title: Neurons, rep1

city: Dubai

first: Muhammad

last: Kumail

state: Dubai

address: Al Razi road

department: CATG

country: United Arab Emirates

institute: Mohammad Bin Rashid University

data_processing:
The fast5 files generated by promethION were basecalled using Guppy. The resulting fastq files were used to produce the normalized and count matrices using epi2me-labs/wf-single-cell (https:// labs.epi2me.io/workflows/wf-single-cell/)
Assembly: GRCh38
Supplementary files format and content: Tab separated count and normalized matrices

source_name: Neurons

extract_protocol:
Neural progenitor cells were generated from human episomal iPSC line (Thermo Fisher Scientific Cat. No.: A18945) by inducing the neural ectoderm for 7 days using neural induction media (NIM, Thermo Fisher Scientific). For this purpose, 5 x 105 cells/mL iPSCs were seeded in a six-well plate precoated with rhLaminin-521 (2.5 lg/mL concentration in DPBS with calcium, magnesium) in the presence of 10 uM Rho kinase inhibitor at 37 C in 5% CO2 incubator. The next day (day 1), the ectoderm formation was induced by replacing culture media with NIM consisting of 1x neurobasal media supplemented with 1x neural induction supplement. The spent media was replaced with fresh media every other day until day 7. On day 8, NIM was removed, and NPCs were maintained in neuronal expansion media (NEM) until 80% confluency. NEM was prepared by mixing 1x neurobasal media and 1x DMEM/F12 KO media supplemented with 0.5x neural induction supplement. NPCs were differentiated into neurons by maintaining the cells in neuronal differentiation medium (NDM) for 15 days. Briefly, after harvesting NPCs, 1 x 106 cells/mL were seeded in NEM on a culture vessel precoated with 50 lg/mL poly-Dlysine and 100 lg/mL rh-Laminin-521 in the presence of 10 lM Rho kinase inhibitor and incubated overnight at 37C in a 5% CO2 incubator. The next day (i.e., day 12), the spent NEM was replaced with fresh prewarmed NDM (1x neurobasal medium and 1x DMEM/F-12 supplemented with 1x B27 supplement, 1x N2 supplement, 10 ng/mL bFGF, and 10 mM GlutaMAX supplement). The media was changed every other day until day 22. The newly  differentiated iPSC-derived neurons were used for experimental analysis after days 27–30. The data was analyzed using scRNAseq.
iPSC-derived NPCs and neurons (day 30 of differentiation) were dissociated using TrypLE Express and washed twice with PBS to remove culture media and strained using 70- lm cell strainers. Finally, the cell pellet was resuspended in PBS þ 0.04% BSA and diluted to achieve 1,200 cells/lL with a target recovery of 10,000 cells. The cell suspension was then subjected to generating barcoded single stranded cDNA molecules using a 10x chromium platform following the manufacturer’s protocol. Barcoded cDNAs (10 ng) were conjugated to Biotin tags and amplified for 13 cycles using LongAmp Hot Start Taq. Later, M280 strepta vidin beads were used to pull down the full-length bar coded cDNA molecules, followed by adapter ligation and sequencing using the PromethION system from Oxford Nanopore Technologies (Oxford, UK). For both NPCs and neurons, 50 fmol barcoded cDNA library was loaded to an independent PromethION flow cell (R10.4.1) for every sample. The average N50 of the mRNA long isoform sequencing was 900 bp

value: Neurons


title: wt 14h IAA BR2

status: Public on Aug 08 2024

type: SRA

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

country: Germany

institute: University Hospital of Freiburg

description: File name 2 has barcodes and UMIs, please see protocols and preprocessing

library_source: transcriptomic

data_processing:
Dropseq tool v1.12 (Macosko et al., 2015) was used for mapping raw sequencing data to the reference genome with default parameters
Create bam file without alignment
java -jar PATHTOPICARD/picard.jar FastqToSam F1=FORWARDREAD F2=REVERSEREAD O=RUNNAME.bam SM=RUNNAME
Sort bam file according to read ID
java -jar PATHTOPICARD/picard.jar SortSam I=RUNNAME.bam O=RUNNAME_sorted.bam SORT_ORDER=queryname
Start Dropseq tool
PATHTODROPSEQTOOLS/Drop-seq_alignment.sh -g PATHTOSTARINDEX -r PATHTOGENOMEREFERENCE -d PATHTODROPSEQTOOLS -s PATHTOSTARALIGNER -o OUTPUTFOLDER RUNNAME_sorted.bam
Get UMI filtered matix
PATHTODROPSEQTOOLS/DigitalExpression' -m 30g -t I=star_gene_exon_tagged.bam O=DGE_Matrix.txt CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM CELL_BC_FILE=BARCODESUSED
Assembly: Gencode gene annotations v28 and the human reference genome GRCh38 were derived from the Gencode homepage (EMBL-EBI).
Supplementary files format and content: Tab-delimited text file includes raw count values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: HaCaT

growth_protocol: Cells were cultured in DMEM (gibco, art N° 41965062), supplemented with 10% FCS (anprotec, art N° AC-SM-0190) and 1% penicillin/streptomycin (gibco, art N° 15140130).

extract_protocol:
Direct-zol™ RNA MicroPrep with TRI Reagent® from Zymo Research, art N° R2061
Total RNA was isolated from purified Treg cells and Tconv cells with RNAeasy Plus micro kit (QIAGEN). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies). RNaseq analysis: library preparation for bulk 30-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 50 ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

treatment_protocol: Auxin (IAA, indole-3-acetic acid) was dissolved in 50mM stock in DMSO. 250K cells were seeded and treated the next day: Media was changed and cells were treated with fresh media supplemented with auxin (20µM) or DMSO as solvent control.

tag: cell line

value: HaCaT

tag: cell type

value: immortalized human keratinocytes

tag: genotype

value: CrisprLV2_iCADE4ko_puro - pFUG147EV16_Tir1_PGK_Hygro_W -  pEF1a_GW_iCADMutE4_mAID_GFP_puro

tag: treatment

value: Auxin (3-indolacetic acid, IAA) 20µM, 14h

tag: time

value: 14 hours


title: WT_IR_2

city: Shanghai

first: Wenwen

last: Li

address: Room 1004, West #5 Building, 280 South Chongqing Road, Shanghai 200025, China

country: China

institute: Shanghai Institute of Immunology; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine

data_processing:
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome
The mapping rate was 96%, on average, across all the samples in the dataset. The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: csv file includes read counts for each sample

organism: Mus musculus

extract_protocol:
total RNA from samples was extracted using Trizol Reagent following standard protocols and 1 ug of total RNA was used for the construnction of sequencing libraries.
RNA libraries for RNA-seq were preparing using bulk RNA-seq following manufacturer's protocols.

treatment_protocol: WT-MC38 (CRISPR-Ctrl) or Piezo2-KO MC38 (Piezo2-gRNA1) tumor cells were subjected to single fraction of X-ray (30 Gy).

value: Epithelial cell line

value: WT

value: IR


title: Mesenchymal stem cells, control, day 21

city: Ljubljana

first: Lucija

middle: Ana

last: Vrščaj

address: Aškerčeva cesta 7

department: Faculty of Pharmacy

country: Slovenia

institute: University of Ljubljana

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low-quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, we chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to look for known miRNA. miRBase20.0 was used as reference.mirdeep2 was used to obtain the potential miRNA.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of data from the specified species itself.
miRNA expression levels were estimated by TPM
Differential expression analysis of two samples was performed using the DEGseq (2010) R package. P-value was adjusted using qvalue qvalue < 0.01 and |log2(foldchange)| > 1 was set as the threshold for significantly differential expression by default.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts and TPM
Supplementary files format and content: tab-delimited text files include diferrential analysis results

source_name: bone

growth_protocol: Human mesenchymal stem cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), L-glutaine and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using miRNeasy kit (Qiagen). 1ug of total RNA was used for library preparation.
3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18-40 bp were ready for sequencing on Illumina NovaSeq 6000. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol:
Osteogenic differentiation was induced by treatment of 1-day post confluent cells with 100nM dexamethasone, 5mM beta-glycerophosphate and 50 mg/mL ascorbic acid-2-phosphate. Media was changed every 2-3 days.
Intermittent teriparatide treatment: 10nM teriparatide was added at every media change for 6h, then fresh osteogenic media without teriparatide was added.
Continuous teriparatide treatment: 10nM teriparatide was added at every osteogenic media change.

tag: tissue

value: bone

value: human bone marrow-derived mesenchymal stem cells

value: mesenchymal stem cells

value: control


title: NPC, rep1

library_source: transcriptomic single cell

source_name: Neural progenitor cells

value: Neural progenitor cells


title: Mesenchymal stem cells, intermittent treatment, day 21

value: intermittent


title: WT_IR_1


title: wt 14h IAA BR1


title: WT_nonIR_2

value: Non-IR


title: wt 14h ut BR4

value: solvent control 0,04% DMSO, 14h


title: PccT3

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

description: Pcc treated with 200 mM NaCl

data_processing:
Raw FASTQ reads were refined by eliminating sequences with suboptimal quality scores, using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). A in-house Python script ensured the alignment of the forward and reverse reads.
Filtered clean reads were mapped to reference genome of each bacteria using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Generated SAM ﬁles were subsequently sorted by genomic coordinates using the SAMtools program.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Burkholderia gladioli BSR3 GCF_000194745.1
Assembly: Pectobacterium carotovorum subsp. carotovorum PCC21 GCF_000294535.1
Assembly: Ralstonia solanacearum GMI1000 GCF_000009125.1
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

growth_protocol: Burkholderia gladioli BSR3 and Pectobacterium carotovorum subsp. carotovorum PCC21 were cultured in LB broth at 28°C. Ralstonia solanacearum GMI1000 were cultured at 28°C in casamino acid peptone glucose (CPG) medium (1 g/L casamino acids, 10 g/L peptone, 5 g/L glucose). All liquid cultures were incubated in a shaker-incubator at 200 rpm. Bacterial cultures in the early exponential phase were prepared for both salt-susceptible and salt-tolerant pathogens. To induce a salt stress response, these cultures were exposed to 200 mM NaCl for 2 hours. Cultures without NaCl addition were used as negative controls.

extract_protocol:
For sequencing library preparation, 4 ml of bacterial cultures were harvested by centrifugation at 5000 × g for 10 minutes and then stabilized using the RNAprotect Bacteria Reagent (Qiagen, CA, USA). Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA quality and quantity were measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (New England Biolabs, MA, USA).
The enriched RNA was then used to construct cDNA libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, CA, USA) according to the manufacturer’s protocol. Paired-end NGS sequencing was performed on the Illumina NovaSeq 6000 platform (Macrogen, Seoul, Korea).

tag: strain

value: 200 mM NaCl

value: wild type

value: 2 hours


title: 201B7, Physical stimulas, rep3 [YOK_4_3]

city: Tokyo

first: Ryutaro

last: Akiyoshi

address: 2-9-32 Nakacho, Musashino-shi

country: Japan

institute: Yokogawa Electric Corporation

data_processing:
Fastq files were generated using the bcl2fastq tool (v. 2.20.0.422). For the quality control, polyA/T sequences, adaptor sequences, and poor quality bases were removed using cutadapt (4.1) Marcel Martin et al 2011 and fastp (v. 0.20.1) Shifu Chen and others, 2018. Trimmed reads were aligned to the human genome assembly GRCh38 by the HiSAT2 tool (v. 2.1.0) Kim, D. 2015. Mapped reads on annotated genes were counted using featureCounts Yang Liao et al, 2014. Read count was converted to transcripts per million (TPM) values for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: xlsx, txt: number of fragments (reads) mapped to each gene using Feature count, Read counts and correction (calculation of TPM values) for each gene.

source_name: skin

extract_protocol:
Total RNA was extracted from iPSC using a RNeasy mini kit (Qiagen), following the manufacturer’s instructions.
The libraries were prepared using a NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490) and a NEBNext Ultra II Directional RNA Library Prep Kit (#E7760)

value: skin

value: iPS

value: Physical stimulas


title: Piezo2_KO_IR_2

value: Epithelial cell line

value: Piezo2 KO


title: PccT1

description: Pcc treated with 200 mM NaCl

organism: Pectobacterium carotovorum subsp. carotovorum


title: PccT2

description: Pcc treated with 200 mM NaCl


title: WT_nonIR_1

value: WT


title: Mesenchymal stem cells, continuous treatment, day 21

value: bone

value: continuous


title: 201B7, Physical stimulas, rep2 [YOK_4_2]


title: PccC3

description: Pcc

value: sterile water


title: MC38_WT_IR_2

treatment_protocol: MC38-WT tumor cells were subjected to single fraction of X-ray (30 Gy).

value: IR


title: wt 14h ut BR2

value: HaCaT

value: immortalized human keratinocytes

value: CrisprLV2_iCADE4ko_puro - pFUG147EV16_Tir1_PGK_Hygro_W -  pEF1a_GW_iCADMutE4_mAID_GFP_puro

value: 14 hours


title: 201B7, Physical stimulas, rep1 [YOK_4_1]


title: MC38_WT_IR_1


title: PccC2

description: Pcc


title: 201B7, Differentiation, rep3 [YOK_3_3]

value: Differentiation


title: Piezo2_KO_nonIR_1

value: Non-IR


title: wt 14h ut BR1

value: solvent control 0,04% DMSO, 14h


title: PccC1

description: Pcc

value: wild type

value: 2 hours


title: MC38_WT_nonIR_2


title: MC38_WT_nonIR_1


title: wt 6h IAA BR3

value: Auxin (3-indolacetic acid, IAA) 20µM, 6h

value: 6 hours


title: 201B7, Differentiation, rep2 [YOK_3_2]

value: skin

value: iPS


title: Injured_vehicle

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

country: France

institute: CNRS UMR8030

data_processing:
RNA-Seq Data Analysis Samples were aligned to the reference genome (Rattus_norvegicus Rnor_6.0.94) with Bowtie2 (Langmead and Salzberg, 2012). Aligned sequenced reads per sample were associated to annotated genes with HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/count.html), followed by an inter-sample quantile normalization to correct for technical differences. Differential expression analysis (relative to the samples issued from non-injured and vehicle treated animals) has been performed with Deseq2.
Assembly: Rattus_norvegicus Rnor_6.0.94
Supplementary files format and content: tab delimited raw counts files

molecule: polyA RNA

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
Frozen micro dissected spinal cord samples were lysed with Teflon-glass homogenisers and QIAshredder columns (Qiagen). Total RNA was isolated with the Qiagen RNeasy® Mini kit. The RNA was assessed for purity and quantity using the Nanodrop 1000 spectrophotometer and assessed for quality on the Agilent Bioanalyzer 2100. RNA was reverse transcribed with a QuantiTect® Reverse Transcription kit (Qiagen).
Four hundred ng of intact high quality total RNA (RIN>7.9) from each sample was then used as input to generate libraries for RNA-sequencing using the NEBNext Ultra II Directional kit (NEB, Cat.no: E7760S) following the manufacturer’s recommendations. This protocol involved an initial step of mRNA selection using a poly-A isolation module (NEB, Cat.no: E7490) to select for mRNA with a mature polyA tail, followed by fragmentation prior to first cDNA synthesis and barcoding second-strand cDNA synthesised with indices for Illumina sequencing for final library amplification (10-cycles). The resulting libraries (342-421bp) were assessed on the Bioanalyzer 2100 for purity. The NEBNext Library Quant Kit for Illumina (NEB, Cat.no: E7630L) was used to calculate the quantity of each library. The quantification data was used to pool the libraries in equal molarity prior to performing a QC run on the MiSeq (MiSeq Reagent Kit v3 (150-cycle); Cat no: MS-102-3001). Further deep sequencing was performed on the pooled library over 2 lanes using a HiSeq4000 (by GENEWIZ) to generate roughly 26 million reads per sample.

value: spinal cord

value: WT

value: spine cord injury


title: wt 6h IAA BR4


title: wt 6h IAA BR2


title: C2C12 cells, ChREBP-β, Day0, rep2

city: Nanning of Guangxi

first: peng

last: wang

address: Xixiangtang

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
The high-quality sequences filtered by fastp were mapped to the mouse reference genome by Bowtie2 (v2.0.0.5) and Tophat (v2.0.0).
Then,themappingreadingswereassembledandGTFfilesweregeneratedbyStringTie(v2.2.0).TheGTFfileswerethenmergedintoonefilebyCuffmerge,fromwhichthecountsofeachgenewereextracted.
The library size (count) was calculated using cheepelev et al. 's protocol, Nucleic Acid Research, 2009. In short, the exons of all the isomers of a gene are combined into a meta-transcript. The number of declining reads in the exon of this meta-transcript is counted according to the meta-transcript size and the library size.
Assembly: GRCg6a
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from cells and tissues using Trizol (Life Technologies, USA), and then used to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse myoblasts

value: ChREBP-beta overexpression.

value: Undifferentiated

value: Day 0


title: 201B7, Low nutrient, rep3 [YOK_2_3]

value: Low nutrient


title: wt 6h IAA BR1

value: HaCaT

value: immortalized human keratinocytes

value: CrisprLV2_iCADE4ko_puro - pFUG147EV16_Tir1_PGK_Hygro_W -  pEF1a_GW_iCADMutE4_mAID_GFP_puro


title: 201B7, Differentiation, rep1 [YOK_3_1]

value: Differentiation


title: C2C12 cells, ChREBP-β, Day0, rep1


title: wt 14h ut BR3

value: solvent control 0,04% DMSO, 14h

value: 14 hours


title: Non-injured_vehicle

value: control


title: Non-injured_C286


title: C2C12 cells, ChREBP-β, Day0, rep3


title: 201B7, Low nutrient, rep1 [YOK_2_1]

value: skin


title: C2C12 cells, GFP, Day0, rep3


title: 201B7, Low nutrient, rep2 [YOK_2_2]

value: iPS


title: wt 6h ut BR3

value: solvent control 0,04% DMSO, 6h

value: 6 hours


title: anti-SIGLEC15 treated 1

first: Zheng

last: Chen

state: Shanghai

address: No.180 Fenglin Road, Xuhui District

department: Department of Liver Surgery and Transplantation, Liver Cancer Institute

institute: Zhongshan Hospital Fudan University

data_processing:
CLC Genomics Workbench v 12.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: csv  files include FPKM values for each sample

source_name: enriched CD8+ T cells in percutaneous tumor graft

extract_protocol:
RNA was harvested using TRI regent (Sigma), and then fragment analyzer was used to examine the quality of extracted RNA.
After quality check, samples were enriched with Oligo-coated beads,and then fragmentation buffer was added to generate transcripts.Then,complementary DNA strains were generated and collected for PCR replication.The samples of cNDA were checked according to protocols, and finally approved samples were loaded onto DNBSEQ-G50 platform for sequencing analysis.

tag: Sex

value: male

value: wild type

value: intraperitoneal injection of SIGLEC15 antibody


title: 201B7, control, rep3 [YOK_1_3]


title: wt 6h ut BR2


title: 201B7, control, rep2 [YOK_1_2]


title: C2C12 cells, GFP, Day0, rep1

value: Mouse myoblasts

value: WT

value: Undifferentiated


title: Injured_C286

value: spinal cord

value: spine cord injury + C286


title: wt 6h ut BR1

value: HaCaT

value: immortalized human keratinocytes

value: CrisprLV2_iCADE4ko_puro - pFUG147EV16_Tir1_PGK_Hygro_W -  pEF1a_GW_iCADMutE4_mAID_GFP_puro


title: CTCF-P4

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

country: USA

institute: NIEHS

library_source: genomic

data_processing:
50nt sequence reads were provided by the NIEHS Core (using Novaseq).
Reads were mapped to the mouse genome mm10 using  Bowtie with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig

molecule: genomic DNA

source_name: uterus

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

treatment_protocol: ovariectomized C57bl/b mice were treated for 1h with 1 mg progesterone (P4) in 0.1 ml sesame oil or with 0.1 ml sesame oil vehicle (V) by sub-cutaneous injection

value: uterus

tag: chip antibody

value: Active Motif, cat # 61311, 4 ug

value: female


title: IgG treated 1

value: enriched CD8+ T cells in percutaneous tumor graft

value: intraperitoneal injection of IgG


title: 201B7, control, rep1 [YOK_1_1]

value: skin

value: iPS

value: control


title: control group (shNC), 3

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Human laryngeal cancer cells


title: wt 6h ut BR4

value: solvent control 0,04% DMSO, 6h

value: 6 hours


title: D3-U360

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

institute: The Third Xiangya Hospital of Central South Uniiversity

data_processing:
Library Preparation included: 1) 3’ -adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~134-160bp PCR amplified fragments (corresponding to ~14-40nt small RNAs).
Completed libraries were quantified using an Agilent 2100 Bioanalyzer.
DNA fragments in well mixed libraries were denatured using 0.1M NaOH to generate single-stranded DNA molecules and loaded using the NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) according to instructions provided by the manufacturer.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
skin were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® was used for library preparation. The NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) was used for sequencing on the Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 6-8 weeks


title: anti-SIGLEC15 treated 2

value: male

value: wild type

value: intraperitoneal injection of SIGLEC15 antibody


title: 21d-Ctcf-f/f V-12

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20.
Remove reads carrying adaptor sequences using cutadapt (v2.7).
Reads were mapped to the mouse genome (mm10) using Tophat
BAM files were uploaded into Partek Genomics Suite and annotated to Refseq.
Supplementary files format and content: RPKM (gene level-RefSeq) was computed and batch effect of the two library preps was removed.

extract_protocol:
RNA was extracted with Trizol and cleaned up (with DNAse) Zymo RNA Clean and Concentrate kit
Illumina Truseq kit

treatment_protocol: 21-day old Ctcf-d/d (PgrCre+Ctcf-flox) or Ctcf-flox (Cre-littermates) mice were treated for 6h with 0.5 mg progesterone (P4) in 0.05 ml sesame oil or with 0.05 ml sesame oil vehicle (V) by sub-cutaneous injection

value: 21 days

tag: library (2_batches)

value: Ctcf-f/f

value: V


title: CTCF-V

value: uterus

value: Active Motif, cat # 61311, 4 ug

value: WT

value: V, 1h


title: 21d-Ctcf-f/f V-10

value: female


title: D1-U360

value: skin


title: control group (shNC), 2

institute: The First Affiliated Hospital of Anhui Medical University

value: control


title: control group (shNC), 1

value: Human laryngeal cancer cells


title: D2-U360


title: C2C12 cells, GFP, Day0, rep2

value: Mouse myoblasts

value: Undifferentiated

value: Day 0


title: 21d-Ctcf-f/f V-7


title: PFKP knockdown (shPFKP), 2

value: PFKP knockdown


title: PFKP knockdown (shPFKP), 3


title: C2-U180

value: 6-8 weeks


title: IgG treated 2

value: male

value: enriched CD8+ T cells in percutaneous tumor graft

value: wild type

value: intraperitoneal injection of IgG


title: HSD17B7_KO_rep3

type: RNA

first: Cene

last: Skubic

state: - None -

address: Zaloška 4

department: Institute for Biochemistry and molecular genetics

institute: University of Ljubljana, Faculty of Medicine

description: Gene expression data from HSD17B7 KO HepG2 cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom_S_Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to(GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays Document Part Number 703174 Publication Number MAN0018137)

scan_protocol: GeneChips were scanned using Scanner GCS 3000 7G.

data_processing: The quality of the raw microarray data was assessed. Microarray images were visually inspected for any visible aberrations. Further quality assessment was done using the arrayQualityMetrics function of the arrayQualityMetrics library, the RLE (Relative Log Expression) and NUSE (normalised unscaled standard errors) functions of the oligo library. All microarrays passed the quality checks. Array data was then processed for background correction, normalisation and summarisation using the robust multichip average algorithm (rma) in Oligo library. Differentially expressed genes were determined by linear models using the Limma. Analysis for KEGG enrichment of gene sets was performed using the clusterProfiler library. A 5% level of significance was considered after correcting for multiple testing using BH-FDR (Benjamini-Hochberg False Discovery Rate) method. All analyses were performed in R software v4.0.2.

label: biotin

source_name: HepG2 cell with HSD17B7 KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays Document Part Number 703174 Publication Number MAN0018137)

growth_protocol: Cell were seeded on 6-well plate in Dulbecco’s Modified Eagle’s Media (DMEM) high glucose (D6429, Sigma Aldrich, St. Louis, MO, USA), supplemented with 10% FBS (F0804, Sigma Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (P0781, Sigma Aldrich, St. Louis, MO, USA). Cells were cultured in constant 37 °C and 5% CO2. After 24h after seeding cell medium was changed with DMEM high glucose, supplemented with 10% LDP (Lipid Depleted Serum Biosera inc., France),  1% penicillin/streptomycin and 30 µg/ml of cholesterol (Sigma Aldrich). 48h after medium change, cell were washed 2 times with PBS and TRI reagent (T9424, Sigma Aldrich, St. Louis, MO, USA) was used for RNA isolation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: HSD17B7 KO


title: PFKP knockdown (shPFKP), 1


title: 21d-Ctcf-f/f V-1a

value: uterus

value: 21 days

value: Ctcf-f/f

value: V


title: HSD17B7_KO_rep1

treatment_protocol: Cell were seeded on 6-well plate in Dulbecco’s Modified Eagle’s Media (DMEM) high glucose (D6429, Sigma Aldrich, St. Louis, MO, USA), supplemented with 10% FBS (F0804, Sigma Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (P0781, Sigma Aldrich, St. Louis, MO, USA). Cells were cultured in constant 37 °C and 5% CO2. After 24h after seeding cell medium was changed with DMEM high glucose, supplemented with 10% LDP (Lipid Depleted Serum Biosera inc., France),  1% penicillin/streptomycin and 30 µg/ml of cholesterol (Sigma Aldrich). 48h after medium change, cell were washed 2 times with PBS and TRI reagent (T9424, Sigma Aldrich, St. Louis, MO, USA) was used for RNA isolation.


title: C1-U180

value: skin


title: C3-U180


title: VMI organoids with unstimulated macrophages-ATAC

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

library_source: genomic single cell

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger-atac pipeline (v2.1.0).
cellranger-atac mkfastq was used for sample demultiplexing and fastq generation.
cellranger-atac count was used to align reads to the 10X pre-built human reference (GRCh38-2020-A-2.0.0), perform peak calling, and extract barcoded and aligned fragment file.
Assembly: GRCh38
Supplementary files format and content: peak and fragment files generated by 10X cellranger-atac count; singlecell.csv.gz stores per-barcode fragment counts & metrics; peaks.bed.gz stores all called peak locations; fragments.tsv.gz stores barcoded and aligned fragments.

source_name: hESC-derived cells

extract_protocol:
Single cells were lysisaccording to the protocol from 10X Genomics (CG000169)
snATAC libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 according to the manufacturer’s instructions.

value: hESC-derived cells

value: organoids with unstimulated macrophages


title: B1-U90

value: 90 mJ/cm2


title: B3-U90


title: SC5D_KO_rep3

description: Gene expression data from SC5D KO HepG2 cell line

source_name: HepG2 cell with SC5D KO

value: SC5D KO


title: 21d-Ctcf-cKO V-13

value: female

value: PgreCre+;Ctcf-f/f (cKO)


title: 21d-Ctcf-cKO V-4


title: A3-control

value: untreated

value: 6-8 weeks


title: VMI organoids with pro-inflammatory macrophages-ATAC


title: 21d-Ctcf-cKO V-11a


title: B2-U90


title: VMI organoids with pro-inflammatory macrophages-RNA

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v7.1.0).
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference (GRCh38-2020-A) and to extract gene expression UMI counts matrix.
Assembly: GRCh38
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
scRNAseq libraries were prepared using the Chromium Next GEM Single Cell 3' v3.1 (Dual index) according to the manufacturer’s instructions.


title: non-coculture cells (Separately cultured cells)-ATAC

value: non-coculture


title: SC5D_KO_rep2


title: 21d-Ctcf-cKO V-5


title: A1-control


title: non-coculture cells (Separately cultured cells)-RNA


title: 21d-Ctcf-f/f V-3


title: DHCR24_KO_rep3

description: Gene expression data from DHCR24 KO HepG2 cell line

source_name: HepG2 cell with DHCR24 KO

value: DHCR24 KO


title: 21d-Ctcf-f/f V-4


title: dog_36_d_ucc_replicate1

city: Cambridge

first: Lajos

last: Kalmar

address: Tennis Court Road

country: United Kingdom

institute: MRC Toxicology Unit, University of cambridge

data_processing:
In command line, saving lines from fastq files including the middle "AACTGTAGGCACCATCAAT" adapter using "zgrep" into a new text file
Using a self-written R-script, generating a table of individual sequences and their count number in each sample using the Unique Molecular Identifiers.
Aligning the sequences to canine mature miRNAs using blast from DEUS pipeline 1.0 with one mismatch and combining the count numbers for sequences that aling to same miRNA.
Assembly: miRbase release 22.1
Supplementary files format and content: csv file including the count numbers for mature miRNAs for each sample

organism: Canis lupus familiaris

source_name: SEC fraction d

growth_protocol: The urine was collected, centrifuged at 2000 x g for 10 minutes (to pellet cellular components) and the cell-free supernatant was frozed at -80C until batch analysis.

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (#217004 Qiagen)  from 500ul of EV and protein fractions.
Libraries were prepared using QiaSeq miRNA library kit (#331505, Qiagen) combined with QIAseq miRNA 48 Index IL kit (#331595, Qiagen). "miRNA" library (SLX-19754) was prepared according to the suggested manufacturer protocol. "Long RNA" library (SLX-19755) was acquired by performing the wash steps to the beads that were meant to be discarded in the first bead purufication step of the official protocol.

treatment_protocol: Protease inhibitor was added in to melted urine, urine was centrifuged at 4000 x g, for 20 minutes at 4 °C, and the supernatant was filtered using 0.22µm syringe PES filters (Millex GP, #SLGP033RS) and concentrated to <130µL using Amicon Ultra centrifugal ultrafiltration columns (100 kDa cut off, #UFC810024, Millipore). The concentrated urine was fractioned using qEV single 70nm SEC columns (Izon Science) and fractions b (EVs) and d (proteins) were used in RNA extraction.

value: SEC fraction d

value: urothelial carcinoma


title: VMI organoids with unstimulated macrophages-RNA


title: unstimulated hESC-derived macrophages-3

data_processing:
Illumina bcl2fastq v2.20 was used for sample demultiplexing and FASTQ generation.
Sequencing reads were trimmed to remove adaptors and low-quality bases using cutadapt v1.18.
The trimmed reads were mapped to the human GRCh37 reference using STAR v2.5.2b.
Read counts per gene were extracted using HTSeq-count v0.11.2.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file include read counts per gene per sample

source_name: hESC-derived macrophages

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: hESC-derived macrophages

value: un-stimulated


title: Stimulated hESC-derived macrophages-3

value: stimulated with LPS and IFN-g


title: SC5D_KO_rep1


title: DHCR24_KO_rep1


title: DHCR24_KO_rep2


title: CYP51 _KO_rep1

description: Gene expression data from CYP51 KO HepG2 cell line

source_name: HepG2 cell with CYP51 KO

value: CYP51 KO


title: CYP51 _KO_rep3


title: 21d-Ctcf-f/f P4-7

value: uterus

value: 21 days

value: Ctcf-f/f


title: A2-control

value: skin


title: CYP51 _KO_rep2


title: Native_rep2

description: Gene expression data from Native HepG2 cell line

source_name: HepG2 cell line control

value: Control


title: Native_rep3


title: 21d-Ctcf-f/f P4-2

value: female


title: 21d-Ctcf-f/f V-2

value: V


title: dog_32_d_ucc_replicate1


title: dog_34_b_hc2_replicate1

source_name: SEC fraction b

value: SEC fraction b

value: healthy control


title: 21d-Ctcf-f/f V-1b


title: 21d-Ctcf-f/f P4-9


title: dog_32_b_ucc_replicate1


title: dog_36_b_ucc_replicate1


title: Stimulated hESC-derived macrophages-1


title: unstimulated hESC-derived macrophages-2


title: Stimulated hESC-derived macrophages-2


title: 21d-Ctcf-f/f P4-1


title: dog_31_b_ucc_replicate1


title: dog_31_d_ucc_replicate1


title: HSD17B7_KO_rep2

value: HSD17B7 KO


title: zap1Δ::ZAP1_biofilm_vs_plank_rep2

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

hyb_protocol: Six hundred nanograms of labelled cDNA were hybridized in the microarray. Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17 h at 65°C.

scan_protocol: Slides were then washed following manufacturer’s instructions and scanned in an Agilent G2565AA microarrays scanner. Probes signal values were extracted using Agilent Feature Extraction Software.

data_processing: Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software 36. Final statistical analysis was carried out using LIMMA package in MeV software (MultiExperiment Viewer 4.8.0) 36 with a cut-off p-value of 0.1.

organism: Nakaseomyces glabratus

label_protocol: cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each strain were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).

growth_protocol: For the transcriptomic profiling an individual colony of C. glabrata zap1Δ and zap1Δ::ZAP1 strains was inoculated in SDB at 37 ºC with orbital agitation (120 rev/min) overnight and then re-inoculated (at 1x105 cells/ml) in 25 ml of RPMI at pH 4 and left to grow for 24h at 37ºC and 120 rev/min, inside Erlenmeyer flaks and microtiter plates, in order to induce planktonic and biofilm growth, respectively.

extract_protocol: The extraction of RNA from the cells was performed using the RiboPure – Yeast Kit (Life Technologies, CA), according to the manufacturer’s instructions.The concentration and purity of the extracted RNA were determined by spectrophotometry and its integrity was confirmed in an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Assay (Agilent Technologies, CA).

tag: growth mode

value: biofilm

value: zap1 delta:ZAP1

value: planktonic


title: dog_30_d_uti_replicate2

value: SEC fraction d

value: urinary tract infection


title: Native_rep1


title: 21d-Ctcf-cKO V-10

value: PgreCre+;Ctcf-f/f (cKO)


title: unstimulated hESC-derived macrophages-1

value: hESC-derived macrophages

value: un-stimulated


title: 21d-Ctcf-cKO V-12

value: uterus

value: 21 days


title: HUVECs,HPHG_1

city: hangzhou

first: Ming

last: Zhang

state: zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: School of Biosystems Engineering and Food Science

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used Bowtie2 and Hisat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion
CIRCExplorer2 and CIRI was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion
For LncRNA analysis, the mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from 6 Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes circRNA expression raw counts for each Sample
Supplementary files format and content: tab-delimited text files includesLncRNA expression raw counts for each Sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM; Hyclone, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin. Culturing was done at 37°C in a humidified incubator with 95% air and 5% CO2.

extract_protocol:
Total RNA was extracted from HUVECs, both with and without HFHG stimulation, utilizing Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions.
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.

treatment_protocol: HUVECs were cultured in high fat/high glucose (PAHG) medium. The medium contained 25 mM glucose and 250 μM saturated free fatty acid (FFA) palmitate (16:C; Sigma, USA) and was incubated for 24 h.

value: HUVECs

value: Primary Human Umbilical Vein Endothelial Cells

value: WT

value: 25 mM glucose and 250 μM  palmitate,24h


title: 21d-Ctcf-cKO P4-8

value: female


title: C42B Xenograft ENZ 3W

city: New Orleans

first: Michael

last: Lan

state: LA

address: 533 Bolivar Street, CSRB Room 623E

department: School of Medicine

institute: LSUHSC

data_processing:
Illumina NovaSeq 6000 (NovaSeq Control Software v1.8; RTA v3)
cellranger-6.1.2 for C4-2B; Alevin-Fry for TRAMP
Seurat V5
Assembly: GRCh38/ mm10
Supplementary files format and content: mtx files of counts

source_name: Xenograft tissue

extract_protocol:
C4-2B xenograft and TRAMP tumor tissues were harvested and dissociated using “Tumor Dissociation Kit, human, #130-095-929” and “Tumor Dissociation Kit, mouse, #130-096-730” from Miltenyi Biotec.
Samples were assessed and processed for single cell 3’ sequencing. GEMs (Gel Bead-in Emulsions) were generated in a Chromium Controller (10x Genomics). RNA contained in the GEMs was reverse transcribed, barcoded, and cDNA was recovered. cDNA was assessed with the Agilent TapeStation D5000 High Sensitivity Kit (Agilent Technologies). All samples underwent manual library processing with the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1: cDNA was fragmented, processed, and size selected. Adaptors were ligated and samples were cleaned up. Dual indexes were attached via PCR. The completed libraries were cleaned up and assessed for quality with the Agilent TapeStation D5000 High Sensitivity Kit. Libraries were quantitated with qPCR (NEBNext Library Quant Kit for Illumina, Bio-rad CFX96 Touch Real-Time PCR). Libraries were normalized to 1.5 pM and pooled. The library pool was denatured and diluted to approximately 300 pM. A library of 1.5 pM PhiX was spiked in as an internal control

value: Xenograft tissue


title: HUVECs,control-2


title: 21d-Ctcf-cKO V-11b

value: V


title: dog_30_d_uti_replicate1


title: HUVECs,HPHG_3


title: HUVECs,HPHG_2


title: zap1Δ::ZAP1_biofilm_vs_plank_rep3

value: biofilm


title: PB004#5, mESC-mix and converted hiPSC, biol rep 3

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing was performed on NovaSeq6000 to target 40M total reads per sample (approximately 6Gb/sample).
Clean data were generated from the raw data by using Trim Galore.
Trimmed sequence reads were mapped to GRCh38 using STAR, and count matrix was generated with RSEM.
TPM was used for evaluation of expression while raw counts were analyzed for differential gene expression with DESeq2.
Assembly: GRCh38
Supplementary files format and content: genes_counts_matrix.tsv: Tab-separated values file includes raw counts for each sample.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (QIAGEN).
Library construction was performed with TruSeq Stranded mRNA library kit (Illumina).

value: Human induced pluripotent stem cell

tag: condition

value: mESC coculture and culture in naive state


title: zap1Δ_biofilm_vs_plank_rep1

value: zap1 delta

value: planktonic


title: dog_30_b_uti_replicate1

value: SEC fraction b

value: urinary tract infection


title: 21d-Ctcf-cKO V-9

value: PgreCre+;Ctcf-f/f (cKO)


title: zap1Δ_biofilm_vs_plank_rep3


title: zap1Δ::ZAP1_biofilm_vs_plank_rep1

value: zap1 delta:ZAP1


title: zap1Δ_biofilm_vs_plank_rep2


title: dog_29_b_hc2_replicate1

value: healthy control


title: 21d-Ctcf-cKO P4-6

value: uterus

value: 21 days


title: HUVECs,control-3

value: HUVECs

value: Primary Human Umbilical Vein Endothelial Cells

value: WT


title: dog_26_b_uti_replicate1


title: dog_28_d_hc2_replicate1

value: SEC fraction d


title: dog_29_d_hc2_replicate1


title: dog_25_b_ucc_replicate2

value: urothelial carcinoma


title: PB004#5, cR hiPSC, biol rep 2

value: Chemical resetting and culture in naive state


title: Antibody treated tumor- scRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: csv
Supplementary files format and content: Tab-separated values files and matrix files

source_name: percutaneous tumor grafts

extract_protocol:
Tumors were trimmed into 2 mm3 pieces in dish before digestion (10 ml of solution with 0.1% DNase I and 0.1% collagenase IV). The mixed solution was then incubated at 37°C for 30min with a speed of 120 rounds/min, which was then applied to a gentle MACS dissociator for further decomposition. 10ml of 2% FACS solution was added to stop digestion, and the mixed solution was filtered through a 70-µm mesh. Centrifugation at 1500 rpm was performed to obtain cell pellets, which was separated by Percoll solution at gradient dilutions of 30% and 70%. Anti-CD45 magnetic beads (StemCell) were used to enrich CD45+ lymphocytes, which were then loaded into platform with original cell pellets at the ratio of 1:1, after viability examination over 90%.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: 6-8 weeks old

value: male

value: wild type

value: percutaneous tumor grafts

value: cells from digested tumors

value: intraperitoneal injection of SIGLEC15 antibody

tag: diet

value: Normal Diet

value: Specific Pathogen Free


title: 21d-Ctcf-cKO P4-5

value: female

value: PgreCre+;Ctcf-f/f (cKO)


title: HUVECs,control-1


title: dog_25_d_ucc_replicate1


title: dog_25_b_ucc_replicate1

value: SEC fraction b


title: PB004#5, cR hiPSC, biol rep 1

value: Human induced pluripotent stem cell


title: 21d-Ctcf-cKO P4-4

value: uterus

value: 21 days


title: PB004#5, primed hiPSC, biol rep 3

value: Culture in primed state


title: AB/Tub larvae, 0.00292 uM TBBPA, Rep 2

city: Saskatoon

first: Morgan

middle: W

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

country: Canada

institute: National Research Council Canada

data_processing:
raw sequence files were trimmed for adapter seqeunce/low quality sequences using cutadapt
trimmed reads were aligned to the GRCz11 reference genome using STAR (default parameters)
raw read per gene counts from STAR were formatted into a matrix and imported into DESeq2 for differential gene expression analysis and pair wise comparison - results were filtered using p-value = 0.05
corrected, normalized DEseq2 data tables were input directly into BMDexpress
Assembly: GRCz11

organism: Danio rerio

source_name: 20 Whole larvae

growth_protocol: Prior to treatment, larvae were stored in nursery baskets on a recirculating system.

extract_protocol:
Total RNA was extracted from each sample of 20 larvae using the Norgen BioTek Corp Total RNA Purification kit (Norgen Cat#17200, Thorold, ON, Canada) with the optional RNase-Free DNase I kit (Norgen Cat#25710, Thorold, ON, Canada).
Sequencing libraries were prepared using the Illumina Truseq Stranded mRNA kit using 1ug of total RNA.

treatment_protocol: At 72 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substance were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, were they were removed and flash frozen prior to RNA extraction.

value: 20 Whole larvae

value: AB/Tub

value: 0.00292 uM TBBPA


title: IgG treated tumor- scRNA-seq

description: 10x Genomics

value: 6-8 weeks old

value: male

value: intraperitoneal injection of IgG


title: PB004#5, mESC-mix and converted hiPSC, biol rep 2

value: mESC coculture and culture in naive state


title: dog_22_b_hc2_replicate1

value: healthy control


title: dog_26_d_uti_replicate1

value: SEC fraction d

value: urinary tract infection


title: PB004#5, mESC-mix and converted hiPSC, biol rep 1


title: TED3, Tal1_R892K, Rep1

city: Bunkyo-ku

first: Sayuri

last: Tsukahara

state: Tokyo

address: Hongo 7-3-1

institute: The University of Tokyo

data_processing:
TED-seq reads were mapped on the Col-CEN genome using Bowtie2 (ver. 2.4.4). The somatic reads were extracted using BEDTools (ver. 2.30.0)
Assembly: Col-CEN_v.1.2
Supplementary files format and content: bedgraph
Library strategy: TED-seq

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

extract_protocol:
Genomic DNA was extracted using Nucelon Phytopure (Cytiva).
TED-seq libraries were constructed using NEB NextUltraII DNA library Kit (NEB).

value: 10-day-old seedlings

value: Tal1 TED-seq


title: AB/Tub larvae, 0.000292 uM TBBPA, Rep 3


title: PB004#5, cR hiPSC, biol rep 3

value: Chemical resetting and culture in naive state


title: AB/Tub larvae, 0.000292 uM TBBPA, Rep 2


title: dog_28_b_hc2_replicate1

value: SEC fraction b


title: dog_21_b_ucc_replicate1

value: urothelial carcinoma


title: dog_26_d_uti_replicate2


title: AB/Tub larvae, 0.000292 uM TBBPA, Rep 1


title: TED3, Tal1_R769K, Rep1


title: dog_21_d_ucc_replicate1


title: AB/Tub larvae, 0.00292 uM TBBPA, Rep 3


title: IWP2, NaHCO3 and 2-DG treated, day 11, rep 2 [18-2-IWP2-NaHCO3-2DG-D11]

city: Taipa

first: Guokai

address: University of Macau E12-3060

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: all.fpkm_anno D7 D11

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (V1.9.1)
FIltered data were aligned to reference genome GRCh37 via software Hisat2 (v2.0.1)
Read count extraction and normalization were performed using HTSeq (v0.6.1)
Assembly: GRCh37
Supplementary files format and content: read counts and FPKM values for each sample

extract_protocol:
RNA was harvested using RNAiso Plus (Takara). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina

tag: treatment/time point

value: IWP2, NaHCO3 and 2-DG treated, day 11

value: ESC

value: WT

value: Cardiac differentiation


title: dog_22_d_hc2_replicate1


title: TED3, Tal1(WT), Rep2


title: PB004#5, primed hiPSC, biol rep 2

value: Human induced pluripotent stem cell

value: Culture in primed state


title: TED3, Tal1_R892K, Rep2


title: AB/Tub larvae, 0.292 uM TBBPA, Rep 3

value: 20 Whole larvae

value: AB/Tub

value: 0.292 uM TBBPA


title: dog_19_d_ucc_replicate1


title: IWP2, NaHCO3 and 2-DG treated, day 11, rep 1 [18-1-IWP2-NaHCO3-2DG-D11]

description: all.fpkm_anno D7 D11


title: AB/Tub larvae, 0.00292 uM TBBPA, Rep 1

value: 0.00292 uM TBBPA


title: PB004#5, primed hiPSC, biol rep 1


title: AB/Tub larvae, 0.0292 uM TBBPA, Rep 3

value: 0.0292 uM TBBPA


title: AB/Tub larvae, 0.292 uM TBBPA, Rep 1


title: dog_19_b_ucc_replicate2


title: Undifferentiated (day 0), rep 2 [19-2-H1-P38]

description: all.fpkm_anno D7 D11

value: Undifferentiated (day 0)


title: AB/Tub larvae, 0.0292 uM TBBPA, Rep 1


title: AB/Tub larvae, 0.0292 uM TBBPA, Rep 2


title: dog_21_d_ucc_replicate2

value: SEC fraction d


title: TED3, Tal1_R769K, Rep2

value: 10-day-old seedlings

value: Tal1 TED-seq


title: Undifferentiated (day 0), rep 1 [19-1-H1-P38]

description: all.fpkm_anno D7 D11


title: dog_18_b_uti_replicate1

value: SEC fraction b

value: urinary tract infection


title: TED3, EVD_K762R, Rep2

value: EVD TED-seq


title: IWP2 treated, day 11, rep 1 [15-1-IWP2-D11]

description: all.fpkm_anno D7 D11

value: IWP2 treated, day 11

value: ESC


title: AB/Tub larvae, 2.92 uM TBBPA, Rep 1

value: 2.92 uM TBBPA


title: TED3, EVD_K762R, Rep1


title: TED3, Tal1(WT), Rep1


title: AB/Tub larvae, 0.292 uM TBBPA, Rep 2


title: IWP2 and NaHCO3 treated, day 11, rep 2 [17-2-IWP2-NaHCO3-D11]

description: all.fpkm_anno D7 D11

value: IWP2 and NaHCO3 treated, day 11

value: WT

value: Cardiac differentiation


title: IWP2 and NaHCO3 treated, day 11, rep 1 [17-1-IWP2-NaHCO3-D11]

description: all.fpkm_anno D7 D11


title: AB/Tub larvae, Carrier Control 0.5% TBBPA, Rep 3

value: 20 Whole larvae

value: AB/Tub

value: Carrier Control 0.5% TBBPA


title: dog_19_b_ucc_replicate1

value: urothelial carcinoma


title: dog_17_d_ucc_replicate1


title: IWP2 treated, day 11, rep 2 [15-2-IWP2-D11]

description: all.fpkm_anno D7 D11


title: TED3, EVD_K854R, Rep2


title: AB/Tub larvae, 2.92 uM TBBPA, Rep 3


title: TED3, EVD_K854R, Rep1


title: dog_18_d_uti_replicate1


title: AB/Tub larvae, 2.92 uM TBBPA, Rep 2


title: AB/Tub larvae, Carrier Control 0.5% TBBPA, Rep 1


title: TED2, EVD_IN2_T, Rep2


title: NaHCO3 treated, day 11, rep 2 [12-2-NaHCO3-D11]

description: all.fpkm_anno D7 D11

value: NaHCO3 treated, day 11


title: AB/Tub larvae, 0.00483 uM BPA, Rep 3


title: dog_17_b_ucc_replicate1


title: TED3, Evade9WT), Rep2

source_name: 3-week-old seedlings

value: 3-week-old seedlings

value: EVD(WT)


title: NaHCO3 treated, day 11, rep 1 [12-1-NaHCO3-D11]

description: all.fpkm_anno D7 D11


title: Differentiation control, day 11, rep 2 [10-2-Ctrl-D11]

description: all.fpkm_anno D7 D11

value: Differentiation control, day 11


title: AB/Tub larvae, Carrier Control 0.5% TBBPA, Rep 2


title: HCl treated, day 11, rep 2 [11-2-HCl-D11]

description: all.fpkm_anno D7 D11

value: HCl treated, day 11


title: dog_15_b_hc2_replicate2

value: SEC fraction b

value: healthy control


title: TED2, EVD_IN2_T, Rep1

value: 10-day-old seedlings

value: EVD TED-seq


title: dog_14_b_ucc_replicate2


title: TED3, Evade(WT), Rep1


title: dog_15_d_hc2_replicate1

value: SEC fraction d


title: TED2, EVD_IN1_T, Rep2


title: TED2, EVD_IN2_T, Rep3


title: HCl treated, day 11, rep 1 [11-1-HCl-D11]

description: all.fpkm_anno D7 D11

value: ESC


title: AB/Tub larvae, 0.00483 uM BPA, Rep 1


title: IWP2, NaHCO3 and 2-DG treated, day 7, rep 2 [9-2-IWP2-NaHCO3-2DG-D7]

description: all.fpkm_anno D7 D11

value: IWP2, NaHCO3 and 2-DG treated, day 7

value: WT


title: dog_14_b_ucc_replicate1


title: dog_15_b_hc2_replicate1


title: dog_14_d_ucc_replicate1


title: TED2, Tal1(ddm1), Rep3

value: Tal1 TED-seq


title: AB/Tub larvae, 0.00483 uM BPA, Rep 2

value: 20 Whole larvae

value: AB/Tub


title: Differentiation control, day 11, rep 1 [10-1-Ctrl-D11]

description: all.fpkm_anno D7 D11

value: Cardiac differentiation


title: TED2, Tal1(ddm1), Rep2


title: IWP2 and NaHCO3 treated, day 7, rep 1 [8-1-IWP2-NaHCO3-D7]

description: all.fpkm_anno D7 D11

value: IWP2 and NaHCO3 treated, day 7


title: IWP2, NaHCO3 and 2-DG treated, day 7, rep 1 [9-1-IWP2-NaHCO3-2DG-D7]

description: all.fpkm_anno D7 D11


title: AB/Tub larvae, 0.0483 uM BPA, Rep 3


title: TED2, EVD_IN1_T, Rep1


title: AB/Tub larvae, 0.0483 uM BPA, Rep 2


title: IWP2 treated, day 7, rep 2 [6-2-IWP2-D7]

description: all.fpkm_anno D7 D11

value: IWP2 treated, day 7


title: dog_13_b_hc2_replicate1


title: AB/Tub larvae, 0.483 uM BPA, Rep 3

value: 0.483 uM BPA


title: TED2, Tal1(WT), Rep3


title: IWP2 and NaHCO3 treated, day 7, rep 2 [8-2-IWP2-NaHCO3-D7]

description: all.fpkm_anno D7 D11


title: dog_13_d_hc2_replicate1


title: AB/Tub larvae, 0.0483 uM BPA, Rep 1


title: dog_13_b_hc2_replicate2


title: AB/Tub larvae, 0.483 uM BPA, Rep 2


title: dog_11_b_uti_replicate2

value: urinary tract infection


title: IWP2 treated, day 7, rep 1 [6-1-IWP2-D7]

description: all.fpkm_anno D7 D11


title: AB/Tub larvae, 0.483 uM BPA, Rep 1


title: TED2, Tal1(WT), Rep2


title: dog_11_d_uti_replicate1


title: TED2, Tal1(ddm1), Rep1


title: AB/Tub larvae, 4.83 uM BPA, Rep 3

value: 4.83 uM BPA


title: dog_11_b_uti_replicate1

value: SEC fraction b


title: NaHCO3 treated, day 7, rep 2 [3-2-NaHCO3-D7]

description: all.fpkm_anno D7 D11

value: NaHCO3 treated, day 7


title: HCl treated, day 7, rep 2 [2-2-HCl-D7]

description: all.fpkm_anno D7 D11

value: HCl treated, day 7


title: NaHCO3 treated, day 7, rep 1 [3-1-NaHCO3-D7]

description: all.fpkm_anno D7 D11


title: dog_10_d_uti_replicate2


title: TED2, Tal1_IN2_E, Rep2

value: 10-day-old seedlings


title: AB/Tub larvae, 4.83 uM BPA, Rep 1


title: AB/Tub larvae, 48.3 uM BPA, Rep 3

value: 48.3 uM BPA


title: TED2, Tal1_IN2_E, Rep1


title: dog_10_d_uti_replicate1

value: SEC fraction d


title: HCl treated, day 7, rep 1 [2-1-HCl-D7]

description: all.fpkm_anno D7 D11

value: ESC


title: Differentiation control, day 7, rep 2 [1-2-Ctrl-D7]

description: all.fpkm_anno D7 D11

value: Differentiation control, day 7

value: WT


title: dog_10_b_uti_replicate1


title: dog_8_b_ucc_replicate1

value: urothelial carcinoma


title: AB/Tub larvae, 48.3 uM BPA, Rep 2

value: 20 Whole larvae

value: AB/Tub


title: TED2, Tal1(WT), Rep1

value: Tal1 TED-seq


title: Differentiation control, day 7, rep 1 [1-1-Ctrl-D7]

description: all.fpkm_anno D7 D11

value: Cardiac differentiation


title: TED2, Tal1_IN1_E, Rep2


title: TED2, Tal1_IN1_E, Rep3


title: TED2, Evade(WT), Rep2

value: Evade(WT)

value: EVD TED-seq


title: TED2, Tal1_IN2_E, Rep3


title: AB/Tub larvae, 48.3 uM BPA, Rep 1


title: TED2, Tal1_IN1_E, Rep1


title: AB/Tub larvae, Carrier Control 0.5% BPA, Rep 2

value: Carrier Control 0.5% BPA


title: IWP2, NaHCO3 and 2-DG treated, day 5, rep 2 [18-2-IWP2-NaHCO3-2DG-D5]

description: all.fpkm_anno D3 D5

value: IWP2, NaHCO3 and 2-DG treated, day 5


title: AB/Tub larvae, Carrier Control 0.5% BPA, Rep 3


title: AB/Tub larvae, 4.83 uM BPA, Rep 2

value: 4.83 uM BPA


title: AB/Tub larvae, Carrier Control 0.5% BPA, Rep 1


title: dog_4_d_ucc_replicate2


title: dog_6_b_ucc_replicate1

value: SEC fraction b


title: TED2, Evade(WT), Rep1

value: 10-day-old seedlings


title: dog_8_d_ucc_replicate1


title: IWP2 and NaHCO3 treated, day 5, rep 1 [17-1-IWP2-NaHCO3-D5]

description: all.fpkm_anno D3 D5

value: IWP2 and NaHCO3 treated, day 5


title: IWP2 and NaHCO3 treated, day 5, rep 2 [17-2-IWP2-NaHCO3-D5]

description: all.fpkm_anno D3 D5


title: dog_6_d_ucc_replicate1

value: SEC fraction d


title: TED2, ddm1, Rep2


title: dog_4_d_ucc_replicate1


title: IWP2 treated, day 5, rep 1 [15-1-IWP2-D5]

description: all.fpkm_anno D3 D5

value: IWP2 treated, day 5

value: ESC


title: IWP2, NaHCO3 and 2-DG treated, day 5, rep 1 [18-1-IWP2-NaHCO3-2DG-D5]

description: all.fpkm_anno D3 D5

value: WT


title: IWP2 treated, day 5, rep 2 [15-2-IWP2-D5]

description: all.fpkm_anno D3 D5


title: dog_4_b_ucc_replicate1

value: urothelial carcinoma


title: TED2, WT Col-0, Rep3


title: dog_2_d_ucc_replicate1


title: TED2, WT Col-0, Rep2


title: NaHCO3 treated, day 5, rep 2 [12-2-NaHCO3-D5]

description: all.fpkm_anno D3 D5

value: NaHCO3 treated, day 5


title: dog_2_b_ucc_replicate1


title: NaHCO3 treated, day 5, rep 1 [12-1-NaHCO3-D5]

description: all.fpkm_anno D3 D5


title: Mut-Y-seq , CMC 2 hr; OH-_RT1306_rep2

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

institute: Boston College

data_processing:
Remove PCR duplication upon deduplication by "BBMap" tools "clumpify.sh" as the library carries the UMI sequence.
Adaptors were trimmed by the “cutadapt” program.
Reads were aligned to the rRNA or the Refseq genome using bowtie2 aligner
Single base reads counting were performed with bam-readcount.
Stop counts and total count coverage were performed with bedtools genomecov.
Assembly: hg38
Supplementary files format and content: For piloting Y-seq libariescsv.gz files for lib1-lib6 were outputs of bam-readcount,  3p.txt and totalcov.txt were the reads counts stop at the postion and total read for the position. For mut-Y-seq libaraies processed  data, the processed.csv files are files containg mutation rate, deletion rate, and insertion rate at single base position; 3p.csv and total.csv files are generated by bedtools genomecov and are used to calculate the stop rate.

source_name: HEK-293T cells

extract_protocol:
RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; poly-A RNA was purified by oligo(dT)25 Dynabeads.
Libraries were constructed using ligation-based library construction approach reported in Methods session in the current work.

value: HEK-293T cells


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, ddm1, Rep2

value: Tal1 TED-seq


title: HCl treated, day 5, rep 1 [11-1-HCl-D5]

description: all.fpkm_anno D3 D5

value: HCl treated, day 5

value: Cardiac differentiation


title: Mut-Y-seq , OH-_SS III


title: Mut-Y-seq , CMC 2 hr; OH-_RT1306_rep1


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, WT, Rep2


title: HCl treated, day 5, rep 2 [11-2-HCl-D5]

description: all.fpkm_anno D3 D5


title: TED2, WT Col-0, Rep1

value: EVD TED-seq


title: Adult testis NONO-delta-ER IP-3

city: nanjing

first: huicong

last: zhai

address: 101 Longmian Avenue, Jiangning District (or 818 Tianyuan East Road)

institute: Nanjing Medical University

description: NONO-delta-ER bind RNA

data_processing:
eCLIP data were analyzed following ENCODE standard eCLIP pipeline.
eCLIP adapters were trimmed by using cutadapt v1.14, barcode and Random-mer were collected for decreasing PCR duplicates loss.
PCR duplicates removed by using a custom python script,  eCLIP reads aligned to the repeat elements from UCSC with STAR (V2.7.6a) and then mapped the rest to mm10 reference genome (GENCODE vM23).
bigWig files were generated using Deeptools. Significantly enriched peaks as those with irreproducible discovery rate cutoff of 0.01 as well as P ≤ 0.001 and fold enrichment ≥ 8
bigWig files were generated using Deeptools. Significantly enriched peaks as those with irreproducible discovery rate cutoff of 0.01 as well as P ≤ 0.001 and fold enrichment ≥ 8
Assembly: MM10
Supplementary files format and content: bigWig files

source_name: Testis

growth_protocol: collect adult NONO and NONO-delta-ER mice testis,

extract_protocol:
Cell Lysates were sonicated, antibody-bound RNA complexes were immunoprecipitated, washed, and RNA was extracted.
RNA was reverse-trascriptioned into cDNA, then cDNA was amplified according to eCLIP protocol provided by Van, Norstrand, et al using adaptors and primers

treatment_protocol: eCLIP-seq

value: Testis

value: testis total cells

value: KI

tag: sample type

value: Adult mice testis


title: TED2, ddm1, Rep1

value: 10-day-old seedlings


title: EpCAM POS 03

city: New Brunswick

first: Victoria

last: da Silva-Diz

address: 195 Little Albany Street

institute: Rutgers University

description: full epithelial cancer cells biological replicate 3

hyb_protocol: 8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix MG-430 PM Array were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label: Biotin

source_name: epithelial cancer cells from WD-SCC

label_protocol: 10 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using (GeneChip Mapping 250K Nsp Assay Kit, Affymetrix catalog  # 900766), according to manufacturer's instructions.

extract_protocol: RNA was isolated using magnetic beads RNA Clean XP (Beckman Coulter; catalog # A63987) from a cells lysate.

tag: tumor type of origin

value: WD-SCC

value: FACS-sorted epithelial cancer cells


title: EpCAM POS plastic 05

description: plastic epithelial cancer cells biological replicate 2

source_name: plastic epithelial cancer cells from MD/PD-SCCs

value: MD/PD-SCC

value: FACS-sorted plastic epithelial cancer cells


title: EpCAM POS plastic 06

description: plastic epithelial cancer cells biological replicate 3


title: EpCAM POS 01

description: full epithelial cancer cells biological replicate 1


title: Mut-Y-seq , CMC 20 min; OH-_SS III_rep2

tag: cell line


title: Mut-Y-seq , CMC 20 min; OH-_SS III_rep1


title: Differentiation control, day 5, rep 1 [10-1-Ctrl-D5]

description: all.fpkm_anno D3 D5

value: Differentiation control, day 5

tag: cell type

value: ESC

value: WT


title: IWP2, NaHCO3 and 2-DG treated, day 3, rep 1 [9-1-IWP2-NaHCO3-2DG-D3]

description: all.fpkm_anno D3 D5

value: IWP2, NaHCO3 and 2-DG treated, day 3

tag: genotype


title: Adult testis NONO IP-3

description: NONO bind RNA

tag: treatment


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, CENH3ox, ddm1, Rep2

value: CENH3ox, ddm1

value: Tal1 TED-seq


title: Differentiation control, day 5, rep 2 [10-2-Ctrl-D5]

description: all.fpkm_anno D3 D5

value: Cardiac differentiation


title: IWP2 and NaHCO3 treated, day 3, rep 2 [8-2-IWP2-NaHCO3-D3]

description: all.fpkm_anno D3 D5

value: IWP2 and NaHCO3 treated, day 3


title: Mut-Y-seq , CMC 20 min; OH-_RT1306_rep2

value: HEK-293T cells


title: EpCAM POS plastic 04

description: plastic epithelial cancer cells biological replicate 1


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, ddm1, Rep1


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, CENH3ox, WT, Rep2

value: CENH3ox, WT


title: Adult testis NONO-delta-ER IP-1

description: NONO-delta-ER bind RNA

value: Testis

value: testis total cells

value: KI


title: IWP2, NaHCO3 and 2-DG treated, day 3, rep 2 [9-2-IWP2-NaHCO3-2DG-D3]

description: all.fpkm_anno D3 D5


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, WT, Rep1

value: 10-day-old seedlings


title: Adult testis NONO-delta-ER input

description: Input RNA

value: Adult mice testis


title: Mut-Y-seq , CMC 20 min; OH-_RT1306_rep1


title: Adult testis NONO IP-1

description: NONO bind RNA


title: IWP2 and NaHCO3 treated, day 3, rep 1 [8-1-IWP2-NaHCO3-D3]

description: all.fpkm_anno D3 D5


title: Adult testis NONO IP-2

description: NONO bind RNA


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, CENH3ox, ddm1, Rep1


title: TED1, Tal1(WT) x CENH3-OX-4 F1

value: CENH3ox, Tal1(WT)


title: Adult testis NONO input

description: Input RNA


title: HD, scRNA-seq

city: Seoul

first: Cho-Rong

last: Lee

address: 1, Gwanak-ro

institute: Seoul national university

description: 10x Genomics

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

source_name: PBMC

extract_protocol:
Freshly collected T cells from HD or patient
Library was performed according to the manufacter's instructions(single cell  5' RNA library v2 protocol, 10x Genomics)

value: PBMC

value: T cells

tag: individual

value: healthy donor


title: Adult testis NONO-delta-ER IP-2

description: NONO-delta-ER bind RNA

tag: tissue


title: TED1, CENH3-OX-4 x Tal1(WT) F1


title: TED1, Tal1(ddm1) x CENH3-OX-1  F2, CENH3ox, WT, Rep1


title: IWP2 treated, day 3, rep 2 [6-2-IWP2-D3]

description: all.fpkm_anno D3 D5

value: IWP2 treated, day 3

value: ESC

value: WT


title: Proband, scRNA-seq

description: 10x Genomics

value: patient


title: IWP2 treated, day 3, rep 1 [6-1-IWP2-D3]

description: all.fpkm_anno D3 D5

value: Cardiac differentiation


title: TED1, Tal1(WT) x CENH3-OX-1 F1

value: Tal1 TED-seq


title: Mut-Y-seq , OH-_RT1306

value: HEK-293T cells


title: 21D testis TEX30 IP-2

data_processing:
library strategy: eCLIP-seq
eCLIP data were analyzed following ENCODE standard eCLIP pipeline.
eCLIP adapters were trimmed by using cutadapt v1.14, barcode and Random-mer were collected for decreasing PCR duplicates loss.
PCR duplicates removed by using a custom python script,  eCLIP reads aligned to the repeat elements from UCSC with STAR (V2.7.6a) and then mapped the rest to mm10 reference genome (GENCODE vM23).
bigWig files were generated using Deeptools. Significantly enriched peaks as those with irreproducible discovery rate cutoff of 0.01 as well as P ≤ 0.001 and fold enrichment ≥ 8
Supplementary files format and content: bigWig files

growth_protocol: collect 21D mouse testis, 3T3L1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: time

value: 21D old mice testis

tag: molecule type

value: TEX30 bind RNA


title: 3T3L1 HA-NONO△ER ip-2

value: 3T3L1 cell line

value: HA-NONO{delta}ER overexpression

value: 48h after transfection

value: HA-NONO△ER bind RNA


title: 21D testis TEX30 IP-1

value: Testis

value: testis total cells


title: NaHCO3 treated, day 3, rep 2 [3-2-NaHCO3-D3]

description: all.fpkm_anno D3 D5

value: NaHCO3 treated, day 3


title: 21D testis TEX30 input

value: Input RNA


title: HCl treated, day 3, rep 2 [2-2-HCl-D3]

description: all.fpkm_anno D3 D5

value: HCl treated, day 3


title: NaHCO3 treated, day 3, rep 1 [3-1-NaHCO3-D3]

description: all.fpkm_anno D3 D5

value: ESC


title: HCl treated, day 3, rep 1 [2-1-HCl-D3]

description: all.fpkm_anno D3 D5

value: WT


title: 3T3L1 HA-NONO△ER ip-1


title: 21D testis PDHA2 IP-2

value: PDHA2 bind RNA


title: 3T3L1 HA-NONO△ER input


title: TED1, CENH3-OX-1 x Tal1(WT) F1

value: 10-day-old seedlings

value: CENH3ox, Tal1(WT)


title: TED1, Tal1(WT), Rep2

value: Tal1 TED-seq


title: 21D testis PDHA2 IP-1

value: 21D old mice testis


title: 21D testis PDHA2 input


title: TED1, Tal1(ddm1), Rep1


title: 3T3L1 HA-NONO input

value: HA-NONO overexpression


title: 3T3L1 HA-NONO IP-2

value: 3T3L1 cell line

value: HA-NONO bind RNA


title: Differentiation control, day 3, rep 1 [1-1-Ctrl-D3]

description: all.fpkm_anno D3 D5

value: Differentiation control, day 3

value: Cardiac differentiation


title: TED1, Tal1(WT), Rep1


title: Cryo_1

status: Public on Aug 07 2024

city: Taichung

first: Chi-Ying

address: No.30-6, Sec. 1, Changping Rd., Beitun Dist., Taichung 406, Taiwan

country: Taiwan

institute: Taiwan IVF center, Lee's women's hospital

data_processing:
CLC Genomics Workbench v  10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus musculus GRCm38
Supplementary files format and content: tab-delimited files include FPKM values for each Sample

source_name: embryo

growth_protocol: Superovulation was induced in 6–8-week-old virgin mice of the C57BL/6JNarl strain throughintraperitoneal injection of pregnant mare serum gonadotrophin (Sigma Chemical Co., St Louis, MO, USA) followed 48h later by injection with 5 IU of human chorionic gonadotrophin(Serono, Rome, Italy).

extract_protocol:
Samples of1 µLwere taken to construct a library using the Ovation SoLo RNA-Seq library preparation kit (NuGEN #0501-32)
Samples of1 µLwere taken to construct a library using the Ovation SoLo RNA-Seq library preparation kit (NuGEN #0501-32)

treatment_protocol: Embryo vitrification was performed using a Cryotech Vitrification Kit (Cryotech, Japan)according to the manufacturer’s instructions and the protocol described by Gutnisky et al

value: embryo

value: Embryo transfer with vitrification and warming


title: Fresh_3

value: Embryo transfer without vitrification and warming


title: Cryo_3


title: Fresh_1


title: Timecourse, sublibrary 7

city: Philadelphia

first: Christopher

middle: M

last: Madl

state: PA

address: 3231 Walnut St

department: Materials Science and Engineering

institute: University of Pennsylvania

description: Parse Biosciences WT v1

data_processing:
Sequencing reads were mapped to the mouse reference genome and correlated with single cell barcodes using the Parse Biosciences analysis pipeline.
Downstream analysis of transcriptomic data was performed using Scanpy.
Assembly: mm10
Supplementary files format and content: H5AD files output from Scanpy analysis with complete sample annotation and processing.

source_name: Hindlimb muscles

growth_protocol: Muscle stem cells were cultured in FluoroBrite DMEM with 15% FBS, L-glutamine, sodium pyruvate, non-essential amino acids, penicillin/streptomycin, and 2.5 ng/mL FGF-2.

extract_protocol:
Cells cultured on hydrogels were washed with PBS and detached from the substrates by treatment with TrypLE Express and manual pipetting. The cells were collected by centrifugation and fixed using the Cell Fixation kit from Parse Biosciences.
Single cell libraries for RNA sequencing were prepared based on a SPLiT-seq approach using the Evercode Mini WT and Evercode WT kits from Parse Biosciences, following the manufacturer's protocols. Library quality was validated using an Agilent Bioanalyzer 2100 at the Stanford Genomics Facility.

treatment_protocol: For samples investigating the effects of RhoA inhibition, cells were treated with DMSO vehicle or rhosin (30 μM) at the time of seeding and refreshed on days 1 and 2 of culture before cells were collected at day 3.

value: Hindlimb muscles

tag: strain

value: muscle stem cells

value: 2 mo or >24 mo


title: Timecourse, sublibrary 6

description: Parse Biosciences WT v1

tag: age


title: TED1, Tal1(ddm1), Rep2


title: Fresh_2


title: Timecourse, sublibrary 2

description: Parse Biosciences WT v1


title: Cryo_2


title: Timecourse, sublibrary 8

description: Parse Biosciences WT v1


title: Timecourse, sublibrary 5

description: Parse Biosciences WT v1


title: Timecourse, sublibrary 4

description: Parse Biosciences WT v1


title: Day 3, Rho inhib, sublibrary 2

description: Parse Biosciences WT Mini v1

value: 2 mo

value: rhosin or vehicle


title: Differentiation control, day 3, rep 2 [1-2-Ctrl-D3]

last: Chen

description: all.fpkm_anno D3 D5

value: ESC

value: WT


title: Timecourse, sublibrary 3

description: Parse Biosciences WT v1


title: polyclonal CD8 cells TCR seq

city: Pittsburgh

first: Jian

last: Cui

address: 5051 Centre Avenue

department: Immunology

institute: University of Pittsburgh

description:
TCR seq
TCR library, read 1 contains barcode and UMI information, and read 2 containsTCR sequences
polyclonal_TCR

library_source: other

data_processing:
After library preparation and quantification, samples were pooled and sequenced on a NovaSeq 6000 using S1 v1.5 kits (150 cycles), with sequencing parameters adjusted for v1 and v2 Chemistry.
Demultiplexing, barcode processing, gene counting, and aggregation were conducted using Cell Ranger software version 6.1.2 and CITE-seq-Count version 1.4.4.
Assembly: mm10
Supplementary files format and content: CellRanger output files: polyclonal_GEX_barcodes.tsv.gz, polyclonal_GEX_features.tsv.gz, polyclonal_GEX_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: polyclonal_TCR_filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files: pMEL_GEX_barcodes.tsv.gz, pMEL_GEX_features.tsv.gz, pMEL_GEX_matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count output files: polyclonal_HTO_barcodes.tsv.gz, polyclonal_HTO_features.tsv.gz, polyclonal_HTO_matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count output files: pMEL_HTO_barcodes.tsv.gz, pMEL_HTO_features.tsv.gz, pMEL_HTO_matrix.mtx.gz

molecule: other

source_name: Tumor and lymph node

extract_protocol:
Single-cell libraries were prepared from sorted live CD8+ T cells derived from either polyclonal mice or CD8+ pMEL cells from an antigen-specific system, utilizing Chromium Single Cell 5’ Reagent (v1 Chemistry) or Chromium Next GEM Single Cell 5’ Reagent (v2 Chemistry Dual Index) immediately post-cell isolation.
Sample multiplexing was achieved via CITEseq, wherein cells were stained with TotalSeq-C anti-mouse hashtag antibodies and additional surface flow cytometry antibodies (TCRβ, CD8). Sorted cells, tagged with uniquely barcoded TotalSeq-C antibodies, were pooled and loaded into parallel lanes for droplet generation, targeting a recovery of 2,000 cells per sample. After droplet partitioning, cells underwent lysis and reverse transcription within droplets.
cDNA was isolated, bulk amplified, and selected with SPRIselect beads. Adaptors were ligated, sample indices were added through PCR, and samples underwent another selection using SPRIselect beads. Library concentration was determined via PCR with KAPA DNA Quantification.

value: Tumor and lymph node

tag: library type

value: TCR


title: Timecourse, sublibrary 1

description: Parse Biosciences WT v1


title: 3T3L1 HA-NONO IP-1

value: HA-NONO overexpression

value: 48h after transfection


title: pMEL CD8 cells citeseq hashtages

description:
Hashtag-derived oligonucleotides
HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.
pMEL_HTO

molecule: protein

source_name: Tumor

value: Tumor

value: HTO

tag: hto

value: m_totalseq_1, Pdcd1L/L Lag3L/L-yfp (WT) - Tumor; m_totalseq_2, Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_3, Pdcd1L/L E8ICre.GFP - Tumor; m_totalseq_4, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - Tumor.


title: polyclonal CD8 cells citeseq hashtages

description:
Hashtag-derived oligonucleotides
HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.
polyclonal_HTO

value: m_totalseq_1, Pdcd1L/L Lag3L/L-yfp (WT) - Tumor; m_totalseq_2, E8ICre.GFP (WT) - Tumor; m_totalseq_3, Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_4, Pdcd1L/L E8ICre.GFP - Tumor; m_totalseq_5, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_6, Pdcd1L/L Lag3L/L-yfp (WT) - ndLN; m_totalseq_7, E8ICre.GFP (WT) - ndLN; m_totalseq_8, Lag3L/L-yfp E8ICre.GFP - ndLN; m_totalseq_9, Pdcd1L/L E8ICre.GFP - ndLN; m_totalseq_10, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - ndLN.


title: pMEL CD8 cells gene expression

description:
polyA RNA
GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript
pMEL_GEX

value: mRNA


title: polyclonal CD8 cells gene expression

description:
polyA RNA
GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript
polyclonal_GEX


title: Soleus, male, Deficient, ZT17, rep3

city: La Jolla

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

institute: Salk Institute for Biological Studies

description:
90_M_H_ZT17_SOL_S351
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

source_name: Soleus

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 500ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

value: CBA/CaJ

value: Soleus

tag: Sex

value: male

value: Deficient

tag: zeitgeber time


title: Soleus, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_SOL_S343
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_SOL_S350
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_SOL_S342
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Control, ZT05, rep3

description:
93_M_L_ZT05_SOL_S352
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: Soleus, male, Control, ZT17, rep2

description:
86_M_L_ZT17_SOL_S349
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Control, ZT17, rep3

description:
94_M_L_ZT17_SOL_S353
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Deficient, ZT17, rep3

description:
60_F_16_5H_SOL_S48_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Soleus, male, Control, ZT17, rep1

description:
78_M_L_ZT17_SOL_S345
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Control, ZT05, rep2

description:
85_M_L_ZT05_SOL_S348
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Control, ZT05, rep1

description:
77_M_L_ZT05_SOL_S344
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Day 3, Rho inhib, sublibrary 1

description: Parse Biosciences WT Mini v1

value: Hindlimb muscles

value: muscle stem cells

value: 2 mo

value: rhosin or vehicle


title: Soleus, female, Deficient, ZT05, rep2

description:
43_F_4_5H_SOL_S42_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Deficient, ZT17, rep2

description:
44_F_16_5H_SOL_S43_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Deficient, ZT05, rep1

description:
35_F_4_5H_SOL_S39_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT17, rep3

description:
48_F_16_5L_SOL_S45_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT17, rep1

description:
32_F_16_5L_SOL_S38_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT17, rep2

description:
56_F_16_5L_SOL_S46_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT05, rep1

description:
31_F_4_5L_SOL_S37_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_SOL_S347
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_TAt_S376
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Tibialis anterior tendon

value: Tibialis anterior tendon


title: Tibialis anterior tendon, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_TAt_S368
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_TAt_S371
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_SOL_S346
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Control, ZT17, rep3

description:
94_M_L_ZT17_TAt_S378
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Control, ZT17, rep2

description:
86_M_L_ZT17_TAt_S374
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Control, ZT17, rep1

description:
78_M_L_ZT17_TAt_S370
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Deficient, ZT05, rep3

description:
59_F_4_5H_SOL_S47_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Deficient, ZT17, rep1

description:
36_F_16_5H_SOL_S40_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Control, ZT05, rep2

description:
93_M_L_ZT05_TAt_S377
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT17, rep2

description:
44_F_16_5H_TAt_S55_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT17, rep3

description:
60_F_16_5H_TAt_S60_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT17, rep3

description:
56_F_16_5L_TAt_S58_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Control, ZT05, rep1

description:
77_M_L_ZT05_TAt_S369
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT05, rep2

description:
39_F_4_5L_SOL_S41_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT17, rep1

description:
36_F_16_5H_TAt_S52_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT05, rep3

description:
59_F_4_5H_TAt_S59_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT05, rep2

description:
43_F_4_5H_TAt_S54_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Soleus, female, Control, ZT05, rep3

description:
47_F_4_5L_SOL_S44_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT17, rep1

description:
32_F_16_5L_TAt_S50_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_TAt_S372
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT17, rep2

description:
48_F_16_5L_TAt_S57_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_TAt_S375
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT05, rep2

description:
39_F_4_5L_TAt_S53_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT05, rep3

description:
47_F_4_5L_TAt_S56_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Control, ZT05, rep1

description:
31_F_4_5L_TAt_S49_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_TA_S364
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Tibialis anterior

value: Tibialis anterior


title: Tibialis anterior tendon, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_TAt_S367
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_TA_S360
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_TA_S356
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_TA_S359
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_TA_S355
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Control, ZT17, rep3

description:
94_M_L_ZT17_TA_S366
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior tendon, female, Deficient, ZT05, rep1

description:
35_F_4_5H_TAt_S51_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Control, ZT17, rep1

description:
78_M_L_ZT17_TA_S358
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Control, ZT05, rep2

description:
85_M_L_ZT05_TA_S361
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Control, ZT05, rep1

description:
77_M_L_ZT05_TA_S357
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Deficient, ZT17, rep3

description:
60_F_16_5H_TA_S24_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Deficient, ZT17, rep2

description:
44_F_16_5H_TA_S19_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Control, ZT05, rep3

description:
93_M_L_ZT05_TA_S365
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv