title: macrophages, ZM-1

description: Library name: Smaple 4


title: UPEC Distal regions Tam+Dtx Rep 1

status: Public on Mar 11 2026

type: SRA

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: Library name: UPEC_DisEpi_TamDtx_1

library_source: transcriptomic

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific reads was done using nf-core RNA-seq pipeline v3.7
Normalization and detection of differentially expressed genes was performed using DESeq2 (v1.42.0)
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

molecule: polyA RNA

organism: Mus musculus

source_name: distal epididymis (Corpus+Cauda)

extract_protocol:
RNA was extracted from testis, proximal (segment 1-5) and distal epididymis (segment 6-10) using the RNeasy Mini Kit (Qiagen) after bead-based tissue homogenization (Tissue homogenizer Retsch, 2.8 mm stainless steel beads)
RNA-seq

tag: tissue

value: distal epididymis (Corpus+Cauda)

tag: genotype

tag: treatment

value: Tamoxifen + Diphtheria toxin


title: PB_3wk_Ctrl_1

city: Fargo

first: Evandro

last: Fortini

address: 1605 Albrecht Blvd N

country: USA

institute: United States Department of Agriculture

description: Library name: PPP3_4

data_processing:
Paired-end reads obtained from the Novaseq 6000 system were processed using Trimmomatic to trim low-quality bases and remove adapter sequences, applying the parameters HEADCROP:10, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the Solanum tuberosum genome assembly version 6.1 (DM1-3516 R44) using HISAT2 (--dta). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools. Transcript abundance was quantified with StringTie (-e, -B flags) using the reference genome annotation in GFF3 format. Gene and transcript count matrices were generated with the prepDE.py3 script.
Assembly: The Solanum tuberosum genome assembly version 6.1 was used for read alignment and analysis. The genome assembly, annotation, and related resources are available in the SpudDB database (Pham et al., 2020; https://spuddb.uga.edu/).
Supplementary files format and content: The processed data files include tab-delimited text files containing gene and transcript count matrices (gene_count_matrix.txt and transcript_count_matrix.txt). These files provide quantified expression levels for differential expression analysis, generated using the prepDE.py3 script based on StringTie outputs.

molecule: total RNA

organism: Solanum tuberosum

source_name: Primary Meristem

extract_protocol:
To extract RNA from primary and secondary meristem samples, roughly 100 mg of tissue was utilized following the protocol described by Rubio-Piña and Zapata-Pérez (2011). Similarly, for flesh tuber RNA extraction, approximately 200 mg of tissue was processed according to the procedure reported by Vennapusa et al. (2020). RNA quality, purity (OD260/280 and OD260/230), and concentration were confirmed using 1% agarose gel electrophoresis, Nanodrop One and Agilent 5400 Bioanalyzer.
RNA-seq

value: Primary Meristem

value: Russet Burbank (Solanum tuberosum L.)

value: Control


title: NOD_8wk_LG_biol rep 2

city: Boston

first: Danny

last: Toribio

state: MA

address: One Kneeland St

department: Basic and Clinical Translational Sciences

institute: Tufts University School of Dental Medicine

description: Library name: 8Week_NOD2

data_processing:
Basecalling and demultiplexing were performed on the raw sequence data using Illumina's bcl2fastq software.
Quality control of the read data was conducted using the FastQC tool.
Sequencing reads from the compressed fastq files were mapped to the mouse reference genome (mm10) using the HISAT2 alignment program.
Raw gene count tables were generated from the resulting alignment files and the mm10 gene annotation files using the featureCounts program from the Rsubread package.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: tab-delimited-value text file with raw count of each sample

source_name: Exorbital Lacrimal Gland

extract_protocol:
Excised lacrimal glands were placed in RNAlater stabilization solution (Thermo Fisher Scientific, Waltham, MA) for storage at -20˚C prior to RNA extraction. Total RNA was extracted and purified using the RNeasy Midi Kit (Qiagen, Germantown, MD) following the manufacturer's instructions. Purified RNA samples were stored at -80°C until downstream use.
100 - 200 ng of total RNA was used for the construction of the sequencing libraries using the Illumina TruSeq stranded mRNA kit, as per the manufacturer’s instructions. The resulted libraries were then analyzed on an Agilent Fragment Analyzer for molar quantification and size distribution, and then pooled at equal molar for sequencing on an Illumina HiSeq 2500 sequencer using V4 chemistry and single read 50 bases format.

value: Exorbital Lacrimal Gland

value: NOR/LtJ


title: macrophages, Ctrl-2

city: Guangzhou

first: Shuo

last: Shi

state: Guangdong Province

address: No.1023, South Shatai Road Baiyun District

department: School of Basic Medical Sciences

country: China

institute: Southern Medical University

description: Library name: Smaple 2

data_processing:
Fastp v0.23.2, Hisat2 v2.2.1, FeatureCounts v2.0.3, and DESeq2 (R package v1.34.0) were used for data processing.
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) , DEGs with \(|log 2 FC|>1\) and \(Padj <0.05\) were considered to be significantly different expressed genes.
Assembly: mm10
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: bone marrow

growth_protocol: BMMs were generated from the bone marrow of 6-week-old C57BL/6 male mice as described previously. The bone marrow cells were then obtained by flushing the bones with a 1 mL syringe. Subsequently, the cells were suspended in α-MEM complete medium supplemented with 10% fetal bovine serum and 30 ng/mL M-CSF. The cells were cultured at 37 ℃ in a 5% CO2 incubator. After three days, the adherent cells were identified as bone marrow-derived macrophages.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Cat.9109, Takara Biotechnology), following the manufacturer’s instructions and using three samples per group. RNA concentration and purity were quantified using a UV spectrophotometer (NanoDropOne, Thermo Fisher Scientific, USA).
RNA libraries for RNA - seq were prepared using ABclonal mRNA - seq Lib Prep Kit following the manufacturer’s protocols.

treatment_protocol: RNA-seq profiling was performed on bone marrow-derived macrophages (osteoclast precursor cells, induced for osteoclast differentiation). The cells were cultured in a complete α-MEM medium containing 10% FBS, supplemented with 30 ng/mL M-CSF and 100 ng/mL RANKL (key factors for osteoclast differentiation); those treated without 10 μM ZM served as the control group, and those treated with 10 μM ZM were the intervention group.

value: bone marrow

tag: cell line

value: primary cell

tag: cell type

value: bone marrow-derived macrophages

value: WT

value: complete α-MEM + 10% FBS + 30 ng/mL M-CSF + 100 ng/mL RANKL（without 10 μM ZM）

tag: batch

value: batch 1


title: NOD_8wk_LG_biol rep 3

description: Library name: 8Week_NOD3


title: PB_OD_Ctrl_3

description: Library name: PPP3_3


title: PB_OD_Ctrl_2

description: Library name: PPP3_2


title: Blood_Control_Short Read 10

city: Boca Raton

first: Massimo

last: Caputi

address: 777 Glades Road

institute: Florida Atlantic University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through customperl 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 lowquality readsfrom raw data. At the same time, Q20, Q30, and GC-content of the rawdatawere calculated. Then, 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 (Langmead et al., 2009) without mismatch to analyze their expression anddistribution on the reference.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: ensembl_82_homo_sapiens_grch38_primary
Supplementary files format and content: sRNA_ADvsControl.Differential_analysis_results.xlsx; differential expression

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
The blood was collected in PAXgene Blood RNA tubes. Total RNA was extracted following the protocol developed by this lab to isolate RNAs of different sizes and low concentration (Paz S, Mauer C, Ritchie A, Robishaw JD, Caputi M. A simplified SARS-CoV-2 detection protocol for research laboratories. PLoS One. 2020 Dec 18;15(12):e0244271). RNA sample quality and quantity were determined utilizing an Agilent TapeStation system and a NanoDrop spectrophotometer. The samples utilized for the cDNA library preparations had an RNA integrity number (RIN) ≥ 7 and an RNA concentration ≥ 30 ng/µL. Ribosomal RNA was removed by Epicentre TruSeq Stranded Total RNA Library Prep Gold/illumina/20020599
A total amount of 2 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

value: Whole Blood


title: NOD_8wk_LG_biol rep 1

description: Library name: 8Week_NOD1


title: Blood_Control_Short Read 11


title: Blood_Control_Short Read 9


title: PB_OD_Ctrl_1

description: Library name: PPP3_1


title: Blood_Control_Short Read 7


title: macrophages, Ctrl-1

description: Library name: Smaple 1


title: Blood_Control_Short Read 8


title: Blood_Control_Short Read 6


title: NOD_3wk_LG_biol rep 3

description: Library name: 3Week_NOD3


title: ZM-3

description:
Library name: Smaple 6
FPKM_ ZM-3

source_name: primary cell

growth_protocol: Primary osteoblasts were isolated from 3 - day - old C57BL/6 mouse calvaria. After removing soft tissue, cut calvaria into fragments, digest with 0.25% trypsin (10 min) and 0.2% type Ⅱ collagenase (90 min). Pipette to get cells, suspend in α - MEM complete medium (10% FBS), and incubate at 37℃ with 5% CO₂.

treatment_protocol: Primary osteoblasts were treated with or without 10 μM ZM in an osteogenic induction medium for 6 days, and the cells were divided into a control group and an intervention group.

value: bone

value: primary osteoblasts

value: osteogenic induction medium, with 10 μM ZM


title: ZM-2

description:
Library name: Smaple 5
FPKM_ ZM-2


title: Z17315, Placenta, Chorionic Villous Tissue, Flu, Female Fetus, Day 5 post-inoculation, Day 131

city: Seattle

first: Kristina

last: Adams Waldorf

state: Washington

address: 750 Republican Street, E Building, Room E360

department: OBGYN

institute: University of Washington

description: Library name: Flu_Z17315

data_processing:
Partek
Reads were aligned to Macaca nemestrina genome v1.0 using STAR in Partek
Count matrix was generated using Partek
Assembly: Mnem_1.0
Supplementary files format and content: csv file includes raw count matrix for each sample

organism: Macaca nemestrina

source_name: placenta (chorionic villous)

extract_protocol:
RNeasy Mini Kit; QIAGEN (250)/Cat #74106
KAPA RNA HyperPrep Kit with RiboErase (HMR)

value: placenta (chorionic villous)

value: Flu Infected

tag: route of_inoculation

value: intratracheal/intranasal/ocular/oral

tag: disease

value: Influenza A virus (A/California/07/2009(H1N1))

tag: dam sex

value: female

tag: fetal sex

tag: days post_inoculation

tag: gestational age_(days)

tag: lung viral_load_(copies_per_mg)


title: NOD_3wk_LG_biol rep 1

description: Library name: 3Week_NOD1

value: Exorbital Lacrimal Gland


title: Z16319a, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 121

description: Library name: Flu_Z16319a

value: male


title: ZM-1

description:
Library name: Smaple 4
FPKM_ ZM-1


title: Blood_Control_Short Read 5

value: Control


title: Ctrl-3

description:
Library name: Smaple 3
FPKM_ Ctrl-3

value: osteogenic induction medium, without 10 μM ZM


title: Ctrl-2

description:
Library name: Smaple 2
FPKM_ Ctrl-2


title: Blood_Control_Short Read 4


title: Z15193, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 135

description: Library name: Flu_Z15193


title: Cecum, Ripk3-/-, TNFα, mouse 1

city: Suzhou

first: li

middle: jing

last: jing

address: No.100 Chongwen Road

institute: Suzhou institute systems medicine

description:
Library name: Sample 11
RIPK3_17_TNF

data_processing:
Gene expression levels were quantified using the FPKM method with HTSeq. Differential gene expression analysis was conducted using the DESeq2 Bioconductor package.
Assembly: Mouse mm10
Supplementary files format and content: txt file includes raw counts and FPKM values for each sample.

source_name: Cecum

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen).
Preparation of sequencing library was constructed according to the manufacturer’s protocol (GENEWIZ).

value: Cecum

value: TNFα


title: Cecum, Ripk3-/-, TNFα, mouse 2

description:
Library name: Sample 12
RIPK3_19_TNF


title: NOD_3wk_LG_biol rep 2

description: Library name: 3Week_NOD2

value: NOR/LtJ


title: Z15060a, Placenta, Chorionic Villous Tissue, Flu, Female Fetus, Day 5 post-inoculation, Day 132

description: Library name: Flu_Z15060a


title: Blood_Control_Short Read 3


title: Cecum, Ripk3D143N/D143N, TNFα, mouse 2

description:
Library name: Sample 10
D143N_12_TNF


title: CD45 enriched 6wk VML PCL replicate 3

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

description: Library name: VML+PCL_6wk_CD45enrich_Rep3

library_source: transcriptomic single cell

data_processing:
Fastq files were aligned using Cell Ranger v6.1.2 using default parameters.
Assembly: GENCODE vM23 annotations and genome
Supplementary files format and content: Processed data files contain standard Cell Ranger outputs (features.csv, barcodes.csv, matrix.mtx).

source_name: Injured Muscle and Fibrotic PCL Implant

extract_protocol:
Quadricep muscles and fibrotic PCL implants were harvested at the 6 wk time point and processed into a single cell suspension. Dead cells were removed with Magnetic-Activated Cell Sorting (MACS) using the Dead Cell Removal kit. MACS with the mouse CD45 MicroBeads was used to separate and collect the CD45+ immune cells (positive fraction) and CD45- stromal cells (negative fraction). Cells were counted in both fractions using a hemocytometer, pooled at in a 1:1 ratio, and processed for 3’ scRNAseq (10x Genomics, v3.1 chemistry)
The CD45+-enriched samples were processed for 3’ scRNAseq (10x Genomics, v3.1 chemistry). Libraries were sequenced using the NovaSeq platform (Illumina) with S2 100 flow cell at a target depth of 100,000 unique reads/cell.

treatment_protocol: PCL particulate was implanted into hindlimb volumetrc muscle loss defects in C57BL/6 wildtype (WT) mice for 6 weeks.

value: Injured Muscle and Fibrotic PCL Implant

value: Mixed

value: C57BL/6 WT

value: 6 wk VML+PCL


title: Ctrl-1

description:
Library name: Smaple 1
FPKM_ Ctrl-1

value: bone

value: primary osteoblasts

value: WT

value: batch 1


title: Z12072, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 139

description: Library name: Flu_Z12072

value: placenta (chorionic villous)

value: Flu Infected

value: intratracheal/intranasal/ocular/oral

value: Influenza A virus (A/California/07/2009(H1N1))


title: Blood_Control_Short Read 1

value: Whole Blood

value: Control


title: Z14061, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 132

description: Library name: Flu_Z14061

value: female

value: male


title: Z11366a, Placenta, Chorionic Villous Tissue, Flu, Female Fetus, Day 5 post-inoculation, Day 139

description: Library name: Flu_Z11366a


title: CD45 enriched 6wk VML PCL replicate 1

description: Library name: VML+PCL_6wk_CD45enrich_Rep1


title: Cecum, Ripk3+/+, TNFα, mouse 1

description:
Library name: Sample 7
WT_1_TNF

value: Cecum

value: TNFα


title: Blood_AD_Short Read 48

value: AD


title: Blood_AD_Short Read 47


title: R06147B, Placenta, Chorionic Villous Tissue, Flu, Female Fetus, Day 5 post-inoculation, Day 143

description: Library name: Flu_R06147B


title: Cecum, Ripk3-/-, PBS, mouse 2

description:
Library name: Sample 6
RIPK3_22_CTRL

value: PBS


title: L07279, Placenta, Chorionic Villous Tissue, Flu, Female Fetus, Day 5 post-inoculation, Day 131

description: Library name: Flu_L07279


title: Blood_Control_Short Read 2


title: Blood_AD_Short Read 46


title: CD45 enriched 6wk VML PCL replicate 2

description: Library name: VML+PCL_6wk_CD45enrich_Rep2

value: Injured Muscle and Fibrotic PCL Implant

value: Mixed

value: C57BL/6 WT

value: 6 wk VML+PCL


title: Cecum, Ripk3-/-, PBS, mouse 1

description:
Library name: Sample 5
RIPK3_21_CTRL


title: L08225a, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 134

description: Library name: Flu_L08225a


title: Cecum, Ripk3D143N/D143N, TNFα, mouse 1

description:
Library name: Sample 9
D143N_11_TNF


title: 12wk PCL Hashed abTCR

description:
Library name: VML-PCL_12wk_hashed_abTCR
HTOs separate individual mice

data_processing:
Fastq files were aligned using Cell Ranger v6.1.2
Cell Ranger's multi command was run to demultiplex samples, after which the bamtofastq function was used to create sample specific fastq files.
Cell Ranger's multi command along with sample specific fastq files was used in conjunction with the  TCR sequencing to align AB TCR sequences.
Cell Ranger's vdj function was used to align the GD TCRs.
Assembly: GENCODE vM23 annotations and genome
Supplementary files format and content: Gene expression files include standard 10x Cell Ranger outputs (barcodes.tsv, features.tsv, matrix.mtx). Data for TCR sequencing (both AB and GD) is included as filtered and annotated contig files.
Library strategy: TCR-Seq

extract_protocol:
Data for scRNA/TCRseq was collected in 3 independent experiments: (1) 1 wk VML+Saline (n=18, pooled) and 1 wk VML+PCL (n=2, pooled), (2) 1 wk VML+PCL (n=5, hashed) and 12 wk VML+PCL (n=5, hashed), and (3) 6 wk VML+PCL (n=3, hashed).Single cell suspensions were stained for viabiliy, surface markers, and TotalSeq-C hashing antibodies. T cells (LiveSSCloCD45+CD3+) were sorted using BD FACSAria Fusion Cell Sorter into dPBS with 1% BSA, centrifuged, and re-suspended in dPBS with 0.01% BSA. Sorted T cells were counted and processed for 5’ paired scRNA/TCRseq with feature barcodes (10x Genomics, v1.1 chemistry).
Library preparations for gene expression, feature barcodes, and abTCRs were performed using standard Chromium Single Cell 5’ library Construction kit v1.1 (10x Genomics PN 1000020) as per manufacturer’s protocols. Library preparation for gdTCRs was performed using previously published custom primers and methods (Lee et al., Nature Communications 2020). Libraries were sequenced using the Illumina NovaSeq platform with S2 100 flow cell at a target depth of 100,000 unique reads/cell.

treatment_protocol: Saline or PCL particulate was implanted into hindlimb volumetric muscle loss defects in C57BL/6 wildtype (WT) mice for 1, 6, or 12 weeks.

value: T Cells

value: 12 wk VML+PCL

value: Batch 2


title: Blood_AD_Short Read 45


title: 12wk PCL Hashed gdTCR

description:
Library name: VML-PCL_12wk_hashed_gdTCR
HTOs separate individual mice


title: Cecum, Ripk3+/+, TNFα, mouse 2

description:
Library name: Sample 8
WT_3_TNF


title: A11251, Placenta, Chorionic Villous Tissue, Flu, Male Fetus, Day 5 post-inoculation, Day 130

description: Library name: Flu_A11251

value: placenta (chorionic villous)

value: Flu Infected

value: intratracheal/intranasal/ocular/oral


title: Cecum, Ripk3D143N/D143N, PBS, mouse 2

description:
Library name: Sample 4
D143N_15_CTRL


title: 12wk PCL Hashed scRNAseq

description:
Library name: VML-PCL_12wk_hashed_GEX
HTOs separate individual mice

data_processing:
Fastq files were aligned using Cell Ranger v6.1.2
Cell Ranger's multi command was run to demultiplex samples, after which the bamtofastq function was used to create sample specific fastq files.
Cell Ranger's multi command along with sample specific fastq files was used in conjunction with the  TCR sequencing to align AB TCR sequences.
Cell Ranger's vdj function was used to align the GD TCRs.
Assembly: GENCODE vM23 annotations and genome
Supplementary files format and content: Gene expression files include standard 10x Cell Ranger outputs (barcodes.tsv, features.tsv, matrix.mtx). Data for TCR sequencing (both AB and GD) is included as filtered and annotated contig files.


title: Z15198, Placenta, Chorionic Villous Tissue, Control, Female Fetus, Day 1 post-inoculation, Day 134

description: Library name: CTRL_Z15198

value: Saline Control

value: choriodecidual space

value: Control


title: Cecum, Ripk3D143N/D143N, PBS, mouse 1

description:
Library name: Sample 3
D143N_14_CTRL

value: Cecum


title: 6wk PCL Hashed gdTCR

description:
Library name: VML-PCL_6wk_hashed_gdTCR
HTOs separate individual mice

value: Batch 3


title: Cecum, Ripk3+/+, PBS, mouse 2

description:
Library name: Sample 2
WT_8_CTRL


title: 6wk PCL Hashed abTCR

description:
Library name: VML-PCL_6wk_hashed_abTCR
HTOs separate individual mice


title: Blood_AD_Short Read 44

value: Whole Blood

value: AD


title: Blood_AD_Short Read 49


title: Blood_AD_Short Read 43


title: 6wk PCL Hashed scRNAseq

description:
Library name: VML-PCL_6wk_hashed_GEX
HTOs separate individual mice

value: Injured Muscle and Fibrotic PCL Implant


title: Blood_AD_Short Read 42


title: R10195, Placenta, Chorionic Villous Tissue, Control, Female Fetus, Day 1 post-inoculation, Day 132

description: Library name: CTRL_R10195

value: female


title: Cecum, Ripk3+/+, PBS, mouse 1

description:
Library name: Sample 1
WT_7_CTRL

value: PBS


title: Afg3l2 GKD, h3k27me3 mark, rep 1

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Afg3l2_h3k27me3

library_source: genomic

data_processing:
Reads were evaluated for their quality using FastQC v0.11.8
Reads were trimmed for adaptor sequences using Trim Galore! v0.6.6
Reads were aligned to the dm6 reference genome version for drosophila melanogaster using Bowtie2 v2.2.8 with parameters -q -I 50 -X 700 --very-sensitive-local --local --no-mixed --no-unal --no-discordant
Binary alignment maps (BAM) files were generated with samtools v1.9
MACS2 v2.1.0 was used to call significant peaks for samples BamRNAi Stwl, WT Stwl and WT BEAF. IgG was used as control to call peaks. Peaks within ENCODE blacklisted regions and repetitive sequences larger than 100 bases were removed
BigWig files were generated from BAM files using deepTools v3.2.1 bamCoverage function with parameters– normalize using RPKM–bin size 10
Assembly: dm6
Supplementary files format and content: bigWig (.bw) files with rpkm-normalized counts
Library strategy: CUT&Run

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Ovary tissue

extract_protocol:
Ovaries were dissected in PBS. PBS was removed and the samples were permeabilized in 1mL of Permeabilization Solution (PBST+1% Triton-X) rotating in RT for 1 hour. Samples were then incubated overnight at 4°C in primary antibody dilutions in freshly prepared BBT+ buffer (PBST + 1% BSA + 0.5 mM Spermidine + 2 mM EDTA + 1 large Roche complete EDTA-free tablets). Primary antibody was replaced with BBT+ buffer and quickly washed twice. Samples were then incubated in ~700 ng/ml of pAG-MNase in BBT+ buffer rotating for 4 hours at 25°C. Samples were then quickly washed twice in wash+ buffer (20 mM HEPES pH7.5 + 150 mM NaCl + 0.1% BSA + 0.5 mM Spermidine + 1 large Roche complete EDTA-free tablets in water). Samples were resuspended in 150 μl Wash+C (wash+ + 100 mM CaCl2) and incubated for 45 minutes on nutator at 4°C. The cleavage reaction was terminated by addition of 150 μl StopR (NaCl final 200 mM + EDTA final 20 mM + 100μg/mL RNaseA) and incubating the sample at 37˚C for 30 minutes. Samples were then centrifuged at 16,000 x g for 5 minutes and 300 μl of the supernatant was collected for DNA discovery. To the supernatant, 2 μL 10% SDS and 2.5 μL of 20 mg /mL Proteinase K was added and incubated at 50°C for 2 hours. Half of this was kept as a backup and half was used in bead cleanup. 20 μL AmpureXP bead slurry and 280 μL MXP buffer (20% PEG8000 + 2.5 M NaCl + 10 mM MgCl2 in water) was added to the sample and mixed thoroughly followed by 15 minutes incubation at RT. The beads were separated by magnet and supernatant was discarded. The beads were carefully washed with 80% ethanol for 30 seconds, while on the magnetic stand and air dried for 2 minutes. The beads were then resuspended in 10 μL DNase free water.
The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection.

value: Ovary tissue

tag: developmental stage

value: Differentiated stages

tag: chip antibody

value: H3K27me3 ab (abcam AB6002)

value: Afg3l2 GKD


title: Blood_AD_Short Read 41


title: 1wk PCL Hashed abTCR

description:
Library name: VML-PCL_1wk_hashed_abTCR
HTOs separate individual mice

value: T Cells

value: C57BL/6 WT

value: 1 wk VML+PCL

value: Batch 2


title: M99183, Placenta, Chorionic Villous Tissue, Control, Male Fetus, Day 7 post-inoculation, Day 143

description: Library name: CTRL_M99183

value: placenta (chorionic villous)

value: Saline Control

value: choriodecidual space

value: male


title: Z15060, Placenta, Chorionic Villous Tissue, Control, Male Fetus, Day 1 post-inoculation, Day 128

description: Library name: CTRL_Z15060

value: Control


title: Wildtype, h3k27me3 mark, rep 2

description: Library name: WT_h3k27me3_2

value: Wildtype


title: Blood_AD_Short Read 40

value: Whole Blood

value: AD


title: 1wk PCL Hashed gdTCR

description:
Library name: VML-PCL_1wk_hashed_gdTCR
HTOs separate individual mice

value: Injured Muscle and Fibrotic PCL Implant


title: Afg3l2 GKD, h3k9me3 mark, rep 1

description: Library name: Afg3l2_h3k9me3

value: Ovary tissue

value: H3K9me3 ab (Active motif 39062)


title: M05267, Placenta, Chorionic Villous Tissue, Control, Male Fetus, Day 7 post-inoculation, Day 145

description: Library name: CTRL_M05267

value: female


title: 1wk PCL Hashed scRNAseq

description:
Library name: VML-PCL_1wk_hashed_GEX
HTOs separate individual mice


title: Blood_AD_Short Read 39


title: L07201, Placenta, Chorionic Villous Tissue, Control, Male Fetus, Day 7 post-inoculation, Day 139

description: Library name: CTRL_L07201


title: Wildtype, h3k27me3 mark, rep 1

description: Library name: WT_h3k27me3

value: Differentiated stages

value: H3K27me3 ab (abcam AB6002)


title: Wildtype, h3k9me3 mark, rep 2

description: Library name: WT_h3k9me3_2


title: 1wk PCL Pooled abTCR

description: Library name: VML-PCL_1wk_pooled_abTCR

value: T Cells

value: C57BL/6 WT

value: Batch 1


title: Mio GKD, h3k27me3 mark, rep 1

description: Library name: Mio_h3k27me3

value: Mio GKD


title: J08186, Placenta, Chorionic Villous Tissue, Control, Female Fetus, Day 1 post-inoculation, Day 136

description: Library name: CTRL_J08186

value: placenta (chorionic villous)

value: Saline Control


title: Blood_AD_Short Read 38


title: Blood_AD_Short Read 37


title: Mio GKD, h3k9me3 mark, rep 1

description: Library name: Mio_h3k9me3


title: Blood_AD_Short Read 35


title: Flesh_12wk_3x_1

description: Library name: PPP3_97

source_name: Flesh

value: Flesh

value: Russet Burbank (Solanum tuberosum L.)


title: Blood_AD_Short Read 36


title: 1wk Saline Pooled gdTCR

description: Library name: VML-Saline_1wk_pooled_gdTCR

source_name: Injured Muscle

value: Injured Muscle

value: 1 wk VML+Saline


title: Flesh_12wk_3x_2

description: Library name: PPP3_98


title: Flesh_12wk_3x_3

description: Library name: PPP3_99


title: Wildtype, h3k9me3 mark, rep 1

description: Library name: WT_h3k9me3

value: Wildtype


title: 1wk Saline Pooled abTCRseq

description: Library name: VML-Saline_1wk_pooled_abTCR


title: UAS-RFP-Rep2

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description: Library name: sample16

data_processing:
The expression of genes and transposons was analyzed and quantified using piPipes(v1.1.0) by family and SQuIRE (v 0.9.9.92) 'Map' and 'Count' function by locus.
Assembly: dm6 and Drosophila TE consensus sequence
Supplementary files format and content: csv,txt; the result files of piPipes and SQuIRE

source_name: pupa 4d hindgut

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Invitrogen, CAT#: 15596018) and precipitated by isopropanol. 10µg of total RNA was treated with DNase and then purified by RNA Clean & Concentrator-5 (Zymo research, CAT#: R1016).
One µg of purified RNA was used for RNA-Seq library preparation by utilizing TruSeq Stranded Total RNA Library Prep kit (Illumina, CAT#: 20020596).

value: pupa 4d hindgut

value: UASP-RFP


title: Flesh_12wk_2x_3

description: Library name: PPP3_96


title: 1wk Saline Pooled scRNAseq

description: Library name: VML-Saline_1wk_pooled_GEX


title: 1wk PCL Pooled scRNAseq

description: Library name: VML-PCL_1wk_pooled_GEX

value: Injured Muscle and Fibrotic PCL Implant

value: 1 wk VML+PCL


title: Blood_AD_Short Read 33

value: Whole Blood

value: AD


title: 1wk PCL Pooled gdTCR

description: Library name: VML-PCL_1wk_pooled_gdTCR

value: T Cells


title: Blood_AD_Short Read 34


title: Flesh_12wk_2x_2

description: Library name: PPP3_95


title: GDKO_Endothelial_Rep4

description: Library name: GDKO_Endothelial_Rep4

data_processing:
Fastq files were aligned using STAR aligner, using the associated counting method to quantify gene expression
Assembly: GRCm38 genome with GENCODE vM23 annotations
Supplementary files format and content: Processed data include raw counts files for each sample.

source_name: Fibrotc tissue around PCL implant and muscle

extract_protocol:
Stromal fibroblasts (LiveCD45-CD31-CD29+) and endothelial cells (LiveCD45-CD31+CD29+) were sorted from the injured murine muscle with fibrotic PCL implants using BD FACSAri Fusion Cell Sorter into sterile RLT Plus Buffer and 1x 2-Mercaptoethanol. RNA was isolated using miRNeasy Mini kit. RNA yield was determined using NanoDrop Spectrophotometer and quality assessed using Agilent Fragment Analyzer (RQN for all samples between 8.7-9.6).
cDNA synthesis and library preparation with unique dual indexes (UDI) was performed using Stranded mRNA Prep, Ligation kit (Illumina 20040532). QC was assessed with Qubit and Agilent Fragment Analyzer. Libraries were pooled and pair-end sequencing performed using the NovaSeq platform (Illumina) with a SP100 flow cell at a targeted depth of 50 million unique reads/sample.

treatment_protocol: PCL particulate was implanted into hindlimb volumetric muscle loss defects in C57BL/6 wildtype (WT) and gamma-delta T cell deficient (TCRd-/- or GDKO) mice for 6 weeks.

value: Endothelial Cell

value: TCRd-/- (GDKO)


title: GDKO_Endothelial_Rep3

description: Library name: GDKO_Endothelial_Rep3

value: Fibrotc tissue around PCL implant and muscle


title: Blood_AD_Short Read 32


title: H3.2K9I-Rep2

description:
Library name: sample14
substituting K9 for isoleucine


title: UAS-RFP-Rep1

description: Library name: sample13


title: Blood_AD_Short Read 30


title: H3.3K9I-Rep1

description:
Library name: sample12
substituting K9 for isoleucine


title: Flesh_12wk_1x_3

description: Library name: PPP3_93


title: H3.3K9I-Rep2

description:
Library name: sample15
substituting K9 for isoleucine


title: GDKO_Endothelial_Rep1

description: Library name: GDKO_Endothelial_Rep1


title: Flesh_12wk_2x_1

description: Library name: PPP3_94


title: Flesh_12wk_1x_1

description: Library name: PPP3_91


title: Blood_AD_Short Read 31


title: GDKO_Endothelial_Rep2

description: Library name: GDKO_Endothelial_Rep2


title: WT_Endothelial_Rep4

description: Library name: WT_Endothelial_Rep4

value: WT


title: H3.2K9I-Rep1

description:
Library name: sample11
substituting K9 for isoleucine


title: Blood_AD_Short Read 28


title: Flesh_12wk_Ctrl_3

description: Library name: PPP3_90

value: Control


title: WT_Endothelial_Rep3

description: Library name: WT_Endothelial_Rep3


title: shwhite_for_shhira_and_shxnp-RNAseq-Rep2

description: Library name: sample10

value: sh-white


title: Flesh_12wk_1x_2

description: Library name: PPP3_92

value: Flesh

value: Russet Burbank (Solanum tuberosum L.)


title: Blood_AD_Short Read 27


title: Blood_AD_Short Read 26


title: Flesh_12wk_Ctrl_2

description: Library name: PPP3_89


title: Blood_AD_Short Read 29


title: Flesh_12wk_Ctrl_1

description: Library name: PPP3_88


title: shxnp-RNAseq-Rep2

description: Library name: sample9

value: sh-xnp


title: WT_Endothelial_Rep1

description: Library name: WT_Endothelial_Rep1


title: WT_Endothelial_Rep2

description: Library name: WT_Endothelial_Rep2


title: shhira-RNAseq-Rep2

description: Library name: sample8

value: sh-hira


title: Flesh_9wk_2x_3

description: Library name: PPP3_87


title: shwhite_for_shhira_and_shxnp-RNAseq-Rep1

description: Library name: sample7

value: pupa 4d hindgut


title: GDKO_Fibroblast_Rep4

description: Library name: GDKO_Fibroblast_Rep4

value: Stromal Fibroblast


title: Flesh_9wk_2x_2

description: Library name: PPP3_86


title: Blood_AD_Short Read 23


title: GDKO_Fibroblast_Rep2

description: Library name: GDKO_Fibroblast_Rep2


title: Blood_AD_Short Read 22


title: shxnp-RNAseq-Rep1

description: Library name: sample6


title: GDKO_Fibroblast_Rep3

description: Library name: GDKO_Fibroblast_Rep3


title: Blood_AD_Short Read 24


title: Blood_AD_Short Read 25


title: Flesh_9wk_2x_1

description: Library name: PPP3_85


title: Flesh_9wk_1x_2

description: Library name: PPP3_83


title: shwhite_for_shcaf1-RNAseq-Rep2

description: Library name: sample4


title: WT_Fibroblast_Rep4

description: Library name: WT_Fibroblast_Rep4


title: shhira-RNAseq-Rep1

description: Library name: sample5


title: Flesh_9wk_1x_1

description: Library name: PPP3_82


title: WT_Fibroblast_Rep3

description: Library name: WT_Fibroblast_Rep3


title: Flesh_9wk_1x_3

description: Library name: PPP3_84


title: Blood_AD_Short Read 20


title: Flesh_9wk_Ctrl_3

description: Library name: PPP3_81


title: WT_Fibroblast_Rep2

description: Library name: WT_Fibroblast_Rep2


title: shcaf1-RNAseq-Rep2

description: Library name: sample3


title: GDKO_Fibroblast_Rep1

description: Library name: GDKO_Fibroblast_Rep1


title: Blood_AD_Short Read 19


title: WT_Fibroblast_Rep1

description: Library name: WT_Fibroblast_Rep1


title: Blood_AD_Short Read 17


title: shcaf1-RNAseq-Rep1

description: Library name: sample1


title: Flesh_9wk_Ctrl_1

description: Library name: PPP3_79


title: sh-white-H3-Input rep2

description: Library name: sample28

data_processing:
Adapters were trimmed via cutadapt (v 4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then using bowtie2 with default parameters aligned reads to dm6 and TE sequences.  Functions “view” and “sort” of samtools (v 1.9) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further deduplicated by picard (v2.18.7) and converted to bed files by the bedtools (v2.25.0) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig.
Assembly: dm6 and Drosophila TE consensus sequence
Supplementary files format and content: bigwig

source_name: Pupa 4d hindgut

extract_protocol:
Tissues were dissected in ice-cold PBS and fixed in 1.8% PFA. Samples were sonicated and protein-DNA complexes were immunoprecipitated. DNA was purified by using Phenol/Chloroform and precipitated by using ethanol.
Libraries for ChIP-Seq were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, CAT#: TD502/TD503). The libraries were purified by RNAClean XP beads and sent to Novogene for quality control and sequencing.

value: Pupa 4d hindgut


title: Blood_AD_Short Read 18


title: Flesh_9wk_Ctrl_2

description: Library name: PPP3_80


title: Blood_AD_Short Read 21


title: shwhite_for_shcaf1-RNAseq-Rep1

description: Library name: sample2


title: Tumor-infiltrating immune cells, creatine-treated

city: Los Angeles

first: Lili

last: Yang

state: CA

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

description: Library name: Sample 2

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger 3.0.2
Assembly: Mus musculus mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Day 14 B16-OVA tumors were harvested from experimental mice to prepare TII suspensions (4 tumors were combined for each group). TII suspensions were then sorted using a FACSAria II flow cytometer to purify immune cells (gated as DAPI−CD45.2+ cells).
Purified TIIs were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 TIIs from each experimental group were loaded on the Chromium platform (10x Genomics), and libraries were constructed using the Chromium Single Cell 3′Library & Gel Bead Kit v2 (catalog no. PN-120237, 10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: 10.5 mg intraperitoneal creatine injection

value: Tumor

value: Creatine


title: Flesh_6wk_1x_3

description: Library name: PPP3_78


title: Tumor-infiltrating immune cells, nontreated

description: Library name: Sample 1

value: PBS


title: sh-white-H3.2-ChIP rep2

description: Library name: sample27


title: Blood_AD_Short Read 16

value: Whole Blood

value: AD


title: sh-caf1-H3-Input rep2

description: Library name: sample25


title: Blood_AD_Short Read 15


title: sh-white-H3.3-ChIP rep2

description: Library name: sample26


title: C57BL/6 liver, Zfp36l1/Zfp36l2 dKO, eight weeks, mouse 3

city: New Hill

first: Yogesh

last: Saini

state: NC

address: 3644 Rail Overlook Drive

institute: NCSU

description:
Library name: dKO3
Column name in FPKM_all_samples.txt: dKO3

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using DEseq2.
Assembly: Mus musculus mm10
Supplementary files format and content: Tab-delimited text file include FPKM values for each sample and gene.

source_name: Liver

growth_protocol: Adult male mice were used to harvest liver.

extract_protocol:
RNA was isolated using Illustra RNAspin Mini RNA isolation kit (Cytiva).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were intrperitoneally challenged with corn oil.

value: Liver

tag: Sex

value: Male

tag: age

value: eight weeks

tag: strain

value: corn oil


title: C57BL/6 liver, Zfp36l1/Zfp36l2 dKO, eight weeks, mouse 4

description:
Library name: dKO4
Column name in FPKM_all_samples.txt: dKO4

tag: tissue

tag: genotype


title: Blood_AD_Short Read 14

tag: cell line


title: Flesh_6wk_1x_1

description: Library name: PPP3_76

tag: treatment


title: Flesh_6wk_1x_2

description: Library name: PPP3_77


title: sh-caf1-H3.3-ChIP rep2

description: Library name: sample23


title: sh-caf1-H3.2-ChIP rep2

description: Library name: sample24


title: Flesh_6wk_Ctrl_3

description: Library name: PPP3_75

value: Control


title: Blood_AD_Short Read 12


title: C57BL/6 liver, Zfp36l1/Zfp36l2 dKO, eight weeks, mouse 2

description:
Library name: dKO2
Column name in FPKM_all_samples.txt: dKO2


title: Blood_AD_Short Read 13


title: sh-white-H3-Input rep1

description: Library name: sample22

value: sh-white


title: C57BL/6 liver, Zfp36l1/Zfp36l2 dKO, eight weeks, mouse 1

description:
Library name: dKO1
Column name in FPKM_all_samples.txt: dKO1


title: Blood_AD_Short Read 11


title: Flesh_6wk_Ctrl_1

description: Library name: PPP3_73

value: Flesh

value: Russet Burbank (Solanum tuberosum L.)


title: Flesh_6wk_Ctrl_2

description: Library name: PPP3_74


title: C57BL/6 liver, Zfp36l1/Zfp36l2 flox control, eight weeks, mouse 4

description:
Library name: Con4
Column name in FPKM_all_samples.txt: Con4


title: Flesh_3wk_1x_3

description: Library name: PPP3_72


title: Blood_AD_Short Read 10


title: Blood_AD_Short Read 9


title: C57BL/6 liver, Zfp36l1/Zfp36l2 flox control, eight weeks, mouse 2

description:
Library name: Con2
Column name in FPKM_all_samples.txt: Con2


title: sh-white-H3.3-ChIP rep1

description: Library name: sample20


title: Flesh_3wk_1x_2

description: Library name: PPP3_71


title: Blood_AD_Short Read 8


title: Flesh_3wk_Ctrl_3

description: Library name: PPP3_69


title: C57BL/6 liver, Zfp36l1/Zfp36l2 flox control, eight weeks, mouse 1

description:
Library name: Con1
Column name in FPKM_all_samples.txt: Con1


title: HA3

city: Changzhou

first: Shuai

last: Chen

state: Jiangsu

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

description:
Library name: sample6
HA3

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: GRCm39.110
Supplementary files format and content: processed data.xlsx

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: HA


title: sh-caf1-H3.2-ChIP rep1

description: Library name: sample18


title: Flesh_3wk_1x_1

description: Library name: PPP3_70


title: sh-caf1-H3.3-ChIP rep1

description: Library name: sample17


title: C57BL/6 liver, Zfp36l1/Zfp36l2 flox control, eight weeks, mouse 3

description:
Library name: Con3
Column name in FPKM_all_samples.txt: Con3


title: sh-white-H3.2-ChIP rep1

description: Library name: sample21


title: Blood_AD_Short Read 6


title: Blood_AD_Short Read 5


title: HA2

description:
Library name: sample5
HA2


title: HA1

description:
Library name: sample4
HA1


title: Flesh_3wk_Ctrl_1

description: Library name: PPP3_67


title: sh-white-H3K9me2-Input rep2

description: Library name: sample16


title: Blood_AD_Short Read 7


title: sh-white-H3K9me2-ChIP rep2

description: Library name: sample15


title: sh-caf1-H3-Input rep1

description: Library name: sample19


title: Flesh_OD_Ctrl_3

description: Library name: PPP3_66


title: Blood_AD_Short Read 4


title: CON3

description:
Library name: sample3
CON3


title: CON2

description:
Library name: sample2
CON2


title: Flesh_OD_Ctrl_2

description: Library name: PPP3_65


title: Blood_AD_Short Read 3


title: Flesh_OD_Ctrl_1

description: Library name: PPP3_64


title: Flesh_3wk_Ctrl_2

description: Library name: PPP3_68


title: sh-caf1-H3K9me2-ChIP rep2

description: Library name: sample13


title: CON1

description:
Library name: sample1
CON1


title: Blood_AD_Short Read 1


title: sh-white-H3K9me2-Input rep1

description: Library name: sample12


title: sh-white-H3K9me2-ChIP rep1

description: Library name: sample11


title: Blood_Control_49

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
For lncRNA and mRNA: (Stringtie- 1.3.3b) was used to count the read numbers mapped to each gene. And then FPKM was calculated, which expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced. FPKM is a simple and mostly common used expression level normalization method. It normalizes for both sequencing depth and genome size.
Prior to differential expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Significantly differential expression genes were screened based on the following criteria: Corrected P-value < 0.05.
For circRNA: The circRNA were detected and identified using find_circ (Memczak et al., 2013) and CIRI2 (Gao et al., 2017). The raw counts were first normalized using TPM (Zhou et al., 2010) Normalized expression level = ( readCount* 1,000,000 ) / libsize ( libsize is the sum of circRNA readcount) . Differential expression analysis of the two groups was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ensembl_82_homo_sapiens_grch38_primary
Supplementary files format and content: ADvsControl.lncRNA.transcript_level.deg.txt ; differential expression
Supplementary files format and content: ADvsControl.mRNA.gene_level.deg.txt ; differential expression
Supplementary files format and content: circRNA_ADvsControl_deg.xlsx; differential expression

extract_protocol:
The blood was collected in PAXgene Blood RNA tubes. Total RNA was extracted following the protocol developed by this lab to isolate RNAs of different sizes and low concentration (Paz S, Mauer C, Ritchie A, Robishaw JD, Caputi M. A simplified SARS-CoV-2 detection protocol for research laboratories. PLoS One. 2020 Dec 18;15(12):e0244271). RNA sample quality and quantity were determined utilizing an Agilent TapeStation system and a NanoDrop spectrophotometer. The samples utilized for the cDNA library preparations had an RNA integrity number (RIN) ≥ 7 and an RNA concentration ≥ 30 ng/µL. Ribosomal RNA was removed by Epicentre TruSeq Stranded Total RNA Library Prep Gold/illumina/20020599
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in first strand synthesis reaction buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: disease state


title: Spheriod_WT10_colon_L2

city: Cleveland

first: Julie

last: Zhou

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic Research Institute

description:
Library name: GC_JZ_1869_12_L2
GC_JZ_1869_12

data_processing:
Raw FASTQ files for checked for quality using FastQC (v0.11.9) followed by removal of adapter sequences and low-quality reads using fastp (v0.21.0). GC_JZ_1869_8 and GC_JZ_1869_13 were combined to make one Spheroid_WT9_jejunum sample.
Reads for each sample were then aligned to the Mus musculus reference genome (GRCm39 with GRCm39.106 annotation) using STAR (v2.7.8a).
A raw counts table was then generated in R (v4.3.1) using the FeatureCounts function from the Rsubread package (v2.14.2).
Normalization of counts and differential expression analysis was performed using the DESeq2 package (v1.40.2) in R.
Pathway analysis on significant genes was done using gprofiler2 package (v0.2.3) in R.
Assembly: Mus musculus reference genome (GRCm39 with GRCm39.106 annotation)
Supplementary files format and content: raw counts, csv file
Supplementary files format and content: normalized counts, csv file

source_name: Intestine (colon)

growth_protocol: Intestinal stem and progenitor cells (ISCs) from mouse jejunum and colon were grown in Matrigel and 50% L-WRN medium. Apoptotic immortalized intestinal epithelial cells (iIECs) were supplemented on day 0.

extract_protocol:
RNA was extracted from FACS purified cells using Qiagen RNeasy Micro Kit.
SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian

treatment_protocol: On day 3 of culture, spheroids and/or adherent cells were lysed using and RNA was extracted.

value: Intestine (colon)

value: ISC

tag: cell type

value: WT


title: Wollemia pollen Bisulfite-seq

city: Cold Spring Harbor

first: W. Richard

last: McCombie

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Library name: Wn_Pollen_BS

data_processing:
Mapping and methylation calls were processed using Bismark v0.23.1
Downstream analyses were performed using deepTools
Assembly: Wnobilis v1.5
Supplementary files format and content: BED files include methylation calls in CG,CHG and CHH contexts  for each sample

organism: Wollemia nobilis

source_name: Pollen

extract_protocol:
Genomic DNA from mature pollen and ovule DNA was isolated using CTAB buffer (2% CTAB, 100 mM Tris-HCl pH 8, 20 mM EDTA, 1.4 M NaCl, 2% PVP).
For the bisulfite conversion, EZ- DNA Methylation Gold kit (Zymo Research) was used according to the manufacturer's instructions.  Converted DNA was then used for the library preparation using the NEXTFLEX Bisulfite-Seq kit (Perkin Elmer) and each library was sequenced on the NextSeq high output platform, paired-end 150-nt.

value: Pollen


title: Wollemia ovule Bisulfite-seq

description: Library name: Wn_Ovule_BS

source_name: Ovule

value: Ovule


title: sh-caf1-H3K9me2-Input rep2

description: Library name: sample14

value: Pupa 4d hindgut


title: Spheriod_WT9_colon_L2

description:
Library name: GC_JZ_1869_11_L2
GC_JZ_1869_11


title: Blood_Control_47

value: Whole Blood


title: Spheriod_WT8_colon_L2

description:
Library name: GC_JZ_1869_10_L2
GC_JZ_1869_10


title: Blood_Control_48


title: sh-caf1-H3K9me2-ChIP rep1

description: Library name: sample9


title: sh-white-H3K9me3-Input rep2

description: Library name: sample8


title: Blood_Control_46


title: sh-caf1-H3K9me2-Input rep1

description: Library name: sample10


title: Spheriod_WT10_jejunum_L2

description:
Library name: GC_JZ_1869_9_L2
GC_JZ_1869_9

source_name: Intestine (jejunum)

value: Intestine (jejunum)


title: sh-white-H3K9me3-ChIP rep2

description: Library name: sample7


title: Blood_Control_45

source_name: Whole Blood


title: Wollemia pollen sRNA replicate3

description: Library name: Wn_Pollen3

data_processing:
For the small RNA annotation, the reads were pre-processed by trimming the adaptors using Cutadapt v3.4, merging the sample files (leaf, ovule, and pollen), and filtering by length (18-26 nt). The filtered file was used as input for miRNA and siRNA annotation using ShortStack v3.8.5
The annotation file generated by ShortStack was used to count the small RNA classes for each tissue (leaf, pollen, and ovules) using the software featureCounts and subsequent analyzes were performed in R
Assembly: Wnobilis v1.6
Supplementary files format and content: tab-delimited text files include feature counts for each sample

extract_protocol:
Total RNA from leaf (4 technical replicates), mature pollen (3 technical replicates) and, ovules (3 technical replicates) was isolated using CTAB buffer (2% CTAB, 2% PVP-K30, 100 mM Tris-HCl pH 8.0, 25 mM EDTA, 2 mM NaCl, 0.5 g/L spermidine, 2% ß-mercaptoethanol).
NEXTFLEX Small RNA-seq kit v3 (Perkin Elmer) was used according to the manufacturer’s instructions to prepare the small RNA libraries.


title: Blood_Control_44


title: Spheroid_WT9_jejunum_2_L2

description:
Library name: GC_JZ_1869_13_L2
GC_JZ_1869_13


title: Wollemia pollen sRNA replicate2

description: Library name: Wn_Pollen2


title: Spheroid_WT8_jejunum_L2

description:
Library name: GC_JZ_1869_7_L2
GC_JZ_1869_7


title: sh-caf1-H3K9me3-ChIP rep2

description: Library name: sample5


title: Blood_Control_43


title: ilEC_CB3_L2

description:
Library name: GC_JZ_1869_6_L2
GC_JZ_1869_6

value: iIEC CB3

value: iIEC

value: Immortalization


title: Spheroid_WT9_jejunum_1_L2

description:
Library name: GC_JZ_1869_8_L2
GC_JZ_1869_8


title: Blood_Control_41


title: Blood_Control_42


title: ilEC_CA4_L2

description:
Library name: GC_JZ_1869_5_L2
GC_JZ_1869_5

value: iIEC CA4


title: Wollemia ovule sRNA replicate3

description: Library name: Wn_Ovule3


title: sh-caf1-H3K9me3-Input rep2

description: Library name: sample6


title: sh-white-H3K9me3-ChIP rep1

description: Library name: sample3


title: Blood_Control_40

value: Control


title: sh-white-H3K9me3-Input rep1

description: Library name: sample4

value: sh-white


title: ilEC_JC4_L2

description:
Library name: GC_JZ_1869_3_L2
GC_JZ_1869_3

value: iIEC JC4


title: ilEC_JA4_L2

description:
Library name: GC_JZ_1869_2_L2
GC_JZ_1869_2

value: iIEC ja4


title: sh-caf1-H3K9me3-ChIP rep1

description: Library name: sample1


title: Blood_Control_39


title: Wollemia pollen sRNA replicate1

description: Library name: Wn_Pollen1


title: Wollemia leaf sRNA replicate4

description: Library name: Wn_Leaf4

source_name: Leaf tissue

value: Leaf tissue


title: Zfrp8 GKD h3k9me3

description: Library name: Zfrp8_h3k9me3

data_processing:
Reads were evaluated for their quality using FastQC v0.11.8
Reads were trimmed for adaptor sequences using Trim Galore! v0.6.6
Reads were aligned to the dm6 reference genome version for drosophila melanogaster using Bowtie2 v2.2.8 with parameters -q -I 50 -X 700 --very-sensitive-local --local --no-mixed --no-unal --no-discordant
Binary alignment maps (BAM) files were generated with samtools v1.9
BigWig files were generated from BAM files using deepTools v3.2.1 bamCoverage function with parameters– normalize using RPKM–bin size 10
Assembly: dm6
Supplementary files format and content: bigWig (.bw) files with rpkm-normalized counts
Library strategy: CUT&Run

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
PBS was removed and the samples were permeabilized in 1mL of Permeabilization Solution (PBST+1% Triton-X) rotating in RT for 1 hour. Samples were then incubated overnight at 4°C in primary antibody dilutions in freshly prepared BBT+ buffer (PBST + 1% BSA + 0.5 mM Spermidine + 2 mM EDTA + 1 large Roche complete EDTA-free tablets). Primary antibody was replaced with BBT+ buffer and quickly washed twice. Samples were then incubated in ~700 ng/ml of pAG-MNase in BBT+ buffer rotating for 4 hours at 25°C. Samples were then quickly washed twice in wash+ buffer (20 mM HEPES pH7.5 + 150 mM NaCl + 0.1% BSA + 0.5 mM Spermidine + 1 large Roche complete EDTA-free tablets in water). Samples were resuspended in 150 μl Wash+C (wash+ + 100 mM CaCl2) and incubated for 45 minutes on nutator at 4°C. The cleavage reaction was terminated by addition of 150 μl StopR (NaCl final 200 mM + EDTA final 20 mM + 100μg/mL RNaseA) and incubating the sample at 37˚C for 30 minutes. Samples were then centrifuged at 16,000 x g for 5 minutes and 300 μl of the supernatant was collected for DNA discovery. To the supernatant, 2 μL 10% SDS and 2.5 μL of 20 mg /mL Proteinase K was added and incubated at 50°C for 2 hours. Half of this was kept as a backup and half was used in bead cleanup. 20 μL AmpureXP bead slurry and 280 μL MXP buffer (20% PEG8000 + 2.5 M NaCl + 10 mM MgCl2 in water) was added to the sample and mixed thoroughly followed by 15 minutes incubation at RT. The beads were separated by magnet and supernatant was discarded. The beads were carefully washed with 80% ethanol for 30 seconds, while on the magnetic stand and air dried for 2 minutes. The beads were then resuspended in 10 μL DNase free water.
The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection. The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection.

value: Ovary tissue

value: H3K9me3 ab (Active motif 39062)

tag: dissection

value: dissected 1-3 days post-eclosion

value: Adult


title: Wollemia ovule sRNA replicate2

description: Library name: Wn_Ovule2

value: Ovule


title: Blood_Control_38


title: sh-caf1-H3K9me3-Input rep1

description: Library name: sample2

value: Pupa 4d hindgut


title: Zfrp8 GKD h3k27me3

description: Library name: Zfrp8_h3k27me3

value: H3K27me3 ab (abcam AB6002)


title: ilEC_JA1_L2

description:
Library name: GC_JZ_1869_1_L2
GC_JZ_1869_1

value: Intestine (jejunum)

value: iIEC JA1

value: WT


title: Wollemia leaf sRNA replicate1

description: Library name: Wn_Leaf1


title: PASMC cells, Hypoxia+Agomelatine3

city: Nanjing

first: yuxian

last: Qian

address: baiziting no.42

institute: Nanjing medical university

description: Library name: Sample 9

data_processing:
Sequencing data were quality controlled using "fastqc" software and rRNA sequencing was removed using "SortMeRNA".
Assembly: hg19
Supplementary files format and content: Csv files with FPKM data.

source_name: PASMC

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

value: PASMC

value: Human smooth muscle cells

value: 1% oxygen+agomelatine (10μM) for 48h


title: PASMC cells, Hypoxia+Agomelatine1

description: Library name: Sample 7


title: Blood_Control_37

value: Whole Blood

value: Control


title: Spheriod_WT10_colon_L1

description:
Library name: GC_JZ_1869_12_L1
GC_JZ_1869_12

value: Intestine (colon)

value: ISC


title: ilEC_CA3_L2

description:
Library name: GC_JZ_1869_4_L2
GC_JZ_1869_4

value: iIEC CA3

value: iIEC

value: Immortalization


title: Nup44A GKD h3k9me3

description: Library name: Nup44A_h3k9me3

value: Ovary tissue

value: H3K9me3 ab (Active motif 39062)

value: dissected 1-3 days post-eclosion

value: Adult


title: PASMC cells, Hypoxia+Agomelatine2

description: Library name: Sample 8


title: Blood_Control_36


title: Spheriod_WT9_colon_L1

description:
Library name: GC_JZ_1869_11_L1
GC_JZ_1869_11


title: Wollemia leaf sRNA replicate2

description: Library name: Wn_Leaf2

value: Leaf tissue


title: Blood_AD_Short Read 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through customperl 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 lowquality readsfrom raw data. At the same time, Q20, Q30, and GC-content of the rawdatawere calculated. Then, 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 (Langmead et al., 2009) without mismatch to analyze their expression anddistribution on the reference.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: ensembl_82_homo_sapiens_grch38_primary
Supplementary files format and content: sRNA_ADvsControl.Differential_analysis_results.xlsx; differential expression

extract_protocol:
The blood was collected in PAXgene Blood RNA tubes. Total RNA was extracted following the protocol developed by this lab to isolate RNAs of different sizes and low concentration (Paz S, Mauer C, Ritchie A, Robishaw JD, Caputi M. A simplified SARS-CoV-2 detection protocol for research laboratories. PLoS One. 2020 Dec 18;15(12):e0244271). RNA sample quality and quantity were determined utilizing an Agilent TapeStation system and a NanoDrop spectrophotometer. The samples utilized for the cDNA library preparations had an RNA integrity number (RIN) ≥ 7 and an RNA concentration ≥ 30 ng/µL. Ribosomal RNA was removed by Epicentre TruSeq Stranded Total RNA Library Prep Gold/illumina/20020599
A total amount of 2 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

value: AD


title: Wollemia leaf sRNA replicate3

description: Library name: Wn_Leaf3


title: Blood_Control_35


title: Wollemia ovule sRNA replicate1

description: Library name: Wn_Ovule1

value: Ovule


title: PASMC cells, Hypoxia3

description: Library name: Sample 6

value: PASMC

value: WT

value: 1% oxygen for 48h


title: Spheriod_WT8_colon_L1

description:
Library name: GC_JZ_1869_10_L1
GC_JZ_1869_10


title: WT h3k9me3

description: Library name: WT_h3k9me3


title: Blood_Control_34

value: Whole Blood


title: Nup44A GKD h3k27me3

description: Library name: Nup44A_h3k27me3

value: H3K27me3 ab (abcam AB6002)


title: PASMC cells, Hypoxia2

description: Library name: Sample 5

value: Human smooth muscle cells


title: PASMC cells, Hypoxia1

description: Library name: Sample 4


title: Blood_Control_33

value: Control


title: Spheroid_WT9_jejunum_2_L1

description:
Library name: GC_JZ_1869_13_L1
GC_JZ_1869_13

value: Intestine (jejunum)

value: ISC


title: CTL 2

city: Jinan

first: Qinghao

last: Yuan

state: Shandong

address: wenhuaxilu 44

institute: Qilu hospital

description:
Library name: Sample5
CTL 2

data_processing:
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- mismatch 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
mm10
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: skin

growth_protocol: HaCaT cells were cultured in Dulbecco’s Modified Eagle Medium, High Glucose (DMEM-H) medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin-streptomycin. Cells were incubated in 37 ℃ with 5% CO2. All cell lines were routinely tested and confirmed to be free of mycoplasma contamination.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
CLC Genomics Workbench v 11.0.1

treatment_protocol: For interferon stimulation, cells were seeded into six-well plates and cultured in complete DMEM (supplemented with 10% FBS and 1% penicillin–streptomycin) at 37 °C in a humidified incubator with 5% CO₂ until they reached approximately 70–80% confluence. Twenty-four hours before total RNA extraction, the culture medium was aspirated and the cells were gently washed once with pre-warmed PBS. For the IFN-treated group, the medium was replaced with serum-free high-glucose DMEM (DMEM-H) containing interferon (IFN, final concentration 160ng/ml unless otherwise specified) and cells were incubated for 24 h. Control cells (CTL) were handled in parallel but received serum-free DMEM-H without IFN. At the end of the 24-h treatment period, the medium was removed, cells were rinsed once with ice-cold PBS, and total RNA was immediately isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

value: skin

value: keratinocytes

value: HaCaT cell

tag: batch

value: unknown


title: PASMC cells, Control3

description: Library name: Sample 3

value: DMSO for 48h


title: Spheroid_WT9_jejunum_1_L1

description:
Library name: GC_JZ_1869_8_L1
GC_JZ_1869_8


title: PASMC cells, Control2

description: Library name: Sample 2


title: Blood_Control_32


title: CTL 3

description:
Library name: Sample6
CTL 3


title: Spheroid_WT8_jejunum_L1

description:
Library name: GC_JZ_1869_7_L1
GC_JZ_1869_7


title: CTL 1

description:
Library name: Sample4
CTL 1


title: Blood_Control_30


title: ilEC_CB3_L1

description:
Library name: GC_JZ_1869_6_L1
GC_JZ_1869_6

value: Intestine (colon)

value: iIEC CB3

value: iIEC

value: Immortalization


title: ilEC_CA4_L1

description:
Library name: GC_JZ_1869_5_L1
GC_JZ_1869_5

value: iIEC CA4

value: WT


title: Blood_Control_28

value: Whole Blood


title: PASMC cells, Control1

description: Library name: Sample 1

value: PASMC


title: RT112 2 µM Trametinib rep3

city: Innsbruck

first: Florian

last: Handle

address: Josef-Wilberger-Str. 9a

country: Austria

institute: XPseq Analytics GmbH

description: Library name: RT112 2 uM Trametinib rep3

data_processing:
Basecalling was performed with dorado (version 1.1.0) using the high accuracy model. Raw sequencing reads were aligned to the human genome (GENCODE Release 47, GRCh38.p14) using the Minimap2 aligner (version 2.28). Read counting was performed with the Rsubread (version 2.22.1).
Assembly: GRCh38
Supplementary files format and content: counts.txt: Tab delimited file containing reads counts for all samples. First column is the ensemble gene identifier.

growth_protocol: UMUC3 cells were cultured in DMEM-low glucose medium. RT112 and 5637 cells were cultured in RPMI 1640 medium. All media were supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, and 1% GlutaMAX. Routine mycoplasma testing was performed for all cell cultures and STR profiling was performed to verify the authenticity of the cell lines.

extract_protocol:
Total RNA was isolated using the FavorPrep Tissue Total RNA purification Mini Kit (FavorGen BioTech Corp.) following the manufacturer’s protocol.
Gene expression analysis was performed using the ExpressoSeq rapid 3' RNA-Seq service (XPseq Analytics GmbH).

treatment_protocol: Cells were seeded in 96 well plates, left to attach for 24 hours before treatment with the EGFR inhibitors neratinib (600 nM) and afatinib (4 µM), the MAPK inhibitor trametinib (2 µM), the FGFR inhibitor erdafitinib (7 µM) or DMSO vehicle for 3 days.


title: RT112 7 µM Erdafitinib rep3

description: Library name: RT112 7 uM Erdafitinib rep3


title: IFNl 3

description:
Library name: Sample3
IFN-treated cell 3

value: IFN-beta


title: WT h3k27me3

description: Library name: WT_h3k27me3

value: Ovary tissue

value: H3K27me3 ab (abcam AB6002)

value: dissected 1-3 days post-eclosion

value: Adult


title: ilEC_CA3_L1

description:
Library name: GC_JZ_1869_4_L1
GC_JZ_1869_4

value: iIEC CA3


title: IFN 2

description:
Library name: Sample2
IFN-treated cell 2

value: skin

value: keratinocytes

value: HaCaT cell


title: Spheriod_WT10_jejunum_L1

description:
Library name: GC_JZ_1869_9_L1
GC_JZ_1869_9

value: Intestine (jejunum)

value: ISC

value: Control


title: IFN 1

description:
Library name: Sample1
IFN-treated cell 1

value: unknown


title: Blood_Control_31


title: Blood_Control_26


title: Blood_Control_27


title: MEF cells, siNFAT5 hyperosmolar 4

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

description: Library name: C94

data_processing:
CLC Genomics Workbench v 21.0.4 with default settings
Reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum read length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2).
They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs.
Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton's UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen).
Trimmed reads were then mapped to the Mouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 gene annotation.
Assembly: GRCm38 v. 80
Supplementary files format and content: xlsx files containing counts, TPM and RPKM values

source_name: MEF

growth_protocol: MEF cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
QIAzol Lysis Reagent according to the manufacturer's protocol
QIAseq UPX 3’ Transcriptome Kit (QIAGEN) according to the manufacturers instruction

treatment_protocol: Gene knockdown was achieved by transfecting cells with target-specific small interfering RNAs (siRNAs). SMARTpool siRNAs (comprising four distinct siRNAs per target gene; ON-TARGETplus Mouse Nfat5 siRNA: #L-058868-01-0020; ON-TARGETplus Non-targeting Pool: #D-001810-10-20) were used at a final concentration of 25 nM. Transfections were performed using DharmaFECT 1 reagent according to the manufacturer’s protocol.

value: MEF

value: embryonic fibroblast

value: NFAT5 knockdown

value: hyperosmosis


title: Blood_Control_29

value: Whole Blood


title: ilEC_JC4_L1

description:
Library name: GC_JZ_1869_3_L1
GC_JZ_1869_3

value: iIEC JC4

value: iIEC

value: WT

value: Immortalization


title: RT112 4 µM Afatinib rep3

description: Library name: RT112 4 uM Afatinib rep3


title: RT112 Control rep3

description: Library name: RT112 Control rep3


title: Blood_Control_25


title: ilEC_JA1_L1

description:
Library name: GC_JZ_1869_1_L1
GC_JZ_1869_1

value: iIEC JA1


title: MEF cells, siNFAT5 hyperosmolar 3

description: Library name: C82


title: RT112 0.6 µM Neratinib rep3

description: Library name: RT112 0,6 uM Neratinib rep3


title: Blood_Control_23


title: ilEC_JA4_L1

description:
Library name: GC_JZ_1869_2_L1
GC_JZ_1869_2

value: iIEC ja4


title: 5637 2 µM Trametinib rep3

description: Library name: 5637 2 uM Trametinib rep3


title: 5637 7 µM Erdafitinib rep3

description: Library name: 5637 7 uM Erdafitinib rep3


title: Blood_Control_24


title: MEF cells, mock hyperosmolar 1

description: Library name: C81


title: 5637 4 µM Afatinib rep3

description: Library name: 5637 4 uM Afatinib rep3


title: MEF cells, mock hyperosmolar 2

description: Library name: C93


title: rmCIRBP-treated Replicate 3

city: hamamatsu

first: Yasutaka

last: Mochizuka

address: handayama

country: Japan

institute: Hamamatsu University School of Medicine

description:
Library name: CIRBP_TRT_3
Primary lung fibroblasts treated with rmCIRBP

data_processing:
Gene expression quantified with featureCounts.
Differential expression analyzed using DESeq2.
All analyses performed in R v4.1.2.
Samples processed in a single batch to avoid technical bias.
Assembly: GRCm38/mm10
Supplementary files format and content: txt file containing normalized counts per gene.

source_name: lung fibroblasts

growth_protocol: Cells were cultured in DMEM with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) per manufacturer's instructions.
Libraries were constructed using a standard Illumina TruSeq mRNA protocol with polyA selection.

treatment_protocol: Cells were serum-starved (0.1% FBS) for 24 h, then treated with rmCIRBP (1 µg/mL) or PBS for 24 h.

value: lung fibroblasts

value: rmCIRBP (1 μg/mL, 24 h)


title: Blood_Control_22


title: ampWC-24H FGF2

city: College Station

first: ling

last: yu

state: TEXAS

address: VMR Bldg 1197  Room 327  Mail Stop 4466

department: VTPP

institute: Texas A&M university

description: Library name: Sample-FGF2

data_processing:
Mapping of reads to transcripts and cells
Assembly: mm10
Supplementary files format and content: QC files include common quality control measures for scRNA-Seq including UMI count per cell and percentage of mitochondrial transcripts. Barcodes, Genes and Matrix files are the output of the 10X pipeline.

source_name: P2 amputation digit

growth_protocol: Passage 1 primary cultures of cells isolated from neonatal non-regenerative digit amputation wounds. Cells were cultured on fibronectin coated dishes in DMEM supplemented with 2mM glutamine, 0.05 mg/ml gentamycin 10 ng/ml EGF, 10 ng/ml PDGF, 0.5 ng/ml LIF and 2% fetal bovine serum in 10 cm culture dishes. Cells were incubated at 37°C under 5% carbon dioxide.

extract_protocol:
Preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10X Genomics.1 mL of cell suspension was pelleted in Eppendorf tubes by centrifugation (400g, 5min). The supernatant was discarded, and the cell pellet was then resuspended in 1X PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150g, 3min). After the second wash, cells were resuspended in ~500 uL 1X PBS with 0.04% BSA followed by gently pipetting mix 10-15 times.
Libraries were prepared using the Chromium Controller (10X Genomics, CA) in conjunction with the single-cell 3’ v3 kit. Briefly, the cell suspension was diluted in nuclease-free water according to manufacturer instructions to achieve a targeted cell count of 10,000. The cDNA synthesis, barcoding and library preparation were then carried out according to the manufacturer's instructions. the library was sequenced in the Molecular Genomic Workspace of the Texas A&M Institute for Genome Sciences on a Novaseq 6000 sequencer (Illumina, San Diego).

treatment_protocol: Treatment  with FGF2(100ng/ml) at 80% cell confluency for 24 hour and collected.

value: P2 amputation digit

value: Fibroblast cell

value: Primary wound cells

value: CD1 mouse

value: Passage 1, 80% confluent wound cells treated with FGF2(100ng/ml) 24H


title: MEF cells, siNFAT5 hyperosmolar 2

description: Library name: C70

value: MEF

value: embryonic fibroblast


title: MEF cells, siNFAT5 hyperosmolar 1

description: Library name: C58

value: NFAT5 knockdown

value: hyperosmosis


title: Blood_Control_21

city: Boca Raton

first: Massimo

last: Caputi

address: 777 Glades Road

institute: Florida Atlantic University

value: Whole Blood

value: Control


title: MEF cells, mock hyperosmolar 6

description: Library name: C46

value: WT


title: rmCIRBP-treated Replicate 1

description:
Library name: CIRBP_TRT_1
Primary lung fibroblasts treated with rmCIRBP


title: MEF cells, mock hyperosmolar 5

description: Library name: C34


title: UMUC3 7 µM Erdafitinib rep3

description: Library name: UMUC3 7 uM Erdafitinib rep3


title: Blood_Control_20


title: Control Replicate 3

description:
Library name: CIRBP_CTRL_3
Primary lung fibroblasts treated with PBS

value: PBS


title: Control Replicate 1

description:
Library name: CIRBP_CTRL_1
Primary lung fibroblasts treated with PBS


title: UMUC3 2 µM Trametinib rep3

description: Library name: UMUC3 2 uM Trametinib rep3


title: Blood_Control_18


title: MEF cells, mock hyperosmolar 4

description: Library name: C22


title: Control Replicate 2

description:
Library name: CIRBP_CTRL_2
Primary lung fibroblasts treated with PBS


title: 5637 0.6 µM Neratinib rep3

description: Library name: 5637 0,6 uM Neratinib rep3


title: JAK_LSK_E

city: Bethesda

first: Shouguo

last: Gao

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: Library name: JAK_LSK_E

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the mm10 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of BMMNCs and LSK cells were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
Assembly: mm10
Supplementary files format and content: matrix file

source_name: mouse bone marrow

extract_protocol:
BM cells were incubated with ACK lysis buffer to lyse RBCs to get BMMNCs. Lin-Sca-1+c-kit+ cells (LSK) were flow-sorted from BM cells to get HSPCs.
Libraries of gene expression of BMMNCs and HSPCs sequencing for mice were generated using Chromium Single Cell 5' Solution Kit from 10XGenomics v2.

treatment_protocol: bone marrow failure mice treated with or without JAK inhibitors: baricitinib, solcitinib, fedratinib, and tofacitinib

value: mouse bone marrow

value: LSK


title: MEF cells, siNFAT5 hyperosmolar 5

description: Library name: C11


title: UMUC3 4 µM Afatinib rep3

description: Library name: UMUC3 4 uM Afatinib rep3


title: rmCIRBP-treated Replicate 2

description:
Library name: CIRBP_TRT_2
Primary lung fibroblasts treated with rmCIRBP

value: lung fibroblasts


title: MEF cells, siNFAT5 hyperosmolar 6

description: Library name: C23


title: Blood_Control_16


title: 5637 Control rep3

description: Library name: 5637 Control rep3


title: UMUC3 0.6 µM Neratinib rep3

description: Library name: UMUC3 0,6 uM Neratinib rep3


title: JAK_LSK_D

description: Library name: JAK_LSK_D


title: UMUC3 Control rep3

description: Library name: UMUC3 Control rep3


title: Blood_Control_15


title: Blood_Control_14


title: Blood_Control_19


title: JAK_LSK_A

description: Library name: JAK_LSK_A


title: BKS_control_JUNB

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

description: Library name: BKS_control_JUNB

data_processing:
ChIP-seq: Single-end reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome using the bwa2 mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2.
ATAC-seq: The adapters were removed and the filtered reads were mapped to GRCm38/mm10 (or GRCh37/hg19) using bwa mem. The duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/) and the reads with quality lower than 20 were filtered.
RNA-seq: The reads were mapped toGRCm38/mm10 (or GRCh37/hg19) using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2.
HiChIP: HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o mm10 (or hg19)_restriction sites.bed hg19.fasta. The raw reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Assembly: GRCm38/mm10 (or GRCh37/hg19)

source_name: aorta

growth_protocol: Mouse aortic endothelial cells (isolated from mouse aorta) and human umbilical vein cells (Cell biology) were cultured in endothelial cell growth medium in T12.5 flasks coated with gelatin (0.1%). Incubate the cells at 37 °C, 5% CO2 until they are 85% - 90% confluent. After 2-3 passages, endothelial cells were treated with Trypsin-EDTA (0.25% Trypsin, 0.02 EDTA in PBS) and collected. The cells were washed with sterile 37 °C PBS before subsequent experiments.

extract_protocol:
ChIP-seq: Chromatin (8 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were precipitated using 4 μg of antibody against H3K27Ac (Active Motif, Cat# 39133) or 10 μg of antibody again JUNB (Activemotif, Cat#39549). The complexes were washed, eluted from the beads with 1% SDS buffer and subjected to RNase and proteinase K treatment overnight at 65°C. The ChIPed DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K in a similar way as ChIPed DNA.
ATAC-seq: Cells grown in tissue culture were pretreated with 200 U/ml DNase (Worthington) for 30 min at 37 °C to remove free-floating DNA and to digest DNA from dead cells. This medium was then washed out, and the cells were resuspended in cold PBS. After the cells were counted, 50,000 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 g for 5 min at 4 °C. Supernatant was carefully aspirated. Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g at 4 °C. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2), 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down at least five times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator-5 kit.
RNA-seq: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
H3K27ac HiChIP: Biotin-labeled proximally-ligated chromatin was prepared using the Arima-HiC kit (Arima Genomics Cat # A510008). Briefly, the crosslinked chromatin was initially digested using a restriction enzyme (RE) cocktail. The 5’-overhangs were subsequently filled in and labeled with a biotinylated nucleotide. Subsequently, the spatially proximal digested ends of DNA were ligated. The resulting proximally-ligated chromatin was fragmented using the Diagenode Bioruptor Pico instrument, bound to an H3K27ac antibody (Abcam Cat # ab4729) overnight and immunoprecipitated on Protein A magnetic beads (Thermo Cat # 10002D). The immunoprecipitated chromatin was reverse crosslinked and purified using the Arima-HiC kit. Subsequently, the Illumina-compatible sequencing libraries were prepared by initial enrichment for biotin using C1 streptavidin beads (Thermo Cat # 65001). The samples were tagmented on-bead utilizing Tagment DNA Enzyme and Buffer (Illumina Cat # 20034197). Subsequently, DNA was ready for PCR enrichment.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated. system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads. Adapter sequences were not trimmed during demultiplexing. ATAC-seq: Libraries were prepared as the description (Buenrostro et al., 2015). RNA-seq: After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA form the total RNA with kit. By using the fragmentation buffer, the mRNA and non-coding RNAs are fragmented into short fragments (about 200~700 bp), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand cDNA. The double strand cDNA is purified with QiaQuick PCR extraction kit and then used for end-polishing. Sequencing adapters are ligated to the fragments , then the second strand is degraded using UNG(Uracil-N-Glyosylase)finally. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.The library products are ready for sequencing analysis via Illunima HiSeq 4000 or Hiseq X Ten. HiChIP: Tagmented DNA was PCR amplified utilizing NPM and the indexing primers from the Nextera XT DNA Library Prep kit (Illumina Cat # FC-131-1024). The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.7X SPRI beads before sequencing.

value: aorta

value: Endothelial cell of aorta


title: JAK_LSK_C

description: Library name: JAK_LSK_C


title: RT112 2 µM Trametinib rep2

description: Library name: RT112 2 uM Trametinib rep2


title: RT112 0.6 µM Neratinib rep2

description: Library name: RT112 0,6 uM Neratinib rep2


title: RT112 7 µM Erdafitinib rep2

description: Library name: RT112 7 uM Erdafitinib rep2


title: BKS_db_JUNB

description: Library name: BKS_db_JUNB


title: STZ_db_H3K27ac_rep2

description: Library name: STZ_db_H3K27ac_rep2

value: Streptozotocin injection


title: Blood_Control_17


title: JAK_BM_9

description: Library name: JAK_BM_9

value: BMMNCs


title: MEF cells, mock hyperosmolar 3

description: Library name: C10


title: Blood_Control_13


title: STZ_control_H3K27ac_rep2

description: Library name: STZ_control_H3K27ac_rep2

value: NaCl injection


title: STZ_control_H3K27ac_rep1

description: Library name: STZ_control_H3K27ac_rep1


title: JAK_LSK_B

description: Library name: JAK_LSK_B


title: RT112 4 µM Afatinib rep2

description: Library name: RT112 4 uM Afatinib rep2


title: Blood_Control_12


title: Blood_Control_10


title: JAK_BM_7

description: Library name: JAK_BM_7


title: RT112 Control rep2

description: Library name: RT112 Control rep2


title: Blood_Control_11


title: STZ_db_H3K27ac_rep1

description: Library name: STZ_db_H3K27ac_rep1


title: Blood_Control_8


title: Blood_Control_9


title: 5637 7 µM Erdafitinib rep2

description: Library name: 5637 7 uM Erdafitinib rep2


title: JAK_BM_5

description: Library name: JAK_BM_5


title: JAK_BM_6

description: Library name: JAK_BM_6


title: 5637 2 µM Trametinib rep2

description: Library name: 5637 2 uM Trametinib rep2


title: JAK_BM_8

description: Library name: JAK_BM_8


title: JAK_BM_4

description: Library name: JAK_BM_4


title: C57BL6_control_H3K27ac_rep2

description: Library name: C57BL6_control_H3K27ac_rep2

value: Normal diet


title: Blood_Control_7


title: C57BL6_db_H3K27ac_rep2

description: Library name: C57BL6_db_H3K27ac_rep2

value: High fat diet


title: JAK_BM_2

description: Library name: JAK_BM_2

value: BMF


title: C57BL6_control_H3K27ac_rep1

description: Library name: C57BL6_control_H3K27ac_rep1


title: C57BL6_db_H3K27ac_rep1

description: Library name: C57BL6_db_H3K27ac_rep1


title: Blood_Control_5


title: BKS_control_H3K27ac_rep1

description: Library name: BKS_control_H3K27ac_rep1


title: 5637 0.6 µM Neratinib rep2

description: Library name: 5637 0,6 uM Neratinib rep2


title: JAK_BM_1

description: Library name: JAK_BM_1


title: Blood_Control_3


title: JAK_BM_3

description: Library name: JAK_BM_3


title: 5637 Control rep2

description: Library name: 5637 Control rep2


title: Blood_Control_2


title: BKS_control_H3K27ac_rep2

description: Library name: BKS_control_H3K27ac_rep2


title: JAK_BM_10

description: Library name: JAK_BM_10


title: UMUC3 7 µM Erdafitinib rep2

description: Library name: UMUC3 7 uM Erdafitinib rep2


title: 5637 4 µM Afatinib rep2

description: Library name: 5637 4 uM Afatinib rep2


title: UMUC3 0.6 µM Neratinib rep2

description: Library name: UMUC3 0,6 uM Neratinib rep2


title: UMUC3 2 µM Trametinib rep2

description: Library name: UMUC3 2 uM Trametinib rep2


title: Blood_Control_4


title: BKS_db_H3K27ac_rep1

description: Library name: BKS_db_H3K27ac_rep1


title: UMUC3 4 µM Afatinib rep2

description: Library name: UMUC3 4 uM Afatinib rep2


title: Blood_Control_1


title: Blood_AD_49

value: AD


title: XF-8_S8

description: Library name: XF-8_S8

data_processing:
The raw data was processed through in-house perl scripts.
Paired-end reads were mapped to the mm10 genome with Hisat2 v2.0.5
Assembly: mm10

extract_protocol:
CD8+ T cells were flow-sorted from BM cells.
Libraries of gene expression of BM CD8+ T cell sequencing for mice were generated using the SMART-Seq mRNA LP kit (Takara Bio, San Jose, CA) .

treatment_protocol: Bone marrow  CD8+ T cells in bone marrow failure (BMF) mice treated with or without baricitinib (BAR) at day 10 and day 14 post BMF induction.

value: CD8+ T cells


title: Blood_Control_6

value: Whole Blood


title: XF-7_S7

description: Library name: XF-7_S7


title: UMUC3 Control rep2

description: Library name: UMUC3 Control rep2


title: Blood_AD_48


title: XF-9_S9

description: Library name: XF-9_S9