: NHA_Enh534_PTMA_RepB_150ng, Batch5_11

value: PTMA


title: donor 1, control, 3h

description:
Library name: Sample 1
Ctl_rep1

value: primary

value: CD4+ T cell (Treg)


title: rad14_cdc13-1_cellular_6h_rep2

description:
Library name: rad14_cdc13-1_cellular_6h_rep2
Replicate 2

value: 6 hr


title: donor 1, LA, 3h

description:
Library name: Sample 2
LA_rep1

value: LA


title: rad14_cdc13-1_cellular_48h_rep2

description:
Library name: rad14_cdc13-1_cellular_48h_rep2
Replicate 2

value: 48 hr


title: E11.5_rep_3


title: rad14_cdc13-1_cellular_24h_rep2

description:
Library name: rad14_cdc13-1_cellular_24h_rep2
Replicate 2

value: 24 hr


title: rad14_cdc13-1_cellular_0h

description:
Library name: rad14_cdc13-1_cellular_0h
Replicate 2

value: 0 hr


title: Esophagus Sample 57

city: Ann Arbor

first: Laura

middle: A

last: Kresty

state: MI

address: 1500 E Medical Center Dr

department: Surgery

institute: University of Michigan

description: Library name: Sample 57

data_processing:
QC and trimming were performed using FastQC and Trimmomatic.
RNA quantification was performed using Kallisto (version 0.46.2) with parameter -g --pseudobam -t 8 -b 100.
Isoform switching analysis was performed using isoformSwitchAnalyzeR package (version 1.14.1) in R (version 4.1.1) with default parameter.
Assembly: Gencode Human Release 34 (GRCh38.p13)
Supplementary files format and content: Table with transcripts that show significant isoform switching events.

source_name: Esophagus

extract_protocol:
RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Esophagus

tag: histopathology

value: EAC


title: E12_rep_1

value: Frontal bone of the calvaria


title: E11.5_rep_2


description:
Library name: rad14_cdc13_naked_post_UV_48h_full_deamination
Replicate 1

data_processing:
Base calling by Azenta
Read1 Fastq files were trimmed using Trimmomatic v0.39 (BOLGER et al. 2014), with the parameters “ILLUMINACLIP:[XR-seq_adapter_file]:2:30:10”
Read1 fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to cytosine bases in dipyrimidine sequence contexts (i.e., TC, CT, CC), corresponding to deaminated CPD lesions, were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools or custom perl script
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA dCPD lesion reads filtered for only cytosines in dipyrimidine mapping sequences and the counts for the trinucleotide context of lesion sites associated with dCPD-seq reads are included.
Library strategy: dCPD-seq

growth_protocol: rad14∆ cdc13-1 yeast were grown overnight in YPDA medium at a permissive temperature (~23C), diluted ~1:7 with pre-warmed (37C) fresh YPDA medium, and incubated with shaking at 37C for six hours to induce G2/M arrest.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with approximately equal volumes of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 7.5-8.0, 1 mM EDTA) and PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and approximately 0.5-0.7 volumes of acid-washed glass beads. Beads were vortexed vigorously twice for 2-3 min each time. After adding additional 1-5xTE buffer (pH7.5), cell lysates were centrifuged and supernatants were mixed with approximately 3-4 volumes of 100% ethanol and stored at -20C to allow DNA precipitation to occur.  After centrifugation, DNA pellets were washed with 75-80% ethanol, dissolved in either 10mM Tris (pH 8) + 0.2 μg/μl RNase A (replicate 1) or 1xTE (pH7.5) + 0.2 μg/μl RNase A (replicate 2) and incubated at 37C for about 15 minutes. This DNA was then quantified using a NanoDrop spectrophotometer.
The dCPD-seq protocol was adapted from the CPDseq 2.0 method (Duan et al. PNAS 2024, 121 (4) e2310854121). Briefly, approximately genomic DNA that had been irradiated in cells and then deaminated at 37C in vitro was incubated with TdT (NEB) and either ddATP or ddGTP to block free 3’ OH ends. After phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation, the DNA was resuspended in water and 10x CPD photolyase buffer (100mM NaCl, 50mM Tris HCl pH 7.5, 20mM DTT, 1mM EDTA, 50% glycerol) to a final concentration of ~1x buffer, and E. coli CPD photolyase and UDG were added to reverse CPDs and excise uracil bases. Reactions were incubated under 365nm light (Spectroline EA-160) to reverse CPDs and then phenol:chloroform:isoamyl alcohol extracted and ethanol precipitated. APE1 (NEB) was then used to cleave the abasic sugar backbone to yield free 3’OH ends that were ligated to a dsS2 splint adaptor labeled with biotin on the complementary 5’ end. Ligated DNA was then fragmented via sonication and cleaned with size selection beads (Cytiva). Adaptor-ligated DNA fragments were captured with streptavidin beads (Invitrogen), washed with 1x SCC (saline sodium citrate) buffer to remove nonspecific binding, and the non-biotinylated strand containing the ligated 3’ A adaptors was eluted with 0.15M NaOH. After synthesis of the complementary strand with EconoTaq (Lucigen) and preparation of DNA ends with NEBNext end repair and NEBNExt dA-tailing modules, a second adaptor ligation with dsF1 adaptors was performed. Each sample was then amplified 10 cycles in a PCR reaction with a primer set containing a unique barcode. Following amplification, libraries were cleaned and submitted to Azenta (Genewiz) for sequencing.

treatment_protocol: Cells were washed with water and exposed to ~600 J/m^2 UVC radiation (duration of exposure was 96 seconds). Genomic DNA was extracted from cells before subjecting them to deamination. For deamination of replicate 1, purified genomic DNA that had been resuspended in 10mM Tris, pH 8.0 was diluted 1:1 with 1xTE, pH 7.5 and either refrozen (0 hr) or incubated in a thermocycler at 37C for the designated length of time (6 hr, 24 hr, or 48 hr). After 48 hr of incubation, this sample was then incubated overnight at 67C to promote complete deamination of the DNA. Samples that had finished incubation were stored at -20C until all samples had finished their designated incubation period. For deamination of replicate 2, purified genomic DNA had been previously resuspended in 1xTE, pH7.5 and was not further diluted. For deamination timepoints, this DNA was incubated at 37C for 6 hr, 24 hr, or 48hr. After 48 hr of incubation, this sample was then incubated overnight at 67C to promote complete deamination of the DNA.


title: Esophagus Sample 55

description: Library name: Sample 55


title: rad14_cdc13_naked_post_UV_24h_rep2

description:
Library name: rad14_cdc13_naked_post_UV_24h_rep2
Replicate 2


title: NHA_Enh168_ANKRD1_RepB_150ng, Batch5_9

value: Normal Human Astrocytes (Lonza, #CC-2565)

value: RepB


title: NHA_Enh219_NEAT1_RepB_150ng, Batch5_7


title: Esophagus Sample 56

description: Library name: Sample 56


title: NHA_Enh538_PTMA_RepB_150ng, Batch5_8


title: E11.5_rep_1


title: NHA_Neg_Library_RepB_150ng, Batch5_6

source_name: NHA, transduced with CRISPRi non-targeting sgRNA

value: Negative control - no enhancer target


title: Esophagus Sample 54

description: Library name: Sample 54


title: E11_rep_3


title: NHA_Enh148_PSAP_RepB_150ng, Batch5_10

value: PSAP


title: NHA_Enh537_PTMA_RepB_150ng, Batch5_5


title: rad14_cdc13_naked_post_UV_0h_rep2

description:
Library name: rad14_cdc13_naked_post_UV_0h_rep2
Replicate 2

value: Yeast cells

value: rad14 cdc13-1

value: UV irradiated 600 J/m2


title: Esophagus Sample 53

description: Library name: Sample 53


title: NHA_Enh220_NEAT1_RepB_150ng, Batch5_4


title: E11_rep_1


title: E11_rep_2


title: CL2 cardiomyocyte 3

city: Melbourne

first: Feng

last: Yan

address: 1G Royal Parade

institute: WEHI

description:
Library name: CL2_3
barcode10_deucp

data_processing:
Basecalling was performed in SUP mode without trimming. Basecalled Nanopore FASTQ files were processed with flexiplex (v1.01; PMID: 38379414) to remove barcodes and identify UMI sequences.
FASTQ files were mapped to genome with minimap2 (v2.26-r1175; PMID: 29750242). For human, the GRCh38 genome and NCBI RefSeq annotation (GCA_000001405.15) were used. For mouse, the GRCm39 genome and NCBI RefSeq annotation (GCF_000001635.27) were used.
UMI-tools (v1.1.6; PMID: 28100584) was used to remove PCR duplicates based on UMIs and genomic coordinates for reads mapped to the Drp1-containing chromosome.
Transcript quantification was performed using Bambu (v3.6.0; PMID: 37308696) with deduplicated BAM files and the corresponding annotation.
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw trancript counts from Bambu for each human sample
Supplementary files format and content: tab-delimited text file includes raw trancript counts from Bambu for each mouse sample

source_name: CL2 induced pluripotent stem cells

extract_protocol:
1) RNA from CERA cardiomyocytes and CL2 cardiomyocytes was extracted using the Illustra RNAspin Mini Kit (Cytiva). 2) RNA from human left ventricle was extracted using the TRIzol reagent with TissueLyser LT (Qiagen). Extracted RNA was treated with Qiagen RNAse-Free Dnase Set and purified usign the RNase Mini kit (Qiagen). 3) RNA from mouse tissues was extracted using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit (BioRad).
300 ng of total RNA was reverse transcribed using Maxima H Minus Reverse Transcriptase with an oligo(dT) primer and a template-switch oligo containing a UMI. The resulting cDNA was purified with SPRIselect beads, PCR-amplified with gene-specific and TSO-binding primers, and subjected to bead-based clean-up. Biotinylated amplicons were captured with streptavidin beads, re-amplified, and purified. Final libraries were prepared using the Oxford Nanopore Native Barcoding Kit (SQK-NBD114.24) and sequenced on a PromethION FLO-PRO114M flow cell.

value: CL2 induced pluripotent stem cells

value: Cardiomyocytes


title: E10.5_rep_3


title: Esophagus Sample 51

description: Library name: Sample 51


title: Esophagus Sample 52

description: Library name: Sample 52


title: NHA_Enh206_MDK_RepB_150ng, Batch5_3

value: MDK


title: Esophagus Sample 50

description: Library name: Sample 50


title: NHA_Pool_PTMA_RepA_150ng, Batch5_2

value: Pool

value: PTMA

value: RepA


title: NHA_Pool_NEAT1_RepB_150ng, Batch5_1


title: CL2 cardiomyocyte 1

description:
Library name: CL2_1
barcode08_deucp


title: E10.5_rep_1


title: Left Ventricle 4

description:
Library name: LV4
barcode07_dedup

source_name: left ventricle

value: left ventricle


title: Left Ventricle 3

description:
Library name: LV3
barcode06_dedup


title: Esophagus Sample 48

description: Library name: Sample 48

value: Esophagus


title: Esophagus Sample 47

description: Library name: Sample 47

value: EAC


title: rad14_cdc13_naked_post_UV_6h_rep2

description:
Library name: rad14_cdc13_naked_post_UV_6h_rep2
Replicate 2

value: 6 hr


title: E10_rep3

value: Frontal bone of the calvaria


title: NHA_Enh220_NEAT1_RepA_150ng, Batch4_11

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: E10_rep2


title: Left Ventricle 2

description:
Library name: LV2
barcode05_dedup


title: NHA_Enh538_PTMA_RepA_150ng, Batch4_10


title: E10_rep1


title: PPI MRC5 229 RNA, 229 Well 6 RNA 24hr

city: Richland

first: Lindsey

middle: N

last: Anderson

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to the human genome version GRCh38.p14 using STAR (https://github.com/alexdobin/STAR).
Aligned reads were mapped to genes using featureCounts from the subread package (https://subread.sourceforge.net/).
Assembly: human genome GRCh38.p14
Supplementary files format and content: tab-delimited columns in .txt files are as follows: Gene ID, chromosome name, gene start site, gene end site, strand orientation, gene length, counts. Counts are in fractions since counting was conducted in fraction mode, where fractions of reads are added to totals when reads map to multiple loci.

source_name: cell line

growth_protocol: A549 cells were grown in Gibco Dulbecco's minimal essential media (DMEM) high glucose 10% Hyclone fetal bovine serum (FBS) 1X antibiotic antimycotic and MRC5 cells were grown in Alpha MEM with 10% FBS and 1x antibiotic antimycotic

extract_protocol:
Following treatment media was removed from cells and 300uL Trizol added to each well (6-well plate). Trizol was collected allowed to sit for 5 minutes and frozen prior to shipment. RNA isolation was performed by Genewiz (Azenta Life Sciences, Chelmsford, MA, USA).
Enrichment using poly-A tailed RNA was performed by Genewiz (Azenta Life Sciences, Chelmsford, MA, USA).

treatment_protocol: Cells were mock-infected (phosphate buffered saline) or infected with human coronavirus 229E (MOI 5) for 24 hours prior to harvest in Trizol.

value: cell line

value: lung fibroblasts cells

value: 24 hours post infection

value: infected


title: CL2 cardiomyocyte 2

description:
Library name: CL2_2
barcode09_deucp


title: E10.5_rep_2


title: Left Ventricle 1

description:
Library name: LV1
barcode04_dedup


title: E9.5_rep_3


title: CERA cardiomyocyte 3

description:
Library name: CERA3
barcode03_dedup

source_name: CERA induced pluripotent stem cells

value: CERA induced pluripotent stem cells


title: PPI MRC5 229 RNA, 229 Well 4 RNA 24hr


title: E9.5_rep_2


title: NHA_Neg_Library_RepA_150ng, Batch4_9

value: Negative control - no enhancer target


title: NHA_Enh465_CNN1_RepA_150ng, Batch4_8


title: Esophagus Sample 49

description: Library name: Sample 49


title: CERA cardiomyocyte 2

description:
Library name: CERA2
barcode02_dedup

value: Cardiomyocytes


title: E9.5_rep_1


title: NHA_Enh537_PTMA_RepA_150ng, Batch4_12


title: PPI MRC5 229 RNA, 229 Well 3 RNA 24hr


title: CERA cardiomyocyte 1

description:
Library name: CERA1
barcode01_dedup


title: NHA_Enh534_PTMA_RepA_150ng, Batch4_6


title: PPI MRC5 229 RNA, 229 Well 2 RNA 24hr


title: E9_rep_3


title: Skeletal muscle 2

description:
Library name: Skeletal_Muscle_2
barcode22_sorted_dedup_merged

source_name: skeletal muscle

value: skeletal muscle


title: PPI MRC5 229 RNA, 229 Well 1 RNA 24hr


title: PPI MRC5 229 RNA, 229 Well 5 RNA 24hr


title: Skeletal muscle 1

description:
Library name: Skeletal_Muscle_1
barcode21_sorted_dedup_merged


title: NHA_Enh206_MDK_RepA_150ng, Batch4_4

value: MDK


title: Kidney 2

description:
Library name: Kidney_2
barcode20_sorted_dedup_merged

source_name: kidney

value: kidney


title: NHA_Enh219_NEAT1_RepA_150ng, Batch4_5

value: RepA


title: NHA_Enh168_ANKRD1_RepA_150ng, Batch4_3


title: E9_rep_2


title: PPI MRC5 229 RNA, Mock Well 5 RNA 24hr

value: mock


title: E8.5_rep_3


title: PPI MRC5 229 RNA, Mock Well 4 RNA 24hr


title: E8.5_rep_2


title: NHA_Enh148_PSAP_RepA_150ng, Batch4_7

value: PSAP


title: PPI MRC5 229 RNA, Mock Well 3 RNA 24hr


title: Heart 2

description:
Library name: Heart_2
barcode16_sorted_dedup_merged

source_name: heart

value: heart


title: Kidney 1

description:
Library name: Kidney_1
barcode19_sorted_dedup_merged


title: NHA_Pool_NEAT1_RepA_150ng, Batch4_2

value: Pool


title: E8.5_rep_1

value: Frontal bone of the calvaria


title: PPI MRC5 229 RNA, Mock Well 2 RNA 24hr


title: NHA_Enh210_FTH1_RepB_150ng, Batch3_12

value: Normal Human Astrocytes (Lonza, #CC-2565)

value: RepB


title: NHA_Pool_PTMA_RepA_150ng, Batch4_1

value: PTMA


title: Spleen 2

description:
Library name: Spleen_2
barcode14_sorted_dedup_merged

source_name: spleen

value: spleen


title: PPI MRC5 229 RNA, Mock Well 1 RNA 24hr

value: cell line

value: lung fibroblasts cells

value: 24 hours post infection


title: HAPC, bone marrow, HSPC, replicate2, scRNAseq

city: Tianjin

first: Peng

last: Wu

address: 288 Nanjing Road

institute: IHCAMS

description:
T17
22x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
FACS-sorted MNC and HSPC from bone marrow
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: hypoxia exposure

value: Bone marrow

value: HSPC

value: Hypoxia


title: HAPC, bone marrow, HSPC, replicate3, scRNAseq

description:
T24
23x Genomics


title: Spleen 1

description:
Library name: Spleen_1
barcode13_sorted_dedup_merged


title: NHA_Enh333_LGALS3_RepB_150ng, Batch3_10


title: NHA_Enh124_FAM107B_RepB_150ng, Batch3_11


title: PPI A549 229 RNA, 229 Well 6 RNA 24hr

value: lung epithelail cells

value: infected


title: PPI MRC5 229 RNA, Mock Well 6 RNA 24hr

value: mock


title: NHA_Enh855_HSPB1_RepB_150ng, Batch3_9


title: Lung 2

description:
Library name: Lung_2
barcode12_sorted_dedup_merged

source_name: lung

value: lung


title: Lung 1

description:
Library name: Lung_1
barcode11_sorted_dedup_merged


title: Control, bone marrow, HSPC, replicate3, scRNAseq

description:
C5
20x Genomics

value: Control


title: HAPC, bone marrow, HSPC, replicate1, scRNAseq

description:
T16
21x Genomics


title: PPI A549 229 RNA, 229 Well 5 RNA 24hr


title: E9_rep_1

source_name: Frontal bone of the calvaria


title: PPI A549 229 RNA, 229 Well 4 RNA 24hr


title: Brain 2

description:
Library name: Brain_2
barcode10_sorted_dedup_merged

source_name: brain

value: brain


title: Heart 1

description:
Library name: Heart_1
barcode15_sorted_dedup_merged

value: heart


title: Control, bone marrow, HSPC, replicate1, scRNAseq

description:
C1
18x Genomics


title: NHA_Enh857_HSPB1_RepB_150ng, Batch3_7

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: PPI A549 229 RNA, 229 Well 3 RNA 24hr


title: NHA_Pool_LGALS3_RepA_150ng, Batch3_8

value: Pool

value: RepA


title: Brain 1

description:
Library name: Brain_1
barcode09_sorted_dedup_merged


title: NHA_Enh334_LGALS3_RepB_150ng, Batch3_6

value: RepB


title: PPI A549 229 RNA, 229 Well 2 RNA 24hr

value: cell line


title: HAPC, bone marrow, MNC, replicate2, scRNAseq

description:
BMT24
13x Genomics

value: MNC


title: MCMV_Acute 3

city: Rijeka

first: Marko

last: Šustić

address: Jonjić's lab

department: Department of Internal Medicine

country: Croatia

institute: University of Rijeka, Faculty of Medicine

description: Library name: Sample 9

data_processing:
RNA-Seq data analysis was performed essentially as previously described6, with minor modifications specific to the particular experimental system employed in this study, and using a workstation equipped with an AMD Ryzen 9 9950X3D, NVIDIA GeForce RTX 4080 SUPER, 96 GB of DDR5 RAM, and running R v4.5.0 and RStudio Desktop (2025.05.0+496) under Ubuntu 24.04.02 LTS (www.ubuntu.com). Operating system, drivers, and all other software packages and tools were updated to the latest versions during analysis. Software packages were used according to their respective manuals, vignettes, or materials published by the Harvard Chan Bioinformatics Core. Initial quality control of the raw sequencing reads obtained from the sequencing core facility was performed using FastQC, and the sequence composition of the FASTQ files was then evaluated with FastQScreen v0.16.09,10 to rule out the presence of technical artefacts and contaminating sequences in the sequencing libraries. In addition, before read mapping and differential gene expression analysis, .
Assembly: Raw sequencing reads were aligned to the mouse genome sequence using STAR  followed by the post-alignment quality control round using QoRTs
Supplementary files format and content: all_contrasts_and_all_analyzed_genes_all_samples containes raw and normalized counts of all samples together with aditional information
Supplementary files format and content: raw_counts files contain raw counts of individual samples

source_name: Heart tissue (ventricles)

extract_protocol:
RNA was isolated with NucleoSpin® TriPrep (Macherey-Nagel®) isolation kit according to manufactures instructions.
RNA-seq libraries were generated using the TruePrep DNA Library Prep Kit for MGI (VAZYME) as per the manufacturer’s recommendations. Single-stranded circle DNA molecules where then replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA was generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS) on DNBSEQ (MGI) sequencing platform in a single end 1x75 base pair run.

value: Heart tissue (ventricles)

value: Acutely infected


title: NHA_Enh332_LGALS3_RepB_150ng, Batch3_5

source_name: NHA, transduced with CRISPRi sgRNA targeting enhancer


title: PPI A549 229 RNA, 229 Well 1 RNA 24hr

value: 24 hours post infection


title: NHA_Enh53_ID3_RepB_150ng, Batch3_4


title: HAPC, bone marrow, MNC, replicate1, scRNAseq

description:
BMT16
12x Genomics

value: Bone marrow

value: Hypoxia


title: MCMV_Acute 2

description: Library name: Sample 8


title: PPI A549 229 RNA, Mock Well 6 RNA 24hr

value: lung epithelail cells


title: Control, bone marrow, MNC, replicate2, scRNAseq

description:
BMC12
11x Genomics


title: Control, bone marrow, HSPC, replicate2, scRNAseq

description:
C12
19x Genomics

value: HSPC


title: Control, bone marrow, MNC, replicate1, scRNAseq

description:
BMC1
10x Genomics


title: NHA_Enh102_ENO1_RepB_150ng, Batch3_3


title: PPI A549 229 RNA, Mock Well 5 RNA 24hr

value: mock


title: MCMV_Acute 1

description: Library name: Sample 7


title: NHA_Pool_HSPB1_RepB_150ng, Batch3_2


title: MCMV_Lat 3

description: Library name: Sample 6

value: Latently infected


title: PPI A549 229 RNA, Mock Well 4 RNA 24hr


title: lung tumor, SD, biol rep3

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

data_processing:
The RNA-seq data were mapped to the reference genome mm10 using the software Hisat2 v2.0.5 based on the default parameters.
The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) estimated each gene expression levels by featureCounts (v1.5.0-p3).
Assembly: mm10

growth_protocol: All mice were kept at a strict 24-hour light-dark cycle, with lights being turned on from 8:00 am (ZT0) to 8:00 pm (ZT12). Food and water were provided ad libitum.

extract_protocol:
Total RNAs were extracted according to TRIzol manufacturer's protocols.1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

treatment_protocol: Mice were placed in SD cages or home cages for 20 hours a day (14:00-10:00) for 7 weeks after virus injection.

value: lung

value: SD


title: MCMV_Lat 2

description: Library name: Sample 5


title: MCMV_Lat 1

description: Library name: Sample 4


title: NHA_Neg_Library_RepB_150ng, Batch3_1

value: Normal Human Astrocytes (Lonza, #CC-2565)

value: Negative control - no enhancer target


title: PPI A549 229 RNA, Mock Well 3 RNA 24hr


title: NHA_Enh334_LGALS3_RepA_150ng, Batch2_12

value: RepA


title: PPI A549 229 RNA, Mock Well 2 RNA 24hr


title: lung tumor, SD, biol rep1


title: lung tumor, SD, biol rep2


title: NHA_Neg_Library_RepA_150ng, Batch2_11


title: Mock 3

description: Library name: Sample 3

value: Non infected


title: PPI A549 229 RNA, Mock Well 1 RNA 24hr

value: cell line


title: Mock 2

description: Library name: Sample 2


title: lung tumor, Ctrl, biol rep3

value: Ctrl


title: Tfh cells, spleen, HSC-transferred, 2

city: Yokohama-shi

first: Yuzo

last: Koda

address: 1000 Kamoshida, Aoba-ku, Yokohama-shi, Kanagawa

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

description: Library name: Sample12

data_processing:
The equally pooled libraries of the samples were sequenced using the Illumina NextSeq 500 in 76-base-pair (bp) single-end reads. Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool. The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.9a. The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies). The read counts allocated for each gene and transcript (Ensembl Database 2016.12.01) were quantified using a Transcripts Per Million (TPM) method. Heatmap was generated using the R package.
Assembly: hg38
Supplementary files format and content: TPM_

source_name: Spleen of humanized mice

extract_protocol:
The spleens were collected from immunodeficient mice transplanted with either human PBMCs depleted of CD8 T cells oe HSCs. Spleens were mechanically dissociated using gentle MACS dissociator (Miltenyi Biotec) and then lysed using HLB solution to remove red blood cells and obtain cell suspensions of mononuclear cells. Finally, the cells were resuspended in fluorescence-activated cell sorting (FACS) buffer and used cell sorting.
RNA-sequencing was performed by isolated cells described in flow cytometry section. Total RNA was isolated from each sample using RNeasy Micro Kit (QIAGEN). The integrity and quantity of the total RNA were measured with an Agilent 2100 Bioanalyzer RNA 6000 Pico Kit (Agilent Technologies). Library preparation was performed using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolab) with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs) following the manufacturer’s instructions. The quality of the libraries was assessed using an Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies).

value: Spleen of humanized mice

value: Infiltrated human cells in humanized mice


title: NHA_Pool_LGALS3_RepA_150ng, Batch2_10

value: Pool


title: Mock 1

description: Library name: Sample 1

value: Heart tissue (ventricles)


title: Tfh cells, spleen, HSC-transferred, 1

description: Library name: Sample11


title: lung tumor, Ctrl, biol rep2


title: lung tumor, Ctrl, biol rep1


title: DN cells. PBMC pre-transfer

description: Library name: Sample10

source_name: Human peripheral blood

value: Human peripheral blood

value: Source PBMC


title: NHA_Enh857_HSPB1_RepA_150ng, Batch2_9


title: Δtor1 , 4h, Rep-2

city: Canakkale

first: Melih

last: GUNAY

address: Izmir Street, Terzioglu Campus,

country: Turkey

institute: Canakkale Onsekiz Mart University

data_processing:
Ion-Torrent Next Generation Sequencing platform were storage in the computer as UBAM (Unaligned BAM) file format. UBAM files converted to “.fastq” file format via Galaxy Platform (www.usegalaxy.org), and Quality control was took place on raw reads by FastQC High Throughput Sequence QC Report (v0.11.9) tool, and the low quality reads were eliminated. All the RNA-Seq reads were mapped with Rhisat2 ( v2.2.1) tool. After alignment process “.bam” files were transformed into “.sam” files by using Rsamtools (v2.18.0). Transcript counts of RNA samples were carried out utilizing featureCounts tools in the R subread package.
Assembly: sacCer3
Supplementary files format and content: each processed data have included these file format: .fastq, .txt

source_name: S. cerevisiae (S288C)

growth_protocol: Yeast strains were  grown in YNBD-HLMU culture (Yeast Nitrogen Base without amino acid and ammonium sulfate; 0.5% Ammonium sulfate; 2% Dextrose, 0.2% Histidine; 0.3% Leucine; 0.2% Methionine; 1% Uracil) at 30°C and constant shaking (120 rpm) up to logarithmic stage (OD600:0.5-0.7), after which yeast cells were used for RNA extraction.

extract_protocol:
Yeast total RNA isolation was carried out by using Invitrogen™ RiboPure™ RNA Purification Kit (AM1926) according to the manufacturer’s instructions. The amount of RNA, RNA quality, RNA purity and RNA integrity was measured by utilizing Qubit® RNA HS Assay Kit in Qubit 3.0 Fluorometer, agarose gel electrophoresis, and Agilent™ Bioanalyzer tools.
Dynabeads® mRNA DIRECT™ Micro and Ion Total RNA-Seq Kit v2 was used to generate the mRNA library according to the manufacturer’s instructors. The cDNA library construction, adaptor ligations, purification, and amplification procedures were executed utilizing the Ion Total RNA-Seq Kit v2 Kit and the Ion Torrent™ Ion Xpress™ RNA-seq Barcode 1-16 kit, respectively.  The Emulsion PCR technique was used to enhance the cDNA concentration and was carried out clonal amplification by utilizing the Ion torrent Ion One Touch System and Ion 540 Kit-OT2.

tag: strain

value: S. cerevisiae (S288C)

value: S288C isogenic yeast strain:BY4741; MATa; his3-1; leu2-0; met15-0; ura3-0; YJR066w::kanMX4


title: lung, SD-ZT24, bio rep3

treatment_protocol: Mice were pre-treated in SD cages or home cages for 20 hours a day (14:00-10:00) for 2 days. Then the lungs of C57BL/6J in Ctrl and SD group were collected per 4 h for 24h beginning at 8:00 am.

value: WT


title: WildType, 4h, Rep-2

value: S288C isogenic yeast strain:MATa; his3-1; leu2-0; met15-0; ura3-0


title: lung, SD-ZT24, bio rep2

value: lung

value: SD


title: Tph cells, spleen,CD8 T cell-depleted PBMC-transferred, 3

description: Library name: Sample9


title: WildType, 4h, Rep-1


title: lung, SD-ZT24, bio rep1


title: Tph cells, spleen,CD8 T cell-depleted PBMC-transferred, 2

description: Library name: Sample8


title: lung, SD-ZT20, bio rep3


title: NHA_Enh53_ID3_RepA_150ng, Batch2_7

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: Tph cells, spleen,CD8 T cell-depleted PBMC-transferred, 1

description: Library name: Sample7


title: NHA_Enh855_HSPB1_RepA_150ng, Batch2_6

value: RepA


title: Tfh cells, spleen,CD8 T cell-depleted PBMC-transferred, 3

description: Library name: Sample6


title: testis, Middle-3

city: Jiang Su

first: ke

last: Ren

address: 608A, Chemistry Building, Northwest Gate, Gulou Campus, Nanjing University, Gulou District, Nanjing City, Jiangsu Province

department: medical college

institute: Nanjing University

description:
Library name: sample6
Column name in processed data.txt: Middle_3

data_processing:
Quality control was performed using the fastp software (version 0.23.0) [@fastp], with the following specific quality control steps: 1. Remove adapter sequences from reads and filter out reads shorter than 15 bp; 2. Filter out low-quality reads (discard if the proportion of bases with a quality score below Q20 exceeds 0.08); 3. Filter out reads with excessive N bases (discard if the number of N bases in a read exceeds 5).
Assembly: GRCm39_release110
Supplementary files format and content: The tab-delimited xls file contains the RPKM values for each sample

source_name: testis

extract_protocol:
Total RNA was extracted from mouse testicular tissue using the Trizol reagent kit, and a sequencing library was constructed using 2400 ng of total RNA.
During library preparation, total RNA was used as input, and the RNA sequencing library was constructed using the KCTM mRNA Library Prep Kit (Wuhan Kangce) following the manufacturer's instructions.

value: testis


title: lung, SD-ZT20, bio rep2


title: NHA_Enh124_FAM107B_RepA_150ng, Batch2_5


title: testis, Middle-2

description:
Library name: sample5
Column name in processed data.txt: Middle_2


title: NHA_Enh332_LGALS3_RepA_150ng, Batch2_2


title: lung, SD-ZT20, bio rep1


title: NHA_Enh102_ENO1_RepA_150ng, Batch2_4


title: Tfh cells, spleen,CD8 T cell-depleted PBMC-transferred, 2

description: Library name: Sample5


title: testis, Middle-1

description:
Library name: sample4
Column name in processed data.txt: Middle_1


title: Tfh cells, spleen,CD8 T cell-depleted PBMC-transferred, 1

description: Library name: Sample4


title: lung, SD-ZT16, bio rep3


title: NHA_Enh333_LGALS3_RepA_150ng, Batch2_8


title: Δtor1 , 4h, Rep-1


title: DN cells, spleen,CD8 T cell-depleted PBMC-transferred, 3

description: Library name: Sample3


title: lung, SD-ZT16, bio rep2


title: testis, Control-3

description:
Library name: sample3
Column name in processed data.txt: Control_3


title: testis, Control-2

description:
Library name: sample2
Column name in processed data.txt: Control_2


title: DN cells, spleen,CD8 T cell-depleted PBMC-transferred, 2

description: Library name: Sample2


title: lung, SD-ZT16, bio rep1


title: lung, SD-ZT12, bio rep3


title: NHA_Pool_HSPB1_RepA_150ng, Batch2_3


title: DN cells, spleen,CD8 T cell-depleted PBMC-transferred, 1

description: Library name: Sample1


title: MD8HB1_4

city: Xiamen

first: Chunlan

last: Xie

address: Daxue

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MC3T3-E1 were cultivated with complete α-MEM essential medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1 % penicillin/ streptomycin (BI, Beit Haemek, Israel) at a temperature of 37°C and a CO2 concentration of 5%.

extract_protocol:
The total RNA of each of above listed samples was isolated using the Trizol Kit (Promega, USA) following by the manufacturer’ s instructions. 2 μg of total RNAs were utilized for the preparation of stranded RNA sequencing libraries with the KCTM Stranded mRNA Library Prep Kit (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China)
RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Under the induction conditions of 50 μg/mL ascorbic acid and 5 mM β-glycerophosphate, MC3T3-E1 were exposed to VDC (5 μM) for 3, 5 and 8 days. 0.1% DMSO was the control treatment.

value: cell line

value: Multipotent precursor cells

value: D5+Osteogenic differentiation+HB-1


title: lung, SD-ZT12, bio rep2