title: WT + aPD-L1 (C1_2)

data_processing:
The sequencing data was processed using CellRanger software (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: exhausted CD8 T cell

extract_protocol:
Mice were sacrificed and spleen isolated. Single cell suspension was created by grinding spleens though a filter. Afterwards, red blood cells were lysed with ACK-buffer for 4min. Splenocytes were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII.
CD8+, PD-1+, TIM-3 negative single-cells were sorted from the spleen of chronically infected mice using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 for the WT untreated sample or v3 for WT sample treated with aPD-L1 (10x Genomics) following the detailed protocol provided by the manufacturer.

treatment_protocol: B/6 Mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d-2 and d0) with 300µg GK1.5 antibody. At the chronic infection phase (> d30), splenocytes were isolated and CD8+, PD-1+, Tim-3 low cells were sorted using FACS AriaIII. Treated mice were injected i.p. 200µg aPD-L1 antibody (clone 10F.9G2) 24h before sacrificing the mice. Cells were pooled form 4 mice per group.

value: spleen

value: exhausted CD8 T cell

value: wild type


title: YFP+ replicate 3

status: Public on May 05 2022

type: SRA

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
reads were trimmed from adapters using cutadapt 3.4
reads were mapped to the genome assembly GRCm38 from Ensembl using STAR 2.7.3a
Genes were counted using FeatureCounts 2.0.1
Differential expression testing was conducted using DESeq2 library 1.24.0.The normalization and dispersion estimation were performed with DESeq2 using the default parameters; statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Assembly: mm10 (GRCm38) from Ensembl
Supplementary files format and content: tab-delimited text files from DESeq2 include raw and norm values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Small intestine

extract_protocol: Cells were isolated by FACS from the small intestine and collected in lysis buffer + 1% ß-mercaptoethanol. Librairies were prepared from total mRNA using the SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio) and sequenced using Illumina NextSeq 500/550 High Output kit v2.5.

tag: tissue

value: Small intestine

tag: cell type

value: CD45-CD31- Stromal cells

tag: genotype

value: YFP-


title: T cells_Control_Day 15_rep2

type: RNA

city: Atlanta

first: Jingru

last: Zhu

state: GA

address: 1365 E Clifton Rd NE Building C

department: Hematology/Oncology

country: USA

institute: Winship Cancer Institute

description:
Control-D15-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for at least 16 hours.

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified.

data_processing: Raw NanoString data (n=24) from both batches was exported from NSolver. Data quality was assessed with the help of QC plots using R package NanoStringNorm5. Three potential outlier samples were excluded from the analysis. The remaining 21 samples were imported and analyzed using R package NanoStringClustR6. Data was normalized using quantile normalization after background subtraction of mean2sd, and count thresholding. Differential expression analysis was carried out using NanoStringClustR and genes were identified as significant with an FDR adjusted p-value of less than or equal to 0.05. Functional enrichment and network analysis for the principal comparison of interest was carried out using an ordered query on gProfiler7.

label: codeset probes

source_name: T cells, Control, Day 15

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString innate immunology mouse panel. Samples were labelled with panel-specific codeset probes.

tag: gender

value: male

tag: strain

tag: treatment

value: T cells, Control

tag: time point

value: Day 15


title: T cells_Control_Day 15_rep1

description:
Control-D15-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_Control_Day 15_rep3

description:
Control-D15-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: Capture-C in E11.5 distal-limbs from R3-only mutant embryos

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

library_source: genomic

data_processing:
Base calling with standard Illumina Software
Paired-end reads from all the Capture-C experiments were aligned using bwa mem local aligner (Li et al. 2009) to a custom reference genome encompassing the captured-region (chr1:71-81Mb of the mm9 assembly) with the region corresponding to the baseline DelBs mutation deleted (chr1:76,388,978-77,858,974). There was one exception, the ΔF-all-Inv mutant Capture-C, in which a different version of the genome was used to account for the inverted coordinates (chr1:77,861,422-78,062,382). The rest of chromosomes, including the remaining chr1, were kept in the custom reference genome to be able to distinguish not-uniquely mapped reads.
Then, following the 4DN consortium recommendations, the resulting bam files were parsed with the pairtools suite (https://github.com/mirnylab/pairtools) to produce 4DN format files containing pairwise interactions. Briefly, bam files were parsed using pairtools parse. Then, not-uniquely mapped reads were filtered out using pairtools select (selecting UU, UR and RU pairs). Subsequently, pairs of reads were sorted and duplicated pairs were removed using pairtools sort and pairtools dedup respectively. Finally, dangling-ends were filtered out using a custom python script.
Filtered 4DN formatted pairs of interactions were then used to construct Knight-Ruiz (KR) normalized Hi-C matrices in hic format with Juicer (Durand et al. 2016).
Genome_build: Custom genome based on the mm9 assembly.
Supplementary_files_format_and_content: multiresolution hic files

molecule: genomic DNA

source_name: E11.5 distal limb buds

growth_protocol: E11.5 mouse limbs were microdissected in 1X PBS and the distal parts of the limb buds were collected and further processed.

extract_protocol:
Fixed nuclei were extracted adding ice-cold custom-made lysis buffer containing the following components: 50mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100, 25X Protease Inhibitor in Milliwater. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed with the following steps: digestion with DpnII RE, re-ligation of the digested fragments, de-crosslinking and DNA purification (3C fragments).
The 3C library was further processed using SureSelectXT Target Enrichment System for the Illumina Platform (Agilent Technology). 200 ng or 3 μg of sample was shared using Covaris sonicator and the following parameters; duty cycle: 10%, intensity: 5, cycle per burst:200, time: 6 minutes, temperature: 4°C. Shared sample was then treated following the kit guidelines (end repair, dA-tailing, adaptor ligation, PCR enrichment of Adaptor ligated DNA, DNA purification, hybridization and capture). The hybridization was performed using SureSelect XT Custom RNA probes (Cat # 5190-4836) and the capture with Streptavidin-Coated Beads (Invitrogen). PCR enrichment and sample indexing were done following Agilent instructions. Capture libraries were sequenced with 75bp paired-end reads.

treatment_protocol: Embryonic tissue was resuspended in Trypsin, dissociated to make a single-cell-suspension using a cell-strainer and finally pelleted. Tissue pellet was then fixed in a 2% PFA/FCS/PBS solution by incubation at room temperature for 10 minutes while tumbling. To stop the fixation process, the sample was quenched on ice and 1.425M Glycine was added.

tag: age

value: distal limb buds


title: AML12 cultured under extremely low frequency weak magnetic fields, 4

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by Trimmomatic v0.39 with parameters PE -threads 8 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36.
Quality controlled reads were mapped to mm10 whole genome by STAR v2.7.4a with parameters using ENCODE standard options for long RNA-seq pipeline (STARmanual.pdf).
Transcripts Per Million (TPM) were calculated by RSEM v1.3.3 with parameters rsem-calculate-expression -p 8 --alignments --paired-end --bam --append-names.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: AML12 cells

extract_protocol:
Total RNA was extracted from AML12 cells incubated under ELF-WMF for 1 h using QuickGene-Mini80 (Kurabo) according to the manufacturer’s instructions.
The extracted RNA was subjected to RNA-seq at Macrogen, Japan. Briefly, a sequencing library was prepared using the TruSeq Stranded mRNA kit (Illumina), and the library was read on Illumina NovaSeq 6000 (150 bp paired-end reads).

treatment_protocol: AML12 cells are exposured with pulsed extremely low frequency weak magnetic fields for 4 msec at increasing frequency of 1, 2, 3, 4, 5, 6, 7, and 8 Hz for 1 sec each. The 1-to-8 Hz pulses over 8 sec were repeated indefinitely. Peak magnetic intensity was 100 mG.  AML12 cells were incubated for 1 h under extremely low frequency weak magnetic fields (treatment group, n = 4) or not (control group, n = 4) .

value: exposure with extremely low frequency weak magnetic fields for 1h


title: Capture-C in E11.5 distal-limbs from ΔR-all mutant embryos

value: [delta]R-all


title: AML12 cultured under extremely low frequency weak magnetic fields, 3


title: WT (F7)

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

molecule: polyA RNA

extract_protocol:
Mice were sacrificed and spleen isolated. Single cell suspnesion was created by grinding spleens though a filter. Afterwards, red blood cells were lysed with ACK-buffer for 4min. Splenocytes were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII.
CD8+, PD-1+, TIM-3 negative single-cells were sorted from the spleen of chronically infected mice using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 for the WT untreated sample or v3 for WT sample treated with aPD-L1 (10x Genomics) following the detailed protocol provided by the manufacturer.

value: untreated


title: ChIP_Rad21_DistalLimb-E11-5_WT_r1

description: ChIP-seq against Rad21 in developing distal limbs of WT mice at E11.5

data_processing:
Base calling with standard Illumina Software
Single-end reads were mapped to the same custom reference genomes as specified in the Capture-C section or to mm9 using Bowtie (Langmead et al. 2009, flags -m1 -S --chunkmbs 500). Reads aligning to more than one location were filtered out by bowtie due to the -m1 flag.
Resulting alignments in SAM format were then converted to bam, sorted and deduplicated using samtools (https://github.com/samtools/samtools).
Deduplicated bam files were converted to normalized coverage tracks in bigwig format. They were generated using deepTools BamCoverage (https://github.com/deeptools) after centering the read locations and extending the signal 300bp (bamCoverage -e 300 --centerReads --normalizeUsing RPGC --effectiveGenomeSize 2620345972)
Genome_build: Custom genome based on the mm9 assembly / mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
The tissues were thawed on ice and resuspended in Chromatin Prep Buffer (High Sensitivity Chromatin Preparation kit (Catalog N. 53046)  from Active Motif) with 1x Protease Inhibitor (Roche); nuclei were released using a dounce homogenizer with a tight pestel (Active Motif Ref. 40415) and centrifuged at 4°C at 1250g for 5 minutes. Nuclei were then resuspended in cold Sonication Buffer (0.25% SDS, 10mM Tris-HCl pH 8.0, 2mM EDTA, 1X Protease inhibitor) and pipetted to facilitate nuclei disruption. The chromatin was sonicated using Diagenode Bioruptor (12 cycles 20´´on 30´´off) to achieve a fragment size ranging from 200-500 bp. Sonicated chromatin was incubated overnight with pre-washed A Dynabeads (Thermofisher Cat. N. 10001D) (previously blocked with 0.1% BSA) and 4μg of RAD21 (Ab992) or 1μg of CTCF (Diagenode, #C15410210). After the washes, samples were tagmented  in Tagmentation Solution (0.25% Tagmentation Buffer, 2mM Tn5 from Illumina 20034197) for 2 minutes at 37°C. Later the chromatin was eluted in ChIP Elution Buffer (10mM Tris-HCl pH8.0, 5mM EDTA pH8.0, 300mM NaCl, 0.4% SDS). Samples were de-crosslinked purified using AmPure Beads (NEB).
Libraries were prepared using KAPA HiFi HotStart ReadyMix (Roche) and indexed primers from Schmidl et al. 2015. Libraries were purified using AmPure Beads (NEB) and sequenced with 30 millions of single end reads of 75 nt, on NextSeq500 platform.

treatment_protocol: Distal limbs from E11.5 embryos were fixed in 1% fixation solution (1%PFA in 10%FCS/1XPBS) for 10 minutes at room temperature while tumbling. The reaction was then quenced on ice by adding Glycin (final concentration 125mM). Samples were then centrifuged at 4°C for 8 minutes at 400 g, then twice washed with cold 1X PBS and finally snap frozen and stored at -80 °C.

value: WT


title: AML12 cultured under extremely low frequency weak magnetic fields, 2


title: ChIP_Rad21_DistalLimb_E11-5_RALL_r2

description: ChIP-seq against Rad21 in developing distal limbs of RALL mice at E11.5

value: R-ALL


title: T cells_WT pDC_Day 15_rep4

description:
WT-D15-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

source_name: T cells, WT pDC, Day 15

value: T cells, WT pDC


title: T cells_WT pDC_Day 15_rep3

description:
WT-D15-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: AML12 cultured under extremely low frequency weak magnetic fields, 1


title: ChIP_Rad21_DistalLimb_E11-5_RALL_r2_input

description: Input from developing distal limbs of RALL mice at E11.5


title: AML12 control, 4

value: untreatment


title: AML12 control, 3


title: ChIP_Rad21_DistalLimb_E11-5_RALL_r1


title: ChIP_Rad21_DistalLimb_E11-5_RALL_r1_input


title: AML12 control, 2


title: T cells_VIP-KO pDC_Day 15_rep4

description:
VIP-KO-D15-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

source_name: T cells, VIP-KO pDC, Day 15

value: T cells, VIP-KO pDC


title: T cells_WT pDC_Day 15_rep1

description:
WT-D15-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_VIP-KO pDC_Day 15_rep3

description:
VIP-KO-D15-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ChIP_Rad21_DistalLimb_E11-5_R1F2_r1_input

description: Input from developing distal limbs of R1F2 mice at E11.5


title: AML12 control, 1


title: T cells_VIP-KO pDC_Day 15_rep2

description:
VIP-KO-D15-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ChIP_Rad21_DistalLimb_E11-5_R1F2_r1

description: ChIP-seq against Rad21 in developing distal limbs of R1F2 mice at E11.5


title: T cells_VIP-KO pDC_Day 15_rep1

description:
VIP-KO-D15-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ≥T2 bladder tumors post-BCG 08

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: The labelled RNA samples were hybridized at 65°C for at least 16 hours but not more than 48 hours in a thermal cycler.

scan_protocol: Each individual lane were scanned 194 Fields of View (FOV). The system images these FOVs separately, and sums the barcode counts of all FOVs from a single lane to form the final raw data count for each unique barcode target. Finally, the system reports the number of FOVs successfully imaged as FOV Counted.

data_processing: The raw data were processed using NanoString nSolver. The raw data were normalized using positive control and housekeeping genes control.

label: biotin

organism: Homo sapiens

source_name: FFPE

label_protocol: 100ng of unamplified total FFPE RNA were labelled with nanoString Reporter CodeSet and Capture ProbeSet, procedure as per MAN-10023-11_nCounter_XT_Assay_User_Manual.

extract_protocol: RNA from the FFPE sections were extracted using QIAGEN RNeasy FFPE Kit (Cat No./ID: 73504).

value: Bladder tumor

value: Post-BCG

tag: case


title: T cells_Control_Day 8_rep2

description:
Control-D8-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

source_name: T cells, Control, Day 8

value: Day 8


title: T cells_Control_Day 8_rep3

description:
Control-D8-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_WT pDC_Day 15_rep2

description:
WT-D15-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ≥T2 bladder tumors post-BCG 03


title: mESC_caRNA_m6A_WT_rep3_Input

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
library strategy: MeRIP-seq
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Peaks were called for each pair of samples by MACS2. Then peaks with at least 5 reads in Input files and more reads in IP files than responsed Input files were kept.
Genome_build: mm10
Supplementary_files_format_and_content: txt; m6A peaks

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.  Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
polyA RNA was purified with the Dynabeads mRNA Purification Kit from mESCs, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
Truseq stranded mRNA library prep according to the manufacturer’s protocols.

value: mESC

value: wild type

tag: antibody

tag: molecule subtype

value: chromatin associated RNA


title: mESC_caRNA_m6A_WT_rep2_Input


title: ChIP_Rad21_DistalLimb_E11-5_FALL_r2_input

description: Input from developing distal limbs of FALL mice at E11.5

value: F-ALL


title: ChIP_Rad21_DistalLimb_E11-5_R3-only_r1_input

description: Input from developing distal limbs of R3-only mice at E11.5


title: ChIP_Rad21_DistalLimb_E11-5_FALL_r2

description: ChIP-seq against Rad21 in developing distal limbs of FALL mice at E11.5


title: ≥T2 bladder tumors post-BCG 11


title: ChIP_Rad21_DistalLimb_E11-5_R3-only_r1

description: ChIP-seq against Rad21 in developing distal limbs of R3-only mice at E11.5


title: T cells_Control_Day 8_rep4

description:
Control-D8-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

value: male

value: T cells, Control


title: ChIP_Rad21_DistalLimb_E11-5_FALL_r1

value: distal limb buds


title: T cells_Control_Day 8_rep1

description:
Control-D8-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ≥T2 bladder tumors post-BCG 02


title: mESC_caRNA_m6A_WT_rep1_IP

value: anti-m6A from EpiMark® N6-Methyladenosine Enrichment Kit


title: ≥T2 bladder tumors post-BCG 01


title: mESC_caRNA_m6A_WT_rep3_IP


title: ChIP_Rad21_DistalLimb_E11-5_FALL_r1_input


title: mESC_caRNA_m6A_WT_rep1_Input


title: T cells_WT pDC_Day 8_rep4

description:
WT-D8-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

source_name: T cells, WT pDC, Day 8


title: mESC_caRNA_m6A_FtoKO_rep3_Input

value: Fto Knockout


title: mESC_caRNA_m6A_WT_rep2_IP


title: ≥T2 bladder tumors post-BCG 06


title: ChIP_Rad21_DistalLimb_E11-5_FALLinv_r2

description: ChIP-seq against Rad21 in developing distal limbs of FALLinv mice at E11.5

value: F-ALL-INV


title: ChIP_Rad21_DistalLimb_E11-5_FALLinv_r2_input

description: Input from developing distal limbs of FALLinv mice at E11.5


title: ≥T2 bladder tumors post-BCG 04


title: T cells_WT pDC_Day 8_rep2

description:
WT-D8-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_WT pDC_Day 8_rep3

description:
WT-D8-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_WT pDC_Day 8_rep1

description:
WT-D8-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: mESC_caRNA_m6A_FtoKO_rep3_IP


title: mESC_caRNA_m6A_FtoKO_rep2_Input


title: T cells_VIP-KO pDC_Day 8_rep4

description:
VIP-KO-D8-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

source_name: T cells, VIP-KO pDC, Day 8


title: ChIP_Rad21_DistalLimb_E11-5_FALLinv_r1


title: mESC_caRNA_m6A_FtoKO_rep1_Input


title: mESC_caRNA_m6A_FtoKO_rep2_IP


title: ≥T2 bladder tumors post-BCG 10


title: ChIP_Rad21_DistalLimb_E11-5_DelBs_r2_input

description: Input from developing distal limbs of DelBs mice at E11.5

value: DelBs


title: ≥T2 bladder tumors post-BCG 09


title: T cells_VIP-KO pDC_Day 8_rep2

description:
VIP-KO-D8-2
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: T cells_VIP-KO pDC_Day 8_rep1

description:
VIP-KO-D8-1
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).


title: ChIP_Rad21_DistalLimb_E11-5_DelBs_r1

description: ChIP-seq against Rad21 in developing distal limbs of DelBs mice at E11.5


title: ChIP_Rad21_DistalLimb_E11-5_FALLinv_r1_input


title: ChIP_Rad21_DistalLimb_E11-5_DelBs_r2


title: ChIP_Rad21_DistalLimb_E11-5_ALL_r2_input

description: Input from developing distal limbs of ALL mice at E11.5

value: ALL


title: 35S::CBP60g, 28C, DC3000 Rep 1

city: Durham

first: Jonghum

last: Kim

state: NC

address: 124 Science Dr

department: Biology

institute: Duke university

data_processing:
Raw single-end RNA sequencing reads were preprocessed to remove sequence adapters and low-quality reads using Trimmomatic version 0.32.
Leading and trailing low-quality bases (below quality score 20) were trimmed, and reads with less than 36 bp in length were removed.
Cleaned reads were aligned to the Arabidopsis thaliana TAIR 10 reference genome using STAR version 2.5.2b.
Reads per gene were counted using featureCounts version 1.22.3.
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Arabidopsis thaliana plants were grown in soil (2:1 “Arabidopsis mix”: perlite) covered with standard Phiferglass mesh for 3-4 weeks at 23°C and 60% relative humidity under a 12 h light/12 h dark regimen (100 ± 10 µmol m-2 s-1).

extract_protocol:
20 to 60 mg of fresh leaf tissues were flash-frozen in liquid nitrogen and ground using a TissueLyser (Qiagen). Plant RNA was extracted using a Qiagen Plant RNeasy Mini Kit following the manufacturer’s protocol, including the recommended on-column DNase I digestion.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS assays. The libraries were divided into two pools of 12 libraries each, combining them in equimolar proportions for multiplexed sequencing. Pools were quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit. Each pool was loaded onto one (1) lane of an Illumina HiSeq 4000 flow cell and sequencing performed in a 1x50bp single read format using HiSeq 4000 SBS reagents. Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.

treatment_protocol: Arabidopsis plants were acclimated at either 23°C (ambient) or 28°C (elevated) for 24h before chemical treatment and/or 48 h before infiltration. Plants were infiltrated with 1 to 2 x 106 Colony Forming Units (CFU) mL of Pst DC3000 (OD600=0.0005), as described previously (Huot et al., 2017 Nature Commun). Plants were returned to the growth chamber at the appropriate temperature and 60% relative humidity.

tag: accession

value: 4 weeks


title: ≥T2 bladder tumors post-BCG 12


title: 35S::CBP60g, 28C, DC3000 Rep 2


title: T1 bladder tumors pre-BCG 06

value: Pre-BCG


title: ≥T2 bladder tumors post-BCG 05

value: Bladder tumor


title: ≥T2 bladder tumors post-BCG 07

value: Post-BCG


title: ChIP_Rad21_DistalLimb_E11-5_ALL_r2

description: ChIP-seq against Rad21 in developing distal limbs of ALL mice at E11.5


title: T cells_VIP-KO pDC_Day 8_rep3

description:
VIP-KO-D8-3
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

value: T cells, VIP-KO pDC

value: Day 8


title: ChIP_Rad21_DistalLimb_E11-5_ALL_r1_input


title: mESC_caRNA_m6A_FtoKO_rep1_IP

value: mESC


title: ChIP_Rad21_DistalLimb_E11-5_ALL_r1


title: T1 bladder tumors pre-BCG 05


title: 35S::CBP60g, 28C, DC3000 Rep 3


title: T1 bladder tumors pre-BCG 12


title: ChIP_CTCF_DistalLimb-E11-5_WT_r1

description: ChIP-seq against CTCF in developing distal limbs of WT mice at E11.5

value: WT


title: 35S::CBP60g, 23C, DC3000 Rep 2


title: T1 bladder tumors pre-BCG 11


title: 35S::CBP60g, 23C, DC3000 Rep 1


title: T1 bladder tumors pre-BCG 04


title: AML patient #116 treated with induction Induction chemotherapy, CD8 cells

city: Baltimore

first: Hanna

middle: A

last: Knaus

state: Maryland

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_6_CD8

hyb_protocol: Hybridization with Human PrimeView expression arrays (Affymetrix) as per manufacturer’s instructions.

scan_protocol: Scanning was performed with M10 scanner using AGCC ScanCom software.

data_processing: R/Bioconductor package 'affy' and  RMA for background processing (PM-MM model), quantile normalization, probe summarization

source_name: AML patient

label_protocol: Total RNA was amplified with the NuGEN™ Ovation Pico WTA system and biotin labelled according manufacturer’s instructions (Affymetrix)

extract_protocol: Total RNA was isolated using TRIzol (Life Techologies) and purified using the RNA Clean&Concentrator Kit (Zymo Research). Sample quality was checked using the Agilent Bioanalyzer Nano kit, and concentrations were verified using the Nanodrop spectrophotometer (Thermo Fisher Scientific). Only specimens with a high RNA integrity (RIN >9) were used for analyses.

treatment_protocol: PBMCs were first separated by T-cell negative selection with a custom made kit (Stem Cell Technologies) containing Abs against CD33, CD34, CD123, CD11c, and CD36. CD3+ CD4+ and CD3+CD8+ T cells were then sorted on a FACSAria II (BSL-2) (BD) to high purity (>98%)

tag: disease state

value: AML

value: peripheral blood (PB)

value: CD8+ T cells

value: Induction chemotherapy only

tag: pairs


title: Col-0, 28C, DC3000 Rep 2


title: Col-0, 28C, DC3000 Rep 3


title: 35S::CBP60g, 23C, DC3000 Rep 3


title: AML patient #19 treated with induction Induction chemotherapy + pomalidomide, CD8 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_3_CD8

value: Induction chemotherapy+pomalidomide


title: AML patient #14 treated with induction Induction chemotherapy, CD8 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_4_CD8


title: T1 bladder tumors pre-BCG 09


title: Salivary gland of control ED mice_2

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.12.0.3).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.12.0.3). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the human reference genome GRCh37 release-75 using CLC Genomics Workbench software (ver.12.0.3) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.12.0.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: Salivary gland

growth_protocol: Ten week old ICR female mice were purchased from CLEA Japan Inc. (Tokyo, Japan). They were housed in a temperature-controlled and pathogen free environment with a 12 h light/dark cycle and were fed a commercial diet (CRF-1, Oriental Yeast Co., Ltd., Tokyo, Japan) with water ad libitum.

extract_protocol:
Total RNA was isolated from the fibroblasts or keratinocyte using the RNeasy Mini Kit (Qiagen). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina Next-seq DNA sequencer with 75 bp pair-end cycle sequencing kit (Illumina).

treatment_protocol: After a 7-day habituation period, mice were divided into two groups (control group and ED group; n = 3) with similar mean body weights. In order to induce atrophic changes in the salivary glands, all mice were injected intraperitoneally with 20 mg/kg/day of 5-FU (Kyowa Hakko Kirin Co., Ltd.) twice per week for 3 weeks. Simultaneously, the ED group received 1.6 kcal/0.8 mL/day of Elental® (Ajinomoto Pharmaceuticals Co., Ltd.) orally (twice/day, 5 times/week for 3 weeks) and the control group received the same amount of saline administered orally (twice/day, 5 times/week for 3 weeks).

tag: diet

value: control diet

value: ICR

value: Salivary gland

value: 10 week old


title: T1 bladder tumors pre-BCG 10


title: AML patient #111 treated with induction Induction chemotherapy, CD8 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_5_CD8


title: Col-0, 28C, DC3000 Rep 1

value: 4 weeks


title: AML patient #7 treated with induction Induction chemotherapy + pomalidomide, CD8 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_1_CD8


title: Salivary gland of control ED mice_1


title: T1 bladder tumors pre-BCG 03

value: Pre-BCG


title: AML patient #10 treated with induction Induction chemotherapy + pomalidomide, CD8 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD8+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_2_CD8


title: Col-0, 23C, DC3000 Rep 3


title: T1 bladder tumors pre-BCG 08

value: Bladder tumor


title: AML patient #116 treated with induction Induction chemotherapy, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_6_CD4

value: CD4+ T cells


title: Salivary gland of ED mice_2

value: elemental diet


title: Col-0, 23C, DC3000 Rep 1


title: Salivary gland of control ED mice_3


title: T1 bladder tumors pre-BCG 02


title: Col-0, 23C, DC3000 Rep 2


title: T1 bladder tumors pre-BCG 01


title: AML patient #111 treated with induction Induction chemotherapy, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_5_CD4


title: AML patient #14 treated with induction Induction chemotherapy, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
C_ELR_4_CD4


title: RD MCU-KD rep 3

status: Public on May 04 2022

first: Reshma

last: Taneja

address: 2 Medical Drive, MD9

department: Physiology

data_processing:
Bcl2fastq is used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5 with parameters mismatch=2. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two condition/groups (three biological replicates per condition) was performed using the DESeq2 R package (v2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table in comma-delimited format with raw gene counts for every gene and every sample

source_name: Embryonal rhabdomyosarcoma

growth_protocol: RD cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin

extract_protocol:
RNA was harvested using Trizol reagent. RNA purity and integrity were assessed with Nanodrop and agarose gel electrophoresis and Agilent 2100 respectively. mRNA fromis purified from total RNA using poly-T oligo-attached magnetic beads The mRNA is first fragmented randomly by addition of fragmentation buffer.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Control and MCU knockdown cells were transfected with scrambled siRNA and MCU-specific siRNA using Lipofectamine RNAiMAX for 48 hours before harvesting for RNA

value: patient-derived RD cell line


title: RD MCU-KD rep 2


title: T1 bladder tumors pre-BCG 07


title: RD WT rep 3


title: Salivary gland of ED mice_1


title: Salivary gland of ED mice_3


title: RD WT rep 2


title: AML patient #7 treated with induction Induction chemotherapy + pomalidomide, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_1_CD4


title: Liver_Vancomycin_PFOS L47

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

description:
Liver_Vancomycin_PFOS
L47

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Rat reference transcriptome from the UCSC website (release rn6, downloaded in August 2020) using BWA version 0.7.4.4  was used to align the second reads
Genome_build: rn6
Supplementary_files_format_and_content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,483 genes detected.

organism: Rattus norvegicus

source_name: Liver

growth_protocol: The animals were kept in cages placed in ScanTainers with  controlled environmental conditions, with reversed light/dark cycles of 12 hours. Feed was given ad libitum with Lucerne free feed based on Altromin 1314. Acidified tap water was given ad libitum in BPA free bottles.

extract_protocol:
RNA was isolated using Kit from Qiagen and stored at -80 ℃.
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.
3'Bulk RNA Barcoding sequencing

treatment_protocol:
8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS
Treatments were administered daily by oral gavage for 7 days from PD56 until PD62. Rats were exposed to 8 mg/kg bw/day Vancomycin, 3 mg/kg bw/day PFOS, 8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS or corn oil (vehicle control).

tag: Stage

value: Adult

value: wild type

tag: sample well

tag: plate

tag: barcode

value: TGCGCG


title: Liver_Vancomycin_PFOS L41

description:
Liver_Vancomycin_PFOS
L41

tag: genotype

value: GGGCGA


title: Liver_Vancomycin_PFOS L43

description:
Liver_Vancomycin_PFOS
L43

value: GGTCCC


title: Liver_Vancomycin_PFOS L46

description:
Liver_Vancomycin_PFOS
L46

value: TCGCGG


title: Liver_Vancomycin_PFOS L48

description:
Liver_Vancomycin_PFOS
L48

value: TGGGCC


title: Liver_Vancomycin_PFOS L44

description:
Liver_Vancomycin_PFOS
L44

value: GTCGCG


title: Liver_Vancomycin_PFOS L45

description:
Liver_Vancomycin_PFOS
L45

value: GTGGGG


title: AML patient #19 treated with induction Induction chemotherapy + pomalidomide, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_3_CD4

value: AML

tag: tissue

value: peripheral blood (PB)

tag: cell type

value: Induction chemotherapy+pomalidomide


title: Liver_Vancomycin_PFOS L38

description:
Liver_Vancomycin_PFOS
L38

tag: strain

value: GGCACG


title: Liver_Vancomycin_PFOS L37

description:
Liver_Vancomycin_PFOS
L37

value: GCTGGG


title: Liver_PFOS L32

description:
Liver_PFOS
L32

treatment_protocol:
3 mg/kg bw/day PFOS
Treatments were administered daily by oral gavage for 7 days from PD56 until PD62. Rats were exposed to 8 mg/kg bw/day Vancomycin, 3 mg/kg bw/day PFOS, 8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS or corn oil (vehicle control).

value: GCCGCA


title: AML patient #10 treated with induction Induction chemotherapy + pomalidomide, CD4 cells

description:
Gene expression data from AML patient treated with induction Induction chemotherapytherapy plus pomalidomide of CD4+ T cells in the peripheral blood (PB) at early lymphocyte recovery (ELR)
CP_ELR_2_CD4

value: CD4+ T cells

tag: treatment


title: Liver_PFOS L36

description:
Liver_PFOS
L36

value: GCGTGG


title: Liver_PFOS L34

description:
Liver_PFOS
L34

value: Adult

value: GCGCCA


title: Liver_PFOS L33

description:
Liver_PFOS
L33

value: wild type

value: GCCTGC


title: Liver_PFOS L31

description:
Liver_PFOS
L31

value: GCCCCT


title: Liver_PFOS L35

description:
Liver_PFOS
L35

value: GCGGCT


title: RD WT rep 1

value: patient-derived RD cell line


title: RD MCU-KD rep 1


title: Liver_PFOS L26

description:
Liver_PFOS
L26

value: CTCCGC


title: Liver_PFOS L30

description:
Liver_PFOS
L30

value: GCAGGC


title: Liver_PFOS L28

description:
Liver_PFOS
L28

value: GACGGG


title: Liver_PFOS L27

description:
Liver_PFOS
L27

value: CTGGGC


title: Liver_PFOS L29

description:
Liver_PFOS
L29

value: GAGGGC


title: Liver_Vancomycin L24

description:
Liver_Vancomycin
L24

treatment_protocol:
8 mg/kg bw/day Vancomycin
Treatments were administered daily by oral gavage for 7 days from PD56 until PD62. Rats were exposed to 8 mg/kg bw/day Vancomycin, 3 mg/kg bw/day PFOS, 8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS or corn oil (vehicle control).

value: CGGGTC


title: Liver_PFOS L25

description:
Liver_PFOS
L25

value: CGTCGC


title: Liver_Vancomycin_PFOS L42

description:
Liver_Vancomycin_PFOS
L42

value: GGGGGT


title: Liver_Vancomycin_PFOS L39

description:
Liver_Vancomycin_PFOS
L39

value: GGCGCT


title: Liver_Vancomycin_PFOS L40

description:
Liver_Vancomycin_PFOS
L40

value: GGGACC


title: Liver_Vancomycin L22

description:
Liver_Vancomycin
L22

value: Adult

value: CGGAGC


title: Liver_Vancomycin L21

description:
Liver_Vancomycin
L21

value: wild type

value: CGCGTG


title: Liver_Vancomycin L19

description:
Liver_Vancomycin
L19

value: CGCAGG


title: Liver_Vancomycin L20

description:
Liver_Vancomycin
L20

value: CGCCTC


title: Liver_Vancomycin L17

description:
Liver_Vancomycin
L17

value: CCTCGG


title: Liver_Vancomycin L18

description:
Liver_Vancomycin
L18

value: CGACGG


title: Liver_Vancomycin L15

description:
Liver_Vancomycin
L15

value: CCGCAG


title: Liver_Vancomycin L13

description:
Liver_Vancomycin
L13

value: CCCCAC


title: Liver_Vancomycin L16

description:
Liver_Vancomycin
L16

value: CCGGGT


title: Liver_Vancomycin L14

description:
Liver_Vancomycin
L14

value: CCCGAG


title: Liver_Ctrl L12

description:
Liver_Ctrl
L12

treatment_protocol:
corn oil (vehicle control)
Treatments were administered daily by oral gavage for 7 days from PD56 until PD62. Rats were exposed to 8 mg/kg bw/day Vancomycin, 3 mg/kg bw/day PFOS, 8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS or corn oil (vehicle control).

value: CCACGC


title: Liver_Ctrl L7

description:
Liver_Ctrl
L7

value: ACGCGC


title: Liver_Ctrl L11

description:
Liver_Ctrl
L11

value: CAGCGC


title: Liver_Ctrl L8

description:
Liver_Ctrl
L8

value: AGCCGC


title: Liver_Ctrl L6

description:
Liver_Ctrl
L6

value: ACCCGG


title: Liver_Ctrl L9

description:
Liver_Ctrl
L9

value: Adult

value: AGGCGG


title: Liver_Ctrl L10

description:
Liver_Ctrl
L10

value: wild type

value: CACCGG


title: Liver_Ctrl L5

description:
Liver_Ctrl
L5

value: CTCTCC


title: Liver_Ctrl L1

description:
Liver_Ctrl
L1

value: GGACAT


title: Thyroid_Vancomycin_PFOS T46

description:
Thyroid_Vancomycin_PFOS
T46

source_name: Thyroid

value: CATCAG


title: Liver_Ctrl L3

description:
Liver_Ctrl
L3

value: TCCAAC


title: Liver_Ctrl L4

description:
Liver_Ctrl
L4

value: TTGTCC


title: Liver_Vancomycin L23

description:
Liver_Vancomycin
L23

value: CGGCTG


title: Thyroid_Vancomycin_PFOS T45

description:
Thyroid_Vancomycin_PFOS
T45

value: ATCGAG


title: Liver_Ctrl L2

description:
Liver_Ctrl
L2

value: GTCAAG


title: Thyroid_Vancomycin_PFOS T48

description:
Thyroid_Vancomycin_PFOS
T48

value: GAAGAC


title: Thyroid_Vancomycin_PFOS T42

description:
Thyroid_Vancomycin_PFOS
T42

value: TTTATG


title: Thyroid_Vancomycin_PFOS T44

description:
Thyroid_Vancomycin_PFOS
T44

value: TTGGAT


title: Thyroid_Vancomycin_PFOS T43

description:
Thyroid_Vancomycin_PFOS
T43

value: TTTTAG


title: Thyroid_Vancomycin_PFOS T38

description:
Thyroid_Vancomycin_PFOS
T38

value: TTACTA


title: Thyroid_PFOS T36

description:
Thyroid_PFOS
T36

value: Adult

value: TGTATT


title: Thyroid_Vancomycin_PFOS T37

description:
Thyroid_Vancomycin_PFOS
T37

value: wild type

value: TTAACT


title: Thyroid_Vancomycin_PFOS T41

description:
Thyroid_Vancomycin_PFOS
T41

value: TTGTTA


title: Thyroid_Vancomycin_PFOS T47

description:
Thyroid_Vancomycin_PFOS
T47

value: CGACTT


title: Thyroid_PFOS T34

description:
Thyroid_PFOS
T34

value: TCTAAT


title: Thyroid_PFOS T32

description:
Thyroid_PFOS
T32

value: TATTAC


title: Thyroid_PFOS T35

description:
Thyroid_PFOS
T35

value: TGAATA


title: Thyroid_Vancomycin_PFOS T40

description:
Thyroid_Vancomycin_PFOS
T40

value: TTCATA


title: Thyroid_PFOS T33

description:
Thyroid_PFOS
T33

value: TCAAAA


title: Thyroid_Vancomycin_PFOS T39

description:
Thyroid_Vancomycin_PFOS
T39

value: TTATCA


title: Thyroid_PFOS T26

description:
Thyroid_PFOS
T26

value: TAACAA


title: Thyroid_PFOS T27

description:
Thyroid_PFOS
T27

value: TAATAG


title: Thyroid_PFOS T29

description:
Thyroid_PFOS
T29

value: TAGAAT


title: Thyroid_PFOS T30

description:
Thyroid_PFOS
T30

value: TATAAG


title: Thyroid_PFOS T31

description:
Thyroid_PFOS
T31

value: TATCAT


title: Thyroid_Vancomycin T21

description:
Thyroid_Vancomycin
T21

value: Adult

value: CTTAAT


title: Thyroid_PFOS T25

description:
Thyroid_PFOS
T25

value: wild type

value: TAAAAC


title: Thyroid_PFOS T28

description:
Thyroid_PFOS
T28

value: TACAAA


title: Thyroid_Vancomycin T20

description:
Thyroid_Vancomycin
T20

value: CTAAAA


title: Thyroid_Vancomycin T24

description:
Thyroid_Vancomycin
T24

value: GTTAAA


title: Thyroid_Vancomycin T18

description:
Thyroid_Vancomycin
T18

value: ATTTTG


title: Thyroid_Vancomycin T17

description:
Thyroid_Vancomycin
T17

value: ATTGTT


title: Thyroid_Vancomycin T16

description:
Thyroid_Vancomycin
T16

value: ATTATC


title: Thyroid_Vancomycin T19

description:
Thyroid_Vancomycin
T19

value: CATAAA


title: Thyroid_Vancomycin T13

description:
Thyroid_Vancomycin
T13

value: ATATGA


title: Thyroid_Vancomycin T15

description:
Thyroid_Vancomycin
T15

value: ATGTAA


title: Thyroid_Vancomycin T14

description:
Thyroid_Vancomycin
T14

value: ATCTAT


title: Thyroid_Ctrl T10

description:
Thyroid_Ctrl
T10

value: AGTATA


title: Thyroid_Ctrl T9

description:
Thyroid_Ctrl
T9

value: AGAATT


title: Thyroid_Ctrl T8

description:
Thyroid_Ctrl
T8

value: ACTAAA


title: Thyroid_Ctrl T12

description:
Thyroid_Ctrl
T12

value: Adult

value: ATAGAT


title: Thyroid_Ctrl T3

description:
Thyroid_Ctrl
T3

value: wild type

value: AACATA


title: Thyroid_Ctrl T5

description:
Thyroid_Ctrl
T5

value: AATATG


title: Thyroid_Vancomycin T23

description:
Thyroid_Vancomycin
T23

value: GATTAA


title: Thyroid_Ctrl T2

description:
Thyroid_Ctrl
T2

value: AAATCA


title: Thyroid_Vancomycin T22

description:
Thyroid_Vancomycin
T22

value: GAATAT


title: Thyroid_Ctrl T4

description:
Thyroid_Ctrl
T4

value: AAGTTA


title: Pituitary_Vancomycin_PFOS P45

description:
Pituitary_Vancomycin_PFOS
P45

source_name: Pituitary

value: GTGGGG


title: Pituitary_Vancomycin_PFOS P47

description:
Pituitary_Vancomycin_PFOS
P47

value: TGCGCG


title: Pituitary_Vancomycin_PFOS P44

description:
Pituitary_Vancomycin_PFOS
P44

value: GTCGCG


title: Pituitary_Vancomycin_PFOS P48

description:
Pituitary_Vancomycin_PFOS
P48

value: TGGGCC


title: Thyroid_Ctrl T1

description:
Thyroid_Ctrl
T1

value: AAACAT


title: Pituitary_Vancomycin_PFOS P42

description:
Pituitary_Vancomycin_PFOS
P42

value: GGGGGT


title: Pituitary_Vancomycin_PFOS P41

description:
Pituitary_Vancomycin_PFOS
P41

value: GGGCGA


title: Pituitary_Vancomycin_PFOS P46

description:
Pituitary_Vancomycin_PFOS
P46

value: TCGCGG


title: Pituitary_Vancomycin_PFOS P43

description:
Pituitary_Vancomycin_PFOS
P43

value: Adult

value: GGTCCC


title: Thyroid_Ctrl T11

description:
Thyroid_Ctrl
T11

value: wild type

value: ATAAGT


title: Pituitary_Vancomycin_PFOS P40

description:
Pituitary_Vancomycin_PFOS
P40

value: GGGACC


title: Thyroid_Ctrl T7

description:
Thyroid_Ctrl
T7

value: AATTTC


title: Thyroid_Ctrl T6

description:
Thyroid_Ctrl
T6

value: AATGTA


title: Pituitary_Vancomycin_PFOS P39

description:
Pituitary_Vancomycin_PFOS
P39

value: GGCGCT


title: Pituitary_PFOS P36

description:
Pituitary_PFOS
P36

value: GCGTGG


title: Pituitary_Vancomycin_PFOS P38

description:
Pituitary_Vancomycin_PFOS
P38

value: GGCACG


title: Pituitary_Vancomycin_PFOS P37

description:
Pituitary_Vancomycin_PFOS
P37

value: GCTGGG


title: Pituitary_PFOS P35

description:
Pituitary_PFOS
P35

value: GCGGCT


title: Pituitary_PFOS P33

description:
Pituitary_PFOS
P33

value: GCCTGC


title: Pituitary_PFOS P30

description:
Pituitary_PFOS
P30

value: GCAGGC


title: Pituitary_PFOS P31

description:
Pituitary_PFOS
P31

value: GCCCCT


title: Pituitary_PFOS P32

description:
Pituitary_PFOS
P32

value: GCCGCA


title: Pituitary_PFOS P29

description:
Pituitary_PFOS
P29

value: GAGGGC


title: Pituitary_PFOS P27

description:
Pituitary_PFOS
P27

value: Adult

value: CTGGGC


title: Pituitary_PFOS P28

description:
Pituitary_PFOS
P28

value: wild type

value: GACGGG


title: Pituitary_PFOS P26

description:
Pituitary_PFOS
P26

value: CTCCGC


title: Pituitary_Vancomycin P23

description:
Pituitary_Vancomycin
P23

value: CGGCTG


title: Pituitary_PFOS P25

description:
Pituitary_PFOS
P25

value: CGTCGC


title: Pituitary_Vancomycin P24

description:
Pituitary_Vancomycin
P24

value: CGGGTC


title: Pituitary_PFOS P34

description:
Pituitary_PFOS
P34

value: GCGCCA


title: Pituitary_Vancomycin P20

description:
Pituitary_Vancomycin
P20

value: CGCCTC


title: Pituitary_Vancomycin P16

description:
Pituitary_Vancomycin
P16

value: CCGGGT


title: Pituitary_Vancomycin P15

description:
Pituitary_Vancomycin
P15

value: CCGCAG


title: Pituitary_Vancomycin P18

description:
Pituitary_Vancomycin
P18

value: CGACGG


title: Pituitary_Vancomycin P22

description:
Pituitary_Vancomycin
P22

value: CGGAGC


title: Pituitary_Vancomycin P14

description:
Pituitary_Vancomycin
P14

value: CCCGAG


title: Pituitary_Ctrl P12

description:
Pituitary_Ctrl
P12

value: CCACGC


title: Pituitary_Vancomycin P13

description:
Pituitary_Vancomycin
P13

value: CCCCAC


title: Pituitary_Vancomycin P17

description:
Pituitary_Vancomycin
P17

value: Adult

value: CCTCGG


title: Pituitary_Vancomycin P19

description:
Pituitary_Vancomycin
P19

value: wild type

value: CGCAGG


title: Pituitary_Ctrl P11

description:
Pituitary_Ctrl
P11

value: CAGCGC


title: Pituitary_Ctrl P2

description:
Pituitary_Ctrl
P2

value: GTCAAG


title: Hypothalamus_Vancomycin_PFOS H45

description:
Hypothalamus_Vancomycin_PFOS
H45

source_name: Hypothalamus

value: ATCGAG


title: Hypothalamus_Vancomycin_PFOS H46

description:
Hypothalamus_Vancomycin_PFOS
H46

value: CATCAG


title: Pituitary_Ctrl P3

description:
Pituitary_Ctrl
P3

value: TCCAAC


title: Pituitary_Vancomycin P21

description:
Pituitary_Vancomycin
P21

value: CGCGTG


title: Pituitary_Ctrl P6

description:
Pituitary_Ctrl
P6

value: ACCCGG


title: Hypothalamus_Vancomycin_PFOS H44

description:
Hypothalamus_Vancomycin_PFOS
H44

value: TTGGAT


title: Hypothalamus_Vancomycin_PFOS H42

description:
Hypothalamus_Vancomycin_PFOS
H42

value: TTTATG


title: Pituitary_Ctrl P8

description:
Pituitary_Ctrl
P8

value: AGCCGC


title: Hypothalamus_Vancomycin_PFOS H39

description:
Hypothalamus_Vancomycin_PFOS
H39

value: TTATCA


title: Hypothalamus_Vancomycin_PFOS H38

description:
Hypothalamus_Vancomycin_PFOS
H38

value: TTACTA


title: Pituitary_Ctrl P10

description:
Pituitary_Ctrl
P10

value: CACCGG


title: Hypothalamus_PFOS H36

description:
Hypothalamus_PFOS
H36

value: Adult

value: TGTATT


title: Hypothalamus_PFOS H34

description:
Hypothalamus_PFOS
H34

value: wild type

value: TCTAAT


title: Hypothalamus_Vancomycin_PFOS H41

description:
Hypothalamus_Vancomycin_PFOS
H41

value: TTGTTA


title: Pituitary_Ctrl P9

description:
Pituitary_Ctrl
P9

value: AGGCGG


title: Pituitary_Ctrl P7

description:
Pituitary_Ctrl
P7

value: ACGCGC


title: Pituitary_Ctrl P4

description:
Pituitary_Ctrl
P4

value: TTGTCC


title: Pituitary_Ctrl P1

description:
Pituitary_Ctrl
P1

value: GGACAT


title: Pituitary_Ctrl P5

description:
Pituitary_Ctrl
P5

value: CTCTCC


title: Hypothalamus_Vancomycin_PFOS H48

description:
Hypothalamus_Vancomycin_PFOS
H48

value: GAAGAC


title: Hypothalamus_PFOS H26

description:
Hypothalamus_PFOS
H26

value: TAACAA


title: Hypothalamus_PFOS H25

description:
Hypothalamus_PFOS
H25

value: TAAAAC


title: W4_3

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

country: China

institute: Zhejiang University

description: Tea samples (one bud and two leaves) planted at the Tea Research Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, China (N30°11'7.21'', E120°03'52.45''), on 15 September with an artificial climate chest (the illumination intensity of 0lux, constant temperature of 25 C).

data_processing:
FASTQC (version 0.10.1) (www.bioinformatics.bbsrc.ac.uk/projects/fastqc.) was used to assess the quality of raw sequence data and Trimmomatic was used to filter low-quality reads
The previously published genome database CSS(cv.Shuchazao) was used as reference genome to map the high-quality reads by using HISAT (v 2.0.5) with default parameters
Stringtie (v 1.3.1) was used to assemble the aligned reads for all sample into transcripts
StringTie-Merge to combine the StringTie assembly results of each sample and the gene expression (FPKM) was calculated using StringTie's own script prepDE.py
The differently expressed genes (DEGs) were identified by using Ballgown
Genome_build: Teaplant_CSS_version2 from TPIA (http://tpia.teaplant.org/download.html)
Supplementary_files_format_and_content: Genes_rcounts.xls

organism: Camellia sinensis

source_name: the leaves samples at 24 hour during withering proces

growth_protocol: Tea samples (one bud and two leaves) planted at the Tea Research Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, China (N30°11′7.21″, E120°03′52.45″), on 15 September with an artificial climate chest (the illumination intensity of 0lux, constant temperature of 25°C).

extract_protocol:
The total RNA isolation from rea leaves according to Thermo GeneJET Plant RNA Purification Mini Kit (Thermo Fisher Scientific Inc, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tea leaves during withering for 0 (W1), 9 (W2), 15 (W3) and 24 (W4) hours

tag: cultivar

value: Camellia sinensis cv. Longjing43

value: leaf


title: Hypothalamus_Vancomycin_PFOS H43

description:
Hypothalamus_Vancomycin_PFOS
H43

value: TTTTAG


title: W4_2


title: Hypothalamus_Vancomycin_PFOS H47

description:
Hypothalamus_Vancomycin_PFOS
H47

value: CGACTT


title: Hypothalamus_Vancomycin_PFOS H40

description:
Hypothalamus_Vancomycin_PFOS
H40

value: Adult

value: TTCATA


title: Hypothalamus_PFOS H35

description:
Hypothalamus_PFOS
H35

value: wild type

value: TGAATA


title: Hypothalamus_Vancomycin_PFOS H37

description:
Hypothalamus_Vancomycin_PFOS
H37

value: TTAACT


title: Hypothalamus_PFOS H32

description:
Hypothalamus_PFOS
H32

value: TATTAC


title: W4_1


title: Hypothalamus_PFOS H33

description:
Hypothalamus_PFOS
H33

value: TCAAAA


title: Hypothalamus_Vancomycin H22

description:
Hypothalamus_Vancomycin
H22

value: GAATAT


title: Hypothalamus_PFOS H29

description:
Hypothalamus_PFOS
H29

value: TAGAAT


title: Hypothalamus_Vancomycin H20

description:
Hypothalamus_Vancomycin
H20

value: CTAAAA


title: Hypothalamus_PFOS H30

description:
Hypothalamus_PFOS
H30

value: TATAAG


title: W3_3

source_name: the leaves samples at 15 hour during withering proces


title: Hypothalamus_PFOS H27

description:
Hypothalamus_PFOS
H27

value: TAATAG


title: Hypothalamus_PFOS H31

description:
Hypothalamus_PFOS
H31

value: TATCAT


title: Hypothalamus_Vancomycin H23

description:
Hypothalamus_Vancomycin
H23

value: GATTAA


title: W3_2

value: Camellia sinensis cv. Longjing43

value: leaf


title: Hypothalamus_PFOS H28

description:
Hypothalamus_PFOS
H28

value: TACAAA


title: Hypothalamus_Vancomycin H19

description:
Hypothalamus_Vancomycin
H19

value: Adult

value: CATAAA


title: Hypothalamus_Vancomycin H24

description:
Hypothalamus_Vancomycin
H24

value: wild type

value: GTTAAA


title: Hypothalamus_Vancomycin H18

description:
Hypothalamus_Vancomycin
H18

value: ATTTTG


title: Hypothalamus_Vancomycin H21

description:
Hypothalamus_Vancomycin
H21

value: CTTAAT


title: Hypothalamus_Vancomycin H17

description:
Hypothalamus_Vancomycin
H17

value: ATTGTT


title: Hypothalamus_Vancomycin H15

description:
Hypothalamus_Vancomycin
H15

value: ATGTAA


title: W2_3

source_name: the leaves samples at 9 hour during withering proces


title: W2_2


title: Hypothalamus_Vancomycin H14

description:
Hypothalamus_Vancomycin
H14

value: ATCTAT


title: Hypothalamus_Vancomycin H16

description:
Hypothalamus_Vancomycin
H16

value: ATTATC


title: W2_1


title: Hypothalamus_Ctrl H10

description:
Hypothalamus_Ctrl
H10

value: AGTATA


title: Hypothalamus_Ctrl H9

description:
Hypothalamus_Ctrl
H9

value: AGAATT


title: W1_1

source_name: the leaves samples at 0 hour during withering proces


title: Hypothalamus_Ctrl H12

description:
Hypothalamus_Ctrl
H12

value: ATAGAT


title: Hypothalamus_Vancomycin H13

description:
Hypothalamus_Vancomycin
H13

value: ATATGA


title: W1_2

value: Camellia sinensis cv. Longjing43


title: W3_1

value: leaf


title: Hypothalamus_Ctrl H8

description:
Hypothalamus_Ctrl
H8

value: ACTAAA


title: Spider late germ-disc 2, scRNA-seq

city: Takatsuki

first: Yasuko

last: Akiyama-Oda

state: Osaka

address: Murasaki-cho 1-1

institute: JT Biohistory Research Hall

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
We used BD Rhapsody WTA analysis pipeline on the Seven Bridges Genomics cloud platform.
After quality filter of read pairs, the cell barcode and the unique molecular index (UMI) were identified from R1 reads, and R2 reads were aligned to the STAR index created form the Paratsteatoda genome reference using STAR-2.5.2b.
Following a UMI error correction step, a cell/gene count matrix, the final output of the pipeline,  was obtained.
Using the Seurat package (v.4.0.3), the count matrix was filtered by the number of unique genes and/or the total number of RNA molecules.
Differentially expressed genes (DEGs) between two ectodermal clusters were removed from the count matrix.
The count matrix was log-normalized.
Assembly: GCF_000365465.2_Ptep_2.0 and GCF_000365465.3_Ptep_3.0
Supplementary files format and content: Comma-separated text files that include the count matrix of the pipeline output.
Supplementary files format and content: Tab-separated text files that include the filtered count matrix.
Supplementary files format and content: Tab-separated text files that include the filtered count matrix after removal of DEGs.
Supplementary files format and content: Tab-separated text files that include the log-normalized count matrix.

organism: Parasteatoda tepidariorum

source_name: 20 whole embryos

growth_protocol: Embryos were incubated at 25 ˚C until they reached the appropriate stages.

extract_protocol:
The spider embryos were dechorionated with 100% commercial bleach, rinsed with distilled water, and transferred into CGBS-CMF (55 mM NaCl, 40 mM KCl, 10 mM Tricine, pH6.95)-0.01% (for cell) or 0.5% (for nucleus) BSA solution, where vitelline membrane was manually removed with forceps. For preparation of dissociated cells, the devitellinized sample was filtered through 40-mm cell strainer (pluriStrainer-Mini) and collected in a 1.5-mL DNA LoBind Tube (Eppendorf). For preparation of nuclei, the devitellinized sample was centrifuged in a 1.5-mL tube (Eppendorf) and suspended in 400 mL homogenization buffer (250 mM Sucrose, 10 mM Tris (pH 8.0), 25 mM KCl, 5 mM MgCl2, 0.1% Triton-X100, 0.1 mM DTT, 100 u/mL RNase Inhibitor (SUPERaseIn RNase Inhibitor: Invitrogen, AM2694), Protease Inhibitor at 1:100 dilution (Nacalai tesque, 25955-11)), where the sample was homogenized with a loose plastic pestle (fisher scientific) by 40 strokes. The sample was then centrifuged and suspended with CGBS-CMF-0.5% BSA-100 u/mL RNase Inhibitor solution, followed by filteration through the 40-mm cell strainer. The centrifugation and resuspension steps were repeated twice. Adding 4 volumes of CellCover (Anacyte Laboratories), the cell and nucleus samples were stored at 4 ˚C until use.
The stored cells or nuclei were centrifuged and resuspended with the CGBS-CMF-based solution, and they were individualized using BD Rhapsody microwell-based platform, followed by library construction according to the manufacture’s instructions. Construction of the single-nucleus RNA-seq library was performed with some modifications; RNase Inhibitor was added to the Sample buffer, and Proteinase K was added to the Lysis buffer, and the lysis step was prolonged from 2 minutes to 5 minutes.
Single-cell and single-nucleus RNA-seq

value: 20 whole embryos

value: all dissociated cells

value: WT

value: late stage 5


title: Hypothalamus_Ctrl H5

description:
Hypothalamus_Ctrl
H5

value: Adult

value: wild type

value: AATATG


title: Hypothalamus_Ctrl H7

description:
Hypothalamus_Ctrl
H7

value: AATTTC


title: solvent control 1

city: nanjing

first: yang

last: niuzi

state: jiangsu

department: College of  Plant Protection

institute: jaas

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150bp paired-end reads were generated.
Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reference genome and gene model annotation files were downloaded from the genome website directly. Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using HISAT2. We selected HISAT2 as the mapping tool so that HISAT2 can generate a database of splice junctions based on the gene model annotation file and thus yield a better mapping result than other non-splice mapping tools. StringTie was used to construct and identify both known and novel transcripts from HISAT2 alignment results.
StringTie was used to count the read numbers mapped to each gene. Clean data were mapped back onto the reference genome. Read counts for each gene were obtained from the mapping results. The FPKM, expected number of Fragments Per Kilobase of transcript sequence per million base pairs sequenced, of each gene, was calculated based on the length of the gene and read counts mapped to this gene.
Genome_build: ASM400044v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples.

organism: Chilo suppressalis

source_name: larva

extract_protocol:
Total RNA was extracted from 6 C. suppressalis larval using TRIzol reagents (Invitrogen, United States) according to the manufacturer’s instructions. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37℃ for 15 min followed by 5 min at 95℃ before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: development stage

value: 3rd instar larval

value: Laboratory sensitive population

value: solvent control


title: solvent control 2


title: Spider late germ-disc 1, scRNA-seq

description: BD Rhapsody

source_name: 10 whole embryos

value: 10 whole embryos


title: Hypothalamus_Ctrl H2

description:
Hypothalamus_Ctrl
H2

value: AAATCA


title: treatmented with (E)-β-farnesene 1

value: treatmented with (E)-β-farnesene


title: Hypothalamus_Ctrl H1

description:
Hypothalamus_Ctrl
H1

value: AAACAT


title: solvent control 3


title: treatmented with (E)-β-farnesene 2


title: Hypothalamus_Ctrl H6

description:
Hypothalamus_Ctrl
H6

value: AATGTA


title: N28M30Ie8

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

data_processing:
base calling - Illumina
alignment - STAR
UMI - collapse_UMI_bam
gene counts - HTSEQ
Genome_build: Mouse mm10

source_name: NOD mouse strain

growth_protocol: Animals were housed in a 12 h dark/light cycle and fed a Chow diet (LabDiet 5001). The morning with presence of a vaginal plug being counted as 0.5 days.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Quant Seq 3'mRNA-Seq Library Kit (FWD) for Illumina from Lexogen, UMI, 75bp cartridge v2.5, total of 4 runs on Nextseq, loaded 1.8pM per run

treatment_protocol: Embryos and their corresponding yolk sac tissue was dissected at 8.5 days of gestation and stored in Trizol at minus 80 deg Celsius.

value: NOD

tag: sex of the embryo

value: male

tag: somite number of the embryo

tag: glucose conc at euthanasia; mg/dl

value: embryo at E8.5, control


title: N28M30Iy8

value: yolk sac at E8.5, control


title: N28M30Hy8

value: female


title: N28M25Ay8


title: irradiated whole skin

city: Jerusalem

first: Jonathan

middle: H.

last: Axelrod

state: n

address: Ein Kerem

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Hebrew University Hospital

data_processing:
Raw data (fastq files) was processed with 'cellranger count', version 3.0.2, with 5000 expected cells, aligning against the mouse GRCm38 genome, with gene annotations from Ensembl release 89.
The 'filtered_feature_bc_matrix' from both samples were loaded to the R package 'Seurat', either version 3.0.2 or 4.0.4, for further analysis.
For each sample, cells were filtered to include ones with at least 200 genes and less than 5% of mitochondrial transcripts, then the data from the two samples was integrated with dimentions 1 to 40.
The integrated data was scaled, centered, subjected to dimension reduction using PCA1 to PCA40 and clustered at 0.6 resolution.
Assembly: GRCm38
Supplementary files format and content: Results of cellranger count are given as is in the HDF5 format (see 10X support for details). In addition, the assignment of cluster and cell type to each cell is given in a tab-delimited text file, with a single header row, followed by data for each cell.

source_name: whole skin

extract_protocol:
Cells for scRNA-seq analysis were prepared from whole skin samples removed from shaved naive or irradiated mice essentially as described (Guerrero-Juarez et al., 2019). Briefly, skin samples were treated by Dispase 2 (Sigma Aldrich) for 60 min at 37° C and separated into dermal and epidermal layers. The separated skin layers were minced into small pieces, pooled, and treated by shaking at 37° C for 100 min in a solution of LiberaseTM Research Grade (Roche)/DNase (Roche) in PBS containing 2% FCS (WS) to disperse the cells. EDTA was added to 7 mM during the final 10 min incubation. Post-incubation, single-cell suspensions were diluted with an equal volume of WS containing 2x cOmpleteTM Protease Inhibitor Cocktail (Sigma Aldrich) and strained through a 70 μM filter to remove large tissue debris. Cell suspensions derived from skin samples of four mice per treatment group were pooled and dead cells were removed using the Dead Cell Removal Kit (MACS) as per the manufacturer’s directions and repeated one time to achieve a suspension of ~90% viable cells. Live cells were suspended in PBS containing 10% FCS and used for cDNA library construction.
cDNA library construction using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics, 6230 Stoneridge Mall Road Pleasanton, CA 94588 USA)

treatment_protocol: Female mice (C57BL/6) aged 6-7 weeks  (n = 4) were exposed to 15 Gy irradiation aimed to the head and neck while immobilized in tubular jigs made of Perspex.  Control mice consisted of unteated female littermates aged 6-7 weeks (n = 4). Fourteen days post-irradiation, whole skin samples were surgically removed from the shaved necks and chest of the irradiated mice and, separatly, from four age-matched naïve control mice while under anesthesia (Xylosine/Ketamine), and immediately used for the preparation of viable single cells for 3’ single-cell RNA-sequencing.

value: irradiated, 15 Gy

value: whole skin

tag: Sex


title: N28M22Ae8


title: Comma1D basal population

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Read processing including demultiplexing, barcode assignment, and UMI quantification was performed by the Cell Ranger analysis pipeline.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

growth_protocol: Cell lines were obtained from the American Type Culture Collection. Comma1-D cells were grown in DMEM:F12 (Gibco) supplemented with 2% FCS, 5 ng/mL murine EGF (Sigma), 10 μg/mL human insulin (Sigma), and 50 μg/mL gentamicin (Gibco).

extract_protocol:
Cells were captured with the Chromium Controller (10x Genomics).
Library preparation was performed with Chromium Single Cell Gene Expression 3′ Kits (10x Genomics)
scRNA-seq

value: Comma1D, Sca-1(H), EpCAM (L)


title: Hypothalamus_Ctrl H11

description:
Hypothalamus_Ctrl
H11

value: Adult

value: wild type

value: ATAAGT


title: treatmented with (E)-β-farnesene 3

value: 3rd instar larval

value: Laboratory sensitive population


title: Hypothalamus_Ctrl H4

description:
Hypothalamus_Ctrl
H4

value: AAGTTA


title: Hypothalamus_Ctrl H3

description:
Hypothalamus_Ctrl
H3

value: AACATA


title: N28M07Jy8


title: N28M30Ay8


title: N28M25Ae8


title: N28M07Je8


title: N28M22Cy8


title: naïve whole skin

value: control


title: N28M07Hy8


title: N28M07He8


title: N28M22Ce8


title: N28M07Ke8


title: Comma1D luminal population

value: Comma1D, Sca-1(L), EpCAM (H)


title: Comma1D bilinage population

value: Comma1D, Sca-1(H), EpCAM (H)


title: Comma1D cell line unsorted population


title: W1_3

value: Camellia sinensis cv. Longjing43

value: leaf


title: N28M22Ay8

value: NOD

value: male

value: yolk sac at E8.5, control


title: N28M06Ee8

value: embryo at E8.5, control


title: N28M06De8


title: N28M07Ky8

value: female


title: N28M06Cy8d

description: duplicate, batch control


title: N28M06Ce8d

description: duplicate, batch control


title: N28M30He8


title: N28M30Ae8


title: N28M06Ce8


title: N28M05Gy8


title: N28M06Je8


title: N28M05Je8


title: N28M07Ey8


title: N28M07Ee8


title: N28M06Hy8


title: N28M06He8


title: N28M05De8


title: N28M06Jy8


title: N28M05Dy8


title: N28M05Cy8


title: N28M06Cy8


title: N28M06Ae8


title: N28M06By8


title: N28M05Jy8


title: N28M03Ce8


title: N28M05Ey8


title: N28M05Ge8


title: N28M06Be8


title: N28M06Ey8


title: N28M03Be8


title: N28M05Ce8


title: N28M06Dy8


title: N24M29Cy8


title: ROC1 tumor cells p53-KD, rep 3

city: Houston

first: Roberto

last: Rangel

state: Texas

address: 1515 Holcomb Blvd

department: Head and Neck Surgery

institute: The University of Texas MD Anderson Cancer Center

description: We assessed the transcriptome analysis in ROC1 p53-KD compared to control cells and identified a dramatic enrichment of proinflammatory cytokines and chemokines confirmed by differential expression gene analysis. Interestingly, the top four pathways altered were the TNF, IL17, chemokine, and cytokine–cytokine receptor interaction pathways, which suggests that mutant p53 modulates the expression and secretion of soluble factors in the TME. Interestingly, our in silico analysis correlated with the qPCR validation of the chemokines and cytokines that were upregulated (Ccl2, Cxcl5, Ccl5, Cxcl16, Il6) and downregulated (Il17c, Il33, St2) in the p53-KD compared to control ROC1 tumor cells.

data_processing:
Sequencing Platform: BGISEQ
Sequencing length: PE100
HISAT to align the clean reads to the reference genome
Bowtie2 to align the clean reads to the reference genes
DESeq ROC1 control vs ROC1 p53-KD
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-delimited text files include TPM and read counts values for each sample.

source_name: ROC1 tumor cells

growth_protocol: ROC1 tumor cells were routinely plated in a 10 cm tissue culture dish plate (1-2 x 106 cells) using DMEM (500 ml) containing 10% FBS, 1X MEM vitamin solution, 1X non-essential aminoacids, 1 mM sodium pyruvate, 2 mM glutamine, 50 I.U. penicillin and 50 ug/ml of streptomycin

extract_protocol:
RNeasy plus micro kit (QIAGEN Cat. No. 74034)
DNBSEQ Transcriptome - BGI genomics

treatment_protocol: Untreated cells, three independent tissue culture dish for RNA extraction for cell tye (Control-shRNA - p53-shRNA)

value: EGFR+ epithelial tumor cells

value: ROC1 tumor cells - untreated


title: N28M03Ee8


title: ROC1 tumor cells p53-KD, rep 1


title: ROC1 tumor cells p53-KD, rep 2


title: N28M03Ey8


title: N28M06Ay8


title: N24M29Be8


title: ROC1 tumor cells control shRNA, rep 3


title: N28M05Ee8


title: N28M03Cy8


title: N24M29Ay8


title: ROC1 tumor cells control shRNA, rep 1


title: N28M03By8


title: SNT16_ICT12h2

city: Shanghai

first: Songmei

last: Wang

address: 131 Rd Dong'an, Xuhui District

institute: Fudan University

data_processing:
Remove reads with adaptors, reads in which unknown bases are more than 10%, and reads of low quality
We use  Bowtie2 to map clean reads to reference gene and use  HISAT to  reference genome.
FPKM.txt  method is used in calculated expression level.
Supplementary files format and content: xls files include FPKM.txt values for each Sample

extract_protocol:
RNA was harvested using Trizol (Life). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy Kit following manufacturer's protocols.

tag: cell line

value: NK/T cell lymphoma cell line

value: WT

value: Icaritin


title: SNT16_ICT12h1


title: N24M21Gy8


title: N24M29Ae8


title: N24M29Ce8


title: SNT16_CON12h1

value: DMSO


title: SNT16_ICT12h3


title: SNK10_CON12h3


title: SNT16_CON12h3


title: N24M29By8


title: SNK10_ICT12h1


title: SNT8_ICT12h3


title: SNT16_CON12h2


title: SNK10_ICT12h2


title: SNT8_ICT12h2


title: N24M21Dy8


title: SNK10_ICT12h3


title: N24M21Ee8


title: SNT8_CON12h2


title: SNK10_CON12h1


title: SNT8_CON12h1


title: SNT8_ICT12h1


title: SNK10_CON12h2


title: ROC1 tumor cells control shRNA, rep 2


title: N24M21Ay8


title: Muscle biopsy_ID09_24h

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

source_name: vastus lateralis muscle

extract_protocol:
Muscle biopsies were obtained from the VL of the right leg using a 5-mm Bergström needle with manual suction following local anesthesia (2% Xylocitin). The location of all incision sites was randomized, and all incisions were 2-3 cm apart at the mid-portion of the VL muscle. After collection of the muscle tissue, the material was cleaned if there was excess blood using blotting paper and frozen in liquid nitrogen. Subsequently, all samples were stored at -80°C for later analysis
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: placebo

tag: time


title: N24M21Ae8


title: SNT8_CON12h3


title: Muscle biopsy_ID09_4h


title: N24M21Ge8


title: N23M31Ey8


title: N23M31Ee8


title: N24M21Ey8


title: Muscle biopsy_ID08_1h

value: verum


title: Muscle biopsy_ID08_24h


title: Muscle biopsy_ID08_Baseline


title: D28M53Gy8

value: yolk sac at E8.5, diabetic


title: Muscle biopsy_ID08_4h


title: Muscle biopsy_ID07_24h


title: 744_500_IFNr-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.7.1) software based on reference genome sequence (Homo sapiens UCSC hg38) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: IFNγ+ABBV-744-treated HepG2 (IFNγ+ABBV-744 500 nM)

growth_protocol: The HepG2 cells were cultured in MEM containing 10% heat-inactivated FBS, penicillin, and streptomycin (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO (Con), ABBV-075 (50 nM), ABBV-744 50 nM, ABBV-744 500 nM, IFNγ, IFNγ+ABBV-075 50 nM, IFNγ+ABBV-744 50 nM, IFNγ+ABBV-744 500 nM.

value: HepG2 cells were treated with IFNgamma+ABBV-744 (500 nM)

value: Hepatocellular carcinoma


title: D28M53Ge8

value: embryo at E8.5, diabetic


title: N24M21De8

value: NOD


title: Muscle biopsy_ID07_Baseline


title: 744_500_IFNr-2


title: Muscle biopsy_ID07_1h


title: 744_500_IFNr-1


title: D28M53Ey8

value: male


title: Muscle biopsy_ID06_4h


title: D28M53Ee8


title: Muscle biopsy_ID09_1h


title: Muscle biopsy_ID06_1h


title: Muscle biopsy_ID06_24h


title: Muscle biopsy_ID09_Baseline


title: D28M53By8


title: Muscle biopsy_ID05_4h


title: Muscle biopsy_ID06_Baseline


title: 744_50_IFNr-3

source_name: IFNγ+ABBV-744-treated HepG2 (IFNγ+ABBV-744 50 nM)

value: HepG2 cells were treated with IFNgamma+ABBV-744 (50 nM)


title: Muscle biopsy_ID05_24h


title: D28M53Be8


title: D28M53Ay8


title: Muscle biopsy_ID05_Baseline


title: Muscle biopsy_ID04_4h


title: Muscle biopsy_ID07_4h


title: Muscle biopsy_ID04_24h


title: Muscle biopsy_ID04_1h


title: D28M53Ae8


title: Muscle biopsy_ID05_1h


title: 744_50_IFNr-1


title: D28M37Be8


title: Muscle biopsy_ID03_4h


title: IFNr-3

source_name: IFNγ-treated HepG2 (IFNγ)

value: HepG2 cells were treated with IFNgamma


title: 075_50_IFNr-1

source_name: IFNγ+ABBV-075-treated HepG2 (IFNγ+ABBV-075 50 nM)

value: HepG2 cells were treated with IFNgamma+ABBV-075 (50 nM)


title: Muscle biopsy_ID04_Baseline


title: Muscle biopsy_ID03_24h


title: Muscle biopsy_ID03_1h


title: 744_50_IFNr-2


title: D28M37Ay8


title: IFNr-2


title: Muscle biopsy_ID30_4h


title: D28M37By8


title: Muscle biopsy_ID30_24h


title: Muscle biopsy_ID03_Baseline


title: IFNr-1


title: Muscle biopsy_ID30_1h


title: 075_50_IFNr-3


title: D28M36Dy8

value: female


title: 075_50_IFNr-2


title: Muscle biopsy_ID02_24h


title: Muscle biopsy_ID30_Baseline


title: ABBV744_500-2

source_name: ABBV-744 500nM-treated HepG2 (ABBV-744 500 nM)

value: HepG2 cells were treated with ABBV-744 (500 nM)


title: Muscle biopsy_ID02_1h


title: ABBV744_500-3


title: D28M36De8


title: D28M36Cy8


title: Muscle biopsy_ID02_Baseline


title: Muscle biopsy_ID29_4h


title: Muscle biopsy_ID29_24h


title: Muscle biopsy_ID29_1h


title: Muscle biopsy_ID28_24h


title: Muscle biopsy_ID28_1h


title: Muscle biopsy_ID28_4h


title: D28M36Ce8


title: ABBV744_500-1


title: Muscle biopsy_ID28_Baseline


title: ABBV744_50-3

source_name: ABBV-744 50nM-treated HepG2 (ABBV-744 50 nM)

value: HepG2 cells were treated with ABBV-744 (50 nM)


title: Muscle biopsy_ID29_Baseline


title: D28M36Be8


title: D28M36By8


title: ABBV744_50-2


title: Muscle biopsy_ID02_4h


title: D28M31Ny8


title: ABBV744_50-1


title: ABBV075_50-3

source_name: ABBV-075 50nM-treated HepG2 (ABBV-075 50 nM)

value: HepG2 cells were treated with ABBV-075 (50 nM)


title: Muscle biopsy_ID27_24h


title: Muscle biopsy_ID27_1h


title: D28M31Ne8


title: Muscle biopsy_ID26_1h


title: Muscle biopsy_ID27_4h


title: ABBV075_50-2


title: D28M31Le8


title: Con-3

source_name: Control HepG2 (Con)

value: HepG2 cells were treated with DMSO


title: Muscle biopsy_ID26_4h


title: D28M37Ae8


title: D28M31Ly8


title: ABBV075_50-1


title: Muscle biopsy_ID27_Baseline


title: D28M31Cy8


title: Muscle biopsy_ID25_24h


title: Con-2


title: Muscle biopsy_ID26_Baseline


title: Muscle biopsy_ID25_Baseline


title: D28M27Cy8


title: D28M27Ce8


title: Muscle biopsy_ID25_1h


title: D28M24Cy8


title: Muscle biopsy_ID24_Baseline


title: Muscle biopsy_ID24_4h


title: Muscle biopsy_ID26_24h


title: Muscle biopsy_ID23_1h


title: Con-1


title: Muscle biopsy_ID23_Baseline


title: Muscle biopsy_ID24_1h


title: D28M23Hy8


title: Muscle biopsy_ID23_24h


title: D28M23He8


title: Muscle biopsy_ID25_4h


title: Muscle biopsy_ID22_4h


title: D28M24Ce8


title: Sc_W3

city: Pittsburgh

first: Chandan

middle: K

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Quality control, clustering and differential gene expression analysis were performed using Seurat v.3.1.0
Genome_build: hg:38
Supplementary_files_format_and_content: barcode files
Supplementary_files_format_and_content: gene names file
Supplementary_files_format_and_content: count matrix file

source_name: human chronic wound edge tissue

growth_protocol: Human tissue samples

extract_protocol:
The tissue was chopped into small pieces and subjected to enzymatic dissociation using whole skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237) (Miltenyi Biotec Inc., San Diego, CA). The samples were incubated in a water bath at 37°C for approximately 3 hours. After incubation, the samples were diluted by adding 0.5 mL of cold cell culture medium in order to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentleMACS™ Octo dissociator and UW human skin dissociation program was performed. The cell suspension was subjected to a pre-Separation Filter, 70 µm, placed on a 15 mL tube in order to remove the debris. RBC were lysed using 10X RBC lysis buffer (cat. no. 420301, BioLegend, San Diego, CA).
The resulting cell suspension was utilized for single cell RNA sequencing using the 10x Genomics platform using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10x Genomics, Inc.) and sequenced on an Illumina NovaSeq 6000 (Illumina, Inc).

treatment_protocol: Single-cell suspensions were generated from the UW human skin and chronic WE biopsies.

tag: gender

value: Female

tag: age (years)


title: Sc_W2

value: Male


title: Muscle biopsy_ID23_4h

value: verum


title: Sc_W1


title: D28M31Ce8


title: D28M23Gy8

value: yolk sac at E8.5, diabetic


title: Muscle biopsy_ID22_24h


title: Sc_Skin4

source_name: human unwounded skin tissue


title: Muscle biopsy_ID24_24h

value: placebo


title: Muscle biopsy_ID21_Baseline


title: Sc_Skin3


title: D28M23Fy8