title: KO-rep3

description: Library name: KO-rep3


title: Nuclear lipid microdomains rep1 [c1_S4]

status: Public on Jul 24 2025

type: SRA

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

library_source: transcriptomic

data_processing:
Reads were demultiplexed, according to the following barcodes, from all the Pool-ID-1 fastq files (B02: CATTCGCGTC, C02: GAGAGCTACT, D02: TGACAGCGTG, E02: ATGTAGGCCT, F02: CCGATGGTTG, G02:GCTTCCATTC)
Reads were mapped to the reference genome (mm10)
The number of mapped reads to each gene or miRNA was quantified
CPM, TPM and RPKM was computed to normalize the number of mapped reads in each gene or miRNA
All steps have been perfomed using the RAP software, GeneGlobe, Quiagen
Assembly: mm10
Supplementary files format and content: miRNA expression (Count, miRNA name and CPM)
Supplementary files format and content: Gene expression (TPM, RPKM, Total exons, Gene name, EnsemblID, Biotype, CPM)

molecule: total RNA

organism: Mus musculus

growth_protocol: Immortalized hippocampal neurons HN9.10e (kind gift of Kieran Breen, Ninewells Hospital, Dundee, UK) were grown in DMEM supplemented with 10% FBS, 2 mMl-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin, and 2.5 μg/mL amphotericin B

extract_protocol:
For nuclei extraction,Triton X-100  (1% in the above buffer) was added to homogenate (0.5:1 v/v). Sample was stirred on a vortex mixer for 30 s and the 1.5 M sucrose in the above buffer was added (0.25:1 v/v). After centrifugation at 2000g × 10 min, the pellet containing the nuclei was washed twice with 0.1M Barnes solution containing 0.085 M KCl, 0.0085 NaCl, 0.0025 M MgCl2, trichloroacetic acid-HCl 0.005 M. For nuclei lipid microdomain extraction, HN9.10 cell nuclei were washed in 10 mM Tris, containing 0.25 M sucrose, 2.5 mM MgCl2, 0.5 mM PMSF, and 1% Triton X-100, pH 7.5, at 0 °C, in order to remove the external nuclear membrane preserving the inner nuclear membrane, and were centrifuged at 1000g for 15 min at 4 °C. The pellet was re-suspended in 0.1 M Barnes solution  at pH 7.4, and was digested with DNase I (120 μg/ml) and RNase cocktail (500 μg/ml) for 15 min at 37 °C. The reaction was stopped on ice with Barnes solution (1:1 by vol.). After centrifugation at 5000 rpm for 5 min, the pellet was resuspended in 30 mM Tris containing 0.4 M ammonium sulphate, which facilitated the RNA precipitation, and 1 mM PMSF, pH 8.4, and then was centrifuged at 10,000 rpm for 15 min.
Paired-end

treatment_protocol: To test the effect of SM and Chol on NM composition, 500x10^3 cells were incubated with 5, 10, 15, 20μM SM-Chol prepared in equimolar ratio as liposomes for 6hrs. The NMs were purified and analyzed.

tag: cell type

value: Immortalized hippocampal neurons

tag: cell line

tag: rna source

value: Nuclear lipid microdomains


title: HeLa_dTAG-13_5K_rPRO-seq_R1

city: Miami

first: Pradeep

middle: Reddy

last: Cingaram

state: FL

address: 1501 N.W. 10th Avenue

department: Human genetics

country: USA

institute: University of Miami

description: Library name: Sample 7

library_source: other

data_processing:
*library strategy: rPRO-seq
Raw fastq PRO-seq data were processed as described previosly (Beckedorff, Blumenthal et al. 2020). Briefly PRO-seq reads were trimmed by Cutadapt 1.14 (Martin, 2011) and Trimmomatic v0.32 (Bolger et al., 2014), and aligned to the human genome (hg19) genome or the drosophila genome (dm3) by bowtie 1.1.2 (Langmead et al., 2009). PRO-seq signal was normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig data, which were used for downstream analyses. Quantification of nascent transcription per region was generated with an in-house script based on pyBigWig [Devon Ryan, B. G. F. R., doi:10.5281/zenodo.45238 (2016)] used to extract the normalized reads (CPM) per position from the bigwig files with a bin size of 1 bp upon merging the signal across two replicates.
Assembly: hg19 and mm10
Supplementary files format and content: The rPRO-seq processed data files are in bigWig format, bigwigs were normalized by Count Per Million produced from DeepTools2. bigwigs were with Bedtools v2.26 with genomecov.

molecule: other

organism: Homo sapiens

growth_protocol:
HeLa  cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.
Mouse E14 embryonic stem cells (ESCs) were acquired from ATCC. These cells were consistently cultured on plates coated with 0.1% gelatin (Stemcell Technologies) in DMEM (high glucose with GlutaMAX Supplement) medium (Thermo Fisher Scientific) that was further supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin and 100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% embryonic stem-cell FBS (all from Thermo Fisher Scientific), and 1000 U/mL recombinant leukemia inhibitory factor (LIF) from Stemcell Technologies. The cells were maintained in a controlled environment at 37°C with 5% CO2. For the non-directed differentiation of the ESCs into embryoid bodies, the medium was adjusted to contain 10% serum and was devoid of LIF.

extract_protocol: For rPRO-seq experiments were conducted following established protocols (see detailed protocol in supplementary file 1). Initially, a mixture of HeLa or mESC nuclei and Drosophila S2 cell nuclei as spike-ins was prepared. Nuclear run-on assays were executed by incubating nuclei at 30°C for 3 minutes with 25 μM Biotin-11-ATP/UTP/CTP/GTP (PerkinElmer). Subsequently, total RNA was extracted using Direct-zol RNA Miniprep and fragmented with 0.2 M NaOH for 10 minutes on ice, followed by purification of biotinylated nascent RNAs using streptavidin beads M-280 (Invitrogen). The 3’ RNA adaptor ligation process employs pre-adenylated single-stranded DNAs (P-3’ App-DNA), and T4 RNA ligase 2, truncated KQ, is utilized, incubated at 25°C for 1 hour. Additionally, on-bead 5’ RNA end repair involved using RppH (NEB) to remove the 5' cap and repair the triphosphate, followed by PNK-mediated repair of the 5' hydroxyl. The hybridization of DBO involves incorporating the dimer blocking oligonucleotide (DBO) into the RNA within the DBO mix. This is followed by a thermocycler program and subsequent combination with the 5’ adaptor ligation mixes in the RNA DBO mix, with a 1-hour incubation at 25°C. After adapter ligation, SuperScript III reverse transcription was employed. PCR amplification generated 140–350 bp libraries, which were size-selected using AMpure XP beads and sequenced using single-read runs on a NovaSeq X.

treatment_protocol: For the depletion of INTS11-dTAG, cells were treated with 500 nm of dTAG-13 and 1 µl/ml DMSO as the control. The treatment duration was predetermined.

value: cervical adenocarcinoma

tag: genotype


title: KO-rep2

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

description: Library name: KO-rep2

data_processing:
Reads were mapped to the mm10 reference genome via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Normalized coverage tracks were generated by STAR v2.5 with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.
Supplementary files format and content: Normalized coverage tracks in bigWig format.

source_name: testis

extract_protocol:
TRIzol was used for RNA preparation, followed by RNA collection via Qiagen RNA Easy kit.
RNA libraries were prepared using the Illumina Total RNA Prep Ligation with Ribo-Zero Plus protocol.

tag: tissue

value: testis

value: Mta3 mutant (lacking BAH domain)

tag: batch


title: HeLa_Ctrl_20K_rPRO-seq_R2

description: Library name: Sample 6


title: TBB30

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: rejection archetype cluster (nr, tcmr/mixed, nkrl, lowsft)

value: NR


title: TBB31

value: NKRL


title: WT-rep3

description: Library name: WT-rep3

value: WT


title: TBB32


title: TBB34


title: KO-rep4

description: Library name: KO-rep4


title: gonads agametic mutant rep 3

city: Sevilla

first: Alicia E.

last: Rosales-Nieves

state: Sevilla

address: HUVR. Edif. IBiS. Lab 109. Av Manuel Siurot S/N

country: Spain

institute: Instituto de Biomedicina de Sevilla-CSIC

description: Gene expression data from drosophila ML3 female gonads

hyb_protocol: the six cDNA collections were hybridized to GeneChip Drosophila Genome 2.0 Arrays from Affymetrix.

scan_protocol: Array scanning was performed using the Affymetrix® Software.

data_processing:
Raw data from  were exported to the R enviroment using LIMMA/Bioconductor packages.
logFC: log2-fold change; AveExpr: average log2-expression level for that gene across all the arrays and channels in the experiment; t: the moderated t-statistic; P.Value: associated p-value; adj.P.Value: p-value adjusted for multiple testing.

organism: Drosophila melanogaster

source_name: FACS-isolated astrocytes control 3m

label_protocol: Affymetrix

growth_protocol: flies were grown at 25C.

extract_protocol:
2 larval gonads (approximately 2000- 3000 cells) per sample (Oregon-R controls and pntaga homozygous; three biological replicas per genotype) were extracted usign Lysis buffer: (20 mM DTT, 10 mM Tris.HCl ph 7.4, 0.5% SDS, 0.5μg/μl proteinase K)
RNA from 2 larval gonads was isolated using magnetic beads. cDNA synthesis, library preparation and amplification (Pico Profiling) are described here (Gonzalez-Roca et al., 2010).
RNA was isolated using magnetic beads from 2 gonads .

treatment_protocol: 96 hours after egg laying the ML3 (mid-third instar larvae) is reached. In this study, ML3 refers to larvae that crawled out of the food but that have not initiated pupariation.

value: larval ML3 gonads

tag: animal age

value: ML3 larvae

tag: gender

value: Female

tag: strain

value: Pnt agametic


title: gonads agametic mutant rep 2


title: TBB33


title: TBB29


title: TBB28

value: lowSFT


title: KO-rep1

description: Library name: KO-rep1


title: HeLa_Ctrl_20K_rPRO-seq_R1

description: Library name: Sample 5


title: TBB27


title: HeLa_Ctrl_10K_rPRO-seq_R2

description: Library name: Sample 4


title: M.Masseter in vivo skeletal muscle tissue

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: M-Masseter

library_source: transcriptomic single cell

data_processing:
CellRanger used for demultiplexing + read mapping + barcode assignment + UMI counting
R package Seurat used for quality control + normalization + dimensionality reduction + clustering
R package SCpubr used for data visualization
Assembly: Bos_taurus_UMD_3.1
Supplementary files format and content: Filtered count matrices from CellRanger

organism: Bos taurus

source_name: skeletal muscle

extract_protocol:
Skeletal muscle tissue was minced and enzymatically digested with a 0.2 % Collagenase II and 1.5 % BSA solution for 1 hour at 37 °C in a shaking waterbath. The cell solution was filtered using a 100 µm cell strainer, followed by red blood cell depletion using ACK lysis buffer. After washing the cells with PBS, the cell solution was filtered using a 40 µm cell strainer followed by a centrigugation step(650 x g for 8 min). The cell pellet was then resuspended in FACS buffer (PBS supplemented with 0.5 % BSA) and sorted for live cells using a cell viability dye (Calcein Violet 50 AM). After counting the cells with a hemocytometer, 20000 cells were used for 10X library prepartation.
Library preparation was performed following the manufacturer's instructions. Library preparation was performed using the Chromium Next GEM Single cell 3’ v3.1, Dual Index kit.

value: skeletal muscle

tag: muscle type

value: Musculus masseter


title: Myoblasts cultured in myoblast medium

description: 10x Genomics

data_processing:
CellRanger used for demultiplexing + read mapping + barcode assignment + UMI counting
R package Seurat used for quality control + normalization + dimensionality reduction + clustering
R package SCpubr used for data visualization
R package velociraptor used for RNA velocity analysis
Assembly: Bos_taurus_UMD_3.1
Supplementary files format and content: Filtered count matrices from CellRanger

source_name: Skeletal muscle

extract_protocol:
Cultures were detached from the cell culture plate using trypsin, filtered and resuspended in PBS and lastly used for 10X Genomics library preparation.
The Chromium Next GEM Single cell 3’ v3.1 protocol was performed according to the manufacturer`s protocol.

value: Skeletal muscle

value: Musculus obliquus externus abdominis

tag: treatment

value: Cultured in myoblast medium

tag: time

value: Day 2


title: HeLa_Ctrl_10K_rPRO-seq_R1

description: Library name: Sample 3

value: cervical adenocarcinoma


title: HeLa_Ctrl_5K_rPRO-seq_R2

description: Library name: Sample 2


title: gonads agametic mutant rep 1


title: Myoblasts cultured in iMPC medium

description: 10x Genomics

value: Cultured in iMPC medium


title: TBB26


title: HeLa_Ctrl_5K_rPRO-seq_R1

description: Library name: Sample 1


title: ITS reads obtained from sample SS3E (SS-NS - Replicate 3)

city: Pisa

first: Giulio

last: Petroni

address: Via A. Volta n°4/6

department: Department of Biology

institute: University of Pisa

description:
Library name: SS3E_ITS
Full-length ITS sequencing

library_source: genomic

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database UNITE (v10)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs

molecule: genomic DNA

organism: activated sludge metagenome

source_name: mixed microbial community

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Kit (QIAGEN, Hilden, Germany)
PacBio Full-Length Amplicon Library Preparation using the SMRTbell Prep Kit 3.0 protocol

value: mixed microbial community


title: ND_dTAG-13_rPRO-seq_R2

description: Library name: Sample 16

source_name: E14 mESC

value: E14 mESC

value: Embryonic stem cell


title: Conventional differentiated cultures

description: 10x Genomics

value: Cultured in conventional differentiation medium (serum withdrawal)

value: Day 10


title: gonads control Wt rep3

value: larval ML3 gonads

value: ML3 larvae

value: oregon-R


title: TBB25

value: lowSFT


title: TBB24

value: NR


title: ND_dTAG-13_rPRO-seq_R1

description: Library name: Sample 15


title: Differentiated cultures with iFRC treatment

description: 10x Genomics

value: Cultured in iMPC medium containing "F"/"R"/"C"


title: M.Abdominis in vivo skeletal muscle tissue

description: Library name: M-Abdominis

value: skeletal muscle


title: gonads control Wt rep1

value: Female


title: TBB23

value: NKRL


title: ND_Ctrl_rPRO-seq_R2

description: Library name: Sample 14


title: ND_Ctrl_rPRO-seq_R1

description: Library name: Sample 13


title: Differentiated cultures with iFR_hi treatment

description: 10x Genomics

value: Skeletal muscle

value: Musculus obliquus externus abdominis

value: Cultured in iMPC medium containing "F"/"R"


title: ITS reads obtained from sample SS33 (SS - Replicate 3)

description:
Library name: SS33_ITS
Full-length ITS sequencing

value: mixed microbial community


title: Myoblasts cultured in myoblast (PM) medium

data_processing:
fastp used for quality control and trimming
Kallisto used for pseudo-alignment and quantification
R package edgeR used for diffferential expression analysis
R package enrichR used for functional enrichment analysis
Assembly: Bos_taurus_UMD_3.1
Supplementary files format and content: tab delimited raw counts

extract_protocol:
Cultures were washed with PBS and total RNA was isolated using the RNAeasy Mini Kit (Qiagen, #74104) following the manufacturer`s instructions.
Total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp.

value: Musculus psoas major

value: Cultured in myoblast medium

value: Day 2


title: ITS reads obtained from sample SS13 (SS - Replicate 1)

description:
Library name: SS13_ITS
Full-length ITS sequencing


title: gonads control Wt rep2


title: TBB20


title: ATRT-340 (ATRT-TYR)

city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

institute: Universität Bern

hyb_protocol: Slide processing and data acquisition was performed automatically by the Xenium In Situ Analyzer according to the manufacturer's protocol (10X genomics)

scan_protocol: Xenium In Situ Analyzer

data_processing:
Data processing was performed by the Xenium In Situ Analyzer according to the manufacturer's protocol (10X genomics)
Slide areas corresponding to distinct tumor samples were manually partitioned using the selection tool in the Xenium Explorer software (v3.0.0).
cell_boundaries.csv.gz: Segmented cell boundaries
cells.csv.gz: Cell summary file
nucleus_boundaries.csv.gz: Segmented nucleus boundaries
transcripts.csv.gz: Transcript location data
cell_feature_matrix.h5: Transcript count tables
overview_scan.png: Low-res overview image of DAPI staining

label: Xenium Human Probe Set

source_name: FFPE ATRT-TYR tissue

label_protocol: Xenium Human Probe Set

extract_protocol: ATRT tissue blocks were processed, and tissue sections were cut using manufacturer’s standard procedures (Xenium in situ for FFPE – tissue preparation guide, 10x Genomics protocol CG000578). In short, tissue blocks were hydrated for 20 minutes in ice bath and then 5μm intact tissue sections were cut using Leica HistoCore Autocut. They were further trimmed in water bath to get the region of interest for spatial profiling. Subsequently, tissue sections were put on 10X Xenium slides and incubated at 42°C for 3h.

value: FFPE ATRT-TYR tissue


title: Myoblasts cultured in myoblast (MM) medium

value: Musculus masseter


title: 18S reads obtained from sample SS3E (SS-NS - Replicate 3)

description:
Library name: SS3E_18S
Full-length 18S rRNA gene sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database EUKARYOME (v1.9)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs


title: TBB22


title: TBB21


title: ATRT-256 (ATRT-SHH)

source_name: FFPE ATRT-SHH tissue

value: FFPE ATRT-SHH tissue


title: ITS reads obtained from sample SS2E (SS-NS - Replicate 2)

description:
Library name: SS2E_ITS
Full-length ITS sequencing


title: Myoblasts cultured in myoblast (MA) medium


title: Myoblasts cultured in iMPC (PM) medium

value: Cultured in iMPC medium


title: TBB18


title: 18S reads obtained from sample SS1E (SS-NS - Replicate 1)

description:
Library name: SS1E_18S
Full-length 18S rRNA gene sequencing


title: ATRT-207 (ATRT-MYC)

source_name: FFPE ATRT-MYC tissue

value: FFPE ATRT-MYC tissue


title: 18S reads obtained from sample SS2E (SS-NS - Replicate 2)

description:
Library name: SS2E_18S
Full-length 18S rRNA gene sequencing


title: 18S reads obtained from sample SS33 (SS - Replicate 3)

description:
Library name: SS33_18S
Full-length 18S rRNA gene sequencing


title: Myoblasts cultured in iMPC (MM) medium


title: TBB16

value: NR


title: ATRT-173 (ATRT-SHH)


title: Myoblasts cultured in iMPC (MA) medium


title: ATRT-15-RV4 (ATRT-TYR)


title: 18S reads obtained from sample SS23 (SS - Replicate 2)

description:
Library name: SS23_18S
Full-length 18S rRNA gene sequencing


title: Conventional differentiated cultures (MM)

value: Cultured in conventional differentiation medium (serum withdrawal)

value: Day 15


title: 18S reads obtained from sample SS13 (SS - Replicate 1)

description:
Library name: SS13_18S
Full-length 18S rRNA gene sequencing


title: ATRT-05 (ATRT-SHH)


title: thrombi contained IVCs, DVT model from Sting mice , 24hours, rep3

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

country: China

institute: Nanjing Medical University

description: abundance measurements

data_processing:
To assess the quality of the data, we utilized FastQC (v.0.11.8). Subsequently, the reads were subjected to further processing to eliminate adaptor and low-quality sequences through the use of Trim Galore (v.0.4.0) software.
The alignment to the mouse reference genome (assembly GRCm39) was performed using HISAT2 (v.2.1.0).
Quantification of gene-level count data was accomplished using featureCounts (v.2.0.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene read counts for each Sample

source_name: thrombi contained IVCs

extract_protocol:
RNA was harvested using R6834 Total RNA Kit I. 2 μg of total RNA was used for the construction of sequencing libraries.
Oligo(dT) attached magnetic beads were used to purifed mRNA from thrombi in three replicates by eliminating rRNA and tRNA in a total amount of 2 μg RNA per sample. Purifed mRNA was fragmented into small pieces with fragment bufer at appropriate temperature. Then, First-strand cDNA was generated by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afer that, RNA Index adapters and A-Tailing Mix were added by incubating to end repair. The fragments of cDNA obtained from previous steps were amplifed by PCR, and the PCR products were purifed by Ampure XP Beads, and dissolved in EB solution. Te products were validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products obtained from previous steps were denatured by heating and circularized by the splint oligo sequence to get the fnal library, and the single stranded circular DNA (ssCir DNA) was formatted as the fnal library. The constructional fnal libraries were further amplifed with phi29 to make DNA nanoball (DNB), DNBs were loaded into the patterned nano-array and paired-end of 150 bp base reads were generated on T7 platform by Wuhan Benagen Technology Co., Ltd.

value: thrombi contained IVCs

value: Stingf/f Lyzm-Cre+/-

value: DVT model


title: 18S reads obtained from sample S102 (LS - Replicate 2)

description:
Library name: S102_18S
Full-length 18S rRNA gene sequencing


title: TBB17


title: thrombi contained IVCs, DVT model from Sting mice , 24hours, rep2

description: abundance measurements


title: Conventional differentiated cultures (PM)

value: Skeletal muscle


title: Differentiated cultures (PM) with iFRC treatment

value: Cultured in iMPC medium containing "F"/"R"/"C"


title: TBB13

value: NKRL


title: TBB15


title: Conventional differentiated cultures (MA)

value: Musculus obliquus externus abdominis


title: TBB12


title: thrombi contained IVCs, DVT model from Sting mice , 24hours, rep1

description: abundance measurements


title: TBB19

value: TCMR/Mixed


title: Differentiated cultures (MM) with iFRC treatment


title: TBB10


title: TBB14


title: TBB11


title: TBB9

value: lowSFT


title: 16S reads obtained from sample SS3E (SS-NS - Replicate 3)

description:
Library name: SS3E_16S
Full-length 16S rRNA gene sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database MiDAS 4 (v5.3)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs

value: mixed microbial community


title: 18S reads obtained from sample S101 (LS - Replicate 1)

description:
Library name: S101_18S
Full-length 18S rRNA gene sequencing


title: Differentiated cultures (MA) with iFRC treatment


title: thrombi contained IVCs, DVT model from WT mice , 24hours, rep3

description: abundance measurements

value: Stingf/f


title: 16S reads obtained from sample SS2E (SS-NS - Replicate 2)

description:
Library name: SS2E_16S
Full-length 16S rRNA gene sequencing


title: thrombi contained IVCs, DVT model from WT mice , 24hours, rep2

description: abundance measurements


title: 18S reads obtained from sample S103 (LS - Replicate 3)

description:
Library name: S103_18S
Full-length 18S rRNA gene sequencing


title: 16S reads obtained from sample SS1E (SS-NS - Replicate 1)

description:
Library name: SS1E_16S
Full-length 16S rRNA gene sequencing


title: thrombi contained IVCs, DVT model from WT mice , 24hours, rep1

description: abundance measurements


title: 16S reads obtained from sample SS33 (SS - Replicate 3)

description:
Library name: SS33_16S
Full-length 16S rRNA gene sequencing


title: Differentiated cultures (MM) with iFR_hi treatment

value: Musculus masseter

value: Cultured in iMPC medium containing "F"/"R"


title: Differentiated cultures (PM) with iFR_hi treatment

value: Musculus psoas major


title: Zea mays B73, primary and seminal root tips (0-1mm), RNA-seq steady-state transcription data, biorep 4

city: Raleigh

first: Linda

last: Hanley-Bowdoin

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
Adapter trimming (trimmomatic-0.36 PE -phred33 -validatePairs ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20)
Contaminants filtration (sortmerna -ref contaminants.fasta -reads $SAMPLE.input.fw.fastq -reads $SAMPLE.input.rv.fastq --out2 True --kvdb $SAMPLE.kvdb --readb $SAMPLE.readb --idx-dir sortmerna.idx-dir --zip-out Yes --fastx true --blast '1 cigar qcov qstrand' --paired_in true --other $SAMPLE.processed)
Read mapping (STAR --genomeDir STAR_2.7.10b.GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterMultimapNmax 1 --readFilesIn $SAMPLE.fw.fastq $SAMPLE.rv.fastq --outFileNamePrefix $SAMPLE.mapped)
Alignments filtering (samtools view -bh -f 0x2 $SAMPLE.bam)
Alignments deduplication (umi_tools dedup -I $SAMPLE.bam -S $SAMPLE.deduplicated.bam --umi-separator=":" --paired )
Genomic coverage (bamCoverage --binSize 50 --normalizeUsing RPGC --effectiveGenomeSize 2209328549 --outFileFormat bigwig --filterRNAstrand forward --bam $SAMPLE.deduplicated.bam --outFileName $SAMPLE.deduplicated.fw.bw )
Read count (htseq-count -f bam --order=pos --stranded=reverse -a 0 -t exon -i gene --nonunique=fraction --mode=union --counts_output=$SAMPLE.counts.tsv $SAMPLE.deduplicated.bam Zm-B73-REFERENCE-NAM-5.0_genomic.with_scaffolds.GENE.coding+non_coding+pseudo.EXONS.gff)
Assembly: GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.fasta
Supplementary files format and content: bigwig files with read density coverage
Supplementary files format and content: tables with raw read counts

organism: Zea mays

source_name: Terminal 1 mm of primary and seminal roots

growth_protocol: B73 seeds were imbibed overnight in autoclaved dH2O with stirring and aeration, and the next day surface sterilized with 0.5% sodium hypochlorite; 0.05% Tween 20 for 15 min at room temperature, rinsed 4X with 1-2 volumes of autoclaved dH2O and germinated in sterilized magenta boxes with paper towels dampened with sterile water. Seedlings were grown in a growth chamber with constant dim light (~500 lux) and 28 C for 3 days.

extract_protocol:
The tissue was ground with mortar and pestle in liquid nitrogen and RNA was extracted using the Invitrogen Plant RNA Purification Reagent. DNA was removed using the Invitrogen Turbo DNA Free kit. Ribosomal RNA was depleted using the Vazyme Ribo-off rRNA depletion kit for plants.
NEBNext Ultra II Directional RNA Library kit for Illumina with NEBNext Multiplex Oligos for Illumina, Unique Dual Index UMI Adaptors RNA set 1.

tag: developmental stage

value: seedling primary and seminal root meristem region

tag: cultivar

tag: age

value: 3-days after germination


title: ecm31D cho2D cells, grown on pantothenate, biol rep 3

city: Groningen

first: Hein

last: Schepers

state: Groningen

address: Hanzeplein 1

department: Internal Medicine

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: Sample 6
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_3C

data_processing:
Differential expression analysis was performed with edgeR package v.4.2.2.
The full set of libraries was normalised by TMM normalisation method
Lowly expressed genes were filtered out using filterByExpr function.
Between-group comparisons were done using pairwise contrasts and quasi-likelihood F (QLF) tests
Benjamini-Hochberg procedure was employed for multiple testing correction
Expression values were exported for further visualisation as counts per million, adjusted for library scaling factors
Assembly: S288C version R64-1-1
Supplementary files format and content: tab-delimited txt file includes raw readcounts for each Sample
Supplementary files format and content: tab-delimited txt file includes normalised CPM values for each Sample

organism: Saccharomyces cerevisiae

source_name: Exponentially growing cells

growth_protocol: Cells were grown in synthetic media with 2% glucose (SMD) and 27mM Pantothenate to OD 1

extract_protocol:
Total RNA was isolated using the RNeasy MicroKit (QIAGEN). 15 ng of total RNA was used for the construction of sequencing libraries
The RNA-seq libraries were prepared at the ERIBA Research Sequencing Facility (Groningen, the Netherlands) according to the Smart-3SEQ protocol (Foley et al, 2019)

value: Exponentially growing cells

value: ecm31D cho2D

value: grown on Pantothenate to OD 1


title: TBB6


title: 16S reads obtained from sample SS13 (SS - Replicate 1)

description:
Library name: SS13_16S
Full-length 16S rRNA gene sequencing


title: ecm31D cho2D cells, grown on pantothenate, biol rep 1

description:
Library name: Sample 4
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_3A


title: ATRT-243 (ATRT-MYC)

value: FFPE ATRT-MYC tissue


title: ecm31D cells, grown on Pantothenate, biol rep 3

description:
Library name: Sample 3
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_2C


title: Zea mays B73, primary and seminal root tips (0-1mm), RNA-seq steady-state transcription data, biorep 3

value: Terminal 1 mm of primary and seminal roots


title: 16S reads obtained from sample S103 (LS - Replicate 3)

description:
Library name: S103_16S
Full-length 16S rRNA gene sequencing


title: ecm31D cells, grown on Pantothenate, biol rep 2

description:
Library name: Sample 2
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_2B


title: 16S reads obtained from sample S102 (LS - Replicate 2)

description:
Library name: S102_16S
Full-length 16S rRNA gene sequencing


title: ecm31D cho2D cells, grown on pantothenate, biol rep 2

description:
Library name: Sample 5
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_3B


title: TBB4


title: ecm31D cells, grown on Pantothenate, biol rep 1

description:
Library name: Sample 1
Column name in 240919HSC11_Wedman_normalized_cpm.txt: 240919HSC11_Wedman_2A


title: 16S reads obtained from sample S101 (LS - Replicate 1)

description:
Library name: S101_16S
Full-length 16S rRNA gene sequencing


title: Differentiated cultures (MA) with iFR_hi treatment

value: Skeletal muscle

value: Day 15


title: Zea mays B73, primary and seminal root tips (0-1mm), RNA-seq steady-state transcription data, biorep 1


title: TBB7

value: NKRL


title: TBB5


title: finfish liver, Wheat Starch; Tank Number - T43

status: Public on Jul 23 2025

city: Fort Pierce

first: David

last: Bradshaw

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

data_processing:
Pre-Assembly Steps - Once sequences were received SortMeRNA (v. 4.3.6) was used to remove any remaining rRNA reads (Kopylova et al., 2012). Trim Galore (v. 0.6.7) was used to remove low quality nucleotides, polyA and polyT tails (Krueger, 2020).
Assembly - Trinity (v. 2.8.5) was used for de novo assembly from pooling all the reads (Grabherr et al., 2011; Griffith et al., 2015; Haas et al., 2013). Busco (v. 5.0.0) was used to determine the resulting transcriptomes completeness (Manni et al., 2021). After Salmon (v. 0.13.1) was used to quantify transcripts (Patro et al., 2017), a series of Trinity scripts were used to generate count and expression (trimmed mean of M-values [TMM] normalization) matrices for transcript isoforms and genes and use DESeq2 (v. 1.38.0) to calculate differentially expressed genes (DEGs) (Haas et al., 2013; Love et al., 2021).
Annotation - Transdecoder (v.  5.7.1) was used to identify long ORFs and predict which ones are coding while Trinotate (v. 4.0.0) was used to annotate the transcripts and genes, and finally a series of scripts from Trinity/Trinotate was used to determine GO (Gene Ontology) Enrichment using GOSeq (v. 1.50.0)(Bryant et al., 2017; Hass, 2022; Young et al., 2010a). If any DEGs had the same annotation, then they were further analyzed to determine if they were potential paralogs or non-overlapping parts of the same gene. BLASTN was used to determine if any of the transcripts associated with these DEGs were overlapping and then BLASTX was used to determine where these DEG transcripts aligned with the UniProt reference sequences associated with these annotations. A set of DEGs were considered to be likely paralogs if they were clustered into different genes but were aligning with an overlapping region of the reference sequence. On the other hand, a set of DEGs were considered to be likely non-overlapping parts of the same gene if they had little significant overlapping with one another (E-value >10) and aligned with completely different regions of the reference sequence.
R Data Processing and Statistical Analysis - Counts, expression matrices, DEGs, and GO enrichment results were analyzed and summarized with RStudio (v.2023.06.1; R version 4.2.0). These tables were converted into a Bray-Curtis dissimilarity matrix which was analyzed with principal coordinates of analysis (PCoA) and permutational analysis of variance (PERMANOVA). PRIMER7/PERMANOVA+ was used to conduct PERMANOVA analysis with Monte Carlo (MC) p-value.
Assembly: De novo
Supplementary files format and content: Trinity.isoform.TMM.EXPR.matrix is the trimmed mean of M-values [TMM] normalization) matrix for transcript isoforms
Supplementary files format and content: Trinity.gene.TMM.EXPR.matrix is the trimmed mean of M-values [TMM] normalization) matrix for transcript isoforms is the trimmed mean of M-values [TMM] normalization) matrix for genes
Supplementary files format and content: Trinotate.txt is the annotation for isoform transcripts and genes.

organism: Trachinotus carolinus

source_name: finfish liver

growth_protocol: A total of 400 fish (approximately 9 g initial weight per fish) were evenly distributed into 20 fiberglass tanks (80 L per tank) with a photoperiod of 12 hours light and 12 hours darkness (lights on at 7am). During experimental period, water quality parameters were kept within acceptable ranges for Florida pompano.

extract_protocol:
Two fish from each tank were euthanized with an overdosed of MS-222 at 300 mg/L for dissection of the liver which was immediately stored at – 80 °C for subsequent transcriptomic analysis. Total RNA was extracted from liver samples using RNeasy purification kit (RNeasy Mini kit, ID:74101, QUIAGEN, Venlo, The Netherlands) following manufacturer’s protocol. RNA quality, purity and quantity were determined using NanoDrop 1000 based on 260/280 and 260/230 absorbance ratios (Thermo Fisher Scientific, Waltham, MA, United States).
Then, RNA samples were sent to GeneWiz (South Plainfield, NJ, USA) for sequencing on an Illumina HiSeq.

treatment_protocol: Five experimental diets were randomly assigned to each tank with four replicates per treatment. After stoking, fish were fed experimental diets two times a day ad libitum (11am and 3pm) every day for 10 weeks.

value: finfish liver

tag: tank number

value: WS


title: finfish liver, Corn Starch; Tank Number - T42

value: CS


title: finfish liver, Whole Wheat Grain Flour; Tank Number - T41

value: WG


title: finfish liver, Dextrin Corn Starch; Tank Number - T40

value: DCS


title: finfish liver, Whole Corn Grain Flour; Tank Number - T39

value: CG


title: finfish liver, Wheat Starch; Tank Number - T38


title: finfish liver, Dextrin Corn Starch; Tank Number - T35


title: finfish liver, Whole Wheat Grain Flour; Tank Number - T34


title: finfish liver, Wheat Starch; Tank Number - T32


title: Zea mays B73, primary and seminal root tips (0-1mm), RNA-seq steady-state transcription data, biorep 2


title: finfish liver, Whole Corn Grain Flour; Tank Number - T31


title: TBB1

value: lowSFT


title: TBB3

value: NR


title: TBB2


title: 16S reads obtained from sample SS23 (SS - Replicate 2)

description:
Library name: SS23_16S
Full-length 16S rRNA gene sequencing

tag: cell type

value: mixed microbial community


title: finfish liver, Whole Wheat Grain Flour; Tank Number - T36


title: finfish liver, Whole Corn Grain Flour; Tank Number - T29


title: finfish liver, Corn Starch; Tank Number - T30


title: GCL_controlwCD31_5

city: Berkeley

first: Kushal

last: Nimkar

state: CA

address: Stanley Hall Room 202

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

description: Average CD31 intensity is in the Anti-Rat column of the metadata

hyb_protocol: The retina was mounted onto a membrane filter (MF-Millipore). The retina and filter paper then underwent two cycles of drying and rewetting and 30% sucrose/PBS, followed by 5 min of drying. The membrane filter was trimmed to be slightly larger than the size of the retina, and the filter paper with the retina was adhered to a flat stage made from tissue freezing medium (EMS), mounted on a cryostat chuck. The retina was embedded in a thin layer of tissue-freezing medium, and the chuck was placed on a block of dry ice to solidify the tissue-freezing medium. The embedded retina was stored overnight at -80°C. Before sectioning, the retina block was equilibrated within the cryostat. Care was taken to maintain the flat orientation of the tissue while trimming and sectioning the block.  Sections of 12µm thickness were collected onto MERSCOPE slides (Vizgen). Each slide was washed with DEPC-treated PBS and incubated in 70% Ethanol at 4°C overnight to permeabilize the tissue. Samples were then either processed for MERFISH imaging or stored in 70% ethanol as flatmount slides at 4°C for up to one month.

scan_protocol: The sample was loaded on the MERSCOPE machine for imaging, which automates the MERFISH probe exchange and readout process.

data_processing: A single biological replicate consisted of four to six separately imaged 12.5 micrometer thick tissue sections. In each tissue section, eight 1.5 micrometer thick optical sections were individually segmented using a fine-tuned Cellpose 2.0 model and stitched together. RNA transcripts were then assigned to each cell using the segmentation boundaries.

source_name: ganglion cell layer, adult control

extract_protocol: To track the orientation of the retina during the flatmount preparation, the nasal side of each mouse eye was marked with a marker pen. The entire globe was subsequently fixed in 4%PFA on ice for 30 min, dissected to remove the cornea and lens, and then placed back into 4%PFA on ice for another 30 min. The sclera was peeled off from the retina, and radial cuts were made to allow for flattening and orientation marking. The retina was then transferred to RNA-grade 30% sucrose/PBS and kept at 4°C until it sank. Once equilibrated, the retina was mounted onto a membrane filter (MF-Millipore). The retina and filter paper then underwent two cycles of drying and rewetting and 30% sucrose/PBS, followed by 5 min of drying. The membrane filter was trimmed to be slightly larger than the size of the retina, and the filter paper with the retina was adhered to a flat stage made from tissue freezing medium (EMS), mounted on a cryostat chuck. The retina was embedded in a thin layer of tissue-freezing medium, and the chuck was placed on a block of dry ice to solidify the tissue-freezing medium. The embedded retina was stored overnight at -80°C. Before sectioning, the retina block was equilibrated within the cryostat. Care was taken to maintain the flat orientation of the tissue while trimming and sectioning the block.  Sections of 12µm thickness were collected onto MERSCOPE slides (Vizgen). Each slide was washed with DEPC-treated PBS and incubated in 70% Ethanol at 4°C overnight to permeabilize the tissue. Samples were then either processed for MERFISH imaging or stored in 70% ethanol as flatmount slides at 4°C for up to one month.

value: ganglion cell layer

tag: costain


title: GCL_controlwOpn4_2

description: Average Opn4 intensity is in the Cellbound3 column of the metadata


title: finfish liver, Wheat Starch; Tank Number - T28


title: GCL_control_3

value: <None>


title: finfish liver, Corn Starch; Tank Number - T26


title: GCL_control_4


title: GCL_controlwOpn4_1


title: GCL_controlwCD31_6


title: finfish liver, Whole Wheat Grain Flour; Tank Number - T25


title: GCL_controlwCD31_2


title: GCL_control_1


title: finfish liver, Corn Starch; Tank Number - T33


title: TBB8


title: pennycress-Leaf-rep2

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

institute: Agriculture and Agri-Food Canada

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to reference transcriptome using salmon (v1.10.0) and gene expression levels were summarized by tximport (version 1.30.0).
Assembly: Camelina sative (GCF_000633955.1); Brassica napus (DH12075 v3.1); Thlaspi arvense (GCA_911865555)
Supplementary files format and content: TPM_N99.csv, TPM_DH12075.csv, TPM_DH55.csv, and TPM_pennycress.csv, all files contain the TPM values summarized by tximport

organism: Thlaspi arvense

source_name: Leaves

extract_protocol:
We collected the fully expanded cotyledons and true leaves from the young seedlings to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

value: Leaves

value: plant cell

value: Field pennycress


title: pennycress-Leaf-rep1


title: pennycress-COT-rep3

source_name: Cotyledons

value: Cotyledons


title: finfish liver, Dextrin Corn Starch; Tank Number - T27


title: pennycress-COT-rep2


title: pennycress-COT-rep1


title: CD4 Tconv Brain day 60 TCR

city: Toulouse

first: Ilan

last: Fijalkow

address: CHU Purpan – BP 3028 – 31024 Toulouse Cedex, 3, Toulouse

country: France

institute: Infinity-Toulouse Institute for Infectious and Inflammatory Diseases

description:
Library name: Tconv-BR-TCR
TCR library

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v9.0.0 and the references provided by 10X : refdata-gex-GRCm39-2024-A for Gene Expression and refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 for VDJ .
Assembly: Mouse (mus musculus) mm39 for GEX & mm10 for VDJ (scRNAseq/TCRseq experiment).
Supplementary files format and content: Tab separated values files and matrix files
Library strategy: TCR-Seq

source_name: Brain

extract_protocol:
EAE was induced in C57BL/6 mice and CD4+ CD44+ GITR- Tconv cells were isolated from the brain and spleen of mice at day 60 post-immunization.
18718 (brain) and 38000 (spleen) CD4+ T conv, were subjected to Chromium Controller (10X Genomics) for single cell libraries generation using Chromium GEM-X Single Cell 5' Reagent Kits v3 (10X Genomics).

value: Brain

value: CD4 T cells

value: WT

value: EAE day 60


title: CD4 Tconv Spleen day 60 TCR

description:
Library name: Tconv-Spleen-TCR
TCR library

source_name: Spleen

value: Spleen


title: CD4 Tconv Brain day 60 RNA

description:
Library name: Tconv-BR-RNA
GEX library

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v9.0.0 and the references provided by 10X : refdata-gex-GRCm39-2024-A for Gene Expression and refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 for VDJ .
Assembly: Mouse (mus musculus) mm39 for GEX & mm10 for VDJ (scRNAseq/TCRseq experiment).
Supplementary files format and content: Tab separated values files and matrix files


title: Day8 Chronic, Replicate 4

city: Columbus

first: Weidong

last: Wu

state: Ohio

address: 2255 Kenny Rd

institute: Ohio State University

description:
Library name: Day8-Acute-post-4
metadata.csv

data_processing:
The raw bulk sequences were checked, trimmed, and filtered by using Fastp (v0.23.4). The filtered reads were mapped to the mouse reference genome mm10 using HISAT2 (v2.2.1), and samtools (v1.17) was used to convert and sort BAM files. Lastly, the subread tool (v2.0.6) was used for gene quantification and generating the raw expression matrix. Raw expression data was first log normalized, and the Limma R package (v3.56.2) was used to fit the model and perform differential expression analysis.
Assembly: GRCm38
Supplementary files format and content: csv

growth_protocol: Mouse spleen CD8+ T cells were isolated and grow in RPMI-1640 with 10% FBS, 1% Pen-Strep, 1 mM Sodium Pyruvate, 1X MEM NEAA, 10mM HEPES and 50 μM 2-mercaptoethanol supplemented with 100 U/ml recombinant human IL-2  in 12-well plates at 37 ℃ and 5% CO2

extract_protocol:
Cells were washed with PBS twice and pellets. Cell pellets were lysed with TRIzol and mixed with chloroform. RNA in the aqueous phase were cleaned up by RNeasy Micro Kit (QIAGEN #74004).
RNA with PolyA selction

treatment_protocol: T cells were first stimulated with 3 μg/ml plate-bound αCD3 and 1 μg/ml αCD28 for 48 hours. Teff were expanded with IL-2 for another 6 days. Tex cells were restimulated with 3 μg/ml plate-bound αCD3 every two days for another 6 days.

tag: cell line

value: Primary mouse CD8+ T cell

value: lymphocyte

value: TCR stimulation

tag: sample group

value: Day8 Chronic


title: pennycress-Leaf-rep3

tag: tissue

tag: genotype


title: CD4 Tconv Spleen day 60 RNA

description:
Library name: Tconv-Spleen-RNA
GEX library


title: Day8 Chronic, Replicate 3

description:
Library name: Day8-Acute-post-3
metadata.csv


title: Day8 Chronic, Replicate 1

description:
Library name: Day8-Acute-post-1
metadata.csv


title: Day8 Acute pre, Replicate 3

description:
Library name: Day8-Acute-pre-3
metadata.csv

value: Day8 Acute pre


title: Day8 Chronic, Replicate 2

description:
Library name: Day8-Acute-post-2
metadata.csv


title: Normoxia_input

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

description: Library name: Normoxia, Input

data_processing:
The data were filtered and trimmed using Trim Galore! (version 0.6.7)
Reads were aligned to the mm10 mouse genome using Bowtie 2 (version 2.3.5.1)
TheBAMfiles were further processed to create bigWig files with the bamCoverage function within the deeptools package (version 3.5.1)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mESCs

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Extraction was performed according to the protocol of the ChIP-Seq High Sensitivity Kit (abcam).
Library construction was performed according to the protocol of the ChIP-Seq High Sensitivity Kit (abcam).

value: mESCs

value: normoxia


title: Day8-Acute-pre, Replicate 1

description:
Library name: Day8-Acute-pre-1
metadata.csv


title: Normoxia_H3K27ac

description: Library name: Normoxia, H3K27ac


title: Hypoxia_H3K27ac

description: Library name: Hypoxia, H3K27ac

value: hypoxia


title: Hypoxia_H3K4me3

description: Library name: Hypoxia, H3K4me3


title: Normoxia_H3K4me3

description: Library name: Normoxia, H3K4me3


title: SSBP3_PRO_seq_DMSO_rep1

city: Philadelphia

first: Xiaokang

last: Wang

state: PA

address: 315 A  Abramson Research Center, 3615 Civic Center Blvd.

department: Hematology

institute: Children's hospital of Philadelphia

description:
Library name: SSBP3_PRO_seq_DMSO_rep1
SSBP3_PRO_seq_DMSO_merge_forward.bw
SSBP3_PRO_seq_DMSO_merge_reverse.bw

data_processing:
Fastq sequencing files were processed by fastp to remove adaptors and low-quality reads and bases; UMI-tools was used to extract UMI from reads; BWA-MEM was used for reads mapping using mm9 genome build; SAMtools was used to convert SAM filefiles to BAM filefiles and BAM file indexing; UMI-tools was used again for deduplication based on the extracted UMI; CPM was used for normalization to generate bigwig from deeptools bamCoverage. Quantifying differential expression was achieved by HOMER (getDiffExpression.pl) (http://homer.ucsd.edu/homer/ngs/peaksReplicates.html).
Assembly: mm9
Supplementary files format and content: bw: tracks of ChIP-seq signals
Library strategy: PRO-Seq

molecule: nuclear RNA

source_name: cell line

extract_protocol:
Nuclei were isolated for PRO-seq, followed by run-on reactions, nascent RNA isolation, and cDNA library preparaion as described in a fast PRO-seq version (https://www.biorxiv.org/content/10.1101/2020.05.18.102277v1)
Library preparaion as described in a fast PRO-seq version (https://www.biorxiv.org/content/10.1101/2020.05.18.102277v1)

value: cell line

value: Erythroblast

value: SSBP3-dTAG subline

value: 1h DMSO


title: Hypoxia_input

description: Library name: Hypoxia, Input


title: SSBP3_PRO_seq_DMSO_rep2

description:
Library name: SSBP3_PRO_seq_DMSO_rep2
SSBP3_PRO_seq_DMSO_merge_forward.bw
SSBP3_PRO_seq_DMSO_merge_reverse.bw


title: Day8 Acute pre, Replicate 4

description:
Library name: Day8-Acute-pre-4
metadata.csv


title: SSBP3_Micro_C_dTAGV1_rep1

description:
Library name: SSBP3_Micro_C_dTAGV1_rep1
NextSeq 2000 for shallow sequencing

data_processing:
.mcool files were generated using the distiller pipeline (v3.3)
Assembly: mm9
Supplementary files format and content: mcool:multi-resolution contact map

extract_protocol:
DNA was digested with MNase and proximity ligated. After overnight decrosslinking and Proteinase K digestion, DNA fragments corresponding to dinucleosomes were isolated by AMPure XP beads.
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440)

value: 1h  dTAGV-1


title: SSBP3_PRO_seq_dTAGV1_rep1

description:
Library name: SSBP3_PRO_seq_dTAGV1_rep1
SSBP3_PRO_seq_dTAGV1_merge_forward.bw
SSBP3_PRO_seq_dTAGV1_merge_reverse.bw


title: SSBP3_PRO_seq_dTAGV1_rep2

description:
Library name: SSBP3_PRO_seq_dTAGV1_rep2
SSBP3_PRO_seq_dTAGV1_merge_forward.bw
SSBP3_PRO_seq_dTAGV1_merge_reverse.bw


title: SSBP3_Micro_C_dTAGV1_rep2

description:
Library name: SSBP3_Micro_C_dTAGV1_rep2
NextSeq 2000 for shallow sequencing


title: SSBP3_Micro_C_DMSO_rep1

description:
Library name: SSBP3_Micro_C_DMSO_rep1
NextSeq 2000 for shallow sequencing


title: SSBP3_Micro_C_DMSO_rep2

description:
Library name: SSBP3_Micro_C_DMSO_rep2
NextSeq 2000 for shallow sequencing


title: Hair cells, 3 days post sham lesion, rep 3

city: New York

first: Rohan

middle: Saleem

last: Roy

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: Library name: Sample 12

data_processing:
Fastq read quality was assessed using the Rfastp package and filtered based on number of unassigned bases (N<5), read length (minimum read length 15), and phred score (minimum 15). Filtered reads were aligned to the reference genomes using the Rsubread package (v 2.8.2) and reads assigned to genes using the featurecounts function. Transcript abundance was calculated using Salmon (v1.8.0). Normalized counts for each sample were generated using the DESeq2 (v.1.34.0) package utilizing the median of ratios methods on transcript quantifications derived from Salmon.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes normalized read counts generated by DESeq2 for each sample.

organism: Danio rerio

source_name: Posterior lateral line hair cells

extract_protocol:
Hair cells were isolated by fluoresence-activated cell sorting directly into lysis buffer, and total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN). 1 ng of total RNA from each sample was used for library preparation.
Full length cDNA was generated using the Clontech Smart-Seq v4 Ultrat Low Input RNA kit. 1 ng of cDNA was then used to prepare libraries using the Illumina Nextera XT DNA sample preparation kit.

value: Posterior lateral line hair cells

value: Uncut


title: Hair cells, 3 days post sham lesion, rep 2

description: Library name: Sample 11

value: WT


title: Hair cells, 3 days post sham lesion, rep 1

description: Library name: Sample 10


title: Hair cells, 3 days post nerve lesion, rep 3

description: Library name: Sample 9

value: Cut


title: Hair cells, 3 days post nerve lesion, rep 2

description: Library name: Sample 8


title: Hair cells, 3 days post nerve lesion, rep 1

description: Library name: Sample 7


title: TAMs, Control, biological replicate 2

city: Tianjin

first: Yu

last: Ren

state: Tianjin

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

description:
Library name: Control 2
tumor-associated macrophages were sorted from PBS-treated mice

data_processing:
Basecalls performed using MGISEQ-2000
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Assembly: mm9
Supplementary files format and content: fpkm values for each sample.

source_name: tumor associated macrophage

extract_protocol:
Total RNA were extracted with Trizol (Solarbio, R1100)
RNA libraries were prepared for sequencing using  oligo -dT beads

value: tumor associated macrophage

value: Equal volume of solvent


title: TAMs, Control, biological replicate 1

description:
Library name: Control 1
tumor-associated macrophages were sorted from PBS-treated mice


title: TAMs, Control, biological replicate 3

description:
Library name: Control 3
tumor-associated macrophages were sorted from PBS-treated mice


title: TAMs, OMVs, biological replicate 3

description:
Library name: OMVs 3
tumor-associated macrophages were sorted from OMVs-treated mice

value: OMVs (12.5 μg vesicle protein per mouse)


title: TAMs, OMVs, biological replicate 2

description:
Library name: OMVs 2
tumor-associated macrophages were sorted from OMVs-treated mice


title: TAMs, OMVs, biological replicate 1

description:
Library name: OMVs 1
tumor-associated macrophages were sorted from OMVs-treated mice


title: TAMs, IN@OMVs, biological replicate 1

description:
Library name: IN@OMVs 1
tumor-associated macrophages were sorted from IN@OMVs-treated mice

value: IN@OMVs (12.5 μg vesicle protein per mouse)


title: TAMs, IN@OMVs, biological replicate 2

description:
Library name: IN@OMVs 2
tumor-associated macrophages were sorted from IN@OMVs-treated mice


title: PUS1-CON-5

city: Shanghai

first: Yanfeng

last: Liu

address: No. 160, Pujian Road, Pudong New Area, Shanghai, China

institute: Ren Ji Hospital, School of  Medicine, Shanghai Jiao Tong University

description:
Library name: sample 16
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv

data_processing:
Illumina Novaseq 6000 PE150 used for sequencing
Paired-end clean reads were aligned to the reference genome using STAR.
Differential expression analysis of two groups was performed using the DESeq R package
Assembly: mm10
Supplementary files format and content: *_counts.xlsx and *_counts.csv include ReadsCount values for each Sample
Supplementary files format and content: *_IRS.csv includes intron retention (IR) scores for each Sample

source_name: liver

extract_protocol:
Total RNA was harvested using Trizol reagent (Invitrogen, 15596018) and mRNA was enriched by Oligo(dT) beads.
The enriched mRNA was fragmented into short fragments using the fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA fragments were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then these cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were then size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000

value: liver

value: control PUS1f/f


title: PUS1-cKO-1

description:
Library name: sample 17
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PUS1-CON-4

description:
Library name: sample 15
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PUS1-cKO-3

description:
Library name: sample 19
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PUS1-CON-1

description:
Library name: sample 13
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PUS1-cKO-2

description:
Library name: sample 18
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PT3-M146-2

description:
Library name: sample 10
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv

value: mutant PUS1 overexpression


title: PUS1-CON-3

description:
Library name: sample 14
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: PT3-WT-4

description:
Library name: sample 8
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv

value: wild type PUS1 overexpression


title: PT3-M146-1

description:
Library name: sample 9
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: PT3-WT-1

description:
Library name: sample 5
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: PT3-WT-2

description:
Library name: sample 6
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: PT3-CON-1

description:
Library name: sample 1
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv

value: control MYC/TP53-/-


title: PT3-CON-3

description:
Library name: sample 3
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: PUS1-cKO-5

description:
Library name: sample 20
PUS1_cKO_counts.csv
PUS1_cKO_IRS.csv
PUS1_cKO_LTR_counts.csv


title: TAMs, IN@OMVs, biological replicate 3

description:
Library name: IN@OMVs 3
tumor-associated macrophages were sorted from IN@OMVs-treated mice


title: brain cells, MCAO,PBS_treated, 14D, rep2

city: Hangzhou

first: An

last: Ping

state: Zhejiang

address: 88, Jiefang Road

institute: Zhejiang University

description:
Library name: PBS_treated_14D_brain_2
PBS_treated_14D_brain_2

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Young (8-10 week-old) transgenic and wild-type male mice on a C57BL/6 background were randomly distributed into PBS group (n=2) and IL2-JES6-1 treated group (n=2). Beginning at 6 hours following MCAO surgery, 7 injections from 6 hours to 14 days after the surgery were intraperitoneally injected into the IL2-JES6-1 treated group, while PBS were intraperitoneally injected into the PBS group. At day 14 after the surgery, cells were dislocated from the ischemic hemisphere of all the mice and sorted for CD45high immune cells using FACS. Immune cells were collected for scRNA-seq. Young (8-10 week-old) transgenic and wild-type male mice on a C57BL/6 background were randomly distributed into PBS group (n=2) and ILC2s-transferred group (n=2). At 6 hours following MCAO surgery, 1*10^6 ILC2s were intravenously transferred into the ILC2s-transferred group, while PBS were intravenously injected into the PBS group. At day 14 after the surgery, cells were dislocated from the ischemic hemisphere of all the mice and were collected for scRNA-seq.
The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaSeq 6000) according to the manufacturer’s instructions (Illumina).

value: Brain

value: Brain cells

value: PBS injections


title: PT3-CON-2

description:
Library name: sample 2
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: brain cells, MCAO,PBS_treated, 14D, rep1

description:
Library name: PBS_treated_14D_brain_1
PBS_treated_14D_brain_1


title: PT3-M146-3

description:
Library name: sample 11
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: CD45high cells, MCAO,IL2-JES6-1_treated, 14D, rep2

description:
Library name: IL2_JES6_1_treated_14D_CD45high_2
IL2_JES6_1_treated_14D_CD45high_2

value: CD45high immune cells

value: IL2/IL2 Ab injections


title: PT3-M146-4

description:
Library name: sample 12
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: brain cells, MCAO,ILC2s_treated, 14D, rep1

description:
Library name: ILC2s_treated_14D_brain_1
ILC2s_treated_14D_brain_1

value: ILC2s transfer


title: brain cells, MCAO,ILC2s_treated, 14D, rep2

description:
Library name: ILC2s_treated_14D_brain_2
ILC2s_treated_14D_brain_2


title: CD45high cells, MCAO,PBS treated, 14D, rep1

description:
Library name: PBS_treated_14D_CD45high_1
PBS_treated_14D_CD45high_1


title: ILC2s, MCAO, brain, 5d, rep6

description: Library name: brain_5d_6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstream analyses were based on the clean data with high quality. 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 thereference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: Mouse mm10
Supplementary files format and content: Comma-separated values file

extract_protocol:
ILC2s from young (8-10 week-old) transgenic and wild-type male mice on a B6.Cg-Tg(CAG-GFP)Smoc were collected for the experiment. First, IL-33 was intraperitoneally injected into mice every 2 days for 7 days for in vivo expansion of ILC2s. Next, ILC2s were collected from the bone marrow and spleen of the mice. Cells negativbe for lineage markers (CD11b, Gr1, CD3ε, CD45R/B220, and Ter119) and positive for CD25 were sorted using MACS. After in vitro culturing for 14 days in the presence of IL-2, IL-7, IL-15 and IL-33, the cells were further sorted by FACS as CD45+Lin-ST2+KLRG1+CD127+ cells. To compare the transcriptional profiles of ILC2s at key time points, we intravenously transferred the isolated ILC2s 6 hours after MCAO and collected them at different time points. We collected the transferred ILC2s from the blood at day 1 (bld_1d, n=6) and day 5 (bld_5d, n=6), also from the brain at day 5 after MCAO (br_5d, n=6) for RNA-seq. In addition, ILC2s directly from culture medium (base, n=5) were also included as a baseline control.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. After the library QC, it is pooled according to the effective concentrationand the target data output required for the experiment, then subjected to Illumina sequencing, which produces 150 bp paired-end reads. The basic principle of the sequencing is "Sequencing by Synthesis," where fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencingcluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

value: ILC2s, MCAO, brain, 5d

tag: batch


title: ILC2s, MCAO, brain, 5d, rep2

description: Library name: brain_5d_2


title: PT3-WT-3

description:
Library name: sample 7
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: ILC2s, MCAO, blood, 5d, rep6

description: Library name: blood_5d_6

source_name: Blood

value: Blood

value: ILC2s, MCAO, blood, 5d


title: ILC2s, MCAO, brain, 5d, rep4

description: Library name: brain_5d_4


title: CD45high cells, MCAO,IL2-JES6-1_treated, 14D, rep1

description:
Library name: IL2_JES6_1_treated_14D_CD45high_1
IL2_JES6_1_treated_14D_CD45high_1


title: ILC2s, MCAO, brain, 5d, rep5

description: Library name: brain_5d_5


title: ILC2s, MCAO, blood, 5d, rep5

description: Library name: blood_5d_5


title: ILC2s, MCAO, brain, 5d, rep1

description: Library name: brain_5d_1


title: ILC2s, MCAO, brain, 5d, rep3

description: Library name: brain_5d_3


title: PT3-CON-4

description:
Library name: sample 4
PT3_PUS1_counts.xlsx
PT3_PUS1_IRS.csv
PT3_PUS1_LTR_counts.csv


title: ILC2s, MCAO, blood, 5d, rep3

description: Library name: blood_5d_3


title: ILC2s, MCAO, blood, 5d, rep4

description: Library name: blood_5d_4


title: ILC2s, MCAO, blood, 5d, rep2

description: Library name: blood_5d_2


title: ILC2s, MCAO, blood, 5d, rep1

description: Library name: blood_5d_1


title: CD45high cells, MCAO,PBS treated, 14D, rep2

description:
Library name: PBS_treated_14D_CD45high_2
PBS_treated_14D_CD45high_2


title: ILC2s, MCAO, blood, 1d, rep6

description: Library name: blood_1d_6

value: ILC2s, MCAO, blood, 1d


title: ILC2s, MCAO, blood, 1d, rep3

description: Library name: blood_1d_3


title: ILC2s, MCAO, blood, 1d, rep4

description: Library name: blood_1d_4


title: ILC2s, MCAO, blood, 1d, rep2

description: Library name: blood_1d_2


title: ILC2s, MCAO, blood, 1d, rep5

description: Library name: blood_1d_5


title: ILC2s, MCAO, blood, 1d, rep1

description: Library name: blood_1d_1


title: ILC2s, base, rep5

description: Library name: base5

value: ILC2s, base


title: ILC2s, base, rep3

description: Library name: base3


title: ILC2s, base, rep2

description: Library name: base2


title: ILC2s, base, rep4

description: Library name: base4


title: snRNA-seq of cortex from Gclc-KO mouse (6 months, replicate 2)

city: Otsu

first: Shoko

last: Hashimoto

state: Shiga

address: Setatsukinowa-cho

country: Japan

institute: Shiga University of Medical Science

description:
Library name: 6M_GclcKO_2
Single-nucleus RNA-seq of Gclc-KO cortex (6M, rep2)

data_processing:
Cell Ranger (10x Genomics) was used to demultiplex raw base call files, align reads to the mm10 genome, and generate gene expression matrices.
Filtering and normalization were performed using Seurat  in R.
Assembly: mm10
Supplementary files format and content: Matrix Market Exchange format files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) generated by Cell Ranger and used for downstream analysis.

source_name: cerebral cortex

growth_protocol: Mice were housed under a 12-h light/12-h dark cycle and fed ad libitum.

extract_protocol:
Nuclei were isolated from mouse cerebral cortex using Nuclei EZ Lysis Buffer (Merck Millipore) according to the manufacturer’s instructions, followed by fluorescence-activated cell sorting (FACS) to enrich for DAPI-positive singlet nuclei.
Single-nucleus RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1 kit, according to the manufacturer's protocol.

treatment_protocol: No treatment was applied before tissue collection.

value: cerebral cortex

value: nucleus

value: Gclc-KO


title: snRNA-seq of cortex from Gclc-KO mouse (6 months, replicate 1)

description:
Library name: 6M_GclcKO_1
Single-nucleus RNA-seq of Gclc-KO cortex (6M, rep1)


title: snRNA-seq of cortex from Gclc-KO mouse (3 months, replicate 2)

description:
Library name: 3M_GclcKO_2
Single-nucleus RNA-seq of Gclc-KO cortex (3M, rep2)


title: snRNA-seq of cortex from Gclc-KO mouse (3 months, replicate 1)

description:
Library name: 3M_GclcKO_1
Single-nucleus RNA-seq of Gclc-KO cortex (3M, rep1)


title: MN1

city: Jinan

first: tian

last: zhihan

address: No. 16369, Jingshi Road

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

description:
Library name: Sample4
Cancer Cachexia
Column name in raw counts All Samples.txt: MN1

data_processing:
The raw image data files obtained from high-throughput sequencing are converted into raw sequencing reads through base calling by CASAVA.
The sequences were filtered using the fastp software to remove those containing sequencing primer adapter sequences, those with bases at the 3' end having a quality score lower than 20, those with a sequence length of less than 25, and ribosome RNA reads of the target species for sequencing.
The software used for sequence alignment was Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5), which employs a spliced mapping algorithm. The species was mouse, and the reference genome version was GRCm39.108.
Gene expression abundance was assessed using FPKM. Differential expression analysis was conducted with the edgeR package, adjusting p-values for multiple testing and applying a Q value threshold (Q < 0.05, |log2 (FC)| > 1, and FPKM > 1).
Assembly: MM10
Supplementary files format and content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: muscle

growth_protocol: Male BALB/c nude mice (6 weeks old, weighing 20–25 g) were kept in individually ventilated cages (IVCs) with 24-hour constant-pressure ventilation, in an environment maintained at 21–24°C with constant humidity and a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the Tianmo#TR205-200 kit. RNA purity and concentration were measured using a Qubit® 3.0 fluorometer (Life Technologies, USA) and a Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA).
1 µg RNA was used for library construction, which was performed according to the instructions of the Stranded RNA-Seq Library Prep Kit (ABclonal, China).

treatment_protocol: CT-26 colon cancer cells (5*10^5 cells) were suspended in 100μL of PBS and injected subcutaneously into the right flank of the mice. An identical amount of PBS was injected into the control group. On the day after tumor injection, the APS high-dose groups were administered APS at a dose of 800 mg/kg by gavage in a volume of 0.2 mL per mouse, while the other groups were given an equal volume of normal saline by gavage.

value: muscle

tag: host strain

value: Six-week-old male BALB/c nude

value: Wild Type


title: MN3

description:
Library name: Sample6
Cancer Cachexia
Column name in raw counts All Samples.txt: MN3


title: MP1

description:
Library name: Sample7
Cancer Cachexia
Column name in raw counts All Samples.txt: MP1

value: colon cancer cells

value: Treatment group

value: APS high-dose


title: MM3

description:
Library name: Sample3
Cancer Cachexia
Column name in raw counts All Samples.txt: MM3

value: Model group


title: MM2

description:
Library name: Sample2
Cancer Cachexia
Column name in raw counts All Samples.txt: MM2


title: MN2

description:
Library name: Sample5
Cancer Cachexia
Column name in raw counts All Samples.txt: MN2


title: MP2

description:
Library name: Sample8
Cancer Cachexia
Column name in raw counts All Samples.txt: MP2


title: Ctrl_d

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: Library name: Ctrl_d

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: featureCounts in xls format

molecule: polyA RNA

source_name: lens

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

value: lens

value: control


title: Mettl3_CKO_c

description: Library name: Mettl3-CKO_c

value: Mettl3 CKO


title: Mettl3_CKO_d

description: Library name: Mettl3-CKO_d


title: MM1

description:
Library name: Sample1
Cancer Cachexia
Column name in raw counts All Samples.txt: MM1


title: Ctrl_c

description: Library name: Ctrl_c


title: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-2

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

description: Library name: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-2

data_processing:
Sequencing reads were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: comma-delimited text files with normalized abundance for every gene and every sample.

source_name: Epi

growth_protocol: Natural mated embryos were dissected from decidua. Peri-implantation stage embryos for 3D in vitro culture were prepared following a previously published protocol (Li et al., Natl Sci Rev. 2023).

extract_protocol:
Approximately 10-100 cells per sample were lysed, and cDNA synthesis was performed directly on the cytoplasmic lysate. Three biological replicates were performed per group. The resulting cDNA was amplified for 17 cycles to generated a full-length cDNA library.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

treatment_protocol: Single cells were collected from E3.5 pre-implantation embryos by fist removing zone pellucida with 20mg/ml PE (Pronase E, Sigma). Embryos were then incubated in Ca2+-free CZB medium and gently pipetting with a fire-polished glass tube to obtain single cells. For peri-implantation embryos (E3.5-E5.5), single cells from different lineages (EPI, PE, and EXE) were collected by separating the embryos from decidua either in vivo or from Matrigel in vitro. The embryos were digested with 0.05% TE (Trypsin-EDTA, Gibco, 25300062) to obtain single cells. All cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals, USA) solution before used.

value: Epi

value: dTAG treatment


title: ILC2s, base, rep1

description: Library name: base1


title: Valid_Zbtb17_RNA-Epi_Control-4.5-2

description: Library name: Valid_Zbtb17_RNA-Epi_Control-4.5-2

value: Wild type


title: Valid_Zbtb17_RNA-Epi_Control-4.5-3

description: Library name: Valid_Zbtb17_RNA-Epi_Control-4.5-3


title: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-3

description: Library name: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-3


title: Valid_Zbtb17_CT-Epi_ZbKO_H3K27me3-4.5-1

description: Library name: Valid_Zbtb17_CT-Epi_ZbKO_H3K27me3-4.5-1

data_processing:
Sequencing reads were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4) with the parameters: --effectiveGenomeSize 2652783500 --extendReads 250 --binSize 20 --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: ChIP signal bigwig file
Library strategy: CUT&Tag

extract_protocol:
Cut&Tag was performed as previously described using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904). Briefly, cells were bound to 10μL of pre-washed ConA beads in a 200μL low-binding tube and incubated overnight at 4°C with 50 μL of antibody buffer containing 0.5μg of the target antibody. After two washes with dig-wash buffer, cells were incubated with 50μL of dig-wash buffer containing 0.5μg of a secondary antibody for 1 hour at room temperature. Following two additional washes with 200μL of dig-wash buffer, tagmentation was performed by adding 1μL of pG-Tn5 in 100μL of dig-300 buffer and incubating for 1 hour at room temperature. After two final washes with 200μL of dig-wash buffer, tagmentation buffer was added, and samples were incubated at 37°C for 1 hour. The reaction was stopped by adding 10% SDS, and tagmented DNA fragments were purified using VAHTS beads. Following purification, libraries were amplified by PCR.
Sequencing libraries were prepared continue using the Hyperactive In-Situ ChIP Library Prep Kit (Vazyme Biotech, TD904). The index used for library preparation were from the TruePrep index Kit V2 for Illumina (Vazyme Biotech, TD202)

value: Zbtb17 Knockout


title: finfish liver, Dextrin Corn Starch; Tank Number - T44

data_processing:
Pre-Assembly Steps - Once sequences were received SortMeRNA (v. 4.3.6) was used to remove any remaining rRNA reads (Kopylova et al., 2012). Trim Galore (v. 0.6.7) was used to remove low quality nucleotides, polyA and polyT tails (Krueger, 2020).
Assembly - Trinity (v. 2.8.5) was used for de novo assembly from pooling all the reads (Grabherr et al., 2011; Griffith et al., 2015; Haas et al., 2013). Busco (v. 5.0.0) was used to determine the resulting transcriptomes completeness (Manni et al., 2021). After Salmon (v. 0.13.1) was used to quantify transcripts (Patro et al., 2017), a series of Trinity scripts were used to generate count and expression (trimmed mean of M-values [TMM] normalization) matrices for transcript isoforms and genes and use DESeq2 (v. 1.38.0) to calculate differentially expressed genes (DEGs) (Haas et al., 2013; Love et al., 2021).
Annotation - Transdecoder (v.  5.7.1) was used to identify long ORFs and predict which ones are coding while Trinotate (v. 4.0.0) was used to annotate the transcripts and genes, and finally a series of scripts from Trinity/Trinotate was used to determine GO (Gene Ontology) Enrichment using GOSeq (v. 1.50.0)(Bryant et al., 2017; Hass, 2022; Young et al., 2010a). If any DEGs had the same annotation, then they were further analyzed to determine if they were potential paralogs or non-overlapping parts of the same gene. BLASTN was used to determine if any of the transcripts associated with these DEGs were overlapping and then BLASTX was used to determine where these DEG transcripts aligned with the UniProt reference sequences associated with these annotations. A set of DEGs were considered to be likely paralogs if they were clustered into different genes but were aligning with an overlapping region of the reference sequence. On the other hand, a set of DEGs were considered to be likely non-overlapping parts of the same gene if they had little significant overlapping with one another (E-value >10) and aligned with completely different regions of the reference sequence.
R Data Processing and Statistical Analysis - Counts, expression matrices, DEGs, and GO enrichment results were analyzed and summarized with RStudio (v.2023.06.1; R version 4.2.0). These tables were converted into a Bray-Curtis dissimilarity matrix which was analyzed with principal coordinates of analysis (PCoA) and permutational analysis of variance (PERMANOVA). PRIMER7/PERMANOVA+ was used to conduct PERMANOVA analysis with Monte Carlo (MC) p-value.
Assembly: De novo
Supplementary files format and content: Trinity.isoform.TMM.EXPR.matrix is the trimmed mean of M-values [TMM] normalization) matrix for transcript isoforms
Supplementary files format and content: Trinity.gene.TMM.EXPR.matrix is the trimmed mean of M-values [TMM] normalization) matrix for transcript isoforms is the trimmed mean of M-values [TMM] normalization) matrix for genes
Supplementary files format and content: Trinotate.txt is the annotation for isoform transcripts and genes.

extract_protocol:
Two fish from each tank were euthanized with an overdosed of MS-222 at 300 mg/L for dissection of the liver which was immediately stored at – 80 °C for subsequent transcriptomic analysis. Total RNA was extracted from liver samples using RNeasy purification kit (RNeasy Mini kit, ID:74101, QUIAGEN, Venlo, The Netherlands) following manufacturer’s protocol. RNA quality, purity and quantity were determined using NanoDrop 1000 based on 260/280 and 260/230 absorbance ratios (Thermo Fisher Scientific, Waltham, MA, United States).
Then, RNA samples were sent to GeneWiz (South Plainfield, NJ, USA) for sequencing on an Illumina HiSeq.

value: finfish liver

value: DCS


title: MP3

description:
Library name: Sample9
Cancer Cachexia
Column name in raw counts All Samples.txt: MP3


title: Valid_Zbtb17_CT-Epi_WT_H3K27me3-4.5-2

description: Library name: Valid_Zbtb17_CT-Epi_WT_H3K27me3-4.5-2

value: wild type


title: Valid_Zbtb17_CT-Epi_ZbKO_H3K27me3-4.5-2

description: Library name: Valid_Zbtb17_CT-Epi_ZbKO_H3K27me3-4.5-2


title: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-1

description: Library name: Valid_Zbtb17_RNA-Epi_Zbtb17KO-4.5-1


title: Valid_Zbtb17_CT-Epi_WT_H3K27me3-4.5-1

description: Library name: Valid_Zbtb17_CT-Epi_WT_H3K27me3-4.5-1


title: Valid_Zbtb17_RNA-Epi_Control-4.5-1

description: Library name: Valid_Zbtb17_RNA-Epi_Control-4.5-1


title: Valid_GSK_CT-Epi_WT_H3K4me3-4.5-2

description: Library name: Valid_GSK_CT-Epi_WT_H3K4me3-4.5-2


title: Valid_GSK_CT-Epi_WT_H3K27me3-4.5-2

description: Library name: Valid_GSK_CT-Epi_WT_H3K27me3-4.5-2


title: Valid_GSK_CT-Epi_WT_H3K4me3-4.5-1

description: Library name: Valid_GSK_CT-Epi_WT_H3K4me3-4.5-1


title: Valid_GSK_CT-Epi_WT_H3K27me3-4.5-1

description: Library name: Valid_GSK_CT-Epi_WT_H3K27me3-4.5-1


title: finfish liver, Whole Corn Grain Flour; Tank Number - T37

value: CG


title: Valid_GSK_CT-Epi_Gsk_H3K4me3-4.5-2

description: Library name: Valid_GSK_CT-Epi_Gsk_H3K4me3-4.5-2

value: GSK treatment


title: Valid_GSK_CT-Epi_Gsk_H3K4me3-4.5-1

description: Library name: Valid_GSK_CT-Epi_Gsk_H3K4me3-4.5-1


title: Invivo_CT-Epi_H3K27me3-5.0_invivo-2

description: Library name: Invivo_CT-Epi_H3K27me3-5.0_invivo-2


title: Valid_GSK_CT-Epi_Gsk_H3K27me3-4.5-2

description: Library name: Valid_GSK_CT-Epi_Gsk_H3K27me3-4.5-2


title: Invivo_CT-Epi_H3K27me3-5.0_invivo-1

description: Library name: Invivo_CT-Epi_H3K27me3-5.0_invivo-1


title: Invivo_CT-Epi_H3K4me3-5.0_invivo-2

description: Library name: Invivo_CT-Epi_H3K4me3-5.0_invivo-2


title: reChIP-ESC_H3K27K4me3-ESC-1

description: Library name: reChIP-ESC_H3K27K4me3-ESC-1

data_processing:
Sequencing reads for RNA were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Sequencing reads for ChIP-seq/CUT&Tag were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4).
Assembly: mm10
Supplementary files format and content: Gene expression quantification in TPM
Supplementary files format and content: ChIP signal bigwig file

source_name: ESC

growth_protocol: Mouse ESCs were cultured on a plate coated with feeders (feeder condition medium collected from mitomycin C-treated mouse embryonic fibroblasts, RPMI 1640 (Thermo) supplemented with 20% FBS, 1% non-essential amino acid, 1mM sodium pyruvate, 100 μM β-mercaptoethanol and 2mM L-glutamine) in Serum medium supplemented with 1,000μmol/L LIF, 1μmol/L PD0325901 (S1036, Selleck) and 3μmol/L CHIR9902 (S1263, Selleck). Cells were cultured at 37°C and 5% CO2 and passaged 1:3-1:10 every 2 days by triturating the colonies into a single cell suspension using 0.05% trypsin-EDTA (25200056, Thermo Fisher Scientific).

extract_protocol:
RNA-seq: RNA was extracted from ESCs and EB spheroids using TRIzol Reagent (Invitrogen) followed by chloroform extraction. RNA was then precipitated using isopropanol with the addition of 1/10 volume of 3M NaAC and 2μL glycogen to the aqueous phase. After two washes with 75% ethanol, RNA was resuspended in nuclease-free water. CUT&Tag: Cells were bound to ConA beads and incubated with primary antibody overnight, followed by secondary antibody incubation. Tagmentation was performed using pG-Tn5, and DNA was purified using VAHTS beads and amplified by PCR. Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904). ULI-NChIP-seq was performed using 200-500 cells/ sample, with two or three biological replicates per group. Isolated cells were washed with PBS/BSA, and the ULI-NChIP procedure was performed as previously described using 1μg of a histone H3K27me3 or H3K4me3 antibody per immunoprecipitation reaction. XChIP-seq: ESCs/sample were used (2 replicates) for ZBTB17 XChIP-seq. Cells were crosslinked (1% formaldehyde), quenched (glycine), lysed, and sonicated (peak power 75, duty factor 20, cycles 200, 10 min). Chromatin was immunoprecipitated using ZBTB17 antibody and protein A/G beads. DNA was eluted, purified, and precipitated. Libraries were prepared using the KAPA Hyper Prep kit. reChIP-seq: ESCs and EPILCs were processed using the same crosslinking, lysis, and sonication steps as the XChIP-seq protocol. Sequential ChIP was performed using the reChIP-IT kit (Active Motif, 53106).
RNA-seq and ChIP-seq: Libraries were prepared using the KAPA Hyper Prep Kit. Sequenced on Illumina Novaseq. CUT&Tag: Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904).

treatment_protocol: Mouse naive ESCs were dissociated with 0.05% trypsin-EDTA and suspended as single cells. A total of 50,000-10,000 2i ESC cells per cm2 were plated on cell culture dishes pretreated with 0.1% Fibronectin in Serum medium supplemented with minimal essential medium (MEM) non-essential amino acids solution, L-glutamine solution, 0.1mM β-mercaptoethanol, 12mg/mL bFGF (Peprotech) and 20ng/mL Activin A (R&D Scientific).

value: ESC


title: Invivo_CT-Epi_H3K4me3-5.0_invivo-1

description: Library name: Invivo_CT-Epi_H3K4me3-5.0_invivo-1


title: Valid_GSK_CT-Epi_Gsk_H3K27me3-4.5-1

description: Library name: Valid_GSK_CT-Epi_Gsk_H3K27me3-4.5-1


title: reChIP-ESC_H3K4K27me3-ESC-1

description: Library name: reChIP-ESC_H3K4K27me3-ESC-1


title: reChIP-ESC_input-ESC-1

description: Library name: reChIP-ESC_input-ESC-1


title: reChIP-EpiLC_H3K27input-EpiLC-1

description: Library name: reChIP-EpiLC_H3K27input-EpiLC-1

source_name: EpiLC

value: EpiLC


title: reChIP-EpiLC_input-EpiLC-1

description: Library name: reChIP-EpiLC_input-EpiLC-1


title: reChIP-EpiLC_H3K27K4me3-EpiLC-1

description: Library name: reChIP-EpiLC_H3K27K4me3-EpiLC-1


title: reChIP-EpiLC_H3K4input-EpiLC-1

description: Library name: reChIP-EpiLC_H3K4input-EpiLC-1


title: Valid_mESC_RNA-ESC2EpiLC_WT-24h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-24h-2


title: Valid_mESC_RNA-ESC2EpiLC_WT-48h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-48h-1


title: Valid_mESC_RNA-ESC2EpiLC_WT-24h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-24h-1


title: Valid_mESC_RNA-ESC2EpiLC_WT-48h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-48h-2


title: reChIP-EpiLC_H3K4K27me3-EpiLC-1

description: Library name: reChIP-EpiLC_H3K4K27me3-EpiLC-1


title: Valid_mESC_RNA-ESC2EpiLC_WT-12h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-12h-2


title: Valid_mESC_RNA-ESC2EpiLC_WT-0h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-0h-1


title: Valid_mESC_RNA-ESC2EpiLC_WT-0h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-0h-2


title: Valid_mESC_RNA-ESC2EpiLC_WT-12h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_WT-12h-1


title: Valid_mESC_RNA-ESC2EpiLC_EedT-48h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_EedT-48h-1

value: EEDi&dTAG


title: Valid_mESC_RNA-ESC2EpiLC_Eedi-48h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_Eedi-48h-1

value: EEDi


title: Valid_mESC_RNA-ESC2EpiLC_Eedi-48h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_Eedi-48h-2


title: reChIP-ESC_H3K27input-ESC-1

description: Library name: reChIP-ESC_H3K27input-ESC-1


title: Valid_mESC_RNA-ESC2EpiLC_dTag-48h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTag-48h-1

value: dTAG


title: reChIP-ESC_H3K4input-ESC-1

description: Library name: reChIP-ESC_H3K4input-ESC-1


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-12h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-12h-1


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-12h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-12h-2


title: Valid_mESC_RNA-ESC2EpiLC_dTag-48h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTag-48h-2


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-24h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-24h-2


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-0h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-0h-2


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-24h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-24h-1


title: Valid_mESC_CUTTag-EpiLC_WT_Eed-EpiLC-1

description: Library name: Valid_mESC_CUTTag-EpiLC_WT_Eed-EpiLC-1

data_processing:
Sequencing reads for RNA were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Sequencing reads for ChIP-seq/CUT&Tag were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4).
Assembly: mm10
Supplementary files format and content: Gene expression quantification in TPM
Supplementary files format and content: ChIP signal bigwig file
Library strategy: CUT&Tag


title: Valid_mESC_RNA-ESC2EpiLC_dTAG-0h-1

description: Library name: Valid_mESC_RNA-ESC2EpiLC_dTAG-0h-1


title: Valid_mESC_CUTTag-EpiLC_WT_Eed-EpiLC-2

description: Library name: Valid_mESC_CUTTag-EpiLC_WT_Eed-EpiLC-2


title: Valid_mESC_ChIP-ESC_Zbtb17-ESC-2

description: Library name: Valid_mESC_ChIP-ESC_Zbtb17-ESC-2


description: Library name: Valid_mESC_CUTTag-EpiLC_dTAG_Eed-EpiLC-2


title: Valid_mESC_RNA-ESC2EpiLC_EedT-48h-2

description: Library name: Valid_mESC_RNA-ESC2EpiLC_EedT-48h-2


title: Valid_mESC_ChIP-ESC_input-ESC-1

description: Library name: Valid_mESC_ChIP-ESC_input-ESC-1


title: Valid_mESC_ChIP-ESC_Zbtb17-ESC-1

description: Library name: Valid_mESC_ChIP-ESC_Zbtb17-ESC-1


description: Library name: Valid_mESC_ChIP-EpiLC_WT_input-EpiLCK4-1


description: Library name: Valid_mESC_ChIP-EpiLC_WT_H3K4me3-EpiLCK4-1


title: Valid_mESC_ChIP-ESC_input-ESC-2

description: Library name: Valid_mESC_ChIP-ESC_input-ESC-2


description: Library name: Valid_mESC_ChIP-EpiLC_WT_input-EpiLCK27-1


description: Library name: Valid_mESC_ChIP-EpiLC_WT_H3K4me3-EpiLCK4-2


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_input-EpiLCK4-1


description: Library name: Valid_mESC_ChIP-EpiLC_WT_H3K27me3-EpiLCK27-2


description: Library name: Valid_mESC_CUTTag-EpiLC_dTAG_Eed-EpiLC-1


description: Library name: Valid_mESC_ChIP-EpiLC_WT_H3K27me3-EpiLCK27-1


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_H3K4me3-EpiLCK4-2


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_H3K27me3-EpiLCK27-2


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_H3K4me3-EpiLCK4-1


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_H3K27me3-EpiLCK27-1


title: Valid_Zbtb17_RNA-Epi_dTAG-5.0-3

description:
Library name: Valid_Zbtb17_RNA-Epi_dTAG-5.0-3
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_Zbtb17_RNA-Epi_dTAG-5.0-1

description:
Library name: Valid_Zbtb17_RNA-Epi_dTAG-5.0-1
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_Zbtb17_RNA-Epi_Control-5.0-57

description:
Library name: Valid_Zbtb17_RNA-Epi_Control-5.0-57
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_GSK_RNA-Epi_GSKJ4-4.5-3

description:
Library name: Valid_GSK_RNA-Epi_GSKJ4-4.5-3
GSK_E4.5_samples_TPM_matrix.csv


title: Valid_Zbtb17_RNA-Epi_dTAG-5.0-2

description:
Library name: Valid_Zbtb17_RNA-Epi_dTAG-5.0-2
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_GSK_RNA-Epi_GSKJ4-4.5-2

description:
Library name: Valid_GSK_RNA-Epi_GSKJ4-4.5-2
GSK_E4.5_samples_TPM_matrix.csv


title: Valid_GSK_RNA-Epi_Control-4.5-3

description:
Library name: Valid_GSK_RNA-Epi_Control-4.5-3
GSK_E4.5_samples_TPM_matrix.csv


title: Valid_GSK_RNA-Epi_Control-4.5-2

description:
Library name: Valid_GSK_RNA-Epi_Control-4.5-2
GSK_E4.5_samples_TPM_matrix.csv