title: 6.5 mo Nf1-mut SN

data_processing:
For Dropseq data, FASTQ sequencing reads were processed, aligned to the mouse genome (mm10), and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2, January 2016 http://mccarrolllab.com/dropseq/).
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix

source_name: Peripheral nerve tumor

extract_protocol: For mouse samples, tumor tissues were dissected and transported in DMEM to the laboratory. For scRNA-seq, the tissues were dissociated into single cells suspensions using a cocktail of collagenase type I (156 U/ml, Worthington) and dispase II protease (1.25 U/ml, Sigma) at 37oC with agitation. Cell concentration was adjusted to a final concentration of 140,000 cells/ml for Dropseq. The libraries were purified, quantified, and then sequenced on an Illumina NextSeq500.

value: Peripheral nerve tumor:sciatic nerves

tag: age

value: 28 weeks


title: Metformin-treated_adipose_1

status: Public on Nov 07 2022

type: SRA

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

country: USA

institute: AbbVie

library_source: transcriptomic

data_processing:
The raw sequence reads, obtained as fastq files were subjected to quality control using OpenGene’s fastp (v0.19.4) preprocessor.
The processed reads were aligned to the mm10 mouse reference genome prebuilt with gene annotations within 10X’s cellranger 3.0.2. software. The alignment was performed using the STAR aligner employed within cellranger 3.0.2.
Gene expression was quantified using each cell-barcode combination’s unique molecular identifiers (UMIs) using the default cellranger 3.0.2. pipeline.
The quantified counts for the raw, unfiltered cell barcodes were stored as a gene x cell matrix and exported for further downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: *_raw_feature_bc_matrix.tar: Tar archive includes raw feature x barcode matrix output from cellranger processing pipeline; barcodes, features and count matrix files.
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar: Tar archive includes filtered feature x barcode matrix output from cellranger processing pipeline; barcodes, features and count matrix files.

molecule: total RNA

organism: Mus musculus

source_name: Adipose SVF

extract_protocol: We applied single-cell RNA-Seq on mouse muscle and adipose tissues using 10X Single Cell 3’ v2 kit using ~3000 cells per lane on the 10X Chromium microfluidics device (10X Genomics, Pleasanton, CA). The libraries were sequenced at a target depth of 50 million reads/sample on Illumina NovaSeq 6000.

tag: tissue

value: Adipose SVF

tag: condition

value: Treated

tag: strain

tag: Sex

value: Male


title: Ca_72hr_1

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) was grown to an OD600 of ~1 in Middlebrook 7H9 medium (Difco) with 0.2 % glycerol, 10% OADC supplement and 0.05% Tween80 medium. Cells were washed twice with Chelex treated Sauton's medium (CTSM) and subculture in CTSM starting at an OD600 of 0.05 and was grown to an OD600 of ~1. The culture was again subcultured in CTSM starting at an OD600 of 0.05 and incubated at 37°C to an OD600 of 0.2.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, cell pellets were resuspended in Trizol and lysed by bead beating for 30sec at 6m/s for three cycles with intermittent cooling on ice. Cell debris were pelleted at 20,000g for 1min, and the supernatant was transferred to a heavy phase lock gel tube containing 300 µl chloroform. The tubes were inverted for 2min and centrifuged at 20,000g for 5min. RNA in the aqueous phase was precipitated using 300 μl isopropanol and 300 μl high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was purified using QIAGEN RNeasy kit and ribosomal RNA was depleted using the Ribo-Zero rRNA removal magnetic kit (Illumina) according to manufacturer's instructions.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit.

treatment_protocol: The cultures were supplemented with or without 1mM CaCl2 in triplicate. Bacteria were harvested at the indicated timepoints.

tag: treatment

tag: time

value: Day 3


title: Young_muscle_1

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle

value: Young


title: Sense2 Total RNA

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Florida

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: N/A
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

source_name: Primary Hippocampal neurons

growth_protocol: Hippocampi were cultured from P0 mice for generating RNA at DIV 16.

extract_protocol:
RNA was extracted using DirectZol RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: DIV 16 neurons from P0 pups


title: Ca_24hr_2

value: Day 1


title: Old_adipose_4

value: Old


title: NoCa_24hr_3

value: No Ca2+


title: 3 mo NPE mut SN2

city: CINCINNATI

first: Lai Man

middle: (Natalie)

last: Wu

state: OH

address: 3333 Burnet Avenue, MLC7013,Lu lab, T6.525

institute: CCHMC

value: 14 weeks


title: Metformin-treated_muscle_4


title: NoCa_72hr_3


title: 1.5 mo Lats1/2-def SN3

value: Lats1/2-def; ccGFP

value: 6 weeks


title: Old_muscle_4


title: ros1_4_rep4_Bisulfite-seq

city: Sheffield

first: Jurriaan

last: Ton

state: South Yorkshire

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic (v0.38) with the parameters: ‘SLIDINGWINDOW:4:25’, ‘HEADCROP:6’, MINLEN:36’.
Trimmed reads were aligned to the TAIR10 genome assembly using Bismark (v0.22.3) and Bowtie2 (v2.3.4.3) with default parameters.
Read deduplication was performed using the 'deduplicate_bismark' tool from the Bismark suite (v0.22.3) with the setting: "--paired".
Methylated and unmethylated read counts per cytosine (C) position were generated using the Bismark (v0.22.3) tool ‘bismark_methylation_extractor’ with the parameters: ‘--paired-end’, ‘--no_overlap’, ‘--ignore_3prime_r2 90’, ‘--comprehensive’, ‘--bedGraph’, ‘--CX’, ‘--cytosine_report’.
Assembly: TAIR10
Supplementary files format and content: Genome-wide cytosine reports output by the 'bismark_methylation_extractor' tool. The column headers in the text files are as follows: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Aerial tissue from two- to three-week-old plants.

growth_protocol: Seeds were stored at 4 °C, in the dark and suspended in deionised H2O (dH2O) for 4 days to break dormancy, after which they were sown onto soil consisting of Levington Advance Pot & Bedding M3 compost (ICL) and sand in a 3:1 ratio and cultivated under the following conditions: 16:8 hr day:night, 22 °C, 60% relative humidity (RH) and 150 μmol m−2 s−1.

extract_protocol:
28-35 seedlings were pooled for each replicate, flash frozen and ground to a powder. Genomic DNA was extracted using the GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich).
Bisulfite treatment, library preparation and 150 bp paired-end sequencing was performed by BGI genomics.

treatment_protocol: Plants were grown under stress free conditions.

tag: genotype

value: Aerial tissue

tag: plant age

value: 2-3 weeks old


title: Metformin-treated_muscle_3


title: NoCa_72hr_2


title: NoCa_72hr_1


title: Col0_JA_rep3_Bisulfite-seq

data_processing:
Reads were trimmed using Trimmomatic (v0.38) with the parameters: ‘PE’, ‘HEADCROP:10’.
Trimmed reads were aligned to the TAIR10 genome assembly using Bismark (v0.21.0) and Bowtie2 (v2.3.4.1) with default parameters.
Read deduplication was performed using the 'deduplicate_bismark' tool from the Bismark suite (v0.21.0) with the setting: "--paired".
Methylated and unmethylated read counts per cytosine (C) position were generated using the Bismark (v0.21.0) tool ‘bismark_methylation_extractor’ with the parameters: ‘--paired-end’, ‘--no_overlap’, ‘--ignore_3prime_r2 90’, ‘--comprehensive’, ‘--bedGraph’, ‘--CX’, ‘--cytosine_report’.
Genome_build: TAIR10
Supplementary_files_format_and_content: Genome-wide cytosine reports output by the 'bismark_methylation_extractor' tool. The column headers in the text files are as follows: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>.

source_name: Leaf tissue from five-week-old plants

growth_protocol: Seeds were stored at 4 °C, in the dark and suspended in deionised H2O (dH2O) for 4 days to break dormancy, after which they were sown onto soil consisting of Scott’s Levington M3 compost (Everris) and sand in a 3:1 ratio and cultivated under the following conditions: 8.5:15.5 hr day:night, 21 °C, 45-70% relative humidity (RH) and 100-150 μE m−2 s−1.

extract_protocol:
12 leaves, 2 from each of 6 plants, were pooled, flash frozen and ground to a powder. Genomic DNA was extracted using the GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich).
Bisulfite treatment, library preparation and 150 bp paired-end sequencing was performed by BGI genomics.

treatment_protocol:
Plants spray treated as two-week-old seedlings with a 1 mM JA solution supplemented with 0.02% of the surfactant silwet L-77.
Plants spray treated as two-week-old seedlings with water (control) or 1 mM JA solutions. The control treatment solution was supplemented with the same percentage ethanol as in the JA solution. All solutions were supplemented with 0.02% of the surfactant silwet L-77.

tag: ecotype

value: Rosette leaves

value: 5 weeks old

value: JA treatment at 2 weeks old


title: 1.5 mo Lats1/2-def SN1

value: Peripheral nerve tumor:sciatic nerves


title: Metformin-treated_muscle_2

value: Treated

value: Male


title: ros1-4_rep2_Bisulfite-seq


title: Ca_24hr_3


title: 3 mo NPE mut SN1


title: Col0_JA_rep2_Bisulfite-seq


title: Ca_6hr_3


title: ros1-4_rep1_Bisulfite-seq


title: 4 mo Lats1/2-def SN2

value: 16 weeks


title: Metformin-treated_muscle_1

value: Gastrocnemius muscle


title: 4 mo Lats1/2-def SN1


title: Ca_24hr_1


title: Ca_6hr_1


title: Col0_WaterControl_rep3_Bisulfite-seq

treatment_protocol:
Plants spray treated as two-week-old seedlings with a water control solution supplemented with the same percentage of ethanol as in the JA solution and 0.02% of the surfactant silwet L-77.
Plants spray treated as two-week-old seedlings with water (control) or 1 mM JA solutions. The control treatment solution was supplemented with the same percentage ethanol as in the JA solution. All solutions were supplemented with 0.02% of the surfactant silwet L-77.

value: Water treatment at 2 weeks old.


title: NoCa_6hr_3


title: NoCa_24hr_2

value: Day 1


title: Col0_WaterControl_rep2_Bisulfite-seq


title: 1.5 mo Lats1/2-def SN2


title: NoCa_24hr_1


title: NoCa_6hr_1


title: Old_muscle_3

value: Old


title: Old_adipose_3

value: Adipose SVF


title: OTI intergenic pool A

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

library_source: transcriptomic single cell

data_processing:
Primary data analysis was performed with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.
Read quality was assessed with the FastQC tool (version 0.11.5)
Raw FASTQ files were processed using STARsolo (STAR version 2.7.9a) for sample demultiplexing, barcode processing, alignement of reads to the mouse genome (mm10) and UMI counting on gene models from Ensembl 102. The options "outFilterType=BySJout", "outFilterMultimapNmax=10", "outSAMmultNmax=1", "outFilterScoreMin=30", "soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts", "soloUMIlen=12", "soloUMIfiltering=MultiGeneUMI_CR", "soloUMIdedup=1MM_CR", "soloCellFilter=None" were used.
For each sample, empty droplets were detected and removed using the emptyDrops() function from the Bioconductor DropletUtils package (version 1.14.0; using 5000 iterations, the option test.ambient = TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%).
Assembly: mm10
Supplementary files format and content: cells_integrated_clustered_annotated.rds: An R .rds file including a Seurat object including the final dataset used in the paper (7017 cells x 21214 genes), with normalized intensities, clustering, annotation and reduced dimensions information
Supplementary files format and content: mm10_ensdb_102_sce.rds: An R .rds file including a SingleCellExperiment class object. All droplets detected as not empty were included (11843 droplets x 55487 genes), see "data processing step" above. Read counts matrix is accessible via "counts(sce)". Information about cells is accessible via colData(sce). Information about genes is accessible via rowData(sce).

molecule: polyA RNA

source_name: Mouse CD8+ OTI T cells

growth_protocol: For the generation of murine antigen-specific Snx9 KO T cells, we harvested spleen and axial, cervical and inguinal lymph nodes from “OTI” mice (C57BL/6-Tg(TcraTcrb)1100Mjb/J, RRID:IMSR_JAX:003831), in which all CD8+ T cells recognize ovalbumin (OVA257-264, H-2Kb). Spleens and lymph nodes were strained over a 70 mm strainer and washed with PBS, incubated in red blood cell lysis buffer for 1min and wash with PBS again. Cells were then resuspended at 1.5 Mio/ml in murine T cell medium (supplemented RPMI medium as above for human T cells, but with 10% heat inactivated FCS instead of human AB+ serum). Cells were then stimulated by addition of 100 ng/ml SIINFEKL (Invivogen, OVA257-264) and 100 U/ml recombinant human IL2 (cross-reactive with murine IL-2 receptor; Proleukin, Clinigen Healthcare) and incubated at 37°C. After two days of stimulation, 900 pmol Alt-R-crRNA (sgSNX9_9 and sgSNX9_IDT_AF; IDT) and 900 pmol Alt-R-tracrRNA (IDT) were annealed by heating to 95°C for 5min, then cooled to 25°C at -0.1°C per minute. 1.5 ml of these aligned crRNA-tracrRNA complexes was then incubated with 15 ml of 40 mM Cas9-NLS protein (Berkeley, QB3) for 30min at room temperature in the dark and used immediately (referred to as Cas9-RNP). 2 days after stimulation, 10mio of the splenocytes and lymphocyte mixture was collected per condition, spun at 90g for 10min and then resuspended in 100ul P4 nucleofection buffer, the Cas9-RNPs and electroporated with the CM137 program. Immediately 900ul medium was added and rested for 20min at 37°C. Then cells were transferred to wells at 1.5 Mio/ml with 100 U/ml IL-2. Cells were expanded to reach 1.5 Mio/ml with fresh 100 U/ml IL-2 daily for 4 days.

extract_protocol:
Sorted single cells were then loaded onto a 10x Genomics Chromium NEXT GEM chip G.
Libraires were prepared following the 10x Genomics protocol for 3′ gene expression profiling (CG000315, Rev C) and cDNA or library quality was assessed using a 4200 TapeStation System (Agilent). A total of four individual libraries were prepared and sequenced using an Illumina NovaSeq 6000 instrument aiming to obtain 50,000 reads per cell.

treatment_protocol: CD57BL/6 mice were injected subcutaneously with 1 Mio MC38-OVA and 1.5 Mio OTI T cells were transferred intravenously 12 days post tumor injection. After 12 days, the tumors (7 per condition) were removed separated from fibrous, necrotic and lymphoid tissue and cut into pieces of 1mm3. These pieces were then digested in the digestion mix as described above and dissociated using a gentle MACS dissociator (Miltenyi, using a C-tube, program m_impTumor_02). The mixture was then incubated for 15min on a rotating shaker (200 rpm) at 37°C. Then the mixture was again dissociated using the m_impTumor_03 program on the gentle MACS dissociator. Cells were then strained through a 100 mm MACS SmartStrainer (Miltenyi) and washed using PBS with 2% FCS. Cells were stained for CD45 (30-F11 clone in V450, BD 560501) and CD19 (1D3 clone in FITC, BD 553785) and analyzed for lymph node contamination. Samples with more than 5% CD19+ cells among CD45+ live cells were excluded due to lymph node contamination (3 samples: 2 intergenic and 1 Snx9 KO). The remaining samples were pooled into 2 pools (2-3 mice) per condition. These pools were sorted for DAPI- CD3e+ F4/80- Ly6G- CD19- CD8a+ CD45.1+ CD45.2- single cells using an AriaIII sorter (intergenic A: 6787 cells, intergenic B: 1975 cells; Snx9 KO A: 6163 cells, Snx9 KO B: 2295).

value: intergenic

tag: timepoint

value: 13 days post transfer


title: Old_adipose_2


title: Ca_6hr_2


title: 4 mo Lats1/2-def paraspinal2

value: Peripheral nerve tumor:paraspinal

value: Lats1/2-def; ccGFP


title: 1.5 mo Lats1/2-def dermal2

value: Peripheral nerve tumor:dermal

value: 6 weeks


title: 4 mo Lats1/2-def paraspinal1


title: Old_muscle_2


title: Old_adipose_1


title: Ca_1hr_2


title: 1.5 mo Lats1/2-def paraspinal1


title: Old_muscle_1


title: Col0_WaterControl_rep1_Bisulfite-seq

value: Rosette leaves

value: 5 weeks old


title: 1.5 mo Lats1/2-def paraspinal2


title: NoCa_6hr_2

value: No Ca2+


title: Col0_JA_rep1_Bisulfite-seq

value: JA treatment at 2 weeks old


title: SRSF10EXP1_S1_L001_001.fastq.gz

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
For bulk RNA-seq, after initial quality control, the clean reads were aligned to the mouse reference genome (mm 9) using Tophat v2.1.1 (TopHat: discovering splice junctions with RNA-Seq). Next, the gene expression was calculated by Cufflinks v2.2.1. And the normalization of the gene expression values was based on the fragments per kilobase of exon per million reads mapped (FPKM).
For Iso-seq, after running the Iso-Seq pipeline, sequence data were processed using the SMRTlink 5.0 software. A circular consensus sequence (CCS) was generated from subread BAM files.Differential splicing events of Iso-seq data were analyzed using SUPPA2 software with the standard protocol.  Additional nucleotide errors in consensus reads were corrected using the Illumina RNAseq data with the software LoRDEC. Then all the consensus reads were aligned to the mouse reference genome (mm 9) using Hisat2.
For Single-cell RNA-seq, raw data were processed using the Cell Ranger Software (version 4.0.0).
Genome_build: mm9
Supplementary_files_format_and_content: For bulk RNA-seq, the txt files for FPKM contain gene names and the FPKM value for samples. For Iso-seq, the  the txt files for the differential PSI value between control and Srsf10cKO.scRNA-Seq: UMI counts matrix with gene and barcode annotations

source_name: P8 testes

growth_protocol: All mice were maintained under specific-pathogen-free (SPF) conditions in compliance with the guidelines of the Animal Care and Use Committee of the Institute of Zoology at the Chinese Academy of Sciences (CAS).

extract_protocol:
Total RNA was extracted from whole testes or enriched cells using RNAzol® RT (Molecular Research Center. Inc, RN 190) following the manufacturer’s instructions. The residual genomic DNA was removed with the DNase I Kit (Promega, M6101)
For Bulk RNA-seq,  a total amount of 1 ug of RNA per sample was used to prepare cDNA libraries generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations. For PacBio Isoform Sequencing (Iso-seq), 5 ug of total RNA per sample was used to prepare the Iso-Seq library using the Clontech SMARTer cDNA synthesis kit and the BluePippin Size Selection System protocol as described by Pacific Biosciences (PN 100-092-800-03). For Single-cell RNA-seq, Single cells were suspended in PBS containing 0.04% BSA and loaded onto the Chromium 3' v3 platform (10x Genomics) to generate single cell libraries according to the manufacturer’s protocol.

treatment_protocol: Testes samples were collected from control and Srsf10cKO mice at P3, P6 and P8, respectively. Isolated spermatogonia (THY1+ cells) for bulk RNA-seq and PacBio Isoform Sequencing (Iso-seq) were enriched from P6 control and Srsf10cKO testes using MACS method anti-THY1 antibody. Isolated spermatogonia for Single-cell RNA-seq  were enriched from P8 control and Srsf10cKO testes using MACS method anti-THY1 and anti-KIT antibody.

value: Testes

value: isolated THY1+ and KIT+ cells


title: Ca_1hr_1


title: SRSF10EXP2_S1_L001_001.fastq.gz


title: SRSF10CON_S1_L001_001.fastq.gz

value: Control


title: Isolated Sp_Srsf10 KO_rep2

source_name: P6 testes

value: isolated THY1+ cells


title: RG5

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

data_processing:
All analysis was conducted within SMRTLINK v10.1
Library strategy: DNA-seq

organism: Enterobacter cloacae

source_name: Intravenous Catheter

growth_protocol: isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

treatment_protocol: The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates

value: bacterial cells


title: Ca_1hr_3


title: 1.5 mo Lats1/2-def dermal1

value: Lats1/2-def; ccGFP (Lats1fl/fl;Lats2fl/+;Dhh-Cre;ccGFP or Lats1fl/+;Lats2fl/+;Dhh-Cre;ccGFP)


title: 211248-002

type: RNA

city: Saitama

first: Koichi

last: Suzuki

state: Saitama

address: 1-847 Amanuma

department: Department  of  Surgery

country: Japan

institute: Jichi  Medical  University, Saitama  Medical Center

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the Clariom S Array, human using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console v4.0 using Thermo Fisher Scientific default analysis settings and global scaling as normalization method. The trimmed mean was used with normalized data.

label: biotin

organism: Homo sapiens

source_name: CP-A 6.4+DCA

label_protocol: cDNA synthesis, amplification and labeling were performed with The WT PLUS Reagent Kit.

growth_protocol: CP-A, a BE metaplastic cell line that was immortalized by stable transfection of the human telomerase reverse transcriptase (TERT) was maintained in MCDB-153 medium with supplementation that included 5% fetal bovine serum, 20 ng/mL recombinant human epidermal growth factor (EGF), 140 μg/mL bovine pituitary extract (BPE), 0.4 μg/mL hydrocortisone, 20 mg/L adenine, 1x ITS supplement, 4 mM glutamine, and 8.4 μg/mL cholera toxin.

extract_protocol: Total RNA was extracted from the cultured cells using the RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: CP-A cells were exposed to the medium with acid and DCA or without them.

tag: cell line

value: CP-A

value: DCA + pH6.4


title: porphyromonas gingivalis W83, trkA mutant, rep3

city: chengdu

first: renjie

last: zou

state: Sichuan

address: Chengdu City, Sichuan Province, Wuhou District people's South Road, three 17

institute: sichuan university

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq X TEN (2 × 150bp read length).
The processing of original images to sequences, base-calling, and quality value calculations were performed using the Illumina GA Pipeline (version 1.6). A Perl program was written to select clean reads by removing low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences.
Trimmed sequence reads were mapped to the reference genome of P. gingivalis W83 (PRJNA393092) through Bowtie2
Read count extraction and normalization were performed using RSEM.
Assembly: porphyromonas gingivalis w83 (PRJNA393092)
Supplementary files format and content: text files include TPM values for each Sample

organism: Porphyromonas gingivalis W83

source_name: bacteria

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA.

value: bacteria

value: trkA knockout


title: 4 mo Lats1/2-def dermal1

value: Lats1/2-def; ccGFP

value: 16 weeks


title: FSK_Total_5

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

extract_protocol:
RNA was extracted using traditional Trizol/chloroform extraction method
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Sample Prep

value: DIV 16 neurons

tag: developmental stage

value: P0 pups

tag: agent

value: FSK


title: Isolated Sp_Srsf10 KO_rep1


title: FSK_Total_6


title: 211248-001

source_name: CP-A control

value: control


title: FSK_Total_4


title: NoCa_1hr_3

value: No Ca2+


title: NoCa_1hr_1


title: NoCa_1hr_2


title: porphyromonas gingivalis W83, trkA mutant, rep1


title: Isolated Sp_Ctrl_rep2

value: Testes


title: porphyromonas gingivalis W83, wild type, rep3

value: wild type


title: porphyromonas gingivalis W83, wild type, rep2


title: FSK_Total_2


title: Csp Iron limitation N3

first: Shiri

last: Graff van Creveld

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washingtom

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana or T. oceanica using Hisat2-2.1.0. De-novo transcriptome assemblies were generated from RNA sequences extracted from isolate cultures of Amphora, Chaetoceros, and Cylindrotheca. Each species' quality-controlled RNA sequencing data was assembled using Trinity v2.12.0 using default settings and with sequences provided as un-merged paired end reads. The pre-assembly RNA sequencing reads were then mapped back to their respective assemblies as a quality control step, and at least 85% of the reads from all cultures successfully mapped onto the resulting assemblies. The assembly resulted in 53,401 contigs for Amphora, 37,507 contigs for Chaetoceros, and 73,553 contigs for Cylindrotheca
We calculated the number of T. pseudonana or T. oceanica reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Assembly: Thaps3 FilteredModels2 or ThaOc_1.0
Supplementary files format and content: csv files include TPM values for each sample,

organism: Chaetoceros sp. CCMP199

source_name: algal cell

growth_protocol: 16:8 hours light:dark cycles and a light intensity of about 100 μmol photons·m-2·sec-1. Specific growth conditions for each species marked under 'growth conditions' as: temprature (C), salts, nutrients, and day of harvest after initiating the experiment, in replete or no iron media. Hydrogen peroxide was added to replete cultures about 2 hours before harvest for RNA-Seq.

extract_protocol:
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols

value: algal cell

value: iron limitation

tag: growth conditions

value: 24C, EASW, L1, 6days


title: Csp Iron limitation N2


title: porphyromonas gingivalis W83, wild type, rep1


title: porphyromonas gingivalis W83, trkA mutant, rep2


title: P8_Testes_Srsf10 KO_rep1

value: Total testes


title: P8_Testes_Ctrl_rep2

value: Control


title: FSK_Total_1


title: RNA_RG3

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Enterobacter bugandensis

source_name: Rectal Swab

value: bacterial cells


title: Isolated Sp_Ctrl_rep1

value: isolated THY1+ cells


title: Csp Control N3


title: DHPG_Total_6

value: DHPG


title: P8_Testes_Ctrl_rep1


title: DHPG_Total_5


title: DHPG_Total_4


title: P6_Testes_Srsf10 KO_rep1


title: P8_Testes_Srsf10 KO_rep2


title: FSK_Total_3


title: Ac Iron limitation N3

organism: Amphora coffeiformis

value: 20C, EASW, L1, 3days


title: P6_Testes_Srsf10 KO_rep2


title: RG8

organism: Enterobacter cloacae complex sp. R_G8


title: Cc Iron limitation N2

organism: Cylindrotheca closterium

value: 24C, Aquil, Aquil, 5days


title: Csp Hydrogren peroxide N1

value: Hydrogen peroxide treated


title: Csp Control N1


title: DHPG_Total_3

value: DIV 16 neurons

value: P0 pups


title: Cc Iron limitation N1


title: P6_Testes_Ctrl_rep2


title: Ac Iron limitation N2


title: DHPG_Total_2


title: P6_Testes_Ctrl_rep1


title: Ac Hydrogren peroxide N3


title: Cc Hydrogren peroxide N3


title: Cc Hydrogren peroxide N2


title: Ac Hydrogren peroxide N2


title: DHPG_Total_1


title: P3_Testes_Srsf10 KO_rep2

source_name: P3 testes


title: P3_Testes_Srsf10 KO_rep1


title: DMSO_Total_4

value: DMSO


title: P3_Testes_Ctrl_rep2


title: Cc Hydrogren peroxide N1


title: Ac Hydrogren peroxide N1


title: DMSO_Total_3


title: Cc Control N1


title: P3_Testes_Ctrl_rep1


title: Ac Iron limitation N1


title: RNA_RG8


title: Ac Control N3


title: DMSO_Total_2


title: Ac Control N2


title: RNA_RA5

organism: Enterobacter asburiae

source_name: Catheter Urine


title: DMSO_Total_1


title: P115Lats1mutparaspinal

data_processing:
For 10X genomics datasets, we used Cellranger v5.0.1 to align reads to the mm10 or hg19 human reference sequence.
Genome_build: mm10 for mouse; hg19 for human

source_name: Peripheral nerve tumor

extract_protocol:
Nerve tumors were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV). Cells were washed in 1x PBS and red blood cells were lysed using RBC lysis buffer (Roche) for 10 minutes at room temperature. Cells were filtered using a 40um strainer followed by lysis in Nuclei EZ buffer for 3-5 min. 1 ml nuclei wash buffer was pipetted into lysed nuclei, which were then centrifuged for 5 min at 500 x g. Nuclei were resuspended at appropriate concentration for scATACseq in Nuclei Buffer supplied by 10X Genomics.
single-cell libraries were generated using the GemCode Single-cell instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10x Genomics, according to the manufacturer’s instructions. The samples were incubated at 37°C for 1 h with 10 μl of transposition mix (per reaction, 7 μl ATAC Buffer, and 3 μl ATAC Enzyme (10x Genomics)). Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) programmed at 72°C for 5 min, 98°C for 30 s, 12 cycles of 98°C for 10 s, 59°C for 30 s, and 72°C for 1 min, and held at 15°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated, cleaned up and amplified. Amplified cDNA and final libraries were assessed on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies) at the Gene Expression Core at CCHMC. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads per sample at the DNA Sequencing Core at CCHMC.

value: paraspinal tumor

value: Lats1/2-def; ccGFP

value: 16 weeks


title: Trpc6-/-+LPS-2 [Z2]

status: Public on Nov 06 2022

city: Yangling

first: Wei

last: Cao

state: Shaanxi

address: No.3 Taicheng Road

department: Department of Pharmacy

institute: School of Chemistry & Pharmacy, Northwest A&F University,

data_processing:
Base calling was performed using Solexa pipeline (Off-Line Base Caller software, version 1.8).
Sequencing data quality was evaluated using FastQC (v0.11.5) and data filtering was performed with Cutadapt (1.14).
Read alignment was carried out using Hisat2 (2.0.5).
Transcriptional abundance estimation was estimated by Stringtie (1.3.1c).
The gene & transcript expression levels (FPKM) value was calculated using Ballgown (2.8.4).
Assembly: mm10
Supplementary files format and content: Expression_Transcript.xlsx

source_name: heart

extract_protocol:
RNA was harvested using the TRIzol reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

value: Adult

value: male

value: Trpc6 knockout

value: LPS challenged

value: 4 h


title: 4 mo Lats1/2-def dermal2

value: Peripheral nerve tumor:dermal


title: WT+LPS-1 [X1]

value: WT


title: Trpc1-/-+LPS-1 [Y1]

value: Trpc1 knockout


title: Trpc1-/-+LPS-2 [Y2]


title: WT+LPS-3 [X3]


title: WT+LPS-2 [X2]


title: WT+vehicle-3 [A3]

value: Vehicle


title: WT+vehicle-1 [A1]


title: Induced culture, biological replicate 3

city: Bozeman

first: Michael

middle: J

last: Franklin

state: MT

address: 109 Lewis Hall

department: Microbiology and Cell Biology

institute: Montana State University

description: Gene expression data from a sample with a 15 minute induction of rpoH

hyb_protocol: Labeled cDNA was hybridized to Affymetrix P. aeruginosa microarrays (part 900339) for 16 h at 50C with constant rotation. Microarrays were stained using a GCOS Fluidics Station 450.

scan_protocol: Microarrays were scanned with an Affymetrix 7G scanner.

data_processing: Affymetrix GCOS v1.4 was used to generate CEL files, which were imported into FlexArray v1.6.1 for quality control, normalization, and data analysis. Microarray data from three biological replicates of 8-hour planktonic arabinose induced PAO1∆rpoH (PBAD-rpoH) cultures and three non-induced PAO1∆rpoH (PBAD-rpoH) cultures were background corrected and normalized using the GC-RMA algorithm in FlexArray v1.6.1. Genes with statistically significant changes in expression (> 2-fold change at p <0.05) were determined by analysis of variance (ANOVA).

label: Biotin

organism: Pseudomonas aeruginosa

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells that were treated with arabinose for 15 minutes, replicate 3

label_protocol: For each sample, 8 μg of Turbo DNase-treated RNA was reverse transcribed, fragmented, and biotin end labeled according to the Affymetrix prokaryotic target labeling protocol (GeneChip expression analysis technical manual, November 2004).

growth_protocol: The PAO1(PBAD-rpoH) strain was cultivated overnight at 37C in Tryptic Soy Broth amended with 40 µg x ml-1 tetracycline and 0.1% arabinose. Two 1 ml aliquots of the overnight culture were washed twice with 1 ml phosphate buffered saline (PBS) pH 7.0 (9k RPM, 1 min) and resuspended in 1 ml PBS. Each washed aliquot of the overnight culture was added to 25 ml of Biofilm Minimal Medium (BMM) in a 125 ml baffled flask and incubated with shaking at 200 rpm at 37C for 7.75 h.

extract_protocol: RNA was isolated from cells using the hot phenol extraction method with chemicals obtained from Fisher Scientific (Waltham, MA). Briefly, pelleted cells were resuspended in 200 µl lysis buffer (0.15 M sucrose, 0.01 M sodium acetate, pH 4.5) and 200 µl 2% sodium dodecyl sulfate. Following the addition of 400 µl phenol, the mixture was incubated for 5 min at 65C with frequent vortexing. A Heavy Phase Lock Gel (PLG) tube (5 Prime Therapeutics, South San Francisco, CA) was used according to the manufacturer’s instructions to separate the phases. A second cleanup was performed in the PLG tube with 400 µl phenol:chloroform:isoamyl alcohol (25:24:1) solution. The aqueous phase was removed, and the RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA) with an on-column DNase treatment according to the manufacturer’s instructions. The purified RNA was then treated with turbo-DNase using the Turbo-DNA free kit (Invitrogen, now Thermo Fisher Scientific, Waltham, MA) following the manufacturer’s instructions. RNA quality was assessed on the Bioanalyzer 2100 using an RNA6000 nano assay (Agilent Technologies, Santa Clara, CA), and all samples were found to be intact with RNA Integrity Number (RIN) scores > 9.

treatment_protocol: For rpoH induction in P. aeruginosa PAO1∆rpoH (PBAD-rpoH), following 7.75 h of growth in BMM, arabinose was added to a final concentration of 0.1%. After 15 minutes, cells were collected from the non-treated control and arabinose treated cultures by centrifugation at 9k RPM for 2 min at 4C. The cell pellets were frozen at -80C for RNA extraction.

tag: induction of rpoh

value: 15 minute arabinose induction


title: Untreated control culture, biological replicate 3

description: Gene expression data from a noninduced control sample

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells, replicate 3

value: Non-induced


title: Induced culture, biological replicate 2

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells that were treated with arabinose for 15 minutes, replicate 2


title: Induced culture, biological replicate 1

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells that were treated with arabinose for 15 minutes, replicate 1


title: Untreated control culture, biological replicate 2

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells, replicate 2


title: Cd1d -/- skin_rep1

city: San Antonio

last: Xiong

state: Texas

address: 7703 Floyd Curl Drive

department: MIMG

institute: UTHSCSA

data_processing:
The Galaxy web platform (usegalaxy.org)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC and RseQC (version 2.6.4)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (version 2.0.4 )
Read count extraction and normalization were performed using R package DESeq2 version 1.16.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was harvested using RNeasy fibrous tissue mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene (https://en.novogene.com/services/research-services/transcriptome-sequencing/) following Novogene's standard protocols.

value: skin

value: Cd1d KO


title: Cd1d +/- skin_rep1


title: Cd1d -/- skin_rep2


title: Cd1d +/- skin_rep2


title: bulk_CTRL_NC3_1_D40

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
NC3-1

data_processing:
For the bulk RNA-seq, RNA-seq reads were aligned to the human reference GRCh38 genome and transcriptome using HISAT2 (v.2.1.0) . RNA differential expression analysis was performed using the DESeq2 package (v.1.30.0) . The cutoff criterion was set as adjusted P value < 0.05, and absolute log2(fold change) ≥ 1
For the scRNA-seq, raw sequencing data was processed with Cell Ranger software version 3.1 (10X Genomics) for FASTQ generation and GRCh38 human reference genome was used for alignments. For filtering and unsupervised clustering, the gene expression matrixs from Cell Ranger results were used for downstream analysis, using R 4.1.1.
Assembly: hg38
Supplementary files format and content: raw counts of bulk RNA-seq and outputs of cellranger software, which include barcodes, gene features and expression matrix for each sample

source_name: hiPSC-derived GABAergic neurons

extract_protocol:
For the bulk RNA-seq, total RNA was extracted using the Trizol reagent kit (Life Technology Inc) and mRNA was enriched by Oligo (dT) beads and then transcripted into cDNA. For the scRNA-seq,  adherent GABAergic neurons were dissociated by 1 ml of trypLE (Life Technology Inc) for 30 min in the condition of 37°C and 5% CO2 into single cell when differentiated in vitro for 35 days. The cell debris and other aggregates were removed by additional low-speed centrifugation. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell platform, version 3. Approximately 5,000 cells were captured for each sample onto a Chromium Single Cell 3’ Chip (10X Genomics, PN-120236), and the released RNA in each cell was barcoded through reverse transcription in individual gel beads in emulsions (GEMs).
For the bulk RNA-seq, library construction and RNA sequencing was completed using the Illumina HiSeqTM 4000 platform. For the scRNA-seq, S1000TM Touch Thermal Cycler (Bio Rad) was used for reverse transcription at 53°C  for 45 min, followed by 85°C for 5 min and final hold at 4°C. The quality of cDNA was accessed on Agilent 4200 (Agilent Technologies). Libraries of scRNA-seq were established by the Chromium Single Cell 3’ Library & Gel Bead Kit V3 (10X Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell.

tag: culture time

value: 40 days in vitro

value: brain

value: hiPSC-derived GABAergic neurons

tag: disease state

value: healthy


title: Trpc6-/-+LPS-3 [Z3]

tag: tissue

value: heart

value: Adult


title: bulk_sMDD_SA005_D40

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
SA005

value: sMDD


title: bulk_CTRL_RC01001_A_D40

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
RC01001-A


title: Cd1d +/- skin_rep3


title: Trpc6-/-+LPS-1 [Z1]

tag: strain

value: male

value: Trpc6 knockout

value: LPS challenged


title: bulk_CTRL_IMR90_4_D40

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
IMR904


title: Untreated control culture, biological replicate 1

source_name: Planktonic PAO1∆rpoH (PBAD-rpoH) cells, replicate 1


title: Pi_deficient_phr1phl4_rep3

first: Dong

state: Select Region

address: School Of Life Sciences

institute: Tsinghua University

data_processing:
The libraries that passed the quality control were sequenced using the Illumina platform by BIONOVA Co. (Beijing).
The clean sequencing data were aligned into the Arabidopsis TAIR 10 genome by Tophat software.
The Q30 values of all RNA-seq samples were greater than 90%, and the ratios of mapped rates to clean reads were above 90%.
Quantification of transcripts and comparative analyses among the mutants were performed with EdgeR software using TPM
Differentially expressed genes were selected using EdgeR software. GO analysis was performed with two online softwares, agrigo v2 and metascape. The Venn diagrams were drawn by Venny 2.1.0.
Assembly: TAIR 10

source_name: root

growth_protocol: Surface-sterilized seeds were sown on agar or agarose plates containing the +Pi or -Pi medium, 1.0% (w/v) sucrose, 0.5% MES, and 1.2% (w/v) agar or 0.8% (w/v) agarose

extract_protocol:
Total RNAs were isolated from roots of 8-day-old seedlings of the WT and various mutants grown under Pi sufficiency and deficiency using the RNeasy plant mini kit (Qiagen, catalog: 74904).
mRNAs were purified from total RNAs using Oligo d(T) beads and were reversely transcribed into cDNAs. The cDNAs were fragmented, and sequencing libraries were prepared by end repairing, “A” tail addition, and adaptor ligation.

treatment_protocol: various mutants grown under Pi sufficiency and deficiency conditions for 8days

value: root

value: -Pi


title: bulk_sMDD_SA004_D40

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
SA004


title: Pi_deficient_phr1phl4_rep1


title: Pi_sufficient_phr1phl4_rep1

value: +Pi


title: bulk_sMDD_SA007_D40

description:
Total RNA from neurons was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was checked on an Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies, Santa Clara, CA, USA). Library construction and high-throughput RNA sequencing (RNA-seq) were performed with the HiSeqTM 4000 sequencing platform (Illumina, California, USA).
sMDD_vs_CTRL_fCount.txt
SA007


title: Pi_deficient_phl4_rep1


title: Trpc1-/-+LPS-3 [Y3]

tag: Sex

value: Trpc1 knockout

value: 4 h


title: WT+vehicle-2 [A2]

value: WT

tag: treatment

value: Vehicle


title: Pi_sufficient_phl4_rep2


title: Pi_deficient_phl4_rep3


title: Pi_deficient_phl4_rep2


title: Pi_deficient_phr1phl2_rep3


title: Pi_deficient_phr1phl3_rep3


title: Pi_sufficient_phl4_rep3


title: Pi_sufficient_phl4_rep1


title: Pi_sufficient_phr1phl4_rep3


title: Pi_deficient_phr1phl1phl2_rep2


title: Pi_deficient_phr1phl1_rep3


title: Pi_deficient_phr1phl2_rep2


title: Pi_deficient_phr1phl2_rep1


title: Pi_deficient_phr1phl3_rep2


title: Pi_deficient_phr1phl4_rep2


title: Pi_deficient_phr1phl1phl2phl3_rep1


title: Pi_deficient_phr1phl1phl2phl3_rep3


title: Pi_deficient_phr1phl1phl2phl3_rep2


title: Pi_deficient_phl3_rep3


title: Pi_deficient_phr1phl1phl2_rep1


title: Pi_deficient_phl3_rep2


title: Pi_deficient_phl2_rep2


title: Pi_deficient_phl3_rep1


title: Pi_deficient_phl1_rep1


title: Pi_deficient_phr1_rep3


title: Pi_sufficient_phr1phl4_rep2


title: Pi_deficient_phr1phl1_rep1


title: Pi_deficient_phr1phl1_rep2


title: Pi_deficient_phr1phl3_rep1


title: Pi_deficient_phl2_rep1


title: Pi_deficient_Col_rep1


title: Pi_deficient_phl2_rep3


title: Pi_deficient_phr1_rep1


title: Pi_deficient_phr1_rep2


title: Pi_sufficient_phr1phl3_rep1


title: Pi_sufficient_phr1phl2_rep2


title: Pi_sufficient_phr1phl3_rep2


title: Pi_sufficient_phr1phl2_rep1


title: Pi_deficient_Col_rep2


title: Pi_sufficient_phr1phl3_rep3


title: Pi_sufficient_phr1phl2_rep3


title: Pi_sufficient_phr1phl1phl2_rep2


title: Pi_sufficient_phr1phl1phl2phl3_rep3


title: Pi_deficient_phr1phl1phl2_rep3


title: Pi_sufficient_phr1phl1phl2_rep1


title: Pi_sufficient_phr1phl1_rep3


title: Pi_sufficient_phr1phl1phl2phl3_rep1


title: Pi_deficient_phl1_rep2


title: Pi_sufficient_phr1phl1phl2phl3_rep2


title: Pi_sufficient_phr1phl1_rep2


title: Pi_deficient_Col_rep3


title: Pi_sufficient_phr1phl1phl2_rep3


title: Pi_sufficient_phl3_rep2


title: Pi_sufficient_phl3_rep1


title: Pi_sufficient_phl2_rep3


title: Pi_sufficient_phl2_rep2


title: Pi_sufficient_phl1_rep2


title: Pi_sufficient_phl2_rep1


title: Pi_sufficient_phl1_rep1


title: Pi_sufficient_phr1_rep3


title: Pi_sufficient_phr1_rep2


title: Pi_sufficient_phl1_rep3


title: Pi_sufficient_Col_rep3


title: Pi_sufficient_phr1_rep1


title: spleen_iNKT_rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC and RseQC (version 2.6.4)
Trimmed sequence reads were aligned to mm9 and transcript quantification was done by RSEM
Read count extraction and normalization were performed using R package DESeq2 version 1.16.1
Assembly: mm9
Supplementary files format and content: tab-separated values and matrix files

source_name: spleen

extract_protocol:
RNA was extracted using RNEasy plus micro kit  (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by SMART-Seq v4 Ultra Low Input RNA Kit (TaKaRa) following manufacture's instruction. The cDNA libraries were sequenced across 75 bp using a paired-end strategy with IIIumina NextSeq 500 sequencing system at the Genome Sequencing Facility Core at the University of Texas Health Science Center at San Antonio.

value: spleen

value: iNKT


title: spleen_iNKT_rep1


title: spleen_iNKT_rep4


title: Pi_sufficient_Col_rep2


title: Pi_sufficient_Col_rep1


title: Pi_sufficient_phr1phl1_rep1


title: skin_iNKT_rep3

value: skin


title: skin_iNKT_rep4


title: skin_iNKT_rep1


title: Pi_sufficient_phl3_rep3


title: skin_iNKT_rep2


title: MP089 (PCA+LTA+MTA) r+l

city: New York

first: Ignacio

last: Hernandez-Morato

state: NY

address: 180 Fort Washington Ave. 8th floor. Room 860

department: Otolaryngology-Head And Neck Surgery

institute: Columbia University

description:
summary.csv
est_counts_transcipts_kallisto.txt
tpm_values_transcripts_kallisto.txt

data_processing:
We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
Assembly: Human: GRCh38; Mouse: GRCm38
Supplementary files format and content: tab-delimited text files include tpm values for each Sample
Supplementary files format and content: computed from tximport R package

organism: Rattus norvegicus

source_name: striated muscle

extract_protocol:
We extracted high-quality RNA from the distinctive intrinsic laryngeal muscles using a spin-column technology.
For STRPOLYA, a poly-A pull-down method is used  to enrich mRNAs from total RNA samples; library construction was proceeded using Illumina TruSeq chemistr.

value: striated muscle

value: Sprague-Dawley

value: Female

tag: anatomical position

value: Both

value: adult

tag: muscle type

value: (PCA+LTA+MTA) r+l


title: Pi_deficient_phl1_rep3

tag: genotype


title: MP087 PCA

value: Male

value: Left

value: PCA


title: a180224_Mm_FL_AP_wt_45s_P55H

city: Chicago

first: François

last: Spitz

state: IL

address: 920 E 58th St

department: Department of Human Genetics

institute: University of Chicago

description: MARS-Seq

data_processing:
The demultiplexing, barcoded processing, transcrit counting and aggregation were made using the MARS-Seq computational pipeline (https://github.com/tanaylab/MARS-SEQ).
Assembly: mm9
Supplementary files format and content: Tab-separated count matrix

source_name: Wild-type forelimb bud, 45s, AP photoconversion, MARS-seq

extract_protocol:
E11.5 mouse embryos were collected. Limbs were dissected and dissociated by incubation at 37˚C with 0.22 Wunsch unit/mL Liberase TM (Roche, 5401119001). The cell suspension was then stained with live (Calcein Violet, Life Technologies, C34858) and dead (Sytox Red, Thermo Fisher Scientific, S34859). Live cells were sorted into 384-well plates by FACS.
Library preparation was performed according to the MARS-Seq protocol (Jaitin et al., Science 2014). Briefly,  single cells were sorted into 384-well capture plates containing lysis solution and barcoded poly(T) RT primers (including UMIs and a well-specific barcode). After evaporation of the lysis buffer, the RT reaction was performed and unused RT primers were digested using Exonuclease I (NEB). Following pooling by half plates. second-strand cDNA synthesis was then performed and products were in vitro transcribed overnight using T7 polymerase (NEB) for linear amplification. RNA was fragmented and a partial Illumina Read1 sequencing adapter containing a plate-specific barcode was single-strand ligated using T4 RNA ligase I (NEB). Products were reverse-transcribed. Finally, the product was purified and PCR-amplified by PCR (14 cycles) with primers containing the Illumina P5-Read1 and P7-Read2 sequences. Concentration of the purified library was assessed with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent Technologies). Libraries were pooled and paired-end sequenced using an Illumina NextSeq 500 sequencer.

value: Forelimb bud

value: KikGR1 het

tag: Stage

tag: embryo id

tag: photoconversion pattern

value: AP

tag: half plate_barcode

value: GGAC

tag: sequencing batch


title: a180224_Mm_FL_AP_wt_45s_P56H

description: MARS-Seq

value: ATGC


title: MP085 LTA

tag: cell line

value: WT

value: Right

tag: developmental stage

value: LTA


title: a180224_Mm_FL_AP_wt_45s_P56A

description: MARS-Seq

value: CTCG


title: a180224_Mm_FL_AP_wt_45s_P55A

description: MARS-Seq

value: GTCC


title: MP084 MTA

value: striated muscle

value: Sprague-Dawley

value: MTA


title: MP082 PCA

value: adult


title: MP081 MTA

value: Male


title: a180224_Mm_FL_AP_wt_45s_P54A

description: MARS-Seq

value: GCAT


title: a180224_Mm_FL_AP_wt_45s_P53H

description: MARS-Seq

value: CGGT


title: a180224_Mm_FL_AP_wt_45s_P54H

description: MARS-Seq

value: Forelimb bud

value: GATC


title: MP088 LTA

value: Left


title: MP080 LTA


title: MP079 PCA

value: PCA


title: MP090 (PCA+LTA+MTA) r

value: Female

value: Both

value: (PCA+LTA+MTA) r


title: a180224_Mm_FL_AP_wt_45s_P53A

description: MARS-Seq

value: KikGR1 het

value: AP

value: TAGA


title: MP077 LTA

value: striated muscle

value: WT

value: LTA


title: MP076 MTA

value: Sprague-Dawley

value: Right

value: adult

value: MTA


title: a180223_Mm_FL_PD_wt_51s_P52A

description: MARS-Seq

source_name: Wild-type forelimb bud, 51s, PD photoconversion, MARS-seq

value: Forelimb bud

value: PD

value: GCTG


title: a180223_Mm_FL_PD_wt_51s_P52H

description: MARS-Seq

value: AAGT


title: MP086 MTA

value: Male


title: a180223_Mm_FL_PD_wt_51s_P51A

description: MARS-Seq

value: GCCA


title: MP075 LTA


title: a180223_Mm_FL_PD_wt_51s_P50H

description: MARS-Seq

value: TAAG


title: MP074 PCA

value: PCA


title: a180223_Mm_FL_PD_wt_51s_P50A

description: MARS-Seq

value: KikGR1 het

value: GTAG


title: MP083 LTA

value: striated muscle

value: Left


title: a180223_Mm_FL_PD_wt_51s_P49H

description: MARS-Seq

value: CGAG


title: MP073 MTA

value: Sprague-Dawley

value: WT


title: MP072 LTA

value: adult

value: LTA


title: spleen_iNKT_rep3

value: spleen

tag: cell type

value: iNKT


title: MP071 PCA


title: MP070 MTA

value: Right

value: MTA


title: a180224_Mm_FL_AP_del_49s_P48H

description: MARS-Seq

source_name: DEL(PolL-SHFM) hom forelimb bud, 49s, AP photoconversion, MARS-seq

value: Forelimb bud

value: KikGR1 het;DEL(PolL-SHFM) hom

value: AP

value: ATGC


title: a180224_Mm_FL_AP_del_49s_P48A

description: MARS-Seq

value: CTCG


title: MP078 MTA

value: Male


title: a180223_Mm_FL_PD_wt_51s_P49A

description: MARS-Seq

value: KikGR1 het

value: PD

value: CTGA


title: MP069 LTA

value: striated muscle

value: Sprague-Dawley


title: a180224_Mm_FL_AP_del_49s_P47H

description: MARS-Seq

value: GGAC


title: a180223_Mm_FL_PD_wt_51s_P51H

description: MARS-Seq

value: AGCT


title: MP067 MTA

value: WT

value: Left

value: adult


title: a180224_Mm_FL_AP_del_49s_P46A

description: MARS-Seq

value: GCAT


title: MP066 LTA

value: LTA


title: a180224_Mm_FL_AP_del_49s_P47A

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het;DEL(PolL-SHFM) hom

value: GTCC


title: MP065 PCA

value: PCA


title: MP063 LTA

value: Male

value: Right


title: MP064 MTA

value: MTA


title: a180224_Mm_FL_AP_del_49s_P45H

description: MARS-Seq

value: AP

value: CGGT


title: a180224_Mm_FL_AP_del_49s_P45A

description: MARS-Seq

value: TAGA


title: a180224_Mm_FL_PD_del_49s_P44H

description: MARS-Seq

source_name: DEL(PolL-SHFM) hom forelimb bud, 49s, PD photoconversion, MARS-seq

value: PD

value: ATGC


title: MP062 PCA

value: striated muscle

value: Sprague-Dawley

value: WT


title: MP060 LTA

value: Female

value: Left

value: adult


title: a180224_Mm_FL_PD_del_49s_P43H

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het;DEL(PolL-SHFM) hom

value: GGAC


title: MP061 MTA


title: MP059 PCA

value: PCA


title: a180224_Mm_FL_PD_del_49s_P43A

description: MARS-Seq

value: GTCC


title: MP056 PCA

value: Right


title: MP058 MTA

value: MTA


title: MP068 PCA

value: Male


title: a180224_Mm_FL_PD_del_49s_P42H

description: MARS-Seq

value: GATC


title: a180224_Mm_FL_PD_del_49s_P41H

description: MARS-Seq

value: PD

value: CGGT


title: a180224_Mm_FL_PD_del_49s_P42A

description: MARS-Seq

value: GCAT


title: a180224_Mm_FL_PD_del_49s_P41A

description: MARS-Seq

value: TAGA


title: a180223_Mm_FL_AER_wt_51s_P40H

description: MARS-Seq

source_name: Wild-type forelimb bud, 51s, AER photoconversion, MARS-seq

value: KikGR1 het

value: AER

value: AAGT


title: a180224_Mm_FL_AP_del_49s_P46H

description: MARS-Seq

value: AP


title: a180223_Mm_FL_AER_wt_51s_P39A

description: MARS-Seq

value: Forelimb bud

value: GCCA


title: a180223_Mm_FL_AER_wt_51s_P40A

description: MARS-Seq

value: GCTG


title: MP051 LTA

value: striated muscle

value: Sprague-Dawley

value: Female

value: WT

value: adult

value: LTA


title: a180223_Mm_FL_AER_wt_51s_P39H

description: MARS-Seq

value: AGCT


title: MP052 MTA

value: Right

value: MTA


title: MP053 PCA

value: Left

value: PCA


title: MP054 LTA


title: MP049 MTA


title: MP048 LTA


title: a180224_Mm_FL_PD_del_49s_P44A

description: MARS-Seq

value: KikGR1 het;DEL(PolL-SHFM) hom

value: PD

value: CTCG


title: MP050 PCA


title: a180223_Mm_FL_AER_wt_51s_P38H

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het

value: AER

value: TAAG


title: a180223_Mm_FL_AER_wt_51s_P38A

description: MARS-Seq

value: GTAG


title: a180223_Mm_FL_AER_wt_51s_P37H

description: MARS-Seq

value: CGAG


title: a180223_Mm_FL_AER_wt_51s_P37A

description: MARS-Seq

value: CTGA


title: MP046 MTA

value: striated muscle

value: Sprague-Dawley

value: Female

value: WT

value: adult


title: MP057 LTA

value: Right

value: LTA


title: a180224_Mm_FL_AER_del_49s_P36H

description: MARS-Seq

source_name: DEL(PolL-SHFM) hom forelimb bud, 49s, AER photoconversion, MARS-seq

value: KikGR1 het;DEL(PolL-SHFM) hom

value: ATGC


title: MP055 MTA

value: Left

value: MTA


title: a180224_Mm_FL_AER_del_49s_P35H

description: MARS-Seq

value: Forelimb bud

value: GGAC


title: a180224_Mm_FL_AER_del_49s_P35A

description: MARS-Seq

value: AER

value: GTCC


title: MP044 PCA

value: PCA


title: MP042 LTA

value: Male


title: a180224_Mm_FL_AER_del_49s_P34A

description: MARS-Seq

value: GCAT


title: a180224_Mm_FL_AER_del_49s_P34H

description: MARS-Seq

value: GATC


title: VAF-02

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description: Total RNA was isolated from post-fertilized ovules

data_processing:
Raw data was processed through a quality check using the FastQC protocol (https://github.com/OpenGene/fastp), and high-quality (Phred score ≥ 30) reads by removing low quality reads (Phred score < 30), reads containing adaptors and poly-N. Further, the GC content of high-quality reads was estimated. Chickpea genome (Cicer arietinum) latest version (GCA_000331145.1) and its annotation file was used for mapping of high quality reads using HISAT2 alignment tool (http://daehwankimlab.github.io/hisat2/main/) using the default parameters.
Fragments Per Kilobase of transcript per Million (FPKM) was used for identification of differentially expressed (DE) genes between pre-fertilized ovules and post-fertilized ovules samples using Cuffdiff (a Cufflinks utility) (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/) using default parameters.
Assembly: ASM33114v1
Supplementary files format and content: csv and FPKM count

organism: Cicer arietinum

source_name: Post-fertilized ovule

extract_protocol:
The total RNA was extracted from pre-and post-fertilized samples using TRI-reagent. The concentration and its purity were checked on the nanodrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). The quality of RNA samples was also cross checked bt RNAase free agarose gel electrophoresis and bioanalyzer (BIO-RAD, USA). Best quality RNA samples with 260/280 ratio and RNA integrity number (RIN≥7) were further selected for transcriptome sequencing.
Total RNA was used for library preparation and paired end sequencing was performed using ILLUMINA platform according to manufacturer's instruction.

tag: cultivar

value: Half opened Flower


title: MP043 MTA

value: striated muscle

value: Sprague-Dawley

value: WT


title: VAF-01


title: VBF-01

description: Total RNA was isolated from pre-fertilized ovules

source_name: Pre-fertilized ovule

value: Closed Bud


title: MP040 MTA

value: Right


title: MP041 PCA


title: Pec, vestimentum

city: Montreal

first: Maeva

last: Perez

state: Qc

address: 1375 Avenue Thérèse-Lavoie-Roux

country: Canada

institute: Université de Montréal

data_processing:
Step1: Decontamination. Genomic ONT reads were mapped onto the mitochondrial (unpublished) and symbiont (unpublished) references with minimap2 (v2.17) and extracted with bbmap (v38.86) filterbyname.sh.
Step2: Nuclear reads were mapped onto the reference genome (Accession: JAHLWY01) with minimap2
Step3: Methylation calling with Nanopolish (v0.13.2). The raw electric signatures (or squiggles) were fetched and aligned back onto their respective mapped reads. Then, the likelihoods of each CpG-containing 6-mer given a 5-base alphabet (with A, T, G, C and M for methylated cytosines) were  calculated and CpG call groups (i.e. sequences containing one or multiple CpG motifs within 10bp of each other) were considered methylated if their log-likelihood of being methylated was twice that of being unmethylated (LLR>2).
Step4: Per-CpG normalisation: We generated a bed file of all CpGs using seqkit (v0.15.0) locate function and mapped to it the respective methylation call coverages and frequencies with bedtools (v2.29.2) map function.
Assembly: JAHLWY01
Supplementary files format and content: tab-delimited text file of methylation call coverage and frequency for all CpGs. The file includes contig_id, start position (the first base on the chromosome is 0), end position (non-inclusive), methylation call coverage (number of reads for which methylation could be assessed), methylation frequency (methylated reads / total reads assessed)
Supplementary files format and content: UCSC Genome Browser bigWig format file of genome-wide CpG methylation frequency : contig_id, start coordinate, stop coordinate, and methylation level (#methylated reads/ total reads called for methylation). Minimum methylation call coverage threshold=10X.
Library strategy: DNA-seq

organism: Paraescarpia echinospica

source_name: vestimentum

extract_protocol:
MagAttract HMV DNA kit (Qiagen, Hilden, Germany)
A whole-genome shotgun library was prepared by Novogene (Beijing, China) for sequencing on the Oxford Technologies Nanopore (ONT) PromethION platform

value: vestimentum


title: a180224_Mm_FL_AER_del_49s_P33A

description: MARS-Seq

value: KikGR1 het;DEL(PolL-SHFM) hom

value: TAGA


title: a180224_Mm_FL_AER_del_49s_P33H

description: MARS-Seq

value: Forelimb bud

value: CGGT


title: MP039 LTA

value: LTA


title: a180224_Mm_FL_AER_del_49s_P36A

description: MARS-Seq

value: AER

value: CTCG


title: MP038 PCA

value: Male

value: PCA


title: a180224_Mm_FL_AER_wt_45s_P32H

description: MARS-Seq

source_name: Wild-type forelimb bud, 45s, AER photoconversion, MARS-seq

value: KikGR1 het

value: AGGG


title: MP045 LTA

value: striated muscle

value: Female

value: adult


title: a180224_Mm_FL_AER_wt_45s_P32A

description: MARS-Seq

value: TCCG


title: MP037 MTA

value: Sprague-Dawley

value: WT

value: Left

value: MTA


title: MP047 PCA


title: a180224_Mm_FL_AER_wt_45s_P31H

description: MARS-Seq

value: Forelimb bud

value: GGTA


title: MP036 LTA

value: LTA


title: VBF-02

value: Closed Bud


title: Young2

city: Durham

first: James

last: White

state: nc

address: 300 N Duke Street

institute: Duke University SOM

data_processing:
STAR software alighnment
FeatureCounts to count Reads per kilobase of exon model per Million mapped reads.
Assembly: mm9
Supplementary files format and content: .txt - matrix of feature counts for each sample

source_name: damaged muscle cell suspension from young control treated muscle

growth_protocol: Cells were not grown ex vivo or in vitro

extract_protocol:
Muscles were dissected, minced, digested, strained and washed to isolate a single cell suspension
NEBNext Ultra RNA Library Prep Kit

treatment_protocol: Muscles were treated in vivo with either PBS or rMetrnl following BaCl2 induded muscle damage

tag: age

value: YOUNG

value: PBS

value: damaged muscle cell suspension


title: OldM3

source_name: damaged muscle cell suspension from old Metrnl treated muscle

value: OLD

value: METRNL

tag: tissue


title: OldM2


title: OldM1


title: Old4

source_name: damaged muscle cell suspension from old control treated muscle


title: Old2


title: Young3


title: Old3


title: MP034 MTA

value: striated muscle

value: Male

value: Right


title: Young1


title: a180224_Mm_FL_AER_wt_45s_P30H

description: MARS-Seq

value: KikGR1 het

tag: strain

value: AER

value: GCGC


title: MP033 LTA

value: Sprague-Dawley

tag: Sex

value: WT


title: a180224_Mm_FL_AER_wt_45s_P30A

description: MARS-Seq

value: Forelimb bud

value: AAAC


title: a180224_Mm_FL_AER_wt_45s_P29H

description: MARS-Seq

value: CGCC


title: Cold

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

country: Taiwan

institute: China Medical University

description: Sample 4

data_processing:
Sequencing was done by NovaSeq 6000 (Illumina) and alignment, demultiplexing, filtering was performed according to the manufacturer's protocol using Cell Ranger.
Assembly: mm10

source_name: inguinal WAT

extract_protocol:
Inguinal WAT (inWAT) from each treatment were dissected from mice (6 mice for each treatment) and cut into small piece (1 mm3) with scissors. Quickly transfer inWAT into a pre-wat 100 μm cell strainer and all together in a petri dish on ice. Add 3 ml ice-cold nuclei preparation buffer [(NPB) 10 mM HEPES (15630-080, Life Technologies) (pH 7.5), 1.5 mM MgCl2 (M1028, Sigma-Aldrich), 10 mM KCl (P9541, Sigma-Aldrich), 250 mM sucrose (S7903, Sigma-Aldrich) and 0.1% IGEPAL CA-630 (NP-40) (I8896, Sigma-Aldrich) in DEPC water] to the inWAT pieces and use syringe plunger to mince inWAT with strainer. Be aware that inWAT should be bathed with ice-cold NPB. Minced inWAT will eventually flow through the strainer and stay at petri dish. Wash the plunger and strainer with 2 ml NPB then filter through the strainer. The homogenate (now is at petri dish, inWAT debris is at upper side of the strainer) was then transferred to a new, pre-cooled 50 ml tube on ice. Centrifuge at 1,000 g for 10 minutes at 4℃. After aspirate the lipid layer, nuclear pellet was resuspended in 100 μl ice-cold nuclei resuspension buffer [(NRB) 1%BSA, 2 mM MgCl2 (M1028, Sigma-Aldrich) and 0.04 U RNase inhibitor (03335399001, Roche) in 1X PBS]. The nuclei were counted using Countess® II FL Automated Cell Counter (Thermo Fisher Scientific) and 12,000 nuclei were submitted for snRNA-seq using the 10X Genomics system.
10X Genomics sequencing libraries were acquired by 10X Chromium Single Cell mRNA Seq 3’ v3.1 reagent kit. Nuclei solutions containing 700-1200 nuclei/μl were loaded into Chromium Controller.
snRNA-seq

value: inguinal WAT

value: Lepr-cre; tdTomato

tag: treatment

value: Cold-treated


title: MP032 PCA

tag: anatomical position

value: PCA


title: EODF

description: Sample 3

value: Fasting-treated


title: MHb, Mutant, Saline

first: Stephanie

last: Caligiuri

state: New York

address: 1 Gustave L. Levy Place,, Box 1662

institute: Icahn School of Medicine

description: Hhiptm1Amc/J Jax stock: 006241

data_processing:
Sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.0, 10X Genomics) against the provided mm10 mouse reference genome. Downstream analyses, such as graph-based clustering, and differential expression analysis/visualization, were performed using the Loupe Cell Browser (version 3.0.1, 10X Genomics) and the Seurat R package.
Further data analyses were run on a Dell Precision T7810 Workstation running Ubuntu 18.04LTS with 128GB RAM and 16 threads. Clustering and differential expression analysis was performed using a combination of ScanPy v1.5.1 and custom Python code (available at github.com/alexcwsmith/singleCellTools). Cells were filtered by <= 5,000 and >= 200 unique genes, and <= 10 percent mitochondrial reads.
Genes expressed in less than 3 cells were then filtered out. Filtered data were then scaled to the median number of unique molecules and log(x+1) transformed. Highly variable genes were defined with a dispersion over 0.3, and total counts and percent mito were then regressed out of the data prior. Principal component analysis was then used to reduce dimensionality to 30.
A neighborhood graph was computed using 25 neighbors and 15 principal components, and visualization used the uniform manifold approximation and projection (UMAP) learning technique. The Louvain algorithm was then used to assign cluster identities with default settings. Following clustering, differential expression analysis was conducted between nicotine and saline treated cells within each cluster using Wilcoxon’s ranked-sign test and corrected with a false-discovery rate of 0.05.
Assembly: mm10 mouse genome assembly
Supplementary files format and content: Matrix files

source_name: brain

extract_protocol:
Warm water bath to 37˚C. Prewarm neuronal culturing medium (NbActiv1) to 37˚C (4 degrees). Prepare papain solution by dissolving papain to a final concentration of 2mg/ml in dissociation solution (Hibernate AB). Add 3.2ml to a vial of 6.4mg papain and mix. Transfer to a 15ml conical tube and incubate at 37˚C for 10 min prior to use – (can use 2 papain vials and divide equally between the tissue). Using a 1000ul wide bore pipette tip, transfer the tissue along with Hibernate AB medium to a new 15ml conical tube and wait until tissue settles at the bottom. Transfer the medium from the tissue to a new 15ml conical tube, leaving only enough medium to cover the tissue. Add 2ml papain solution (divide equally the 6.4ml prepped from above so will be under 2ml) to tissue and incubate at 37˚C for 20 minutes. Gently swirl to mix, repeat 2-3x during the incubation. Remove and discard the papain solution without disrupting the tissue at the bottom, leaving only enough solution to cover the tissue. Add medium from step 5 back to the tissue. Aspirate the tissue with the medium into a fire polished silanized Pasteur pipette (laurens bench) and immediately dispense the contents back to the tube. Triturate with 8-10x MAXIMUM passes through the pipette from when the first piece of tissue is taken up. The goal is to achieve 85% dissociation. Allow the tissue debris to settle for 1 minute. Transfer the supernatant containing dispersed cells to a new 15ml conical tube, leaving tissue debris at the bottom. Centrifuge cells at 200rcf for 2 minutes. Remove and discard the supernatant without disturbing the cell pellet. Leave only enough media to cover the cell pellet. Use a regular bore pipette tip and resuspend the cell in 1ml pre warmed NbActiv1 by gently pipetting 20x or until cells are completely suspended. This volume results in a cell concentration of 2000cells/ul approx.
Single cell RNA Seq was performed on these samples using the Chromium platform (10X Genomics, Pleasanton, CA) with the 3’ gene expression (3’ GEX) V3 kit, using an input of ~12,000 cells. Briefly, Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis. Libraries were sequenced in paired end mode on a NovaSeq instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.  Sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.0, 10X Genomics) against the provided mm10 mouse reference genome. Downstream analyses, such as graph-based clustering, and differential expression analysis/visualization, were performed using the Loupe Cell Browser (version 3.0.1, 10X Genomics) and the Seurat R package. Further data analyses were run on a Dell Precision T7810 Workstation running Ubuntu 18.04LTS with 128GB RAM and 16 threads. Clustering and differential expression analysis was performed using a combination of ScanPy v1.5.1 and custom Python code (available at github.com/alexcwsmith/singleCellTools). Cells were filtered by <= 5,000 and >= 200 unique genes, and <= 10 percent mitochondrial reads. Genes expressed in less than 3 cells were then filtered out. Filtered data were then scaled to the median number of unique molecules and log(x+1) transformed. Highly variable genes were defined with a dispersion over 0.3, and total counts and percent mito were then regressed out of the data prior. Principal component analysis was then used to reduce dimensionality to 30. A neighborhood graph was computed using 25 neighbors and 15 principal components, and visualization used the uniform manifold approximation and projection (UMAP) learning technique. The Louvain algorithm was then used to assign cluster identities with default settings. Following clustering, differential expression analysis was conducted between nicotine and saline treated cells within each cluster using Wilcoxon’s ranked-sign test and corrected with a false-discovery rate of 0.05.

value: brain

value: Medial Habenula

value: HHIP Mutant

value: Saline


title: CL

description: Sample 2

value: CL316243 injected


title: MHb, WT, Nicotine

description: Hhiptm1Amc/J Jax stock: 006241

value: Wild-Type

value: Nicotine

value: 1.0 mg/kg BW free base nicotine injection s.c for 3 consecutive days. Tissues collected 24 hours post last injection


title: MHb, Mutant, Nicotine

description: Hhiptm1Amc/J Jax stock: 006241


title: MHb, WT, Saline

description: Hhiptm1Amc/J Jax stock: 006241


title: PBS

description: Sample 1

value: non-treated, PBS group


title: a180224_Mm_FL_AER_wt_45s_P29A

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het

value: AER

value: ACTT


title: MP031 MTA

value: striated muscle

value: Sprague-Dawley

value: Male

value: WT

value: Left

tag: muscle type

value: MTA


title: a180224_Mm_FL_AP_wt_45s_P28H

description: MARS-Seq

tag: genotype

value: AP

value: TCTA


title: MP035 PCA

value: PCA


title: a180224_Mm_FL_AP_wt_45s_P27H

description: MARS-Seq

tag: Stage

value: ATCA


title: a180224_Mm_FL_AP_wt_45s_P28A

description: MARS-Seq

tag: embryo id

value: TGAT


title: ND_AOM_DSS1

city: Hangzhou

first: Chenxiao

last: Ye

address: Puyan street

institute: zhejiang chinese medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: genes_fpkm_expression.txt include FPKM values for each sample

source_name: colonic tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: colonic tissue

value: tissue

value: chow diet


title: BBR3

value: berberine


title: ND_AOM_DSS3


title: HFD_AOM_DSS2

value: high fat diet


title: HFD_AOM_DSS1


title: ND_AOM_DSS2


title: MP029 PCA

source_name: striated muscle


title: a180224_Mm_FL_AP_wt_45s_P27A

description: MARS-Seq

source_name: Wild-type forelimb bud, 45s, AP photoconversion, MARS-seq

value: Forelimb bud

value: KikGR1 het

tag: photoconversion pattern

value: CTAC


title: BBR2


title: MP030 LTA

value: striated muscle

value: Sprague-Dawley

value: Male

value: LTA


title: BBR1

value: WT


title: MP026 MTA

value: Left

value: MTA


title: a180224_Mm_FL_AP_wt_45s_P26H

description: MARS-Seq

value: AP

tag: half plate_barcode

value: ACAG


title: MP025 LTA


title: a180224_Mm_FL_AP_wt_45s_P26A

description: MARS-Seq

value: TTGG

tag: sequencing batch


title: a180224_Mm_FL_AP_wt_45s_P25H

description: MARS-Seq

value: CATG


title: a180224_Mm_FL_AER_wt_45s_P31A

description: MARS-Seq

value: AER

value: TTTC


title: Ins2 Tomato negative gut cells from cultured mGOs biol rep1

first: Wen

last: Du

address: 1150 ST NICHOLAS AVE

department: Medicine

data_processing: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.

source_name: Small intesine

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen).
We use the Clontech Ultra Low v4 kit for cDNA synthesis followed by NexteraXT.

value: Small intesine

tag: cell line

value: mice gut organoids

value: Epithelial cells

value: RipCre; Rosa26tdtomato

value: combination treatment


title: RipTomato+ pancreatic beta cells biol rep 1

source_name: islets

value: islets

value: primary cells

value: Pancreatic beta cells


title: MP024 PCA

value: striated muscle

value: Sprague-Dawley

value: Male

value: WT

tag: developmental stage

value: PCA


title: Ins2 Tomato positive gut cells from cultured mGOs biol rep2

tag: cell type


title: RipTomato+ pancreatic beta cells biol rep 2


title: HFD_AOM_DSS3

value: colonic tissue

value: tissue

value: high fat diet


title: Ins2 Tomato positive gut cells from cultured mGOs biol rep1


title: a180224_Mm_FL_AP_wt_45s_P25A

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het

value: AP

value: AGTC


title: MP028 LTA

value: Right

value: LTA


title: MP023 MTA

value: MTA


title: MP027 PCA


title: MP022 LTA


title: CD24neg/Ngn3Tomato+ Biol rep3 [DW025]

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38
Supplementary files format and content: counts_table_normalized

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.

value: Small intesine

tag: cell subtype

value: Primary epithelial cells

value: Neurog3Cre-FoxO1 f/f; Rosa26tdtomato


title: Ngn3Tomatoneg Biol rep2 [DW030]


title: a180126_Mm_FL_PD_del_44s_P20A

description: MARS-Seq

source_name: Wild-type forelimb bud, 44s, PD photoconversion, MARS-seq

value: PD

value: TCCG


title: a180126_Mm_FL_PD_del_44s_P20H

description: MARS-Seq

value: AGGG


title: Ngn3Tomatoneg Biol rep3 [DW027]


title: CD24neg/Ngn3Tomato+ Biol rep2 [DW028]


title: CD24+/Ngn3Tomato+ Biol rep2 [DW029]


title: CD24+/Ngn3Tomato+ Biol rep3 [DW026]


title: Ins2 Tomato negative gut cells from cultured mGOs biol rep2

value: mice gut organoids

value: Epithelial cells

value: RipCre; Rosa26tdtomato

value: combination treatment


title: a180126_Mm_FL_PD_del_44s_P19H

description: MARS-Seq

value: Forelimb bud

value: GGTA


title: MP021 PCA

value: striated muscle

value: Sprague-Dawley

value: Male

value: WT

value: PCA


title: Ngn3Tomatoneg Biol rep1 [DW033]

value: Small intesine


title: MP020 MTA

value: Female

value: Left

value: MTA


title: CD24+/Ngn3Tomato+ Biol rep1 [DW032]

value: Primary epithelial cells

value: Neurog3Cre-FoxO1 f/f; Rosa26tdtomato


title: MP019 LTA

value: LTA


title: CD24neg/Ngn3Tomato+ Biol rep1 [DW031]


title: a180126_Mm_FL_PD_del_44s_P19A

description: MARS-Seq

value: KikGR1 het

value: PD

value: TTTC


title: NFKO, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: small intestine

extract_protocol:
The whole small intestine pooled from 4-5 mice was used for cell isolation. The attached pancreata were carefully removed under a dissection microscope to avoid pancreatic β-cell contamination. The preparation process of single intestinal cells was as described (Magness et al., 2013). Cells were sorted using a BD Influx. After sorting, cells were pellet at 500g for 5min, then resuspended in 1:1 DMEM/F12 +10% FBS medium for scRNAseq.Viability >90% was obtained for all samples was determined by trypan blue staining.
10x Genomics 3’ Single Cell Gene Expression (GEX) microfluidic cell processing, library preparation and sequencing were performed by the Columbia Genome Center as described (Capdevila et al., 2020).

value: Epithelial cells

value: small intestine

value: NFKO

tag: age

value: 4-6 weeks old


title: MP018 PCA

tag: tissue

value: striated muscle

value: Sprague-Dawley


title: a180126_Mm_FL_PD_del_44s_P18A

description: MARS-Seq

value: Forelimb bud

tag: strain

value: AAAC


title: a180126_Mm_FL_PD_del_44s_P18H

description: MARS-Seq

value: GCGC


title: MP017 MTA

tag: Sex

value: Female

value: WT

value: Right


title: scATAC_seq_E16.5

first: fang

last: li

address: 22# Xinong Road

institute: Northwest A&F University

description: The group information is prefixed with 165 in the column of processed data file

data_processing:
We used Cell Ranger ATAC 1.2.0 to analyze the sequencing data and generated the single cell information.
Assembly: mm10
Supplementary files format and content: Filtered peak barcode matrix in hdf5 format

source_name: skin

extract_protocol:
The mouse fetus at desired dates was isolated using cesarean operation when the pregnant mice were anesthetic with the compound ketamine. The skin tissues (0.5 cm × 0.5 cm) were isolated from the fetus back skin and were immediately transferred to the ice-cold DMEM/F12 media (Gibco, Beijing, China) with 50 U/ml penicillin and 50 mg/ml streptomycin (HyClone, Beijing, China). After washing three times with DMEM/F12 to remove contaminative blood cells, the skin tissues were then dissociated into single cells prior to sequencing. For E13.5 and E16.5 skin tissues, the obtained skin tissues were firstly incubated with 2 mg/ml collagenase IV (Sigma, St Louis, MO, USA) for 30 min at 37 °C, and then the skin tissues were mechanically dissociated into single-cell suspensions with a 1ml pipette tip. For P0 skin tissues, the skin tissues were firstly cut into ~3 mm skin pieces and then incubated with 2 mg/ml collagenase IV for 30 min. After incubation, the hair follicles within the skin tissues were isolated with a pair of precise forceps and the pooled hair follicles were further dissociated into single cells with TypLE Express (Gibco, Grand Island, NY, USA) for 30 min at 37 °C. The obtained single-cell suspensions were then washed three times with PBS supplemented with 0.04% BSA (Sigma, St Louis, MO, USA) and were filtered with a 40 μm cell strainer (BD Falcon, BD Biosciences, San Jose, CA, USA) to remove debris and cell aggregations. For each stage, the samples were obtained from at least 3 different mouse fetus and for each fetus mouse, the single-cell suspension was prepared separately until finally pooled together prior to single-cell barcoding.
Single-cell ATAC-seq libraries were prepared using 10x Chromium Single Cell ATAC Library & Gel Bead Kit (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

value: skin


title: scATAC_seq_P0

description: The group information is prefixed with P0-2 in the column of processed data file


title: a180126_Mm_FL_PD_del_44s_P17H

description: MARS-Seq

value: CGCC


title: scATAC_seq_E13.5

description: The group information is prefixed with E135 in the column of processed data file


title: Double AAV

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: mRNA in splenic cells

data_processing:
All RNA-seq reads were processed using the 10x Cell Ranger pipeline v5.0.1. Fragments were aligned to the mm10 genome assembly using STAR aligner v2.7.2a.
Reads within coding regions were counted and normalized using Cell Ranger v5.0.1
Assembly: mm10
Supplementary files format and content: TSV and MTX files are tab-delimited text files specifying total numbers of reads overlapping each gene for each unique cell barcode (altogether in MEX format). H5 files are binary files in H5 format containing the matrix of transcript read counts for each barcode.

source_name: Spleen

extract_protocol:
Mice spleens were homogenized and filtered with a 70μm cell strainer and live cells (stained with Calcein AM) were sorted using a Flow Sony MA900 Cell Sorter.
All libraries were barcoded and prepared for sequencing using standard 10x protocols (Single cell 5' RNA-seq) and Illumina protocols.

treatment_protocol: AAV was administered to animals via intravenously tail-vein injections. Spleens were collected 1 week after the last AAV dose.

tag: times exposed


title: a180126_Mm_FL_PD_del_44s_P17A

description: MARS-Seq

value: KikGR1 het

value: ACTT


title: MP015 PCA

tag: anatomical position

value: PCA


title: Control

description: mRNA in splenic cells


title: MP014 MTA

value: Left

tag: muscle type

value: MTA


title: a180126_Mm_FL_PD_wt_45s_P12H

description: MARS-Seq

source_name: Wild-type forelimb bud, 45s, PD photoconversion, MARS-seq

tag: genotype

value: PD

value: TCTA


title: Single AAV

description: mRNA in splenic cells


title: MP016 LTA

value: striated muscle

value: LTA


title: a180126_Mm_FL_PD_wt_45s_P12A

description: MARS-Seq

value: Forelimb bud

tag: Stage

value: TGAT


title: a180126_Mm_FL_PD_wt_45s_P11H

description: MARS-Seq

tag: embryo id

value: ATCA


title: RNA-seq, DN1 cells, Tle134 mutant (KO3)

city: Xi'an

first: Xiaoke

last: Ma

address: No.2 South TaiBai Road

institute: Xidian University

data_processing:
Sequence reads were trimmed using trimmomatic (v0.38) with cutoff Quality Phred score  25
Trimmed sequence reads were mapped to mm9 genome using Tophat2 (v2.1.1)
Read count extraction were performed using featureCounts (v2.0.1), and only unique mapped reads are used for downstream analysis
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM value for each gene

source_name: Thymocyte at DN1 stage

growth_protocol: WT or Tle134-deficient DN1 (Lin–TCRb–CD8a–CD25–CD44+) thymocytes were sort-purified for downstream analysis.

extract_protocol:
DN1 thymocytes were used for total RNA extraction using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: Thymocyte at DN1 stage

value: 5-8 weeks old


title: RNA-seq, DN1 cells, Tle134 mutant (KO1)


title: RNA-seq, DN1 cells, Tle134 mutant (KO2)


title: MP012 PCA

value: Sprague-Dawley

value: Female

value: WT


title: a180126_Mm_FL_PD_wt_45s_P11A

description: MARS-Seq

value: KikGR1 het

tag: photoconversion pattern

value: CTAC


title: WT, scRNAseq

description: 10x Genomics

value: Epithelial cells

value: small intestine

value: Neurog3Cre; Rosa26tdtomato

value: 4-6 weeks old


title: MP013 LTA

value: Left


title: 20220628_dusp4 silencing 28062022_12 cre scr_12

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

country: Germany

institute: University of Regensburg

hyb_protocol: Nanostring hybridization protocol by manufacturer

scan_protocol: nCounter digital analyzer

data_processing: nsolver advanced analysis

label: nanostring reporter and capture probes

source_name: AKT/NRAS Cre DUSP4 SCR 3

label_protocol: Nanostring label protocol by manufacturer

growth_protocol: Growth in DMEM medium in incubator

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: DUSP4 siRNA vs. SCR

value: AKT/NRAS Cre

value: cell line (derived from AKT/NRAS double injected hepatocellular carcinoma in a mouse by hydrodynamic injection) with Cre knockout for AKT

value: AKT/NRAS Cre DUSP4 SCR


title: 20220628_dusp4 silencing 28062022_11 cre scr_11

source_name: AKT/NRAS Cre DUSP4 SCR 2


title: RNA-seq, DN1 cells, WT3


title: MP011 MTA

value: striated muscle

value: MTA


title: 20220628_dusp4 silencing 28062022_10 cre scr_10

source_name: AKT/NRAS Cre DUSP4 SCR 1


title: RNA-seq, DN1 cells, WT1

value: Thymocyte at DN1 stage


title: a180126_Mm_FL_PD_wt_45s_P10A

description: MARS-Seq

value: Forelimb bud

value: PD

tag: half plate_barcode

value: TTGG


title: MP010 PCA

value: Sprague-Dawley

value: Female

value: WT

value: PCA


title: RNA-seq, DN1 cells, WT2

value: 5-8 weeks old


title: a180126_Mm_FL_PD_wt_45s_P10H

description: MARS-Seq

value: KikGR1 het

value: ACAG

tag: sequencing batch


title: MP009 MTA

tag: cell line

value: Right