title: S0h3

first: xi

last: zhen

data_processing:
1. Quality control and De novo assembly
2. Functional annotation
3. Unigene quantification, analysis of differentially expressed unigenes (DEGs), cluster analysis, GO and KEGG enrichment
Assembly: No reference genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Leaf tissue

extract_protocol:
A. Add 600 uL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 uL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 uL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.E. Apply 350 uL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube. F. The 10 uL DNase I and 70 uL Buffer RDD QIAGEN (#79254) were mixed. Then  the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15  min. G. Apply 350 uL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube. H. Apply 500 uL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw  it through the Filter Cartridge as in the previous step. Repeat with a second 500 uL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer  the Filter Cartridge into a fresh Collection Tube. Apply 100 uL of pre-heated (95°C)  Elution Solution to the center of the filter. Leave it at the room temperature for 2 min.  Spin for ~20-30 sec at maximum speed to recover the RNA. Collect the eluate (which  contains the RNA) and store it at -70°C.
1. Purify and Fragment mRNA;2.Synthesize First Strand cDNA;3. Synthesize Second Strand cDNA;4. Adenylate 3’Ends;5. Ligate Adapters;6. Enrich DNA Fragments;7.Purification;8.Validate library

value: Leaf tissue

value: wild P. apocinae

value: nutrient solution (containing 300 mmol/L NaCl)

tag: time point


title: secreted round 2 rep A

status: Public on Apr 09 2024

type: SRA

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files
for genomic target loci, sequences were aligned to the human genome using STAR v2.5.3a 42 with the following flags: scoreDelBase 0, scoreDelOpen 0, scoreInsOpen 0, scoreInsBase 0, alignIntronMin 300, alignIntronMax 299. The indel rate was calculated as the fraction of reads containing insertions or deletions based on the CIGAR sequence.
Assembly: hg19
Supplementary files format and content: sgRNA_counts.csv is a coma separated file where each line contains an sgRNA name, the gene it targets and the read counts in each of the samples in the paper
Supplementary files format and content: indel_counts.tsv is a tab separated file listing the number of reads containing indels (Indel.reads) and the number of reads without mutations (WT.reads), in each sample. Samples are defined by targeted gene and by time point (tp)
Library strategy: amplicon sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: HFF

extract_protocol:
DNA from cells and virus pellets was extracted using a published protocol (Chen et al. 2015, Cell). The viral and cell pellets resuspended in 300 µl and 6 ml of NK buffer, respectively, and DNA extraction was continued normally with volumes adjusted to the 300 µl start, and GlycoBlue™ (Thermo-Fisher, catalog number AM9516) was added at the stage of DNA precipitation.
the region of interest (sgRNA casette or targeted genomic locus) was PCR amplified with addition of illumina adaptors, followed by SPRI bead size selection and purification of the product.

tag: experiment type

value: VECOS library screen

tag: time

value: 10 dpi

tag: cell line

value: HFF

tag: selection round

tag: replicate

value: A

tag: targeted gene


title: Ocab(fl/fl)

city: Salt Lake City

first: Erik

middle: Peter

last: Hughes

state: Utah

address: 2000 Cir of Hope Dr.

department: Pathology

country: USA

institute: University of Utah

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: CNS

extract_protocol:
At relapse timepoint, brain and spinal cord cells were FACS sorted for CD3e+ cells.
The Chromium Next GEM Single Cell 5’ Reagent kits v2 (PN-1000265) was used to barcode individual cells with oligonucleotides containing an Illumina R1 sequence, a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and  a 13 nt template switch oligo (TSO) according to the manufacture.  The following protocol based on 10x Genomics user guide (CG000331) was performed by High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah.  Filtered CD3e+ cells  with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip K (PN-1000287) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets.  Within individual GEMs, barcoded cDNA generated from captured poly-adenylated mRNA was synthesized by reverse transcription (RT) with a master mix containing reverse transcription reagents and poly d(T) RT primer at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 4150 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842).  Multiple libraries were then normalized, pooled and sequenced on NovaSeq 6000 with 150x150 paired-end mode

treatment_protocol: NOD Ocab(fl/fl) and Ocab(fl/fl);CD4-Cre mice were induced with EAE

tag: tissue

value: CNS

value: NOD Primary

tag: cell type

tag: genotype

value: Ocab(fl/fl)

tag: treatment

value: EAE Relapse


title: WT 7d IMQ male biol rep 2 [ADT]

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

description: 10X Genomics

library_source: other

data_processing:
Raw data was filtered, aligned, and aggregated using Cellranger v.6.0.0 and feature-barcode matrix analysis was performed in Rstudio with the Seurat v4 R package. A total of 135,825 cells were filtered based on mitochondrial content and feature count. Cells with >20% mitochondrial DNA were filtered from analysis, leaving a total of 135567 cells. Normalization, scaling, and dimensionality reduction were performed using default parameters, with resolution at 0.8 and 30 dimensions for the reduction. For CITE-seq, RNA and protein data were integrated using weighted nearest neighbor analysis (65). The CellSelector function was used to separate single-positive CD4 and CD8 populations based on surface protein expression, and the CD4 and CD8 populations were renormalized using the same procedure. Non-T cell contaminants were removed from analysis. Clusters were manually annotated based on CD44 and CD62L surface protein expression and by expression of canonical genes found in literature. Differential gene expression was calculated using the ‘FindMarkers’ function and the default Wilcoxon rank-sum test. Seurat, EnhancedVolcano, ggplot2, and dittoseq R packages were used for data visualization. T cell clonotypes were assigned and clonotype dynamics were analyzed using the ScRepertoire R package (66). Clonotypes were assigned using the ‘cloneCall=strict’ function, which integrates the VDJC genes of the TCR and the nucleotide sequence of the CDR3 region to define clonotype.
Assembly: mm10
Supplementary files format and content: R object (RDS file ). Contains filtered data and dimension reduction (umap)
Supplementary files format and content: aggregated and  filtered h5  cell matrix

molecule: protein

source_name: cervical lymph node

extract_protocol: 5’ GEX v2 libraries were generated and dual indexed with VDJ and surface immune receptor sequencing following the manufacturer’s instructions, loading 30,000 cells per well (10X Genomics). Libraries were sequenced and processed by the Genome Technology Access Center at the McDonnell Genome Institute at Washington University School of Medicine following the manufacturer’s instructions (10X Genomics)

treatment_protocol: 5% imiquimod (IMQ) cream (Taro) was applied to the dorsal and ventral sides of both ears for 7 consecutive days. Mice received approximately 5 mg IMQ daily. Bulk T cells were isolated from the cervical lymph nodes of 2 untreated and 2 IMQ-treated WT and STAT3 GOF littermates (1 male and 1 female per group; 8 separate groups/mice) using the EasySep Mouse T cell Isolation Kit (StemCell) following the manufacturer’s instructions. 1 x106 purified T cells were labeled with anti-mouse CD3e (C0182), TCRβ (C0120), CD4 (C0001), CD8a (C0002), CD44 (C0073), and CD62L (C0112) Totalseq-C antibodies (Biolegend) for CITE-seq

value: cervical lymph node

value: CD3+ T cells

value: WT

value: 7 day imiquimod

tag: library type

value: ADT

tag: antibodies/tags

value: CD3e (TotalSeq-C0182), TCRβ (TotalSeq-C0120), CD4 (TotalSeq-C0001), CD8a (TotalSeq-C0002), CD44 (TotalSeq-C0073), and CD62L (TotalSeq-C0112)


title: secreted round 2 rep B

value: B


title: secreted round 2 rep C

value: C


title: WT NT male biol rep 2 [ADT]

description: 10X Genomics

value: no treatment


title: scRNA-seq gene expression, DCs, lane2

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description:
HTO_features_DCs.csv
DCs_lane2_matrix.mtx.gz
DCs_lane2_features.tsv.gz
DCs_lane2_barcodes.tsv.gz
DC_SeuratObj.rds

library_source: transcriptomic

data_processing:
Data were filtered and mapped to mm10 reference genome by using Cellranger 6.1.1 (10X Genomics). Data were normalized in Seurat.
Assembly: mm10
Supplementary files format and content: csv files for HTO libraries to run cellranger count
Supplementary files format and content: csv files for features and barcodes - output of cellranger count
Supplementary files format and content: mtx files for count matrix - output of cellranger count
Supplementary files format and content: rds files for Seurat objects

source_name: skin

extract_protocol:
Skin lymphocytes (CD45+ Thy1.2+, exclude γδTCRhi population) or skin dendritic cells (CD45+ Lin- Ly6G- Siglec-F- CD11c+ MHC-II+) from 8-9-week-old female and male mice were sorted from samples labeled with TotalSeqC hashtags antibodies (BioLegend) on a Sony MA900 cell sorter.
10X Genomics 5' kit
All DC and all T cell samples were pooled together in two separate vials, and 45,000 cells were loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate cells into droplets. Libraries were prepared using a Chromium Single Cell 5’ Reagent Kit (10X Genomics) following manufacturer's instructions and the HTO library was prepared according to a previous publication (M. Stoeckius et al, 2019). Libraries were then sequenced on an Illumina Nextseq500 (Next Seq 500/550 High Output Kit v2, Illumina).

value: skin

value: dendritic cells

value: WT male and female

value: Control and S. epidermidis


title: RNAseq_keratinocytes_female_Sepi_rep4

data_processing:
Sequencing reads were mapped to the C57BL/6 mouse genome (GRCm38: mm10) and differential gene expression was calculated by DESeq2
Assembly: mm10
Supplementary files format and content: txt

extract_protocol:
RNA was extracted with the Qiagen microRNA kit following manufactuer's instruction
Sequencing library was prepared using the Ovation SoLo RNA-Seq library preparataion kit (Tecan) following manufacture’s instructions.

value: keratinocytes

value: WT female

value: S. epidermidis


title: STAT3 GOF 7d IMQ female biol rep 1 [ADT]

description: 10X Genomics

value: STAT3 GOF


title: RNAseq_keratinocytes_female_Sepi_rep3


title: STAT3 GOF 7d IMQ male biol rep 2 [ADT]

description: 10X Genomics

value: cervical lymph node


title: WT 7d IMQ female biol rep 1 [ADT]

description: 10X Genomics

value: CD3+ T cells


title: RNAseq_keratinocytes_female_Sepi_rep2


title: STAT3 GOF NT female biol rep 1 [ADT]

description: 10X Genomics


title: RNAseq_keratinocytes_female_Sepi_rep1


title: RNAseq_keratinocytes_male_Ctrl_rep1

value: WT male

value: Control


title: STAT3 GOF NT male biol rep 2 [ADT]

description: 10X Genomics

value: ADT


title: cells round 2 rep C

value: VECOS library screen

value: 10 dpi

value: HFF


title: RNAseq_keratinocytes_female_Ctrl_rep3


title: RNAseq_keratinocytes_female_Sepi_rep5


title: STAT3 GOF 7d IMQ male biol rep 2 [TCR]

description: 10X Genomics

value: 7 day imiquimod

value: TCR

value: CD3e (TotalSeq-C0182), TCRβ (TotalSeq-C0120), CD4 (TotalSeq-C0001), CD8a (TotalSeq-C0002), CD44 (TotalSeq-C0073), and CD62L (TotalSeq-C0112)


title: cells round 2 rep B

value: B


title: secreted round 1 rep A

value: A


title: cells round 2 rep A


title: RNAseq_keratinocytes_female_Ctrl_rep1

value: skin

value: keratinocytes


title: WT NT male biol rep 2 [TCR]

description: 10X Genomics

value: WT

value: no treatment


title: progeny round 1 rep B


title: sustained CeA male MR1 68_CeA

city: Mainz

first: Anna

last: Wierczeiko

address: Hanns-Dieter-Hüsch-Weg 15

department: Institute for Human Genetics

country: Germany

institute: University Medical Center, Johannes Gutenberg University Mainz

description: sustained CeA male MR1

data_processing:
Sequence reads were trimmed for adapter sequence and low-quality sequence using BBDuk.
Trimmed sequence reads were mapped to GrCM38/mm10 using the STAR aligner with default parameters.
Read count extraction were performed using FeatureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw gene counts per sample

source_name: CeA

extract_protocol:
Mouse brains were snap-frozen on dry ice and stored at -80°C. Regions of interest (ACC, BNST, BLA, and CeA) were isolated by a brain punching technique from the whole-mount brain in the cryostat Leica CM3050 S (Leica Biosystems, Nussloch, Germany) at -20°C using biopsy pens EMS Rapid-Core (Electron Microscopy Sciences, Hatfield, USA). To localize the subregions of interest in the brain, punching was carried out by referencing toluidine blue staining of brain slices (Franklin & Paxinos, 2007).  ACC was sampled approximately from 1.34 to 0.5mm (from bregma) using a 1mm pen. BNST (0.5: -0.22)mm, BLA (-0.94: -2.06)mm, and CeA (-0.94: -1.82)mm were sampled bilaterally using a 0.5mm pen. Biopsies were stored at -80°C for further RNA extraction. RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
All steps were carried out on ice. Tissue biopsies were moved to precooled Precellys tubes containing ice-cold ceramic beads for homogenization via Precellys 24 (Peqlab, Erlangen, Germany) (600 g, 20 s). Extraction was performed using RNeasy® mini kit (Qiagen, Hilden, Germany) according to the protocol provided by the manufacturer.

tag: strain

value: CeA

tag: Sex

value: male

tag: phenotype

value: sustained


title: sustained CeA male MR1 81_CeA

description: sustained CeA male MR1


title: progeny round 1 rep C

value: C


title: WT NT female biol rep 1 [ADT]

description: 10X Genomics

value: cervical lymph node

value: CD3+ T cells

value: ADT


title: progeny round 1 rep A

value: VECOS library screen

value: 10 dpi

value: HFF


title: sustained CeA male MR1 84_CeA

description: sustained CeA male MR1


title: STAT3 GOF NT female biol rep 1 [TCR]

description: 10X Genomics

value: STAT3 GOF

value: TCR

value: CD3e (TotalSeq-C0182), TCRβ (TotalSeq-C0120), CD4 (TotalSeq-C0001), CD8a (TotalSeq-C0002), CD44 (TotalSeq-C0073), and CD62L (TotalSeq-C0112)


title: Input 3

value: input


title: secreted round 1 rep C


title: WT NT female biol rep 1 [TCR]

description: 10X Genomics


title: WT 7d IMQ male biol rep 2 [TCR]

description: 10X Genomics

value: 7 day imiquimod


title: secreted round 1 rep B

value: B


title: STAT3 GOF NT male biol rep 2 [TCR]

description: 10X Genomics

value: no treatment


title: STAT3 GOF 7d IMQ female biol rep 1 [TCR]

description: 10X Genomics


title: cells round 1 rep C


title: sustained CeA male MR1 79_CeA

description: sustained CeA male MR1

value: CeA


title: STAT3 GOF 7d IMQ male biol rep 2 [mRNA]

description: 10X Genomics

molecule: polyA RNA

value: mRNA


title: Input 1


title: WT 7d IMQ female biol rep 1 [TCR]

description: 10X Genomics

value: WT


title: phasic CeA male MR1 80_CeA

description: phasic CeA male MR1

value: male

value: phasic


title: STAT3 GOF NT male biol rep 2 [mRNA]

description: 10X Genomics

value: cervical lymph node

value: CD3+ T cells


title: WT NT male biol rep 2 [mRNA]

description: 10X Genomics


title: phasic CeA male MR1 65_CeA

description: phasic CeA male MR1


title: cells round 1 rep B

value: VECOS library screen


title: pDONR plasmid library

description: pDONR

value: VECOS library cloning


title: RNAseq_keratinocytes_female_Ctrl_rep2

value: skin

value: keratinocytes

value: WT female

value: Control


title: sustained CeA male MR1 85_CeA

description: sustained CeA male MR1

value: sustained


title: Input 2

value: HFF

value: input


title: STAT3 GOF 7d IMQ female biol rep 1 [mRNA]

description: 10X Genomics

value: STAT3 GOF

value: 7 day imiquimod

value: CD3e (TotalSeq-C0182), TCRβ (TotalSeq-C0120), CD4 (TotalSeq-C0001), CD8a (TotalSeq-C0002), CD44 (TotalSeq-C0073), and CD62L (TotalSeq-C0112)


title: WT 7d IMQ female biol rep 1 [mRNA]

description: 10X Genomics

value: WT

value: mRNA


title: phasic CeA male MR1 76_CeA

description: phasic CeA male MR1

value: CeA

value: male

value: phasic


title: sustained CeA male MR1 77_CeA

description: sustained CeA male MR1


title: GW-BAC library

description: BAC


title: WT 7d IMQ male biol rep 2 [mRNA]

description: 10X Genomics

value: cervical lymph node

value: CD3+ T cells


title: timp_1a

city: Cambridge

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw data reads were trimmed with Trim Galore v.0.6.7, and aligned to the human genome (GRCh38) with Kallisto v.0.46.2.
Count files were generated from transcript level estimates using tximport v.
Trimmed Mean of M-values (TMM) normalization was conducted and GSEA performed (Subramanian et al, 2005).
Assembly: GRCh38
Supplementary files format and content: unnormalized count files

source_name: aortic VSMC

growth_protocol: VSMCs were established from human aortic explants. Following outgrowth, cells were maintained in promocell smooth muscle cell growth medium 2

extract_protocol:
RNA extracted with qiagen Rneasy extraction kit
Libraries were prepared from oligo-dT-purified mRNA and sequenced on an Illumina Novaseq 6000 (150 bp paired end reads).

treatment_protocol: Bulk RNA-seq was conducted on total RNA isolated from of six different hVSMC isolates following 3 hours serum starvation in serum free media containing 0.1% BSA, followed by 6 hours TIMP1 (or vehicle) treatment in serum free media containing 0.1% BSA.

value: aortic VSMC

value: primary cells

value: VSMC

tag: source age

tag: source gender

value: Female

value: TIMP1 (500 ng / mL) for 6 hours


title: heec,rep2

city: Jinan

first: Dianhao

last: Guo

address: 6699 Qingdao Road

department: Institute of Basic Medicine

country: China

institute: shandong first medical university

data_processing:
The raw data were analyzed for quality using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic) would remove the low-quality sequences and adaptor-contaminated sequences.
The filtered data was mapped to the human hg19 genome using HISAT2(https://daehwankimlab.github.io/hisat2/) and generated with the SAM files, which were converted to the BAM format by SAMtools
HTseqwas used to count the number of reads mapped on each gene.
Read count extraction
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count for each Sample

source_name: heec

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 oC

extract_protocol:
RNA was isolated using Trizol extraction method (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02) following manufacturer's protocols.

treatment_protocol: without any treatment

value: heec

value: normal esophageal

tag: disease state

value: normal


title: sustained ACC male MR1 81_ACC

description: sustained ACC male MR1

source_name: ACC

value: ACC

value: sustained

tag: time point


title: heec,rep1

tag: cell line


title: timp_13a

value: Male


title: cells round 1 rep A

tag: experiment type

value: VECOS library screen

tag: time

value: 10 dpi

value: HFF

tag: selection round

value: A


title: sustained ACC male MR1 68_ACC

description: sustained ACC male MR1

tag: tissue

value: male


title: sustained ACC male MR1 79_ACC

description: sustained ACC male MR1


title: STAT3 GOF NT female biol rep 1 [mRNA]

description: 10X Genomics

value: cervical lymph node

tag: cell type

value: CD3+ T cells

value: STAT3 GOF

value: no treatment

value: mRNA

value: CD3e (TotalSeq-C0182), TCRβ (TotalSeq-C0120), CD4 (TotalSeq-C0001), CD8a (TotalSeq-C0002), CD44 (TotalSeq-C0073), and CD62L (TotalSeq-C0112)


title: ctrl_15a

value: aortic VSMC

value: primary cells

value: VSMC

value: serum starved for 3 hours


title: WT NT female biol rep 1 [mRNA]

description: 10X Genomics

tag: genotype

value: WT


title: kyse150,rep1

value: esophageal squamous cell carcinoma

value: tumor


title: kyse150,rep2


title: ctrl_13a

value: Male

tag: treatment


title: ctrl_1a

value: Female


title: timp_15a

value: TIMP1 (500 ng / mL) for 6 hours


title: Liver AAV8-TBG-Control (GFP) 2

city: Boston

first: Huan

last: Liu

state: Massachusetts

address: 185 Cambridge Street

department: CVRC

institute: Massachusetts General Hospital

description:
Sample 14 GFP
CG2
NGvsCG_deg.csv

data_processing:
Trimmed sequence reads were mapped to GRCm38 (mm10).
Assembly: mm10
Supplementary files format and content: Comma-separated text files include normalized counts, counts and FPKM values.

source_name: Liver

growth_protocol: We studied C57BL/6J mice on a FPC NASH diet and sugar water for 16 weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control), or AAV8-H1-shRNA to knockdown of Gpnmb or scramble control in liver. In addition, we used C57BL/6J mice treated with GFP, on a standard chow diet for 16 weeks as the control.

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.
TruSeq stranded mRNA kit (Illumina Corp.) following manufacturer's protocols.

value: Liver

value: Standard chow diet and normal water

value: 16 weeks


title: sustained ACC male MR1 85_ACC

description: sustained ACC male MR1

value: ACC

value: male

value: sustained


title: phasic CeA male MR1 63_CeA

description: phasic CeA male MR1

value: CeA

value: phasic


title: timp_14a

value: aortic VSMC

value: primary cells


title: Liver AAV8-TBG-Control (GFP) 1

description:
Sample 13 GFP
CG1
NGvsCG_deg.csv


title: kyse30,rep1


title: RNAseq_keratinocytes_male_Sepi_rep3

value: skin

value: keratinocytes

value: WT male

value: S. epidermidis


title: sustained ACC male MR1 77_ACC

description: sustained ACC male MR1


title: SRRM2_TSAseq

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

data_processing:
TSA-seq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.5.0; (Langmead and Salzberg, 2012)). Read counts were computed and normalized using “bamCoverage” from deepTools (version 3.5.0; (Ramirez et al., 2014)) using a bin size of 50bp. “bamCompare” from deepTools was used to compute the log2 ratio for each bin after normalized the data for sequencing depth.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Coverage tracks were calculated as the number of reads per bin normalized by genome coverage. TSAseq track shows log2 ratio between SRRM2 TSAseq and noAb TSAseq.
Library strategy: TSA-seq

growth_protocol: Mouse embryonic stem cells (E14) were cultured in N2B27 medium with LIF/2i.

extract_protocol:
1% formaldehyde was added to 7.5x10^6 mouse ESCs to cross-link proteins to DNA. Cells were then permeabilized in PBS with TritonX-100 0.5% for 5 min on ice and 10 min at RT. Next, cells were resuspended in 1.5% H2O2 to quench the endogenous peroxidases by slowly nutating at RT for 1 hr. After three washes with PBS-TritonX-100 0.1% (PBST), cells were resuspended in GS blocking buffer (1% BSA in PBST) for 1 hr at RT. Cells were then incubated with antibody anti-SRRM2 (Novus Biologicals, NBP2-55697) 1:500 in GS blocking buffer overnight at 4°C. For the no-antibody control sample, cells were incubated in GS blocking buffer only. After washing, cells were incubated with HRP conjugated secondary antibody (Vector Laboratories, PI-1000-1) 1:1000 in GS blocking buffer for 2 hr at RT. Cells were then incubated in Buffer A (50% sucrose, 0.0015% H2O2, 1:2500 tyramide-biotin 8 mM (Sigma-Aldrich, SML2135) for 10 min nutating at RT.
For monitoring TSA labeling by immunostaining, a small aliquot of each sample was placed on a glass coverslip, air dried for few minutes and fixed on the coverslip with 3.7% formaldehyde in PBS for 10 min at RT. After washing in PBST three times, coverslips were incubated 30 min at RT with streptavidin-Alex Fluor 594 (Invitrogen, S11227) 1:1000 and Alex Fluor 488 secondary antibody (Thermo Fisher, A11034) 1:1000 in GS blocking buffer. After washing, the coverslips were mounted using VECTASHIELD® Antifade Mounting Medium with DAPI.
To shear the DNA, cells were resuspended in MNase digestion buffer (0.3M Sucrose, 50mM Tris pH 7.5, 30mM KCl, 7.5mM NaCl, 4mM MgCl2, 1mM CaCl2, 0.125% NP-40, 0.25% NaDeoxycholate, supplemented with cOmplete™ Protease Inhibitor Cocktail (Roche)) with 100U MNase (Roche) at 37°C for 30 minutes. The digestion was then stopped with 5mM EDTA and the digested chromatin was solubilized in 200mM NaCl and five pulses of 30sec sonication using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode). For the affinity purification of biotinylated DNA, 10μl/106 cells of Dynabeads™ M-270 streptadivin (Invitrogen) were washed with Wash and Binding (W&B) buffer (5mM Tris pH 7.5, 0.5 mM EDTA, 1M NaCl) before being added to the samples. Beads were then washed four times with W&B buffer, with TSE 500 (20 mM Tris pH 8, 1% TritonX-100, 0.1% SDS, 2 mM EDTA pH 8, 500 mM NaCl), again with W&B buffer and then with TE buffer. After the final wash, beads were resuspended in Proteinase K buffer (10 mM Tris pH 7,5, 10 mM EDTA pH 8, 0.5% SDS) supplemented with free biotin 0.1 mM and 40 μg of Proteinase K (Thermo Scientific) and incubated at 50°C for 3 h and reverse cross-linked at 65°C, overnight. DNA was isolated by Phenol:Chloroform extraction following original protocol’s instructions.
Quantity and quality of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). The NEBNext® Ultra™ II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L) was used following the manufacturer’s protocol. Briefly, TSA and input samples (10 ng) were end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer and the 4200 TapeStation System (Agilent). Sequencing was performed on an Illumina NovaSeq6000 machine with single-end 100 bp reads.

value: Mouse embryonic stem cells (ESCs)

value: Wild type

tag: antibody


title: timp_8a

value: VSMC

value: female

value: TIMP1 (500 ng / mL) for 6 hours


title: phasic ACC male MR1 76_ACC

description: phasic ACC male MR1


title: timp_3a


title: APO2 Input replicate 3

city: Changchun

first: Yiling

last: Miao

address: Xian Street NO.5333

institute: Jilin University

data_processing:
bcl2fastq2 V2.2 software used for base calling and parameter is default inhouse scripts used for filtering
Bowtie-0.12.8 used for alignment
MACS2 V1.4.2 used for peak-calling
Bigwig files were generated using the bamCoverage V3.5.4.
narrowPeak files were generated using MACS2 with default settings.
Assembly: IRGSP-1.0
Supplementary files format and content: bigwig, narrowPeak (except for Input samples)

organism: Oryza sativa

source_name: young inflorescence meristems

extract_protocol:
Plant tissues were fixed with 1%formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonifier 250 (Branson)
Libraries were prepared according to Illumina's instructions, including DNA fragment, End repair,dA-Tailing, Adaptor ligation and the KAPA HiFi DNA Polymerase for PCR amplification

value: young inflorescence meristems

tag: chip antibody


title: sustained ACC male MR1 84_ACC

description: sustained ACC male MR1

tag: strain

value: ACC


title: APO2 Input replicate 4


title: noAb_TSAseq


title: APO2 Input replicate 2


title: Input_SRRM2_TSAseq


title: Liver AAV8-TBG-Control (GFP) 3

description:
Sample 15 GFP
CG3
NGvsCG_deg.csv

value: Liver

tag: Sex

value: Male

value: Standard chow diet and normal water

value: 16 weeks


title: phasic ACC male MR1 63_ACC

description: phasic ACC male MR1

value: male

tag: phenotype

value: phasic


title: ctrl_14a

value: aortic VSMC

value: primary cells

tag: source age

value: serum starved for 3 hours


title: RNAseq_keratinocytes_male_Ctrl_rep3

value: skin

value: keratinocytes

value: WT male

value: Control


title: kyse30,rep2

value: esophageal squamous cell carcinoma

value: tumor


title: ctrl_8a

value: VSMC

tag: source gender

value: female


title: Input_noAb_TSAseq

value: Mouse embryonic stem cells (ESCs)

value: Wild type


title: ctrl_3a


title: APO2 Input replicate 1

value: young inflorescence meristems


title: H3K27me3_ChIPseq_BAZ2A_dTAM

data_processing:
ChIPseq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.5.0; (Langmead and Salzberg, 2012)). Read counts were computed and normalized using “bamCoverage” from deepTools (version 3.5.0; (Ramirez et al., 2014)) using a bin size of 50bp.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bigWig: Coverage tracks were calculated as the number of reads per bin normalized by genome coverage. Samples were then scaled by a normalization factor calculated on the least uniquely counted reads aligning against D. melanogaster genome (dm6).

extract_protocol:
1% formaldehyde was added to cultured cells to cross-link proteins to DNA. For H3K27me3 ChIPs, isolated nuclei were then lysed and sonicated using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris–HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Sepharose beads for 2 h at 4°C. Pre-cleared chromatin was incubated overnight with ChIP-grade antibody raised against H3K27me3. The next day, Dynabeads™ Protein A (Invitrogen, 10002D) were added and incubated for 4 h at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon Proteinase K (Thermo Scientific) digestion (50°C for 3 h) and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform, ethanol precipitated and quantified by qPCR.
For BAZ2A ChIPs, crosslinked chromatin has been fragmented into mono-nucleosomes through digestion with MNase. Briefly, isolated and crosslinked nuclei were MNase digested in 400µl MNase digestion buffer (0.3M Sucrose, 50mM Tris pH 7.5, 30mM KCl, 7.5mM NaCl, 4mM MgCl2, 1mM CaCl2, 0.125% NP-40, 0.25% NaDeoxycholate, supplemented with cOmplete™ Protease Inhibitor Cocktail (Roche)) with 100U MNase (Roche) at 37°C for 30 minutes. The digestion was then stopped with 5mM EDTA and the digested chromatin was solubilized in 1% SDS and three pulses of 30sec sonication using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode). 200µg of pre-cleared chromatin was immunopurified with incubation of 20µl of Anti-FLAG® M2 Affinity Gel (Sigma, A2220) over night. The samples were subsequently washed, eluted and the DNA was purified as for histone ChIPs.
For ChIPseq normalization with D. melanogaster spike-in chromatin, the samples were prepared and processed as above but with the addition of 200 ng of D. melanogaster S2 chromatin and 0.5 μg of H2Av antibody (Active Motif, 61686) for BAZ2A ChIP and 50 ng of D. melanogaster S2 chromatin and 0.2 μg of H2Av antibody for H3K27me3 ChIP.
Quantity and quality of the isolated DNA was determined with Qubit® 4 Fluorometer (Life Technologies). The NEBNext® Ultra™ II DNA Library Prep for Illumina (New England Biolabs, E7645S and E7645L) was used following the manufacturer’s protocol. Briefly, ChIP and input samples (10 ng) were end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer and the 4200 TapeStation System (Agilent). Sequencing was performed on an Illumina NovaSeq6000 machine with single-end 100 bp reads.

treatment_protocol: For siRNA and Antisense LNA GapmeR transfection, 4.5x10^5 parental ESCs were seeded into gelatin-coated 10 cm plate. Cells were let to attach for 4 hour and then transfected with 2 μl of 40 μM siRNA stock or 0.4 μl of a 50 μM GapmeR stock using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778150) following the manufacturing instructions.

value: Flag and HA tagged BAZ2A <delta>TAM resistant to the siRNA inserted by PiggyBac transposase

value: ESCs were transfected with siRNA targeting Baz2a and collected 3 days post transfection


title: Input_H3K27me3_ChIPseq_BAZ2A_dTAM

value: Flag and HA tagged BAZ2A wt resistant to the siRNA inserted by PiggyBac transposase


title: APO2 ChIP replicate 3

value: α-GFP antibody (ab292, Abcam)


title: phasic CeA female MR1 97_CeA

description: phasic CeA female MR1

value: CeA

value: phasic


title: phasic ACC female MR1 97_ACC

description: phasic ACC female MR1

value: ACC


title: H3K27me3_ChIPseq_BAZ2A_wt


title: APO2 ChIP replicate 4

value: α-GFP antibody (ab293, Abcam)


title: exp2_EIF4ENIF1_GFP_OE_2_transcription

city: Beijing

first: Yuxi

last: Ding

address: D110, Medical Building, 30 Shuangqing Road

institute: Tsinghua University

description:
exp2_GFP_2_ZL
exp2_count_matrix.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
Reads were mapped to  hg19 whole genome using Hisat2 (v2.1.0) with default parameters.
Gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: 293FT cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco 11965092), supplemented with 10% FBS (genimi 900-108), 1% penicilin- streptomycin (Gibco 15070063), 1% glutamax (Gibco 35050079), 1% MEM NEAA (Gibco 11140050) and 1mM sodium pyruvate (Gibco 11360070). The cells were placed in a cell incubator of 37°C, 5% CO2 with humidified atmosphere.

extract_protocol:
10,000 293FT cells from each group were lysed in sample buffer (Vazyme N712) and divided into two subgroups at a 20:80 ratio. The major subgroup was used for translatome sequencing and the minor subgroup for transcriptome sequencing. Twenty percent of the lysate was used directly for reverse transcription by the SMART-seq2 strategy using Vazyme Single Cell Full Length mRNA-Amplification Kit (Vazyme N712). Eighty percent of the lysate was incubated with pre-activated ribosome magnetic beads (IMMAGINA RL001) to capture actively translating ribosomes. The beads were then washed, and the captured ribosomes were digested with proteinase K to release bound mRNAs. The released mRNAs were purified using clean VAHT RNA beads (Vazyme N412-01-AA) for reverse transcription and library construction, as described above.
DNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's instructions.

treatment_protocol: For T&T seq, 293FT cells of each well on a 6-well plate were transfected using opti-MEM (ThermoFisher 31985070) and lipofectAMINE 2000(ThermoFisher 11668019) with 2 μg of the desired plasmids following the manufacturer's guidance. The cells were changed with fresh medium 24 hours after transfection, and collected with TrypLE (ThermoFisher 12605028) for further experiments another 24 hours after.

value: embryonic kidney epithelial cells

value: GFP overexpression


title: exp2_EIF4ENIF1_GFP_OE_1_translation

description:
exp2_GFP_1_FY
exp2_count_matrix.txt


title: exp2_EIF4ENIF1_GFP_OE_2_translation

description:
exp2_GFP_2_FY
exp2_count_matrix.txt


title: sustained CeA female MR1 95_CeA

description: sustained CeA female MR1

value: sustained


title: phasic ACC male MR1 65_ACC

description: phasic ACC male MR1

value: male


title: APO2 ChIP replicate 2

value: α-GFP antibody (ab291, Abcam)


title: phasic ACC male MR1 80_ACC

description: phasic ACC male MR1


title: Input_H3K27me3_ChIPseq_BAZ2A_wt


title: sustained ACC female MR1 95_ACC

description: sustained ACC female MR1

value: female


title: exp2_EIF4ENIF1_R208H_OE_2_translation

description:
exp2_R208H_2_FY
exp2_count_matrix.txt

value: EIF4ENIF1 R208H overexpression


title: BAZ2A_ChIPseq_NegCtrl_GapmeR

value: Mouse embryonic stem cells (ESCs)

value: BAZ2A endogenously Flag and HA tagged

value: ESCs were transfected with indicated GapmeR and collected 3 days post transfection

value: anti-FLAG


title: sustained CeA female MR1 92_CeA

description: sustained CeA female MR1


title: exp2_EIF4ENIF1_R208H_OE_2_transcription

description:
exp2_R208H_2_ZL
exp2_count_matrix.txt


title: APO2 ChIP replicate 1

value: young inflorescence meristems

value: α-GFP antibody (ab290, Abcam)


title: sustained ACC female MR1 93_ACC

description: sustained ACC female MR1


title: exp2_EIF4ENIF1_R208H_OE_1_translation

description:
exp2_R208H_1_FY
exp2_count_matrix.txt


title: exp2_EIF4ENIF1_GFP_OE_1_transcription

description:
exp2_GFP_1_ZL
exp2_count_matrix.txt


title: BAZ2A_ChIPseq_Malat1_GapmeR


title: C666-1,-SG2

city: Nanchang

first: Yishan

last: Xiong

state: Jiangxi Province

address: 永外正街17号

institute: 南昌大学第一附属医院

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2(v2.3.4.3) was applied to align the clean reads to the reference genome. Gene expression was calculated by RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: The 'gene_expression' excel file includes read counts for each sample.
Supplementary files format and content: The 'gene_expression' excel file includes FPKM and TPM values for each sample.

growth_protocol: C666-1 cells were cultured in CM (complete medium) and-SG (serine-and glycine-removed medium) supplemend with 10% dialyzed fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃。

extract_protocol:
RNA was extracted using Trizol reagent.
The experimental procedures of mRNA library preparation included mRNA fragmentation, cDNA synthesis, end repair, addition of a single ‘A’ nucleotide, adaptor ligation, PCR, and circularization. The produced library was subjected to high-throughput sequencing in the DNBSEQ platform.

treatment_protocol: C666-1 cells were cultured in CM (complete medium)  or -SG (serine-and glycine-removed medium) for 24h.Complete medium was prepared from 10% dialyzed fetal bovine serum (Procell, China), MEM essential media (excluding non-essential amino acid components, Procell, China), 1% streptomycin mixture, D-glucose (4.5g / L), glycine (0.4 mmol/L), and serine (0.4 mmol/L). Serine-and glycine-removed medium contained the same components as the complete medium, except for serine and glycine.

value: Human nasopharyngeal carcinoma cells

value: -SG (serine-and glycine-removed medium)


title: C666-1,-SG3


title: Input_BAZ2A_ChIPseq_GapmeR


title: BAZ2Aend_ChIPseq_TPL

value: ESCs were treated for 4 hours with 1uM triptolide (TPL)


title: mg_screen1_ascl1_oe

city: Seattle

first: Amy

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: single nucleus RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Brotman Baty sci-RNA-seq demultiplexing and processing pipelines (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The hashes were incorporated into the output and further analysis was performed using Monocle3
Assembly: GRCm38
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv), Monocle3 cds object (RDS file), Count matrix from 10x (.mtx),

source_name: Muller glia from dissected retina

growth_protocol: The Muller glia were cultured as in Todd et al. Sci Adv. (2022)

extract_protocol:
In a 48-well plate, the cells were  rinsed with 200ul HBSS and then 200ul of Accutase. Accutase was removed, and the cells were incubated at 37°C for 5 minutes. Cells were then resuspended in 200 uL of 1% tet-FBS-reduced growth medium with a wide-bore P200 pipette tip to isolate single cells.
The library was prepared by the original sci-RNA-seq2 protocol  (Cao et al., 2017) in combination with hashing as presented by sci-Plex (Srivatsan et al., 2019). Nuclei were fixed in the presence of a barcoded polyA DNA oligo. A reverse transcription reaction with barcoded RT primers captured 3'-polyAdenylated transcripts and the barcoded oligo. Using FACs, nuclei were sorted into wells of 96-well plates where second strand synthesis was followed by tagmentation of dsDNA. PCR was performed with barcoded primers and the library was size-selected. The unique combination of barcodes in the RT and PCR steps enable the reconstruction of individual cells in silico.

treatment_protocol: Retinal cells were dissociated,  cultured until confluent (~7 days), and then frozen. Cells were thawed and cultured for 1-2 days before being induced to express Ascl1 through 2 ug/mL of doxycycline for 1-5 days. At the same time, cells were also exposed to one of 92 different compounds from the Tocriscreen Stem Cell Library at a dose of 0.1 uM, 1 uM, or 10 uM. Cells were harvested 5 days from the start of Ascl1 expression + drug treatment.

value: Muller glia from dissected retina

value: rtTa:tetO-Ascl1-ires-GFP (a gift from M. Nakafuku, U. Cincinnati)


title: exp2_EIF4ENIF1_R208H_OE_1_transcription

description:
exp2_R208H_1_ZL
exp2_count_matrix.txt

value: embryonic kidney epithelial cells


title: Input_BAZ2Aend_ChIPseq


title: C666-1,CM3

value: CM (complete medium)


title: phasic ACC female MR1 113_ACC

description: phasic ACC female MR1

value: ACC

value: phasic


title: BAZ2Aend_ChIPseq_untreated


title: exp2_EIF4ENIF1_WT_OE_2_translation

description:
exp2_WT_2_FY
exp2_count_matrix.txt

value: EIF4ENIF1 WT overexpression


title: phasic ACC female MR1 112_ACC

description: phasic ACC female MR1

value: female


title: exp2_EIF4ENIF1_WT_OE_2_transcription

description:
exp2_WT_2_ZL
exp2_count_matrix.txt


title: BAZ2A_dTAM_ChIPseq

value: Mouse embryonic stem cells (ESCs)

value: Flag and HA tagged BAZ2A <delta>TAM resistant to the siRNA inserted by PiggyBac transposase

value: ESCs were transfected with siRNA targeting Baz2a and collected 3 days post transfection


title: sustained CeA female MR1 93_CeA

description: sustained CeA female MR1

value: CeA

value: sustained


title: exp2_EIF4ENIF1_WT_OE_1_translation

description:
exp2_WT_1_FY
exp2_count_matrix.txt


title: C666-1,CM1


title: phasic CeA female MR1 111_CeA

description: phasic CeA female MR1


title: BAZ2A_wt_ChIPseq

value: Flag and HA tagged BAZ2A wt resistant to the siRNA inserted by PiggyBac transposase

value: anti-FLAG


title: phasic ACC female MR1 111_ACC

description: phasic ACC female MR1


title: exp2_EIF4ENIF1_WT_OE_1_transcription

description:
exp2_WT_1_ZL
exp2_count_matrix.txt


title: Input_BAZ2A_ChIPseq


title: scCOLORseq_R3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
We performed basecalling on the raw pod5 data using Derado in GPU mode from Oxford Nanopore Technologies running on four A100 graphics card. For each read we identify the barcode and UMI sequence by searching for the polyA region and flanking regions before and after the barcode/UMI. Accurately sequenced barcodes were identified based on their dual nucleotide complementarity. Unambiguous barcodes were then used as a guide to error correct the ambiguous barcodes in a second pass correction analysis approach. Fastq data was processed using TallyTrin pipelines (https://github.com/cribbslab/TallyTriN). Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. The transcript name was then appended to the bam XT flag using the xt_tag_nano script before umi_tools count module was used to count the features using the following settings: --per-gene --gene-tag=XT --per-cell --dual-nucleotide. The umi_tools used to correct for the dimer UMIs is located in the AC-dualoligo in a fork at the repository: https://github.com/Acribbs/UMI-tools.
Assembly: hg38 and mm10
Supplementary files format and content: Tab seperated files and market matrix gz files
Supplementary files format and content: log files: the calculation of polyA positive data that is integral for an up and coming manuscript. The data contained in these files is the output of our analysis workflow.

organism:
Homo sapiens
Mus musculus

source_name: 5TGM1 and Jurkat

growth_protocol: Jurkat and 5TGM1 cells were cultured in complete RPMI medium supplemented with 10% Foetal Calf Serum

extract_protocol:
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
scCOLOR-seq v2 protocol was used.

value: 5TGM1 and Jurkat


title: RNAseq_ESC_BAZ2A_dTAM_rep4

data_processing:
The quality of the 100 bp single end reads generated by the machine was checked by FastQC (Andrews, 2010). The quality of the reads was increased by applying: a) SortMeRNA (Kopylova, 2012) (version 2.1) tool to filter out ribosomal RNA; b) Trimmomatic (Bolger, 2014) (version 0.36) software package to trim the sorted (a) reads. The sorted (a), trimmed (b) reads were mapped against the mouse genome (mm10) using the default parameters of the STAR (Spliced Transcripts Alignment to a Reference, version 2.4.0.1) (Dobin et al., 2013). For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: mm10 (GRCm38)
Supplementary files format and content: RPKM_BAZ2A_wt_BAZ2A_dTAM.csv: Comma-separated text file includes RPKM values for each Sample.
Supplementary files format and content: RNAseq_BAZ2AdTAM_vs_wt.xlsx: Excel file includes the DESeq2 computed mean of normalized count of all samples based on sequencing depth.

extract_protocol:
Total RNA was purified with TRIzol reagent (Life Technologies).
The quality of the isolated RNA was determined with a Qubit® 4 Fluorometer and 4200 Tape Station system. Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5-2 were further processed. The TruSeq Stranded mRNA (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® 4 Fluorometer. The product is a smear with an average fragment size of approximately 260 bp. Libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The Novaseq6000 (Illumina) was used for cluster generation and sequencing according to standard protocol. Sequencing was single end at 100 bp.

treatment_protocol: 8x10^4 parental ESCs were seeded into gelatin-coated 6 cm plate. Cells were let to attach for 4 hour and then transfected with 2 μl of 40 μM siRNA stock using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778150) following the manufacturing instructions.


title: ETC_tgirt60_repC

city: State College

first: Catherine

middle: A

last: Douds

state: Pennsylvania

department: BMMB

institute: Penn State University

data_processing:
trimming: Paired end sequencing reads were first trimmed with cutadapt to remove sequencing primers and the 10 nt random sequence from the adaptase step (cutadapt -a NNNNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGA -g AGATCGGAAGAGCGTCGTGTAGGGAAAGA -G TGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNN -q 30,30 -m 20)
mapping/ identification of mutation rates: For analysis without filtering mutations, trimmed reads were then processed using ShapeMapper2 with bowtie2 alignment and a random primer length of 10 nt. The mutation types were quantified using the output from --output-counted-mutations. To apply mutation filtering, the --dms flag was used.
normalization: Background-subtracted mutation rates from ShapeMapper2 were 2-8% normalized with all four residues together within a transcript for final reactivity calculations. As in ShapeMapper2, any residue with untreated modification rate over 0.05% was removed from analysis.
Assembly: genomebuild_assembly.txt
Supplementary files format and content: All profile.txt files are formatted as a csv that includes the RNA transcript (RNA), nucleotide number (Nucleotide), nucleotide sequence (Sequence), number of mutations in the modified sample (Modified_mutations), read depth in the modified sample (Modified_read_depth), effective read depth in the modified sample (Modified_effective_depth), mutation rate of modified sample (Modified_rate), depth of off target reads in modified sample (Modified_off_target_mapped_depth), depth of low quality reads in the modified sample(Modified_low_mapq_mapped_depth), the total depth of the modified sample(Modified_mapped depth), number of mutations in the untreated sample (Untreated_mutations), read depth in the untreated sample (Untreated_read_depth), effective read depth in the untreated sample (Untreated_effective_depth), mutation rate of untreated sample (Untreated_rate), depth of off target reads in untreated sample (Untreated_off_target_mapped_depth), depth of low quality reads in the untreated sample(Untreated_low_mapq_mapped_depth), the total depth of the untreated sample(Untreated_mapped depth), background subtracted mutation rates (raw_reactivity), and normalized reactivity values (norm_reactivity).
Supplementary files format and content: File names that contain "merge" are counts from the three pooled bioreplicates. Files names that contain "filt" applied mutation signature filtering.
Library strategy: DMS/ETC MaP-seq

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: E. coli cells were grown by shaking in LB to mid exponential phase at 37°C

extract_protocol:
Cell growth was arrested by transferring all 6 mL of treated cell cultures to 6 mL of a frozen slurry containing 10 mM Tris-HCl (pH 7.2), 5 mM MgCl2, 25 mM NaN3, 1.5 mM chloramphenicol, and 12.5% ethanol, followed by incubation for 5 min on ice. Cells were harvested by centrifugation for 20 min. For ETC- treated cells that resisted standard lysis protocols, cell pellets were resuspended in 100 μL of 10 mg/mL lysozyme and incubated for 10 min at room temperature with brief vortexing every 2 min. The cell mixture was transferred to a 2 mL screw cap tube along with 700 μL of RLT buffer from the RNeasy Mini kit (Qiagen) and 700 μL of 150-212 μm acid washed glass beads (Sigma). Cells were lysed with a bead-beater at max speed for 2.5 min three times; cells were incubated for 5 min on ice between rounds. For untreated, EDC, and DMS treated cells, cell pellets were resuspended in 100 μL of 3 mg/mL lysozyme and incubated for 20 min at 37°C for cell lysis. The rest of the extraction followed the RNeasy Mini Kit instructions. Purified RNA samples were treated with RQ1 DNase (Promega), and then the DNase was inactivated with the provided stop solution by incubating for 5 min at 65°C . RNA was then ethanol precipitated by adding 10 μL 5M NaCl, 1 μL GlycoBlue™ (Thermofisher), and 250 μL of 100% ethanol for every 100 μL of sample. If the sample volume surpassed 100 μL, 1 μL of GlycoBlue™ was added and the remaining volume was supplemented with colorless, Invitrogen UltraPure glycogen (Fisher Scientific).
Sequencing libraries for Illumina paired-end 150x150 Next-Seq 2000 were prepared by adapting the xGen Broad-Range RNA Library Preparation Kit (IDT) protocol. 150 ng of total RNA was brought to 7 μL in water and mixed with 1 μL of RNA Reagent F1, 4 μL of RNA Buffer F3, and 2 μL of RNA Buffer F4. This mixture was heated for 3 min to 94°C to fragment the RNA and then it was immediately chilled for 2 min on ice. Library preparation varied only at the RT reaction and libraries were prepared as follows. For libraries with TGIRT-III, a mixture of 2 μL of TGIRT-III enzyme (Ingex), 1 μL of R1 (RNase inhibitor), and 2 μL of 50 mM DTT was added to the fragmented RNA and incubated for 10 min at room temperature before 2 μL of RNA Reagent F2 (dNTPs) was added. The RT reaction was carried out at for 20 min 20°C, for 30 min 42°C, and for 45 min at 50°C, 55°C, 60°C, or 65°C. For libraries with Marathon RT, a mixture of 1 μL Marathon RT enzyme (Kerafast), 1 μL of R1, 0.5 μL of 200 mM DTT, 0.5 μL of 80 mM MnCl2, and 4 μL of 100% glycerol was added to the fragmented RNA and incubated for 10 min at room temperature before 2 μL of RNA reagent F2 was added. The RT reaction was carried out for 3 h at 42°C. For libraries with SuperScript-II, a mixture of 2 μL SuperScript-II enzyme (ThermoFisher), 1 μL of R1, 1 μL of 200 mM DTT, and 1 μL of 60 mM MnCl2 was added to the fragmented RNA and incubated for 10 min at room temperature before 2 μL of RNA reagent F2 was added. The RT reaction was carried out for 3 h at 42°C. For libraries with HIV-RT, a mixture of 2 μL HIV RT enzyme (Worthington Biochemical Corporation), 1 μL of R1, and 2 μL of 100 mM DTT was added to the fragmented RNA and incubated for 10 min at room temperature before 2 μL of RNA reagent F2 was added. The RT reaction was carried out for 1 h at 37°C. Following RT, RNA was degraded with 1 μL of 4M NaOH and incubated for 3 min at 95°C and then cooled to 4°C. An equal amount of HCl was added to neutralize the mixture and then 26 μL of low EDTA TE buffer provided by the library kit was added to bring the sample to 50 μL. A size-selection clean-up with AMPure XP beads (Beckman Coulter) was done with 90 μL of beads and eluted in 12 μL of low EDTA TE buffer. Ten μL of the eluate was transferred to a fresh tube before continuing with the Adaptase, Extension, Ligation, and Indexing PCR as instructed in the kit. Rather than a final AMPure XP bead clean-up, amplified cDNA was purified by an 8% non-denaturing polyacrylamide gel extraction (150-600 bps) and ethanol precipitation.

treatment_protocol: Cells were exposed to modifying reagent for 5 min, quenched with 5 molar excess DTT for 2 min.

value: bacterial cells

value: ETC

tag: group


title: exp1_EIF4ENIF1_ctrl_2_transcription

description:
exp1_P2K7_2_ZL
exp1_count_matrix.txt

value: empty vector transfection


title: phasic CeA female MR1 113_CeA

description: phasic CeA female MR1

tag: time point


title: ETC_tgirt60_repB


title: C666-1,-SG1

tag: cell line

value: Human nasopharyngeal carcinoma cells

value: -SG (serine-and glycine-removed medium)


title: exp1_EIF4ENIF1_ctrl_2_translation

description:
exp1_P2K7_2_FY
exp1_count_matrix.txt

value: embryonic kidney epithelial cells


title: sustained ACC female MR1 109_ACC

description: sustained ACC female MR1

value: ACC


title: phasic CeA female MR1 112_CeA

description: phasic CeA female MR1

value: phasic


title: RNAseq_ESC_BAZ2A_dTAM_rep3


title: RNAseq_ESC_BAZ2A_dTAM_rep2


title: ETC_tgirt60_repA


title: exp1_EIF4ENIF1_ctrl_1_translation

description:
exp1_P2K7_1_FY
exp1_count_matrix.txt


title: C666-1,CM2

value: CM (complete medium)


title: exp1_EIF4ENIF1_ctrl_1_transcription

description:
exp1_P2K7_1_ZL
exp1_count_matrix.txt


title: UT_tgirt60_repC

value: UT


title: exp1_EIF4ENIF1_(1-684)_OE_2_translation

description:
exp1_TR_2_FY
exp1_count_matrix.txt

value: EIF4ENIF1 (1-684) overexpression


title: RNAseq_ESC_BAZ2A_dTAM_rep1

value: Mouse embryonic stem cells (ESCs)

value: Flag and HA tagged BAZ2A <delta>TAM resistant to the siRNA inserted by PiggyBac transposase

value: ESCs were transfected with siRNA targeting Baz2a and collected 3 days post transfection


title: sustained ACC female MR1 107_ACC

description: sustained ACC female MR1

value: female

value: sustained


title: UT_tgirt60_repB


title: RNAseq_ESC_BAZ2A_wt_rep4

value: Flag and HA tagged BAZ2A wt resistant to the siRNA inserted by PiggyBac transposase


title: UT_tgirt60_repA

value: bacterial cells


title: exp1_EIF4ENIF1_(1-684)_OE_2_transcription

description:
exp1_TR_2_ZL
exp1_count_matrix.txt


title: RNAseq_ESC_BAZ2A_wt_rep3


title: DMS_tgirt55_repC

value: DMS


title: sustained CeA female MR1 103_CeA

description: sustained CeA female MR1

value: CeA


title: sustained CeA female MR1 109_CeA

description: sustained CeA female MR1


title: exp1_EIF4ENIF1_(1-684)_OE_1_translation

description:
exp1_TR_1_FY
exp1_count_matrix.txt


title: RNAseq_ESC_BAZ2A_wt_rep2


title: DMS_tgirt55_repB


title: exp1_EIF4ENIF1_(1-684)_OE_1_transcription

description:
exp1_TR_1_ZL
exp1_count_matrix.txt


title: RNAseq_ESC_BAZ2A_wt_rep1


title: exp1_EIF4ENIF1_Q842P_OE_2_translation

description:
exp1_Q842P_2_FY
exp1_count_matrix.txt

value: EIF4ENIF1 Q842P overexpression


title: sustained ACC female MR1 103_ACC

description: sustained ACC female MR1


title: phasic ACC female MR1 102_ACC

description: phasic ACC female MR1


title: phasic CeA female MR1 102_CeA

description: phasic CeA female MR1


title: exp1_EIF4ENIF1_Q842P_OE_2_transcription

description:
exp1_Q842P_2_ZL
exp1_count_matrix.txt


title: phasic BNST female MR1 97_BNST

description: phasic BNST female MR1

source_name: BNST

value: BNST


title: phasic ACC female MR1 105_ACC

description: phasic ACC female MR1


title: ETC_tgirt55_repB

description:
ETC_tgirt55_merge_profile.txt
ETC_tgirt55_filtmerge_profile.txt

value: ETC


title: Liver AAV8-H1-shRNA Gpnmb 3

data_processing:
Trimmed sequence reads were mapped to GRCm38 (mm10)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized counts, counts and FPKM values

growth_protocol: We studied C57BL/6J mice on a FPC NASH diet and sugar water for 16 Weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control), or AAV8-H1-shRNA to knockdown of Gpnmb or scramble control in liver. In addition, we used C57BL/6J mice treated with GFP, on a standard chow diet for 16 weeks as the control.

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.
TruSeq stranded mRNA kit (Illumina Corp.)  following manufacturer's protocols.

value: Liver

value: Male

value: NASH diet and sugar water

value: 16 weeks


title: exp1_EIF4ENIF1_Q842P_OE_1_translation

description:
exp1_Q842P_1_FY
exp1_count_matrix.txt

value: embryonic kidney epithelial cells


title: phasic BLA female MR1 97_BLA

description: phasic BLA female MR1

source_name: BLA

value: BLA

value: phasic


title: phasic CeA female MR1 105_CeA

description: phasic CeA female MR1


title: Liver AAV8-H1-shRNA Gpnmb 1


title: Liver AAV8-H1-shRNA Gpnmb 2


title: Liver AAV8-H1-shRNA Sramble control 3


title: sustained BNST female MR1 95_BNST

description: sustained BNST female MR1


title: ETC_tgirt55_repA


title: sustained BLA female MR1 95_BLA

description: sustained BLA female MR1


title: exp1_EIF4ENIF1_Q842P_OE_1_transcription

description:
exp1_Q842P_1_ZL
exp1_count_matrix.txt


title: Liver AAV8-H1-shRNA Sramble control 2


title: exp1_EIF4ENIF1_WT_OE_2_translation

description:
exp1_WT_2_FY
exp1_count_matrix.txt

value: EIF4ENIF1 WT overexpression


title: Liver AAV8-H1-shRNA Sramble control 1


title: exp1_EIF4ENIF1_WT_OE_2_transcription

description:
exp1_WT_2_ZL
exp1_count_matrix.txt


title: UT_tgirt55_repC

value: UT


title: DMS_tgirt55_repA


title: UT_tgirt55_repA


title: sustained BLA female MR1 93_BLA

description: sustained BLA female MR1

value: female

value: sustained


title: UT_tgirt55_repB

value: bacterial cells


title: exp1_EIF4ENIF1_WT_OE_1_translation

description:
exp1_WT_1_FY
exp1_count_matrix.txt


title: ETC_tgirt55_repC


title: ETC_tgirt50_repC

description:
ETC_tgirt50_merge_profile.txt
ETC_tgirt50_filtmerge_profile.txt


title: Liver AAV8-TBG-Activin A 3


title: phasic BNST female MR1 105_BNST

description: phasic BNST female MR1


title: exp1_EIF4ENIF1_WT_OE_1_transcription

description:
exp1_WT_1_ZL
exp1_count_matrix.txt


title: Liver AAV8-TBG-Activin A 2


title: sustained BLA female MR1 92_BLA

description: sustained BLA female MR1


title: Liver AAV8-TBG-Activin A 1


title: HSAPN, IP

first: yanru

last: duan

state: Beijing

address: Beijing, Chaoyang

institute: Capital Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the Wig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01.
Wig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. Bed files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: Wig, bed (except for Input sample)

source_name: HUVEC

growth_protocol: ECM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: HUVEC

value: Human umbilical vein

tag: condition

value: siAPPL1 cultured with adiponectin-treated high glucose and high lipid medium


title: ETC_tgirt50_repB


title: ETC_tgirt50_repA


title: Liver AAV8-TBG-Control 3

tag: time


title: HSAPN, Input


title: UT_tgirt50_repC


title: phasic BNST female MR1 113_BNST

description: phasic BNST female MR1

value: BNST


title: HAPN, IP

value: Adiponectin-treated high glucose and high lipid medium


title: phasic BLA female MR1 113_BLA

description: phasic BLA female MR1


title: UT_tgirt50_repB


title: phasic BNST female MR1 112_BNST

description: phasic BNST female MR1


title: HAPN, Input


title: Liver AAV8-TBG-Control 2

value: Liver


title: UT_tgirt50_repA


title: Liver AAV8-TBG-Control 1

value: Male


title: phasic BLA female MR1 112_BLA

description: phasic BLA female MR1


title: ETC_hivrt

value: ETC


title: HGHL, Input

value: High glucose and high lipid culture medium


title: Sample 6_Mouse PBMCs EBV DNA Treated rep3

city: Riad El-Solh

first: Elias

middle: A.

last: Rahal

state: Beirut

department: Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

data_processing:
Base-calling was performed using Real-Time Analysis (RTA) 3 on the NovaSeq 6000 system.
Sequences were trimmed using Trimmomatic and reads were alligned to the reference genome using HISAT2 followed by read enumeration with featureCounts.
Differential expression analysis was performed using Limma-Voom.
Genome_build: mm10
Supplementary_files_format_and_content: A matrix table with raw transcript counts per sample.

source_name: Peripheral Blood_EBV DNA Treated

growth_protocol: Cells were cultured in complete RPMI at 37° C in the presence of 5% CO2.

extract_protocol:
RNA extraction was performed using Qiazol (Qiagen, Hilden, Germany) per manufacturer recommendations.
Libraries were constructed using an Illumina TruSeq RNA Sample Prep Kit v2 emplyed as per manufacturer instructions.

treatment_protocol: Three replicates were treated with EBV DNA.

value: BALB/c

value: Peripheral Blood Mononuclear Cells

value: EBV DNA


title: phasic BNST female MR1 111_BNST

description: phasic BNST female MR1

value: phasic


title: Control, IP

value: Normal culture medium


title: sustained BNST female MR1 93_BNST

description: sustained BNST female MR1

value: female


title: UT_hivrt

value: UT


title: Sample 5_Mouse PBMCs EBV DNA Treated rep2


title: phasic BLA female MR1 111_BLA

description: phasic BLA female MR1

value: BLA


title: Sample 4_Mouse PBMCs EBV DNA Treated rep1


title: Control, Input

value: HUVEC


title: ETC_ssii

value: bacterial cells


title: Sample 3_Mouse PBMCs Untreated rep3

source_name: Peripheral Blood_untreated

value: Untreated


title: UT_ssii


title: sustained BNST female MR1 109_BNST

description: sustained BNST female MR1

value: BNST

value: sustained


title: sustained BLA female MR1 109_BLA

description: sustained BLA female MR1


title: SFB-Ku80 PAR-Clip

city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

institute: Westlake University

data_processing:
The gene annotation (GTF format) of CHM13 is generated with parameters: gffread chm13.draft_v1.1.gene_annotation.v4.gff3 -o chm13.draft_v1.1.gene_annotation.v4.gtf
The STAR reference of human CHM13 genome assembly v1.1 is built with parameters: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir hsa_chm13v1.1_genanno_v4 --genomeFastaFiles chm13.draft_v1.1.fasta --sjdbGTFfile chm13.draft_v1.1.gene_annotation.v4.gtf --sjdbOverhang 150
The BLAST database of human ribosomal DNA is built with parameters: makeblastdb -in Hsa_rDNA_Kim.fa -dbtype nucl -out HsaKimrDNA -parse_seqids
RNA-seq reads are aligned to the pre-built human CHM13 v1.1 using STAR version 2.7.6a with the following parameters: STAR --runMode alignReads --genomeLoad NoSharedMemory --runThreadN 8 --readFilesCommand gunzip -c --genomeDir [dir_of_hsa_CHM13v1.1] --readFilesIn [read1.fq.gz] [read2.fq.gz] --chimOutJunctionFormat 1 --outReadsUnmapped Fastx --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --twopassMode Basic --outFileNamePrefix [outdir_bam] --sjdbOverhang 150 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --outFilterMultimapNmax 50
Gene count data is generated using featureCounts version 2.0.2 with the following parameters: featureCounts -T 8 -p -t exon -g gene_id -a [location_of_hsa_CHM13v1.1_gtf] -o [output_featurecounts.txt] [star_align_output_sorted.bam]
The unaligned reads are converted to FASTA format and the reads shorter than 18nt are excluded using seqkit version 2.1.0: seqkit fq2fa -j 16 [unmapped_reads] | seqkit seq -m 18 -o [unmapped_reads_filtered.fa]
The unaligned sequences are aligned with human ribosomal DNA sequence (KY962518.1) using BLAST 2.11.0+ with following parameters: blastn -db [path_of_blastdb_HsaKimrDNA] -query [unmapped_reads_filtered.fa] -outfmt '6 qseqid sseqid pident length slen qlen mismatch gapopen qstart qend sstart send evalue bitscore' -out [blast_results_table]
The BLAST data are filtered, only results in 45S region are kept. These results were splitted into bins of 10nt.
Assembly: human CHM13 v1.1, and the reference sequence of human ribosomal DNA is extracted from NCBI (GenBank: KY962518.1).
Supplementary files format and content: FASTA (reference sequence of Human ribosomal DNA)
Supplementary files format and content: TXT (readpergene table generated from STAR)
Supplementary files format and content: TXT (featurecounts table generated from featurecounts)
Supplementary files format and content: TXT (10nt binned blast results)

source_name: Embryonic kidney

growth_protocol: 293T cells stably expressing SFB empty vector, SFB-Ku80 cells were incubated with DMEM in 37℃,5% CO2 incubator.

extract_protocol:
Cells were incubated with 0.1 mM of 6SG for overnight followed by 0.4 Jcm2 365nm wavelength UV treatment. RNA were isolated with PAR-Clip by streptavidin resin and Flag resin.
Library preparation and sequencing were finished by Geneseed Technology CO., Ltd., Guangzhou, China. The protocol is as follows: 1) RNA quality and RNA sample assessment; 2) RNAs were fragmented, add adapters and indexes; 3) PCR; 4)Separation and cyclization; 5) Accurate quantification; 6) Sequencing.

treatment_protocol: PAR-Clip extract Ku80/Ku70 associated RNA

value: Embryonic kidney


title: Sample 2_Mouse PBMCs Untreated rep2


title: ETC_marathon


title: SFB empty vector PAR-Clip

value: SFB empty vector

value: PAR-Clip by streptavidin resin and Flag resin


title: sustained BNST female MR1 107_BNST

description: sustained BNST female MR1

data_processing:
Sequence reads were trimmed for adapter sequence and low-quality sequence using BBDuk.
Trimmed sequence reads were mapped to GrCM38/mm10 using the STAR aligner with default parameters.
Read count extraction were performed using FeatureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw gene counts per sample

extract_protocol:
Mouse brains were snap-frozen on dry ice and stored at -80°C. Regions of interest (ACC, BNST, BLA, and CeA) were isolated by a brain punching technique from the whole-mount brain in the cryostat Leica CM3050 S (Leica Biosystems, Nussloch, Germany) at -20°C using biopsy pens EMS Rapid-Core (Electron Microscopy Sciences, Hatfield, USA). To localize the subregions of interest in the brain, punching was carried out by referencing toluidine blue staining of brain slices (Franklin & Paxinos, 2007).  ACC was sampled approximately from 1.34 to 0.5mm (from bregma) using a 1mm pen. BNST (0.5: -0.22)mm, BLA (-0.94: -2.06)mm, and CeA (-0.94: -1.82)mm were sampled bilaterally using a 0.5mm pen. Biopsies were stored at -80°C for further RNA extraction. RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
All steps were carried out on ice. Tissue biopsies were moved to precooled Precellys tubes containing ice-cold ceramic beads for homogenization via Precellys 24 (Peqlab, Erlangen, Germany) (600 g, 20 s). Extraction was performed using RNeasy® mini kit (Qiagen, Hilden, Germany) according to the protocol provided by the manufacturer.


title: HGHL, IP

value: Human umbilical vein

value: High glucose and high lipid culture medium


title: Sample 1_Mouse PBMCs Untreated rep1

value: BALB/c

value: Peripheral Blood Mononuclear Cells


title: UT_marathon


title: sustained BNST female MR1 92_BNST

description: sustained BNST female MR1


title: sustained BLA female MR1 107_BLA

description: sustained BLA female MR1


title: KO3

city: shanghai

first: hongshang

last: chu

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.

source_name: distal part of the auricle

growth_protocol: no

extract_protocol:
Distal part of the auricle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (Sigma) was dissolved in corn oil and administered peritoneally to mice at 120 mg kg−1 body weight daily for 3 days.

value: distal part of the auricle

value: male

value: 60 days

value: Tamoxifen


title: ETC_tgirt70

value: ETC


title: vsp_2

city: nanjing

last: Yang

state: 选择一项...

address: 江苏省南京市卫岗一号南京农业大学

institute: Nanjing Agricultural university

data_processing:
BGISEQ-500
Assembly: NBI_Gossypium_hirsutum_v1.1
Supplementary files format and content: mm10
Supplementary files format and content: FPKM values

organism: Gossypium hirsutum

source_name: Leaves

extract_protocol: A polysaccharides and polyphenols RNA extraction kit (Tiangen, Beijing) was used to extract RNA from leaves. 1.3 μL of total RNA was used for the construction of sequencing libraries

value: Leaves

value: MSmsv1v1 (Virescent mutant)


title: vsp_1

address: 江苏省南京市卫岗一号南京农业大学


title: DMS_tgirt65

value: bacterial cells

value: DMS


title: UT_tgirt70

value: UT


title: KO2


title: vsp_3

address: 江苏省南京市卫岗一号南京农业大学


title: WT_3

address: 江苏省南京市卫岗一号南京农业大学

value: msmsv1v1 (WT)


title: KO1


title: phasic BLA female MR1 105_BLA

description: phasic BLA female MR1

value: BLA

value: female

value: phasic


title: sustained BLA female MR1 103_BLA

description: sustained BLA female MR1

value: sustained


title: WT3


title: phasic BNST female MR1 102_BNST

description: phasic BNST female MR1

value: BNST


title: WT_2

address: 江苏省南京市卫岗一号南京农业大学


title: 1.5XETC_tgirt65


title: ETC_tgirt65


title: phasic BLA female MR1 102_BLA

description: phasic BLA female MR1


title: WT1


title: UT_tgirt65


title: WT_skin_2

status: Public on Apr 08 2024

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

description:
WT2_S12
Raw_Read_Counts_per_Gene
CPM_Normalized_counts

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.  The alignment was performed using STAR [70] with mouse reference genome mm10. The mm10 - Ensembl Transcripts release 100 gtf was used for gene feature annotation.
Partek flow software version 11.0 was used to determine read counts normalized by CPM and data analysis.
Assembly: mm10
Supplementary files format and content: txt file with raw read counts
Supplementary files format and content: txt file with CPM normalized counts

source_name: dorsal skin

extract_protocol:
TSK mice and WT littermates were used for dorsal skin isolation. After shaving the mice, the dorsal skin was removed and processed for RNA isolation using the RNAeasy kit (Qiagen). Samples in RT buffer were submitted to the Technology Center for Genomics & Bioinformatics Core at UCLA to be processed for RNA-Seq.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit with RiboErase Kit. The workflow consisted of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentaion. First strand cDNA synthesis was done using random priming followed by second strand synthesis to convert cDNA:RNA hybrids to double-stranded cDNA (dscDNA) and incorporate dUTP into the second cDNA strand. cDNA generation was followed by A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq 3000 for SE 1x50 run.

value: dorsal skin

value: WT

value: Female

tag: age

value: 6-8 weeks old


title: TSK_skin_1

description:
Fbn4_S14
Raw_Read_Counts_per_Gene
CPM_Normalized_counts

tag: tissue

value: TSK


title: TSK_skin_3

description:
Fbn6_S16
Raw_Read_Counts_per_Gene
CPM_Normalized_counts


title: WT_skin_3

description:
WT3_S13
Raw_Read_Counts_per_Gene
CPM_Normalized_counts


title: TSK_skin_2

description:
Fbn5_S15
Raw_Read_Counts_per_Gene
CPM_Normalized_counts


title: WT_skin_1

description:
WT1_S11
Raw_Read_Counts_per_Gene
CPM_Normalized_counts


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep5

type: RNA

city: Baltimore

first: Apurva

last: Borcar

state: MD

address: 685 W. Baltimore Street, MSTF 5-34

department: Anesthesiology

institute: University of Maryland School of Medicine

hyb_protocol: ss-cDNA was fragmented and labeled before hybridization onto the microarray chips, which were washed and processed using an Affymetrix GeneChip system 3000 7G.

scan_protocol: Affymetrix image data (.CEL files) was further analyzed using the R statistical analysis tool. The R ‘oligo' package was used to access the intensity values which were normalized using the ‘Robust Multichip Average (RMA)’ normalization method provided by the R ’limma’ package.

data_processing:
The samples were assessed and corrected for any batch effects before downstream analyses. Principal component analysis was utilized to identify and exclude any outlier samples. A general linear model was utilized to fit the expression values for each gene.
TXT files are available along with the CEL files. TXT files compared treatment groups to the control group after outliers were removed. The list of .TXT files and associated .CEL files are found on the Matrix table. We used the analyzed data within TXT files for our results and conclusions.

label: Biotin

organism: Rattus norvegicus

source_name: Left hippocampus

label_protocol: 150 ng RNA was transcribed to double-stranded cDNA, followed by synthesis and purification of cRNA. 2nd-cycle ss-cDNA was then synthesized and then purified after RNA hydrolysis using RNase H.

growth_protocol: Rats were subjected to different levels of hypobaria and/or hyperoxia for different durations of time at room temp. Immediately after "flight", rats were anesthetized and euthanized and tissue was collected.

extract_protocol: All tissues were processed for RNA via commercially available and appropriate kits (trizol for solid tissue, PAXgene kit for blood).

treatment_protocol: Heart, lung, and hippocampus samples were placed on dry ice immediately. Blood was collected in PAXgene blood RNA stabilization tubes and frozen. Solid tissues were placed in RNAlater ICE before processing.

value: Left hippocampus


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep6


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep6


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep5


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep5


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep6


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep6


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep6


title: WT2

value: distal part of the auricle

value: male

value: 60 days

value: Tamoxifen


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep6


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep6


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep6

description: These were the control group animals, therefore they were used as reference for differential expression of the treated groups and do not have a separate processed data file.


title: WT_1

address: 江苏省南京市卫岗一号南京农业大学

value: Leaves


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep4


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep2


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep5


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep6


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep6


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep1


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep3


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep2


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep5


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep1


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep4


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep1


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep2


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep2


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep2


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep1


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep1


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep1


title: Left hippocampus of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep2


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep2


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep1


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep2


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep1


title: Left hippocampus of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep2


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep1


title: Left hippocampus of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep4


title: Left hippocampus of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep2


title: lasR gene knockout strain (PAO1ΔlasR)  rep3

city: wenzhou

first: Changrui

last: Qian

state: zhejiang

address: wenzhou medical university

institute: wenzhou medical university

data_processing:
The RNA-seq data of 6 samples was filtered with fastp.
The clean reads were mapped to the reference genome using HISAT2.
Expression level of gene was calculated by featureCounts.
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: PAO1
Supplementary files format and content: gene_counts_matrix.txt

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: Pseudomonas aeruginosa PAO1, PAO1ΔlasR were cultured in LB medium at 37℃ with constant shaking (200 rpm) for 16 h.

extract_protocol: Bacterial cells were pelleted and flash frozen on dry ice. Pellets were shipped to Genewiz for RNA extraction, Illumina Ribo-Zero rRNA removal, Illumina library construction, and sequencing.


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep3


title: Left hippocampus of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep1


title: lasR gene knockout strain (PAO1ΔlasR)  rep1


title: lasR gene knockout strain (PAO1ΔlasR)  rep2


title: wild type PAO1 rep2

value: wild type


title: S23

city: Xi’an

first: Chunsheng

last: Wang

address: No. 157, West Fifth Road

institute: Second Affiliated Hospital of Xi’an Jiaotong University

data_processing:
CLC Genomics Workbench v 11 0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: subchondral bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)- 1.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: subchondral bone

tag: cell type

value: Subchondral bone cells


title: S20


title: wild type PAO1 rep1

tag: genotype


title: S13


title: S10


title: S12


title: S21


title: LMH cells_PP2V4

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

description: LMH cells, PP2

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Assembly: Gallus_gallus-4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: LMH

growth_protocol: LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LMH cells with or without ILTV infection were treated with PP1 dissolved in DMSO at a final concentration of 2 μM or PP2 dissolved in DMSO at a final concentration of 20 μM.

value: LMH

value: liver cells

tag: treatment

tag: infection

value: ILTV infection


title: LMH cells_PP2V3

description: LMH cells, PP2


title: LMH cells_PP2V2

description: LMH cells, PP2


title: LMH cells_PP2C3

description: LMH cells, PP2

value: no infection


title: LMH cells_PP2C1

description: LMH cells, PP2


title: LMH cells_PP2C2

description: LMH cells, PP2


title: LMH cells_PP1V4

description: LMH cells, PP1


title: LMH cells_PP1V1

description: LMH cells, PP1


title: LMH cells_PP1V3

description: LMH cells, PP1


title: LMH cells_PP1C4

description: LMH cells, PP1


title: wild type PAO1 rep3


title: LMH cells_PP1C2

description: LMH cells, PP1


title: LMH cells_PP1V2

description: LMH cells, PP1


title: LMH cells_PP1C3

description: LMH cells, PP1


title: LMH cells_PP1C1

description: LMH cells, PP1


title: Effector replicate 2 (ATACseq)

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Reads were trimmed in paired-end mode using Trim_Galore version 0.4.5_dev
Trimmed reads were aligned to GRCm38.p6 using BWA MEM v0.7.17
The resulting bam files were deduplicated with MarkDuplicates (Picard) v2.19.0
Bam converted to bedGraph using genomeCoverageBed from bedtools
bedGraph coverted to Bigwig using bedGraphToBigWig from KentUtils
Assembly: GRCm38.p6
Supplementary files format and content: Bigwig (bw)

source_name: CD8+ T cells

extract_protocol:
60h after transfer, undivided (Naïve) or divided (Tolerance, Effector) CD45.1+ OT-I cells were sorted from either the spleen (Naïve, Effector) or pooled sacral and pancreatic LNs (Tolerance)
ATACseq library preparation was conducted based on a published protocol (Buenrostro et al, Nat Methods, 2013).

treatment_protocol: CTV labelled CD45.1+ OT-I mice were injected i.v. into untreated B6 mice (Naïve), RIP-OVAhi mice (Tolerance) or LM-OVA infected B6 mice (Effector)

value: OT-I CD8+ T cell

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into B6 mice simultaneously infected i.v. with 10^6 cfu LM-OVA

value: CD45.1+ OT-I TCR transgenic

tag: timepoint


title: Tolerance replicate 2 (ATACseq)

tag: strain

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice


title: Tolerance replicate 1 (ATACseq)


title: Effector replicate 1 (ATACseq)


title: Naïve replicate 1 (ATACseq)

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into B6 mice


title: LMH cells_PP2V1

description: LMH cells, PP2


title: mouse muscle healthy SS2_20_031_P19

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

description:
Smartseq2
SS2_20_031_P19

data_processing:
The raw sequencing data was converted to demultiplexed FASTQ files using deindexer (https://github.com/ws6/deindexer) based on the Nextera index adapters and the 384 well layout.
Reads were then aligned to the mouse genome (GRCm38) using STAR v2.7.7a (Dobin et al., 2013), and FeatureCounts v2.0.1 (Liao et al., 2014) was subsequently used to extract raw gene expression counts matrix from the algnments.
Scanpy v1.7.1 package (Wolf et al., 2018) was used to convert the resulting cells-by-genes table to AnnData object and for further analysis for scRNA-seq data. Cell libraries were filtered out if: (1) the percentages of mitochondrial and ribosomal gene families were above 10%; (2) the number of unique genes in a cell was below 500; (3) predicted doublet by Scrublet v0.2.3 (Wolock et al., 2019). In total, 1425 cells were retained for downstream analysis. Genes detected in less than three cells along with mitochondrial genes were excluded from the analysis, leaving 38,178 genes in count matrix.
Python version of velocyto v0.17.17 (La Manno et al., 2018) run_smartseq2 command was used to count unspliced transcripts from the alignments masking out expressed repeat annotation downloaded from UCSC genome browser. The resulting loom file was read and the unspliced counts were added to AnnData object in ‘layers’ using scvelo v0.2.4 (Bergen et al., 2020)
Assembly: GRCh38, vM25
Supplementary files format and content: matrix.csv stores the gene by cell count matrix, with its correpsonding metadata meta.csv; adata file is an anndata object that contains the count matrix, meta data, spliced and unspliced counts and umap coordinates.

source_name: gastrocnemous muscle

growth_protocol: Cx3cr1-CreERT2 mice (Yona et al., 2013) were crossed with R26-TdTomato mice (Madisen et al., 2010), resulting in a heritable expression of tdTomato in myeloid cells and tissue-resident macrophages upon tamoxifen administration. For simultaneous in situ detection of PDGFRβ expression, the generated mouse line was crossed with the PdgfrβeGFP reporter mouse line.

extract_protocol:
Ischemic gastrocnemius muscle was removed and minced into very small pieces with a scalpel. The tissue was then mechanically and enzymatically dissociated by incubating in collagenase II (500 U/ml) (#17101015; Gibco) in RPMI1640 in 37°C for 30 minutes during intermittent pipetting. After washing the tissue with ice-cold DPBS, it was incubated for further 30 minutes with collagenase IV (15 U/ml) (#17104019; Gibco) and dispase (2.4 U/ml) (#17105041; Gibco) in RPMI1640, with intermittent pipetting. Thereafter, the tissue suspension was passed through a 23G 0.6 mm needle 8-10 times, and filtered through a 70 µm cell strainer. Once a single-cell suspension was obtained, live/dead cell staining was carried out using CellTrace Calcein Violet, AM (C34858; Invitrogen), according to manufacturer’s instructions. Lastly, tdTomato+PDGFRβ+/- cells and tdTomato-PDGFRβ+ cells were FACS sorted into SMART-Seq2 plates, using BD FACSAria™ III Cell Sorter with 4 lasers configuration (405, 488, 561, 633 nm) (BD Biosciences).
RNA libraries were prepared according to Smart-seq2 protocol.

treatment_protocol: CreERT2-mediated recombination was initiated by oral gavage of 2 mg of tamoxifen (Sigma) in corn oil once every 24 hours for 5 days, followed by a 5-days washout period. After this perior, the mice were anesthetized (Isoflurane, 2.5%, Forene, Abbott Laboratories) and the fur was removed from the left leg. Hindlimb ischemia was induced as described before (Niiyama et al., 2009). Briefly, the left femoral artery was separated from the femoral vein, followed by ligation and cutting of the femoral artery above the superficial epigastric artery branch. Post-operative pain relief was achieved with sub-cutaneous administration of carprofen (5 mg/kg). Animals were terminated by cervical dislocation before gastrocnemius muscle extraction.

value: gastrocnemous muscle

tag: Sex

value: female

value: Healthy


title: mouse muscle healthy SS2_20_031_P17

description:
Smartseq2
SS2_20_031_P17