title: HSPCs_IFNα_72h, scRNAseq_Hashtag

city: Heidelberg

first: Yasmin

middle: Essam

last: Demerdash

state: Germany

address: Im Neunheimer Feld, 280

department: Inflammatory Stress in Stem Cells

institute: DKFZ

description: 10x Genomics

data_processing:
The cellranger pipeline (version 3.1.0) was used to align all reads to the mm10 genome and count the coverage of each gene in each cell. CITEseqCount v1.4.3 was used for the hashtag count matrix generation.
Assembly: mm10
Supplementary files format and content: Tab separated values files and comma separated values files
Supplementary files format and content: AnnData object and Seurat object [The data in the object is filtered (low quality genes and cells are removed), but has not been processed (no scaling, normalization, log transform etc.)]

source_name: Bone Marrow

extract_protocol: Library was performed using the Chromium Next GEM single cell 3‘ reagent kits v3.1 following the official instruction manual (https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry).Briefly, cells were super-loaded according to the manufacturer’s instructions up until the cDNA amplification step. 1 ul/sample of HTO primers was spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3.1 protocol aiming for a targeted cell recovery of 500-6000 cells. Following PCR, cDNA cleanup was performed by using SPRI to separate the HTO-derived cDNAs (in the supernatant) from the mRNA-derived cDNAs (retained on beads). The cDNA fraction was processed according to the manufacturer's protocol to generate the transcriptome library.

treatment_protocol: Mice were injected subcutaneously with 50.000 international units (IU) of recombinant mouse IFNα per 20g mouse. Recombinant mouse IFNα was diluted in PBS and control mice were injected with 100 µl PBS.

value: hematopoetic stem and progenitors

value: Bone Marrow

value: Wildtype

tag: age

value: 12-14 weeks old


title: GK002_Mn

status: Public on Apr 05 2023

type: RNA

city: Kraków

first: Marcin

last: Czepiel

address: Anny 12

department: Clinical Immunology

country: Poland

institute: Jagiellonian University Medical College

data_processing:
After processing OpenArray miRNA Expression run, the data analysis was performed. Quality control images (QC Images) were exported and investigated to find potential loading errors. The result files created by QuantStudio Software v1.2.3 were uploaded to ThermoFisher Cloud and analyzed with Relative Quantification qPCR Application. miRNA Panel A and B were analyzed in separate analysis groups
The Processed (normalized) Data is organized in separate excel files - each file for each target (miRNA). This data has been normalised to U6 rRNA Ct values coming from the relevant Raw Data files namely: "Panel_A_Sample Results.csv" and "Panel_B_Sample Results.csv". In these raw data files you will find the Sample name, target name and Ct values in columns 1, 2 and 3 respectively (column names: Sample Name, Target Name, Mean Equivalent Cq).
The expression of each miRNA type was calculated using 2−ΔΔCT method and snRNa U6 was used as a control to all miRNA analysis

molecule: total RNA

organism: Homo sapiens

source_name: Healthy Control 2 - Non-classical Monocytes

label_protocol: cDNA was pre‐amplified to increase its quantity before performing the OpenArray qPCR. Preamplification products were prepared in two separate reactions for Megaplex™ PreAmp Primers Pool A and Pool B, corresponding to the Megaplex™ RT Primers Pool used previously for reverse transcription. For each pre-amplification we used 2,5 µl cDNA and 22,5 μL of PreAmp Reaction Mix, containing Megaplex™ PreAmp Primers Pool A or Pool B (2,5 µl), 2x TaqMan® PreAmp Master Mix (12,5 µl) and nuclease-free water (all reagents by ThermoFisher Scientific, Waltham, MA, USA). Pre-amplification reaction tubes with reagents were incubated on ice for 5 minutes before performing RUN on SimplyAmp Thermal Cycler (Applied Biosystems by ThermoFisher Scientific, Waltham, MA, USA). The following thermal conditions were used to run pre-amplification: 95°C for 10 minutes, 55°C for 2 minutes, 72°C for 2 minutes, 12 cycles including 95°C for 15 seconds and 60°C for 4 minutes, hold step with 99,9°C for 10 minutes and final hold step 4°C. Negative control was used for each preamplification. Every single preamplification product was diluted 1:20 with nuclease-free water and used for the next step within 12 hours. For each sample, qPCR reaction was prepared by mixing 22,5 µl 2x TaqMan® OpenArray® Real‐Time PCR Master Mix and 22,5 µl pre-amplification product on 96-well plate. Next, the qPCR reaction mixes with samples (5 µl) were transferred by pipetting to 384-well plate according to protocol created in OpenArray Sample Tracker Software (ThermoFisher Scientific, Waltham, MA, USA) and loaded to OpenArray plates by OpenArray™ AccuFill™ System (ThermoFisher Scientific, Waltham, MA, USA). OpenArray cases were sealed according to guidelines within 90 seconds. Ready OpenArray Plates were put into the QuantStudio 12K Flex Real-time PCR System with OpenArray block and processed.

extract_protocol: RNAs were isolated using miRVana microRNA isolation kit (Thermo Fisher Scientific) and transcripted into cDNA using Megaplex™ RT Primers and TaqMan® MicroRNA Reverse Transcription Kit

tag: cell type

value: Non-Classical Monocytes

tag: tissue

value: peripheral blood

tag: disease state

value: Healthy Control


title: CD161P-HBV, HBV-infected patients, CD161+CD8+ non-MAIT cells,  biol rep1

type: SRA

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

country: China

institute: Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
Illumina novaseq 6000 platform used for basecalling.
Raw image Data files obtained by Illumina nova are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads per Kilobase per Million Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: peripheral blood

extract_protocol:
Total RNAs were extracted from enriched cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
circulating CD161-CD8+ T cells(CD161N) from HD
circulating CD161+CD8+ non-MAIT cells(CD161P) from HD
circulating MAIT cells from HD
circulating CD161+CD8+ non-MAIT cells(CD161P) from HBV-infected patients
hepatic CD161+CD8+ non-MAIT cells from HBV-infected patients(AST>40 and AST<40)

value: circulating CD161+CD8+ non-MAIT cells (CD161P)

tag: infection

value: HBV-infected


title: castration-resistant prostate cancer1

city: Guangzhou

first: wen

last: tao

address: Tianhe Road 600

institute: The Third Affiliated Hospital, Sun Yat-sen University

description:
Ribosomal-depleted RNA
B1A
sample paired with:
B1

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were subjected to trimming process with Trimmomatic (v.0.32)
High-quality reads were aligned to the Homo sapiens reference genome (GRCH37/hg19) by BWA (v.0.7.12). The resulted sequence alignment files (bam formatted file) were then sorted by reference position as required by SAMtools(v.2.6.2).
CircRNAs was identified and quantified by CIRI2
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: text file with abundance data, logFC,  logCPM,  Pvalue,  FDR. circRNAs are identified by their chromosome coordinates (chromosome:position1|position2).

source_name: plasma exosome

extract_protocol:
Isolation of exosomes using ExoQuick（SBI,Palo Alto,CA,US) according to the manufacturer's instructions.Exosomal RNA was isolated from samples using RNAiso Plus Total RNA extraction reagent (TAKARA, Dalian, China) according to the manufacturer's instructions and the RIN number was checked to detect RNA integrity by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Further purification of qualified total RNA using RNAClean XP Kit (Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set(QIAGEN, GmBH, Germany).
The total RNA were treated with the RiboZero rRNA Removal Kit (Epicentre, WI, USA) to delete rRNA and digested linear RNA using RNase-R (Epicentre, WI, USA) according to the manufacturer’s instructions. Next, strand-specific libraries were constructed by using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, CHN) following the manufacturer’s instructions. In brief, The enriched circRNAs were fragmented using fragmentation buffer and then reverse transcribed into first-strand cDNA and second-strand cDNA in orderly. Then, the cDNA fragments were purified, subjected to end-repair, and modified to add poly (A) to the 3’ end. The sequencing adapters were ligated to the cDNA fragments. The double strand cDNA are digested by uracil-DNA glycosylase (UDG) (Cwbio, Beijing, CHN) to remove the second-strand cDNA before sequencing. The purified ligation products were performed 13-15 cycles of PCR amplification. The PCR amplification products of cDNA were purified with Agencourt AMPure XP Beads(Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and then sequenced by Illumina Hiseq X Ten system (Illumina, San Diego, CA, USA) on paired-end(PE) mode with length 150 bases following the vendor’s recommended protocol.

tag: subject id

value: plasma

tag: tissue compartment

value: exosome

tag: patient diagnosis

value: castration-resistant prostate cancer

tag: Sex

value: male


title: HSPCs_IFNα_24h, scRNAseq_Hashtag

country: Germany

description: 10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: genotype

tag: treatment


title: HSPCs_IFNα_3h, scRNAseq_Hashtag

description: 10x Genomics


title: GK001_Mn

source_name: Healthy Control 1 - Non-classical Monocytes


title: MAIT, HD biol rep2

value: circulating MAIT cells

value: HD (control)


title: HSPCs_Control_PBS, scRNAseq_Hashtag

description: 10x Genomics


title: metastasis castration-resistant prostate cancer15

description:
Ribosomal-depleted RNA
W6
sample paired with:
W6g

value: castration-resistant prostate cancer with metastasis


title: metastasis castration-resistant prostate cancer14

description:
Ribosomal-depleted RNA
W5
sample paired with:
W5g


title: MAIT, HD biol rep3


title: OS028_Mk

source_name: Axial SpA Patient 28 - Classical Monocytes

value: Classical Monocytes

value: Axial SpA Patient


title: CD161P, CD161+CD8+ T cells, HD biol rep3


title: metastasis castration-resistant prostate cancer12

description:
Ribosomal-depleted RNA
W3
sample paired with:
W3g


title: MAIT, HD biol rep1


title: HSPCs_IFNα_72h, scRNAseq

description: 10x Genomics

value: hematopoetic stem and progenitors

value: Bone Marrow


title: HSPCs_IFNα_24h, scRNAseq

description: 10x Genomics

value: Wildtype

value: 12-14 weeks old


title: OS026_Mk

source_name: Axial SpA Patient 26 - Classical Monocytes

value: peripheral blood


title: HSPCs_IFNα_3h, scRNAseq

description: 10x Genomics


title: metastasis castration-resistant prostate cancer11

description:
Ribosomal-depleted RNA
W2
sample paired with:
W2g


title: CD161P, CD161+CD8+ T cells, HD biol rep2


title: HSPCs_Control_PBS, scRNAseq

description: 10x Genomics


title: metastasis castration-resistant prostate cancer10

description:
Ribosomal-depleted RNA
W1
sample paired with:
W1g


title: CD161P, CD161+CD8+ T cells, HD biol rep1


title: OG2 mESC, SUZ12-KO,rep2

city: guangzhou

first: Xinjie

last: Li

address: gongming street 66

institute: sun yat-sen university

data_processing:
FastQC v 0.11.9 was used for qulity control.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.0.1.
The remaining reads were mapped to the reference genome (mm10) with hisat2 v 2.2.1. Only uniquely mapping reads were retained.
Read count extraction and normalization were performed using HTSeq v 2.0.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: OG2 mESC

growth_protocol: OG2 mESC cells were maintained on gelatin-coated plate in DMEM supplemented with 15% fetal bovine serum (FBS)and 2iL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Kit I (Omega Bio-Tek)  and then total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell line

value: OG2 mESC

value: mouse embryonic stem cells

value: SZU12 knockout


title: OS024_Mk

source_name: Axial SpA Patient 24 - Classical Monocytes


title: CD161N, CD161-CD8+ T cells, HD biol rep3

value: circulating CD161-CD8+ T cells (CD161N)


title: metastasis castration-resistant prostate cancer9

description:
Ribosomal-depleted RNA
X19
sample paired with:
X11

value: plasma

value: exosome


title: OS022_Mk

source_name: Axial SpA Patient 22 - Classical Monocytes


title: OG2 mESC, SUZ12-KO

value: SUZ12 knockdout


title: OS030_Mk

source_name: Axial SpA Patient 30 - Classical Monocytes


title: metastasis castration-resistant prostate cancer8

description:
Ribosomal-depleted RNA
B8
sample paired with:
B8A

value: male


title: CD161N, CD161-CD8+ T cells, HD biol rep2

value: HD (control)


title: OS021_Mk

source_name: Axial SpA Patient 21 - Classical Monocytes


title: OS027_Mk

source_name: Axial SpA Patient 27 - Classical Monocytes


title: OS020_Mk

source_name: Axial SpA Patient 20 - Classical Monocytes


title: OG2 mESC, EED-KO, rep2

value: EED knockdout


title: CD161N, CD161-CD8+ T cells, HD biol rep1


title: metastasis castration-resistant prostate cancer13

description:
Ribosomal-depleted RNA
W4
sample paired with:
W4g

value: castration-resistant prostate cancer with metastasis


title: metastasis castration-resistant prostate cancer7

description:
Ribosomal-depleted RNA
B7
sample paired with:
B7A


title: OG2 mESC, EED-KO


title: GM21 fibroblasts, shPOU2F2 #325, Day 27 post RAS overexpression rep2

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

country: USA

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

data_processing:
fastq files were quality checked with multiqc
fastq files were aligned using bowtie 2 with the local option in paired-end mode
read counts per exon were obtained using summarized overlaps
count normalization was performed using DESeq2
Assembly: hg19
Supplementary files format and content: BigWig
Supplementary files format and content: tab-delimited text file include normalized counts per Sample

molecule: polyA RNA

growth_protocol: Human somatic GM21 foreskin fibroblasts (Coriell Institute, Camden, NJ) and WI-38 human fetal lung fibroblasts (European Collection of Authenticated Cell Cultures, Porton Down, UK) were cultured in a DMEM medium containing 10% fetal bovine serum (FBS) and 1× penicillin/streptomycin (Corning) at 37 °C in a 2% oxygen atmosphere

extract_protocol:
Macherey-Nagel RNA XS columns. At least 200 ng RNA with RIN number 9 were used for library construction.
NEB UltraII Directional with poly A selection.

treatment_protocol: GM21-RASV12 fibroblasts and their empty vector counterparts were generated by retroviral transduction. GM21 fibroblasts constitutively expressing non-targeting and POU2F2-targeting shRNAs (pLKO.1-Neo-CMV-tGFP, pLKO.1-Neo-CMV-tGFP-TRCN0000245324 and pLKO.1-Neo-CMV-tGFP-TRCN0000245325) (Millipore-Sigma, Saint Louis, MO) were generated by lentiviral transduction and selected with 400 µg/ml neomycin for seven days. Cells were subsequently retrovirally transduced with RASV12

value: H-RAS-G12-V overexpression

value: skin fibroblast

value: POU2F2 knockdown #2

tag: time

value: Day 27


title: OS019_Mk

source_name: Axial SpA Patient 19 - Classical Monocytes

value: Classical Monocytes

value: Axial SpA Patient


title: OS025_Mk

source_name: Axial SpA Patient 25 - Classical Monocytes

value: peripheral blood


title: GM21 fibroblasts, shPOU2F2 #325, Day 27 post RAS overexpression rep1


title: OG2 mESC, rep2

value: OG2 mESC

value: mouse embryonic stem cells

value: WT


title: metastasis castration-resistant prostate cancer5

description:
Ribosomal-depleted RNA
B5
sample paired with:
B5A

value: plasma


title: OG2 mESC


title: GM21 fibroblasts, shPOU2F2 #324, Day 27 post RAS overexpression rep2

value: POU2F2 knockdown #1


title: metastasis castration-resistant prostate cancer4

description:
Ribosomal-depleted RNA
B4
sample paired with:
B4A

value: exosome


title: metastasis castration-resistant prostate cancer3

description:
Ribosomal-depleted RNA
B3
sample paired with:
B3A

value: male


title: GM21 fibroblasts, pLKO, Day 27 post RAS overexpression rep2

value: pLKO


title: GM21 fibroblasts, shPOU2F2 #324, Day 27 post RAS overexpression rep1


title: OG2 mESC, SUZ12-KO [SUZ12-KO_input]

library_source: genomic

data_processing:
FastQC v 0.11.9 was used for qulity control.
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.0.1.
ChIP-seq reads were aligned to mm10 genome using Bowtie v 2.4.5. Only uniquely mapping reads were retained.
Peaks were called uing MACS v 2.2.7.1 the significance cut-off q-value <=0.05.
bigWig files were generated using deeptools v 3.5.1.  Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig (sample normalized coverage adjusted by input)

molecule: genomic DNA

growth_protocol: OG2 mESC cells were maintained on gelatin-coated plate in DMEM supplemented with 15% fetal bovine serum (FBS) and 2iL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
After the DNA samples quality control:(1) The DNA fragments are repaired, dA-tailed;(2) The DNA fragments with A tail are ligated to sequencing adaptors;(3) The final DNA library is obtained by size selection and PCR amplification.

value: SZU12 knockout

tag: chip antibody


title: OS015_Mk

source_name: Axial SpA Patient 15 - Classical Monocytes


title: metastasis castration-resistant prostate cancer2

description:
Ribosomal-depleted RNA
B2
sample paired with:
B2A

value: castration-resistant prostate cancer with metastasis


title: OG2 mESC, SUZ12-KO [SUZ12-KO_H3K27me3]

value: H3K27me3 (Active Motif, 39055)


title: OS013_Mk

source_name: Axial SpA Patient 13 - Classical Monocytes


title: OG2 mESC, SUZ12-KO [SUZ12-KO_LSD1]

value: LSD1 (Abacm,ab17721)


title: OS012_Mk

source_name: Axial SpA Patient 12 - Classical Monocytes


title: GM21 fibroblasts, pLKO, Day 27 post RAS overexpression rep1

value: H-RAS-G12-V overexpression

value: skin fibroblast


title: GM21 fibroblasts, shPOU2F2 #325, Day 14 post RAS overexpression rep2

value: POU2F2 knockdown #2

value: Day 14


title: OG2 mESC, SUZ12-KO [SUZ12-KO_H3K4me3]

value: H3K4me3 (abcam, ab8580)


title: metastasis castration-resistant prostate cancer1

description:
Ribosomal-depleted RNA
B1
sample paired with:
B1A


title: metastasis castration-resistant prostate cancer6

description:
Ribosomal-depleted RNA
B6
sample paired with:
B6A


title: OS011_Mk

source_name: Axial SpA Patient 11 - Classical Monocytes

value: Classical Monocytes

value: peripheral blood

value: Axial SpA Patient


title: GM21 fibroblasts, shPOU2F2 #325, Day 14 post RAS overexpression rep1


title: P28_CX_Gabbr1_control, YC162

city: Houston

first: Yi-Ting

last: Cheng

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
P28_Gabbr1_CX_normalized.csv
YC162

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression between different samples.
Assembly: mm10
Supplementary files format and content: csv files include FPKM normalized abundance measurements from astrocytes

source_name: cortical astrocytes

extract_protocol:
Tissue was dissociated as previously described. (Lin et al., Nat Neurosci 2017)
Illumina sequencing libraries were constructed from 500pg - 1ng of total RNA using the Trio RNA-seq (Nugen)

value: cortical astrocytes

value: Gabbr1 control

value: tamoxifen


title: OS018_Mk

source_name: Axial SpA Patient 18 - Classical Monocytes


title: OG2 mESC, SUZ12-KO [SUZ12-KO_H3K4me1]

value: OG2 mESC

value: mouse embryonic stem cells

value: SUZ12 knockdout

value: H3K4me1(Abcam, #ab8895)


title: P28_OB_Gabbr1_cKO, YC161

description:
P28_Gabbr1_OB_normalized.csv
YC161

source_name: olfactory bulb astrocytes

value: olfactory bulb astrocytes

value: Gabbr1 cKO


title: OG2 mESC, EED-KO, rep2 [rep2_EED-KO_input]

value: EED knockdout


title: OS010_Mk

source_name: Axial SpA Patient 10 - Classical Monocytes


title: OS009_Mk

source_name: Axial SpA Patient 9 - Classical Monocytes


title: OS016_Mk

source_name: Axial SpA Patient 16 - Classical Monocytes


title: GM21 fibroblasts, shPOU2F2 #324, Day 14 post RAS overexpression rep2

value: H-RAS-G12-V overexpression

value: skin fibroblast

value: POU2F2 knockdown #1


title: P28_HC_Gabbr1_cKO, YC160

description:
P28_Gabbr1_HC_normalized.csv
YC160

source_name: hippocampal astrocytes

value: hippocampal astrocytes


title: GM21 fibroblasts, shPOU2F2 #324, Day 14 post RAS overexpression rep1

value: Day 14


title: OG2 mESC, EED-KO, rep2 [rep2_EED-KO_H3K27me3]

source_name: OG2 mESC

value: H3K27me3 (Active Motif, 39055)


title: OG2 mESC, EED-KO, rep2 [rep2_EED-KO_H3K4me3]

value: H3K4me3 (abcam, ab8580)


title: GM21 fibroblasts, pLKO, Day 14 post RAS overexpression rep2

value: pLKO


title: P28_OB_Gabbr1_control, YC158

description:
P28_Gabbr1_OB_normalized.csv
YC158

value: Gabbr1 control


title: OS008_Mk

source_name: Axial SpA Patient 8 - Classical Monocytes

value: Classical Monocytes

value: peripheral blood

value: Axial SpA Patient


title: P28_CX_Gabbr1_cKO, YC159

description:
P28_Gabbr1_CX_normalized.csv
YC159

value: cortical astrocytes

value: tamoxifen


title: OS007_Mk

source_name: Axial SpA Patient 7 - Classical Monocytes


title: P28_CX_Gabbr1_control, YC157

description:
P28_Gabbr1_CX_normalized.csv
YC157


title: OS006_Mk

source_name: Axial SpA Patient 6 - Classical Monocytes


title: GM21 fibroblasts, pLKO, Day 14 post RAS overexpression rep1


title: OS005_Mk

source_name: Axial SpA Patient 5 - Classical Monocytes


title: P28_OB_Gabbr1_cKO, YC156

description:
P28_Gabbr1_OB_normalized.csv
YC156

value: olfactory bulb astrocytes


title: OG5 mESC, EED-KO [EED-KO_LSD1]

value: OG2 mESC

value: mouse embryonic stem cells

value: LSD1 (Abacm,ab17721)


title: H460 PON1-N253G secretome replicate 2

city: Daejeon

first: Yoosik

last: Kim

state: Daejeon

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Chemical and biomolecular engineering

country: South Korea

institute: KAIST

data_processing:
Basecalls performed using bcl2fastq (Version 2.20)
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with HISAT2 v2.1.0 using default parameters except with the option '--dta'.
Stringtie v2.0.6 was used to quantify the expression of genes and transcripts by employing transcriptome information from GENCODE v27.
Ballgown package was used to perform differential gene expression analysis generating FPKM for each gene.
Genome_build: hg38
Supplementary_files_format_and_content: tar.gz of stringtie output containing coverage data for the reference transcripts given with the -G option.

source_name: H1993-gefitinib resistant

growth_protocol: Low densitiy H1993-gefitinib resistant was grown under indicated conditions in the original paper for 48 h.

extract_protocol:
Total RNA was extracted using the RNAeasy mini kit.
2x101 paired-end RNA-seq library was constructed using TruSeq stranded total RNA H/M/R prep kit and sequenced using the Illumina NovaSeq 6000 system.

value: H460 PON1-N253G secretome


title: OG2 mESC, EED-KO, rep2 [rep2_EED-KO_H3K4me1]

value: EED knockdout

value: H3K4me1(Abcam, #ab8895)


title: H460 PON1-N253G secretome replicate 1


title: OS004_Mk

source_name: Axial SpA Patient 4 - Classical Monocytes


title: H460 PON1 secretome + PNGase F replicate 2

value: H460 PON1 secretome + PNGase F


title: P28_HC_Gabbr1_cKO, YC155

description:
P28_Gabbr1_HC_normalized.csv
YC155

value: hippocampal astrocytes

value: Gabbr1 cKO


title: OG4 mESC, EED-KO [EED-KO_H3K27me3]

value: H3K27me3 (Active Motif, 39055)


title: P28_OB_Gabbr1_cKO, YC153

description:
P28_Gabbr1_OB_normalized.csv
YC153


title: OG2 mESC, EED-KO [EED-KO_H3K4me1]


title: OS001_Mk

source_name: Axial SpA Patient 1 - Classical Monocytes


title: H460 PON1 secretome + PNGase F replicate 1


title: OS002_Mk

source_name: Axial SpA Patient 2 - Classical Monocytes


title: OS003_Mk

source_name: Axial SpA Patient 3 - Classical Monocytes


title: P28_OB_Gabbr1_control, YC150

description:
P28_Gabbr1_OB_normalized.csv
YC150

value: Gabbr1 control


title: H460 PON1 secretome replicate 2

value: H460 PON1 secretome


title: OG2 mESC [rep2_OG2_input]

value: WT


title: P28_HC_Gabbr1_control, YC149

description:
P28_Gabbr1_HC_normalized.csv
YC149


title: OG6 mESC, EED-KO [EED-KO_input]


title: P28_HC_Gabbr1_cKO, YC146

description:
P28_Gabbr1_HC_normalized.csv
YC146


title: H460 CC secretome replicate 2

value: H460 CC secretome


title: OG3 mESC, EED-KO [EED-KO_H3K4me3]

value: H3K4me3 (abcam, ab8580)


title: H460 PON1 secretome replicate 1


title: OB021_Mk

source_name: Peripheral SpA Patient 21 - Classical Monocytes

value: Classical Monocytes

value: peripheral blood

value: Peripheral SpA Patient


title: OG2 mESC [rep2_OG2_H3K4me3]

value: OG2 mESC

value: mouse embryonic stem cells


title: OB019_Mk

source_name: Peripheral SpA Patient 19 - Classical Monocytes


title: H460 CC secretome replicate 1


title: OG2 mESC [rep2_OG2_H3K4me1]


title: P28_HC_Gabbr1_control, YC143

description:
P28_Gabbr1_HC_normalized.csv
YC143

value: tamoxifen


title: H1993 1 uM gefitinib secretome replicate 2

value: H1993 1 uM gefitinib secretome


title: OG2 mESC [OG2_input]


title: P28_HC_Gabbr1_cKO, YC152

description:
P28_Gabbr1_HC_normalized.csv
YC152


title: OB018_Mk

source_name: Peripheral SpA Patient 18 - Classical Monocytes


title: OG2 mESC [OG2_LSD1]

value: LSD1 (Abacm,ab17721)


title: OB017_Mk

source_name: Peripheral SpA Patient 17 - Classical Monocytes


title: H1993 1 uM gefitinib secretome replicate 1


title: OG2 mESC [OG2_H3K27me3]


title: H1993 DMSO secretome replicate 2

value: H1993 DMSO secretome


title: OS000_Mk

source_name: Axial SpA Patient 0 - Classical Monocytes

value: Axial SpA Patient


title: OG2 mESC [rep2_OG2_H3K27me3]


title: Kras p53 Notch1 Tumour Rep 18

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Beatson Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: Matrix of raw counts

source_name: Primary Tumour

extract_protocol:
RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

tag: source tissue

value: Small Intestine

tag: genetic background

value: VilCreER KrasG12D/+ p53 fl/fl Notch1Tg/+

value: Primary Tumour


title: Kras p53 Notch1 Tumour Rep 17


title: OB015_Mk

source_name: Peripheral SpA Patient 15 - Classical Monocytes


title: OB014_Mk

source_name: Peripheral SpA Patient 14 - Classical Monocytes


title: OG2 mESC [OG2_H3K4me1]

source_name: OG2 mESC

value: H3K4me1(Abcam, #ab8895)


title: NF_WT_8_3

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (paired-end, 100 bp) were aligned to mouse reference genome mm9 using bowtie2 with the options of ‘-k 4 -X 2000’. Only properly paired reads were retained for the following analysis.
The Picard tool was used to mark and remove duplicates. All samples were randomly down-sampled to 56,000,000 reads to exclude library-size effect.
Peak calling was performed using MACS2 with the default cutoff of P ≤ 1 × 10-3. The peaks overlapped with any ENCODE mm9 ‘blacklist’ regions were excluded.
Common peaks in two replicates were determined by bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: Common peaks between two replicates in bed format.

source_name: liver

extract_protocol:
Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396 (please see manuscript for further methods details)
ATAC–seq samples were sequenced using the Illumina HiSeq 2000 .

tag: strain

value: C57BL/6J background

value: WT

value: nighttime feeding

value: 8-12 weeks

value: male

value: liver


title: Kras p53 Notch1 Tumour Rep 16

value: Mixed


title: NF_WT_8_4

tag: age


title: P28_OB_Gabbr1_control, YC144

description:
P28_Gabbr1_OB_normalized.csv
YC144

source_name: olfactory bulb astrocytes

tag: cell type

value: olfactory bulb astrocytes

value: Gabbr1 control


title: Kras p53 Notch1 Tumour Rep 15

tag: tissue


title: NF_WT_20_4


title: OB013_Mk

source_name: Peripheral SpA Patient 13 - Classical Monocytes

value: Classical Monocytes

value: peripheral blood

tag: disease state

value: Peripheral SpA Patient


title: OB012_Mk

source_name: Peripheral SpA Patient 12 - Classical Monocytes


title: Kras p53 Notch1 Tumour Rep 19


title: Kras p53 Notch1 Tumour Rep 14


title: Wild-type LP Trm cells_rep2

city: Newark

first: Alexander

last: Lemenze

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Demultiplexing with cellranger v3.1.0 mkfastq, bcl2fastq v2.20.0.422
Barcode and UMI deconvolution, mapping with cellranger v3.1.0 count
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

source_name: LP Trm cells

growth_protocol: T cells were isolated from the lamina propria for sequencing.

extract_protocol:
Five to ten thousand single cells at >90% viability were resuspended in PBS with 0.05% bovine serum albumin
GEMs (Gel Beads-in-Emulsion) were generated using the Chromium Single Cell 3ʹ Reagent Kits v3 and 10X Chromium Controller
10X scRNA 3' GEX

treatment_protocol: Mice were infected with Y.psuedotuberculosis 35 days prior to cell isolation.

value: lamina propria

value: Wild-type


title: Wild-type LP Trm cells_rep1

description: WT


title: Kras p53 Notch1 Tumour Rep 13

value: Small Intestine

value: VilCreER KrasG12D/+ p53 fl/fl Notch1Tg/+


title: Stat4-/- LP Trm cells_rep2


title: OB011_Mk

source_name: Peripheral SpA Patient 11 - Classical Monocytes


title: Kras p53 Notch1 Tumour Rep 12

value: Primary Tumour


title: OB016_Mk

source_name: Peripheral SpA Patient 16 - Classical Monocytes


title: NF_RE_8_3

value: C57BL/6J background

value: Bmal1 Liver-reconstituted


title: H1993 DMSO secretome replicate 1

source_name: H1993-gefitinib resistant

value: H1993 DMSO secretome


title: OB010_Mk

source_name: Peripheral SpA Patient 10 - Classical Monocytes


title: NF_RE_8_2

value: nighttime feeding

value: 8-12 weeks


title: Stat4-/- LP Trm cells_rep1

description: KO


title: OG2 mESC [OG2_H3K4me3]

value: OG2 mESC

value: mouse embryonic stem cells

value: WT

value: H3K4me3 (abcam, ab8580)


title: OB009_Mk

source_name: Peripheral SpA Patient 9 - Classical Monocytes

value: Classical Monocytes


title: KO_ZT20_2

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 using Tuxedo bowtie
Mapping results filtering performed using Tuxedo cuffquant
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: genes_fpkm_table.tsv  (FPKM value for each gene in tsv table format)

extract_protocol:
Total RNA was extracted from liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
Library construction was performed according to the Illumina TruSeq Total RNA stranded protocol.  The input quantity for total RNA was 1ug and rRNA was depleted  using ribo-zero rRNA gold removal kit (human/mouse/rat). The rRNA depleted RNA was chemically fragmented for three minutes.  First strand synthesis used random primers and reverse transcriptase to make cDNA.  After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated.  Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.  The concentrations for the libraries were normalized and then multiplexed together.  The concentration for denaturation was 2nM and the final concentration for clustering was 200pM.  The multiplexed libraries were sequenced by the Genomics High-Throughput Facility at the University of California – Irvine on six lanes using single end 100 cycles chemistry for the Ilumina instrument.   The version of HiSeq control software was HCS 3.4.0.38 with real time analysis software, RTA 2.7.7.

value: mKO

value: liver


title: Kras p53 Notch1 Tumour Rep 11

value: Mixed


title: NF_RE_20_3

value: male


title: OB008_Mk

source_name: Peripheral SpA Patient 8 - Classical Monocytes

value: peripheral blood

value: Peripheral SpA Patient


title: Kras p53 Notch1 Tumour Rep 10

value: Small Intestine

value: VilCreER KrasG12D/+ p53 fl/fl Notch1Tg/Tg

value: Primary Tumour


title: NF_RE_20_2

value: C57BL/6J background

value: Bmal1 Liver-reconstituted


title: Kras p53 Rep 9

value: VilCreER KrasG12D/+ p53 fl/fl


title: KO_ZT20_1


title: KO_ZT20_0


title: OB007_Mk

source_name: Peripheral SpA Patient 7 - Classical Monocytes


title: NF_WT_20_3

value: nighttime feeding

value: 8-12 weeks


title: Kras p53 Rep 7


title: NF_KO_8_1


title: Kras p53 Rep 8


title: KO_ZT16_1


title: OB006_Mk

source_name: Peripheral SpA Patient 6 - Classical Monocytes


title: NF_KO_20_4


title: NF_KO_8_2


title: OB005_Mk

source_name: Peripheral SpA Patient 5 - Classical Monocytes


title: OB004_Mk

source_name: Peripheral SpA Patient 4 - Classical Monocytes


title: KO_ZT16_2


title: NF_KO_20_3


title: Kras p53 Rep 5

source_name: Primary Tumour


title: OB002_Mk

source_name: Peripheral SpA Patient 2 - Classical Monocytes


title: KO_ZT12_2


title: OB001_Mk

source_name: Peripheral SpA Patient 1 - Classical Monocytes


title: Kras p53 Rep 6


title: KO_ZT12_1


title: AL_WT_8_6

source_name: liver

value: WT

value: ad libitum feeding


title: Kras p53 Rep 4


title: AL_WT_8_5


title: Braf p53 Notch1 Tumour Rep 7

value: VilCreER BrafV600E/+ p53fl/fl Notch1Tg/+


title: KO_ZT12_0

value: mKO


title: GK021_Mk

source_name: Healthy Control 21 - Classical Monocytes

value: Classical Monocytes

value: Healthy Control


title: AL_WT_20_5

value: male

value: liver


title: KO_ZT8_2


title: GK019_Mk

source_name: Healthy Control 19 - Classical Monocytes

value: peripheral blood


title: AL_WT_20_4


title: Braf p53 Notch1 Tumour Rep 6

value: Small Intestine

value: Mixed


title: GK018_Mk

source_name: Healthy Control 18 - Classical Monocytes


title: KO_ZT8_1


title: KO_ZT16_0


title: Braf p53 Notch1 Tumour Rep 4

value: Primary Tumour


title: GK017_Mk

source_name: Healthy Control 17 - Classical Monocytes


title: Braf p53 Notch1 Tumour Rep 5


title: AL_RE_8_1

value: C57BL/6J background


title: KO_ZT4_2


title: Braf p53 Notch1 Tumour Rep 3


title: Braf p53 Notch1 Tumour Rep 2


title: AL_RE_20_4

value: Bmal1 Liver-reconstituted


title: KO_ZT8_0


title: KO_ZT4_1


title: Braf p53 Notch1 Tumour Rep 1


title: AL_RE_20_3


title: GK016_Mk

source_name: Healthy Control 16 - Classical Monocytes


title: AL_KO_8_2


title: Braf p53 Tumour Rep 4

value: VilCreER BrafV600E/+ p53fl/fl


title: GK013_Mk

source_name: Healthy Control 13 - Classical Monocytes


title: AL_KO_8_1


title: KO_ZT0_2


title: Braf p53 Tumour Rep 3


title: GK012_Mk

source_name: Healthy Control 12 - Classical Monocytes


title: AL_KO_20_5


title: AL_RE_8_2


title: Braf p53 Tumour Rep 2


title: KO_ZT0_0


title: WT_ZT20_2


title: AL_KO_20_4


title: Braf p53 Tumour Rep 1


title: GK010_Mk

source_name: Healthy Control 10 - Classical Monocytes


title: GK015_Mk

source_name: Healthy Control 15 - Classical Monocytes


title: GK009_Mk

source_name: Healthy Control 9 - Classical Monocytes


title: GK014_Mk

source_name: Healthy Control 14 - Classical Monocytes


title: KO_ZT4_0


title: WT_ZT20_1


title: Apc Kras Tumour Rep 6

value: VilCreER Apcfl/+ KrasG12D/+


title: Apc Kras Tumour Rep 5

value: Colon


title: Apc Kras Tumour Rep 4


title: GK008_Mk

source_name: Healthy Control 8 - Classical Monocytes


title: WT_ZT20_0

value: WT


title: KO_ZT0_1


title: GK006_Mk

source_name: Healthy Control 6 - Classical Monocytes


title: Apc Kras Tumour Rep 3

source_name: Primary Tumour

value: Unknown


title: GK005_Mk

source_name: Healthy Control 5 - Classical Monocytes


title: Braf_T21 repeat 2

city: Worcester

first: Ichiro

last: Onoyama

address: 364 Plantation St

institute: University of Massachusetts Medical School

description: bisulfite converted genomic DNA

data_processing:
Samples were run on an Illumina HiSeq 2000 and images were analyzed using OLB 1.9 and CASAVA_v1.8.2.
Sequences were binned and trimmed according to the barcodes using a perl script written in house.
Binned Sequences were mapped to mm10 genome using BSMAP v2.89, which was also used for extracting the methylation ratio of mapped cytosines.
Mouse CpG island track from mm10/GRCm38 assembly was downloaded from UCSC genome browser. Mappedcytosines were assigned to CpG islands and nearest genes using ChIPpeakAnno package in R.
Arcsin transformed methylation ratios were compared among groups for each CpG,CpG island, as well as 200 bp window using limma package in R. To adjust for multiple comparisons, p-values were adjusted using the Benjamini-Hochberg (BH) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the methylation ratios from BSMAP mapping results for each sample, and the Arcsin transformed methylation ratios among groups for each CpG,CpG island, as well as 200 bp window, and p value, adjusted p value for the comparisons.

source_name: Braf KI MEFs 21 days after 4-OHT treatment

growth_protocol: MEFs were cultured in DMEM supplemented with 10% FBS. Cells were replated every 3 days with 2.4x106 cell/15cm dish.

extract_protocol:
Genomic DNA was extracted with Purelink genomic DNA kit from Invitrogen according to the manufacturer’s guidelines.
Libraries were prepared according to "Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling" (Nature Protocols, 6(4), 468-481. 2011).

treatment_protocol: To induce Cre recombinase, cells were treated with 0.1uM 4-OHT for 7 days.

value: mixed

tag: gender

value: female

value: Mouse embryonic fibroblast

tag: genotype/variation

value: Rosa26-CreERT2; Braf+/LSL


title: WT_ZT16_2


title: GK011_Mk

source_name: Healthy Control 11 - Classical Monocytes

value: Classical Monocytes

value: Healthy Control


title: GK004_Mk

source_name: Healthy Control 4 - Classical Monocytes

value: peripheral blood


title: Braf_T21 repeat 1

description: bisulfite converted genomic DNA


title: WT_ZT16_0

value: liver


title: Apc Kras Tumour Rep 2


title: Braf_T0 repeat 2

description: bisulfite converted genomic DNA

source_name: Braf KI MEFs without 4-OHT treatment


title: Braf_T0 repeat 1

description: bisulfite converted genomic DNA


title: Braf_T21 repeat 3

description: bisulfite converted genomic DNA


title: WT_ZT12_2


title: GK003_Mk

source_name: Healthy Control 3 - Classical Monocytes


title: Apc Kras Tumour Rep 1


title: wt_T21 repeat 3

description: bisulfite converted genomic DNA

source_name: WT MEFs 21 days after 4-OHT treatment

value: Rosa26-CreERT2; Braf+/+


title: Apc Tumour Rep 6

value: Mixed

value: VilCreER Apcfl/+

value: Primary Tumour


title: GK002_Mk

source_name: Healthy Control 2 - Classical Monocytes


title: WT_ZT12_1


title: Apc Tumour Rep 5

value: Small Intestine


title: wt_T21 repeat 2

description: bisulfite converted genomic DNA


title: WT_ZT12_0


title: Braf_T0 repeat 3

description: bisulfite converted genomic DNA


title: Apc Tumour Rep 4


title: WT_ZT8_2


title: wt_T21 repeat 1

description: bisulfite converted genomic DNA


title: WT_ZT16_1


title: microorganism2.0, tetracycline treatment,OD600=2.0

city: Nibong

first: Li

middle: Ya

address: 818 Fenghua Road

institute: Ningbo university

data_processing:
llumina Casava1.7 software used for basecalling
After the extracted RNA was tested qualified, mRNA was obtained by removing the ribosomal RNA (rRNA) in Total RNA. Then the mRNA was randomly broken into short fragments by adding fragmentation buffer, and the library was constructed according to strand specificity
After library construction, the library was initially quantified using Qubit2.0 Fluorometer, diluted to 1.5ng/ul, and then the insert size of the library was detected using Agilent 2100 bioanalyzer. qRT-PCR was used to accurately quantify the effective concentration of the library (library effective concentration higher than 2nM) to ensure the quality of the library
After passing the library inspection, different libraries were pooled according to the requirements of effective concentration and target off-machine data volume for Illumina sequencing. The basic principle of Sequencing is Sequencing by Synthesis. In the sequencing of the flow cell with four kinds of fluorescence labeled dNTP, primers for amplification, DNA polymerase and joint in each sequence complementary chain clusters, each to join a fluorescently labeled dNTP can release the corresponding fluorescence, sequencing machine by capturing the fluorescent signal, and through the computer software to convert optical signals into sequencing peak, Thus, the sequence information of the fragment to be tested is obtained
The raw sequencing sequence obtained by sequencing contains spliced or low-quality reads. In order to ensure the quality of information analysis, raw reads must be filtered to obtain clean reads
Assembly: the genome of V. atlanticus strain LGP32 (FM954973.2) using Bowtie2
Supplementary files format and content: tab-delimited text fies include FPKM values for each Sample

organism: Vibrio splendidus

source_name: bacterial cells

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods, followed by strict quality control of RNA samples, mainly through Agilent 2100 bioanalyzer: accurate detection of RNA integrity and total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacterial cells

tag: culture stage

value: tetracycline


title: wt_T0 repeat 3

description: bisulfite converted genomic DNA

source_name: WT MEFs without 4-OHT treatment


title: wt_T0 repeat 2

description: bisulfite converted genomic DNA


title: Apc Tumour Rep 2

value: Colon


title: WT_ZT8_0

value: WT


title: microorganism0.6, tetracycline treatment,OD600=0.6


title: wt_T0 repeat 1

description: bisulfite converted genomic DNA

value: mixed


title: microorganism1.2, tetracycline treatment,OD600=1.2


title: Apc Tumour Rep 1


title: WT_ZT4_2


title: GK001_Mk

source_name: Healthy Control 1 - Classical Monocytes


title: microorganism, coelomic fluid with tetracycline treatment ,  OD600=2.0

value: coelomic fluid with tetracycline


title: WT_ZT4_1


title: 3_SOR_ONC_S22

city: Pittsburgh

first: Kun-Che

last: Chang

state: PA

address: 1622 Locust St

department: Department of Ophthalmology

institute: University of Pittsburgh School of Medicine

description: Total counts 3_SOR_ONC_S22 (GE)

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench v22 (QIAGEN Digital Insights). Reads were aligned to the GRCm39/mm39 version of the mouse reference genome using default settings
Assembly: mm39
Supplementary files format and content: CSV file-matrix table with total raw counts for every gene and every sample

source_name: Retina

extract_protocol:
Qiagen RNeasy Plus micro (https://www.qiagen.com/us/resources/download.aspx?id=1961e574-091d-42cc-8b51-1bc3747da874&lang=en) We followed manufactures instructions, including DNA elimination. For elution we passed the elute through the column twice.
Reverse stranded libraries, library prep kit (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/stranded-total-rna-prep.html). 100ng of input RNA used

value: Retina

value: wildtype

value: Sorbinil- treatment


title: UCD52CR, replicate 3, RNAseq

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Raw sequence data (.bcl files) was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Initial quality control on the fastq files was performed with FastQC v.0.11.8 and MultiQC v.1.8.
Reads were trimmed for adaptor sequence/low-quality bases using Cutadapt v.1.15
Trimmed sequence reads were mapped to the merged GRch38/GRCm38 M12 genome using STAR v2.5.2b (parameters: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1)
Read counts were extracted using Salmon v0.8.2 "quant" algorithm with the library type set to "IU".
Differential expression was performed using the R package edgeR v.3.36.0.
Assembly: GRch38; GRCm38 M12
Supplementary files format and content: tab-delimited quantification file produced by Salmon

organism:
Homo sapiens
Mus musculus

source_name: Basal-like triple-negative breast cancer patient-derived xenograft; UCD52

growth_protocol: UCD52 PDX cells were grown in mammary fat pads of female NSG mice. Tumors were harvested when ~ 10mm x 10mm in size and 500K cells were injected into the right mammary gland of female NGS mice.

extract_protocol:
RNA was harvested using the Rneasy mini kit (Qiagen).
NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s protocols (New England Biolabs).

treatment_protocol: Once tumors reached 25-50 mm^2 in size, carboplatin resistance was induced by administering three intraparitoneal 40mg/kg doses of carboplatin spaced out over four days. Tumors were harvested once growth resumed and serially passaged into new recipient NGS mice, and was repeated until the tumor was unresponsive to carploplatin treatments. The carboplatin-resistant phenotype was maintained by continuing the carboplatin treatment regimen.

value: carboplatin resistant tumor from UCD52 PDX model

tag: phenotype

value: carboplatin-resistant

value: carboplatin


title: microorganism, coelomic fluid with tetracycline treatment ,  OD600=1.2


title: 1_SOR_ONC_S20

description: Total counts 1_SOR_ONC_S20 (GE)


title: UCD52CR, replicate 2, RNAseq

value: Basal-like triple-negative breast cancer patient-derived xenograft; UCD52


title: UCD52CR, replicate 1, RNAseq


title: 3_DMSO_ONC_S19

description: Total counts 3_DMSO_ONC_S19 (GE)

value: DMSO- control


title: WT_ZT4_0

value: liver


title: microorganism, coelomic fluid with tetracycline treatment , OD600=0.6


title: microorganism, active, OD600=2.0


title: UCD52PR, replicate 3, RNAseq

value: primary tumor from UCD52 PDX model

value: primary tumor

value: untreated


title: microorganism, active, OD600=1.2

value: bacterial cells


title: UCD52PR, replicate 2, RNAseq


title: 1_DMSO_ONC_S17

description: Total counts 1_DMSO_ONC_S17 (GE)


title: WT_ZT0_0


title: Apc Tumour Rep 3

value: Small Intestine

value: VilCreER Apcfl/+

value: Primary Tumour


title: WT_ZT8_1

value: WT


title: UCD52PR, replicate 1, RNAseq


title: WT_ZT0_2


title: 10b

status: Public on Apr 04 2023

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

institute: University of Agriculture in Krakow

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences, and also reads that did not pass quality filteration criteria (phred quality <20)
The raw reads were aligned to the Equus caballus (EC3)  genome  as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Assembly: EquCab3.0
Supplementary files format and content: Files containing gene counts for every gene and every sample created with htseq-count software

organism: Equus caballus

source_name: blood

extract_protocol:
RNA was isolated from tissue using using TRIzol reagent (Invitrogen, Carlsbad, California) in combination with a Direct-zol RNA kit (Zymo Research)
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

value: blood

tag: subject

value: after run


title: 9b


title: 6b


title: 8b


title: 7b


title: 2_DMSO_ONC_S18

description: Total counts 2_DMSO_ONC_S18 (GE)

value: Retina

tag: genotype

value: wildtype


title: 4b

tag: treatment


title: 2b


title: 5b


title: 1b


title: 10a

value: before run


title: microorganism, active, OD600=0.6


title: 3b


title: 9a


title: 8a


title: WT_ZT0_1


title: 7a


title: 6a


title: 5a


title: 4a


title: 3a


title: 2a


title: 1a


title: m.Vastus Lateralis_X017_30_6H

city: Durham

first: Christopher

last: Vann

state: NC

address: 300 N Duke St

department: Molecular Physiology Institute

institute: Duke University School of Medicine

description: X017 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM

hyb_protocol: RNA was prepared for Clariom S Human whole transcrioptome (WT) microarrays by North American Genomics in accordance with manufacturers specifications.

scan_protocol: Human Clariom S microarrays were ran on the GeneTitan MC platform (ThermoFisher) in accoradance with manufacturers specifications.

data_processing:
CEL files were uploaded to Transcriptome Analysis Console ver4.0 (ThermoFisher) and subsequently normalized using the robust multi-array average (RMA) method.  Following normalization,  the Hg38 build of the human genome was used to generate reference annotations.  Following annotation, pairwise comparisons were used to determine if differences existed in the PRE values from each bout of exercise.  Subsequently, a 2X2 RM-ANOVA with eBayes correction factor was used to determine differentially expressed mRNAs.  mRNAs with a p-value <0.01 and fold-change >±1.5 were considered significant.
Clariom_s_Human.r1.pgf
Clariom_s_Human.r1.mps

label: Biotin

source_name: previously resistance trained m. vastus lateralis muscle

extract_protocol: Approximately 10mg of skeletal muscle was placed into 500uL of Trizol in 1.7mL polypropelene tubes.  The muscle was hymogenized using a tight fitting pestle for ~30 seconds and stored at -80 degrees C overnight to increase RNA yield.  The following day, RNA was removed from overnight storage and thawed at room temperature.  100 uL of bromochloropropane was added to samples and then samples were shaken for 15 seconds followed by incubation at room temperature for 2 minutes.  Samples were then centrifuged at 12,000g for 15 minutes yielding three distinct phases.  Following centrifugation, the remainder of the protocol was performed on ice.  200uL of the aqueous phase was removed from each sample and placed into a new 1.7mL polypropelene tube with 500uL of isopropanol and subsequently centrifuged to form the RNA pellet.  Following removal of residual isopropanol, the RNA pellet was reconstituted in DEPC water and stored at -80 degrees C until shipment to commercial laboratory (North American Genomics) on dry-ice for analysis using the Clariom S Human array (Thermo Fisher).

tag: Sex

value: male

tag: individual

value: muscle biopsy


title: m.Vastus Lateralis_X017_30_PRE

description: X017 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM

label_protocol: RNA was prepared for Clariom S Human whole transcrioptome (WT) microarrays by North American Genomics in accordance with manufacturers specifications.


title: m.Vastus Lateralis_X016_30_PRE

description: X016 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X015_80_3H

description: X015 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X016_80_PRE

description: X016 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X016_80_3H

description: X016 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X017_30_3H

description: X017 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X015_30_3H

description: X015 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X015_30_6H

description: X015 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X014_80_3H

description: X014 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X014_30_PRE

description: X014 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X015_80_PRE

description: X015 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X015_30_PRE

description: X015 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X014_80_6H

description: X014 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X014_80_PRE

description: X014 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X016_30_6H

description: X016 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X017_80_6H

description: X017 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X014_30_6H

description: X014 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X012_80_PRE

description: X012 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X014_30_3H

description: X014 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X012_30_PRE

description: X012 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X017_80_3H

description: X017 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X016_80_6H

description: X016 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X016_30_3H

description: X016 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X012_80_3H

description: X012 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X015_80_6H

description: X015 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X012_30_3H

description: X012 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X011_80_6H

description: X011 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X011_80_PRE

description: X011 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X017_80_PRE

description: X017 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X011_30_PRE

description: X011 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X011_80_3H

description: X011 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X010_80_3H

description: X010 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X011_30_6H

description: X011 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X010_80_6H

description: X010 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X011_30_3H

description: X011 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X005_80_6H

description: X005 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X010_30_6H

description: X010 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X005_80_PRE

description: X005 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X004_80_PRE

description: X004 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X004_30_3H

description: X004 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X005_80_3H

description: X005 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X004_80_3H

description: X004 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X005_30_3H

description: X005 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X002_30_3H

description: X002 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X004_80_6H

description: X004 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X010_30_PRE

description: X010 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X010_80_PRE

description: X010 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X005_30_6H

description: X005 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X002_80_3H

description: X002 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X002_80_6H

description: X002 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X010_30_3H

description: X010 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X002_30_PRE

description: X002 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X004_30_6H

description: X004 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X002_30_6H

description: X002 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X005_30_PRE

description: X005 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: m.Vastus Lateralis_X001_80_PRE

description: X001 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X002_80_PRE

description: X002 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X001_80_6H

description: X001 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X001_80_3H

description: X001 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.8 estimated 1RM


title: m.Vastus Lateralis_X001_30_PRE

description: X001 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: severe group 21

city: Shanghai

first: Yunjie

address: No.800 Xiangyin Road

institute: Naval Medical University

data_processing:
Using FLASH v1.2.7 software, the reads of each sample are spliced by overlap, and the spliced sequence is the raw Tags.Using Trimmomatic v0.33 software, the Raw Tags obtained by splicing were filtered to obtain high-quality Tags data (Clean Tags)
Using UCLUST in QIIME(version 1.8.0) software to cluster Tags at the similarity level in ninety-seven percent, OTU was obtained, and the OTU was taxonomically annotated based on Silva (bacteria) and UNITE (fungi) taxonomic databases.
Comparing the representative sequence of the OTUs with a microbial reference database to obtain species classification information corresponding to each OTU, and counting the composition of each sample community at each level,
The Alpha diversity index of samples was evaluated using the Mothur (version v.1.30) software. In general, the index of diversity was compared among samples, and the number of sequences contained in samples was standardized for analysis.
The PICRUSt software was used to deduce the functional gene composition in samples by comparing the species composition information obtained from 16S sequencing data, so as to analyze the functional differences between different samples or subgroups.
Assembly: mm10
Library strategy: 16s-rDNA

organism: gut metagenome

source_name: intestinal lavage fluid

extract_protocol:
Extraction of total genomic DNA through the DNA Extraction Kit (Tiangen Biotechnology Company, Beijing, China) was conducted following the instructions of the kit.
DNA libraries for 16s-rDNA sequencing were prepared using SMARTER DNA-Seq Library Prep Kit following manufacturer's protocols.

value: intestinal lavage fluid

tag: group

value: severe


title: severe group 22


title: severe group 20


title: severe group 18


title: severe group 23


title: severe group 15


title: m.Vastus Lateralis_X001_30_3H

description: X001 male participant m.Vastus Lateralis muscle 3 hours  post acute resistance exercise at 0.3 estimated 1RM


title: severe group 13


title: severe group 14


title: severe group 12


title: severe group 11


title: m.Vastus Lateralis_X004_30_PRE

description: X004 male participant m.Vastus Lateralis muscle PRE acute resistance exercise at 0.3 estimated 1RM


title: severe group 10


title: severe group 8


title: severe group 6


title: severe group 4


title: severe group 17


title: severe group 7


title: severe group 19


title: severe group 5


title: severe group 9


title: severe group 3


title: 6 h post-treatment with suppresor tRNA

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
Global analysis of nuclearly encoded tRNAs
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the  tRNA standards e.g. tRNA standards E. coli tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

source_name: Mouse liver tissue

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. Total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9)
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol: All mice were purpose-bred and experimentally naïve at the start of the study. Mice were housed 5 per cage in a pathogen-free environment in Innovive disposable IVC rodent caging system with a 12h light/dark cycle. Ad libitum access to standard diet (2018, Global 18% protein rodent diet from Envigo+++, San Diego, CA, USA) and pre-filled acidified water from Innovive (pH 2.5-3.0) were used throughout the study period. The bedding material was hardwood chips (Sani-Chips, Cat# 7115, Envigo++++, CA, USA) and cages were changed biweekly. All in vivo procedures involving animals were performed in accordance with guidelines established by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol: The whole organs were pulverized in liquid nitrogen and lysed by grinding in 500 µL TRIzol. Total RNA from cells was isolated using the TRIzol-method according to manufacturer’s instructions and RNA integrity was assessed by 10%-denaturing polyacrylamide gel electrophoresis.

treatment_protocol: Four female wild-type mice were i.v. dosed with proprietary LUNAR-LNPs formulated with vitro transcribed suppressor tRNA (tSA1T5). Post mortem, liver was dissected at 6 and 72h post-treatment for analysis

value: liver

value: treated with suppressor tRNA

tag: time

value: Liver tissue from mouse treated with PBS


title: m.Vastus Lateralis_X001_30_6H

description: X001 male participant m.Vastus Lateralis muscle 6 hours  post acute resistance exercise at 0.3 estimated 1RM


title: 72 h post-treatment with suppresor tRNA


title: severe group 1


title: severe group 2


title: mild group 17

value: Ctrl


title: severe group 16


title: mild group 16


title: mild group 13


title: mild group 15


title: mild group 14


title: mild group 7


title: mild group 8


title: mild group 10


title: mild group 1


title: mild group 11


title: mild group 9


title: mild group 12


title: mild group 4


title: mild group 2


title: mild group 5


title: mild group 6


title: mild group 3


title: Smchd1 MD43 GFP, replicate 2, CaptureC

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

country: Australia

institute: WEHI

description:
Capture-C_probe_coverage.bed
CaptureC_Smchd1_MD43-GFP_MD43-GFP.hic

data_processing:
Reads were mapped using HiCUP v0.8.3 to the mm10 assembly of the mouse reference genome, providing a DpnII-digested version of the same.
BAM files were then imported into CHiCANE v0.1.8 in R v4.2.0. DpnII restriction fragments of the genome were intersected with coordinates of regions covered by capture probes, limiting to unique fragments of at least 20bp. Replicates were merged (method=’sum’) and significant interactions were determined with an FDR cutoff of 0.05.
Heatmaps were generated using the cloud-base implementation of Juicebox v2.2.6 after merging replicate BAM files, converting them to .txt format with a script provided in HiCUP then to .hic format by the pre function from Juicer_tools v2.20.00.
Assembly: mm10
Supplementary files format and content: Tab-separated file of capture-probe covered genomic domains and .hic processed files (Juicer pipeline format) for each replicate set of libraries.
Library strategy: Capture-C

source_name: Tailbud containing PSM from E8.5 somite matched embryos

extract_protocol:
Tail-bud tissue was dissected in ice-cold PBS. Immediately after dissection, the tissue was mechanically dissociated then fixed with 1% formaldehyde in PBS at room temperature for 10 min, then quenched by addition of glycine to a final concentration of 0.2M for 5 min. After pelleting, nuclei were extracted with cold lysis buffer (10mM Tris-Cl pH 8.0, 10mM NaCl, 0.2% IGEPAL CA-630 (Sigma-Aldrich) and cOmplete Ultra protease inhibitors (Roche)). After pelleting, most of the supernatant was removed and fixed nuclei were frozen and stored at -80C.
Upon thawing, 2-3 tailbud samples per genotype were pooled and in situ Hi-C was performed as described in Jansz et al. Nat Struct Mol Biol. 25(9):766-777 using DpnII as a the restriction enzyme. Hi-C libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) kit according to the manufacturer’s instructions and amplified with 9 PCR cycles. Samples were then quantified with a high sensitivity D1000 Tapestation (Agilent Technologies) and high sensitivity dsDNA Qubit then pooled at equimolar ratios. Capture C was carried out on the pooled libraries using the Agilent SureSelect Target Enrichment Kit (Roche) according to the manufacturer’s instructions. Baits for SMCHD1 targets of interest were designed using the online Agilent Technologies SureDesign Custom Design Tool (table below). The captured pool was then sequenced on the Illumina NextSeq platform with 75bp paired-end reads.

value: pre-somitic mesoderm


title: Smchd1 MD43 GFP, replicate 1, CaptureC

value: Tailbud containing PSM from E8.5 somite matched embryos


title: Smchd1 GFP, replicate 4, CaptureC

description:
Capture-C_probe_coverage.bed
CaptureC_Smchd1_GFP_GFP_merged.hic


title: Smchd1 GFP, replicate 1, CaptureC


title: Smchd1 MD43 GFP, replicate 3, CaptureC


title: Smchd1 MD43 GFP, replicate 4, CaptureC


title: Smchd1 GFP, replicate 3, CaptureC


title: Smchd1 wt, replicate 2, CaptureC

description:
Capture-C_probe_coverage.bed
CaptureC_Smchd1_wt_wt_merged.hic


title: Smchd1 GFP, replicate 2, CaptureC


title: Smchd1 wt, replicate 1, CaptureC


title: Smchd1 MD43, replicate 2, CaptureC

description:
Capture-C_probe_coverage.bed
CaptureC_Smchd1_MD43_MD43_merged.hic


title: NSC, CTCF, Smchd1-GFP, whole cell extract, input

description:
input
CTCF_ChIPseq_merged_peaks_and_normalized_counts.txt

data_processing:
Basecalls were performed witth the NextSeq2000 RTA3 software
Adapter trimming was performed with Trim Galore! v0.4.4 with Cutadapt v2.9, library QC was assessed with FastQC v0.11.8 before mapping with Bowtie2 v2.3.4.1 and Samtools v1.7 with default parameters to the GRCm38.p5 version of the reference mouse genome.
SeqMonk v1.48.1 was used to read in BAM files (extending by 180bp for all libraries as determined by cross-correlation plots using CSAW v1.30.1 in R v4.2.0) and call peaks over each replicate set of libraries.
Assembly: GRCm38.p5
Supplementary files format and content: Tab-delimited text file containing the list of peaks, called individually for each replicate set then merged into a single list of unique CTCF binding sites of interest (overlapping peaks were merged into single domains). The file also contains one column of counts for each replicate set, normalized by total counts per million and log2-transformed.

source_name: NSC

growth_protocol: Cortices of E14.5 embryos were dissociated and grown as an adherent monolayer on tissue culture treated plates. Growth media was NeuroCult NSC Basal Medium (Mouse) containing NeuroCult Proliferation Supplement (Mouse) (StemCell Technologies),  recombinant human EGF (20 ng/mL), recombinant human basic FGF (20ng/mL, all from Stem Cell Technologies) and 10 ng/ml laminin (Sigma Aldrich). Primary cells were maintained for a maximum of 20 passages.

extract_protocol:
CTCF ChIP-seq libraries were prepared from approximately 15 million female NSCs using the ChIP-IT High Sensitivity kit (Active Motif), according to the manufacturer's instruction and 10 µg of CTCF antibody (Cell Signalling Technologies, D31H2).
Libraries were generated with an Illumina TruSeq DNA Sample Preparation Kit. 200- to 400-bp fragments were size-selected with AMPure XP magnetic beads. Libraries were quantified with a D100 tape in a 4200 Tapestation (Agilent). Libraries were pooled and sequenced on the Illumina NextSeq2000 platform, with 75-bp single-end reads.

treatment_protocol: Female Smchd1 del-del cells were produced by transduction of Smchd1 flox-flox cells with VSVg pseudotyped MSCV-Cre-puromycin retrovirus and culturing them under drug selection for one week.

tag: cell line

value: NSC

value: Primary neural stem cells

value: Smchd1 GFP/GFP

tag: chip antibody


title: Smchd1 MD43, replicate 1, CaptureC

tag: age


title: NSC, CTCF, Smchd1 null, rep2

description:
Smchd1_del
CTCF_ChIPseq_merged_peaks_and_normalized_counts.txt

tag: cell type

value: Smchd1 del/del

tag: strain

value: Cell Signalling Technologies, D31H2


title: NSC, CTCF, Smchd1MD43-GFP, rep3

description:
MommeD43-GFP
CTCF_ChIPseq_merged_peaks_and_normalized_counts.txt

value: Smchd1 MommeD43-GFP/MommeD43-GFP


title: Smchd1 MD43, replicate 3, CaptureC

tag: tissue


title: NSC, CTCF, Smchd1MD43-GFP, rep2


title: NSC, CTCF, Smdhd1MD43-GFP, rep1


title: FNP, Smchd1 MD1, replicate 2

description:
MD1_male_rep2
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated txt file containing mean values across biological replicates, and values for individual replicates of log2-transformed RPKM counts normalized by sequencing depth for all genes. Transcript isoforms were merged.

source_name: FNP tissue

extract_protocol:
Tissue was dissected from E10.5 embryos. RNA was extracted and treated with DNAse I with the Quick RNA kit (Zymo) as per the instructions.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep kit v2 (Illumina) as per the manufacturer's instructions.

value: FNP tissue

value: frontonasal prominence

value: Smchd1 MD1/MD1

tag: mouse strain

value: FVB/NJ


title: FNP, Smchd1 WT, replicate 4

description:
WT_female_rep4
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt

value: Smchd1 WT/WT

value: female


title: FNP, Smchd1 WT, replicate 6

description:
WT_female_rep6
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: FNP, Smchd1 WT, replicate 5

description:
WT_female_rep5
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: NSC, CTCF, Smchd1GFP wild-type, rep3

description:
Smchd1GFP
CTCF_ChIPseq_merged_peaks_and_normalized_counts.txt


title: NSC, CTCF, Smchd1-GFP wild-type, rep2


title: FNP, Smchd1 WT, replicate 1

description:
WT_male_rep1
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt

value: male


title: FNP, Smchd1 WT, replicate 2

description:
WT_male_rep2
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: FNP, Smchd1 WT, replicate 3

description:
WT_male_rep3
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: RNA-Seq Astrocytes, Untreated, 72h, 2

city: New Delhi

first: Kartikeya

last: Singh

address: Outer Ring road

country: India

data_processing:
Fastq files contain raw sequenced data and FastQC tool was used for quality check.
The fastq data was trimmed to remove bad quality reads using Trim Galore and trimmed reads were then aligned to the transcriptome using STAR aligner.
STAR produces unsorted BAM files as output, which were then sorted using Samtools.
We used the sorted files as input for Feature Counts to get gene expression counts.
Assembly: mm10
Supplementary files format and content: RNA-seq counts dataframe (GeneID x SampleID)

source_name: Astrocyte

growth_protocol: We isolated primary NSCs from the ventricular zone of single wild type mouse brains (C57BL/6J, Harlan, The Netherlands) at embryonic day 14 (E14) as described before. Primary cultures of neurospheres (NSPs) were kept under proliferating conditions in neurobasal medium (DMEM F12; Lonza) supplemented with 1% B27 without vitamin A (Life Technologies), penicillin (100 U/ml; Lonza), streptomycin (100 g/ml; Lonza), and 20 ng/ml EGF (Epidermal Growth Factor; Life Technologies). We differentiated NSPs into astrocytes on 6-well or 12-well plates coated with poly-L-ornithine and by exchanging the proliferation medium with DMEM containing 10% FBS (Fetal Bovine Serum; Gibco), penicillin (100 U/ml; Lonza), and streptomycin (100 g/ml; Lonza). We differentiated cells into astrocytes at different time points (24, 48, 72 hours and 1 week) at 37°C in 5% CO2 and we kept them under normal conditions or treated with TNF (50 ng/ml; R&D Systems).

extract_protocol:
We extracted total RNA with TRIzol (Invitrogen) following the manufacturer’s recommendations. We added a DNase treatment to the RNA extraction using DNA-free kit DNase Treatment and Removal Reagents (Ambion-Thermofisher cat #AM1906) following manufacturer’s instructions. We checked the RNA quality using a Fragment Analyzer Systems (Agilent Technologies), RQN were between 3.4 and 10.
We converted total RNA into Stranded Total RNA Library for RNA-sequencing by using the TruSeq Stranded Total RNA Library Prep workflow with Ribo-Zero Gold kit according to Illumina’s instructions. Briefly, ribosomal RNA was removed from 300 ng of total RNA using biotinylated, target-specific oligos combined with Ribo-Zero Gold beads that deplete cytoplasmic and mitochondrial rRNA. Then, RNA was fragmented using divalent cations under elevated temperature. Cleaved RNA fragments are double stranded cDNA converted keeping strand-specificity. A single index adapter was ligated to each sample and DNA fragments were enriched using a polymerase. All libraries have been quantified using a Qubit HS dsDNA kit (Thermofisher) and the library quality check has been performed using a High Sensitivity NGS Fragment Analysis Kit on a Fragment Analyzer System (Agilent Technologies). We normalized indexed DNA libraries and pooled them at 10 nM.

treatment_protocol: For RNA-sequencing analyses, murine NSPs were kept under proliferation conditions or were differentiated into astrocytes for 24 and 72 hours without or with TNF treatment and for 1 week under normal conditions.

value: Astrocyte

value: Untreated


title: RNA-Seq Astrocytes, Untreated, 0h, 1

source_name: NSP

value: NSP


title: RNA-Seq Astrocytes, Untreated, 72h, 1


title: RNA-Seq Astrocytes, Untreated, 72h, 3


title: RNA-Seq Astrocytes, Untreated, 0h, 2


title: RNA-Seq Astrocytes, TNF treated, 72h, 3

value: TNF treated


title: RNA-Seq Astrocytes, TNF treated, 72h, 2


title: RNA-Seq Astrocytes, Untreated, 0h, 3


title: RNA-Seq Astrocytes, TNF treated, 72h, 1


title: RNA-Seq Astrocytes, Untreated, 24h, 3


title: RNA-Seq Astrocytes, Untreated, 24h, 2


title: RNA-Seq Astrocytes, Untreated, 24h, 1


title: NSC, CTCF, Smchd1 null, rep1

value: NSC


title: FNP, Smchd1 MD1, replicate 4

description:
MD1_female_rep4
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: NSC, CTCF, Smchd1-GFP wild-type, rep1

value: Primary neural stem cells


title: FNP, Smchd1 MD1, replicate 1

description:
MD1_female_rep1
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: RNA-Seq Astrocytes, TNF treated, 24h, 1


title: RNA-Seq Astrocytes, Untreated, 1 week, 3

value: 1 week


title: RNA-Seq Astrocytes, TNF treated, 24h, 2


title: D1TA_shPten_3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Mouse embryonic fibroblasts_D1TA_shPten

growth_protocol: Cells were cultured in 10%FBS DMES usign standard prrocedure

extract_protocol:
Total RNA was extracted by Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Mouse embryonic fibroblasts


title: Astrocytes, Untreated, 0h, 3

data_processing:
We used the FastQC tool to perform quality check on fastq files containing raw sequenced reads and bad quality reads were removed using Trim Galore.
The trimmed fastq reads were aligned to the genome using Bowtie2.
We used Samtools to convert the SAM output files from Bowtie2 into sorted BAM files and to remove reads aligned to mitochondrial chromosomes.
We used MACS2 to call chromatin accessibility peaks and the peaks that were found in the blacklisted regions of the genome (ENCODE) were removed before further analyses.
Assembly: mm10
Supplementary files format and content: ATAC-seq peak counts dataframe

extract_protocol:
800 μl of resuspension buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) were added to the cells. Following cell counting, we centrifuged 50,000 cells at 500 g for 10 min in a pre-chilled (4°C) fixed-angle centrifuge. The cell pellet was re-suspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl transposase, 17 μl PBS, 0.5 μl 10% Tween-20 and 5 μl water). Transposition reactions were incubated at 37°C for 40 min in a thermomixer with shaking at 1’000 rpm. Reactions were cleaned up with MinElute Raction purification kit (Qiagen) following manufacturer’s recommendations.
Library fragments were amplified using 1× NEBnext PCR master mix and 0.6 μM of custom PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Full libraries were amplified for five cycles, after which an aliquot of the PCR reaction was used together with 9 μl of the PCR cocktail with Sybr Green at a final concentration of 0.05×. We ran this reaction for 30 cycles to determine the additional number of cycles needed for the remaining reaction. Libraries were purified using AMPure XP magnetic beads (Beckman Coulter), quantified using qubit fluorimeter and diluted to make 4nM final concentration.

treatment_protocol: Cells grown as either free floating spheres (NSPs) or as astrocytes (for 24h and 72h non-treated or treated with TNF and for 1 week without TNF treatment) in poly-L-ornithine coated plates were washed once with ice-cold PBS and were spun at 500 g for 5min in a pre-chilled (4°C) fixed-angle centrifuge. We then re-suspended the cells in 200 μl of lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) and incubated them for 20 min on ice.


title: FNP, Smchd1 MD1, replicate 3

description:
MD1_male_rep3
FNP_MD1_and_wt_raw_RNAseq_counts.txt
FNP_MD1_and_wt_normalized_RNAseq_counts.txt


title: D1TA_shPten_1


title: Astrocytes, Untreated, 0h, 2


title: D1TA_3

source_name: Mouse embryonic fibroblasts_D1TA


title: Astrocytes, TNF treated, 24h, 1


title: Astrocytes, TNF treated, 24h, 2


title: D1TA_2


title: Astrocytes, Untreated, 0h, 1


title: Astrocytes, Untreated, 24h, 3


title: Astrocytes, TNF treated, 24h, 3


title: Astrocytes, Untreated, 24h, 2


title: D1TA_1


title: shPten_3

source_name: Mouse embryonic fibroblasts_shPten

value: shPten


title: RNA-Seq Astrocytes, TNF treated, 24h, 3


title: shPten_2


title: RNA-Seq Astrocytes, Untreated, 1 week, 2


title: CRF423 vehicle control

city: Swansea

first: Benjamin

middle: James

last: Jenkins

address: Singleton Park

institute: Swansea University

description: CRF423 V

hyb_protocol: RNA samples stored at -80°C were thawed on ice prior to hybridisation reactions. Reporter probes were diluted in 70 μl of hybridisation buffer and gently mixed to create a master mix. To set up the hybridisation reactions, 5 μl of each sample was added to 8 μl of master mix. Hybridisation reactions were then completed by adding 2 μl of Capture ProbeSet and incubation at 65°C for 20 h. Probe set-target RNA hybridisation solution is then further diluted to a final volume of 35 μl. 33 μl of the diluted hybridisation solution is loaded onto a SPRINT microfluidic cartridge, with an air bubble also inserted to the stop point.

scan_protocol: Detection and scanning were performed by the nCounter® SPRINT Profiler analysis system (Nanostring).

data_processing: Raw data appraisal, quality control and normalisation were all performed using the nSolver™ analysis software. Quality control included an imaging QC of > 75% FOV registration, binding density QC within a range of 0.1 - 2.25, positive control linearity QC with R2 ≥ 0.95, and a positive control limit of detection QC set as 0.5 fM positive control above 2 standard deviations above the negative controls. Normalisation was performed using negative controls, positive controls and housekeeping genes selected by the nSolver™ normalisation module and normalised data was used as input for further analysis.

label: Nanostring capture and reporter codeset

source_name: human peripheral blood

label_protocol: Sample RNA is hybridised with target-specific capture and reporter probes in order to create a library of unique target-probe complexes. Each target is labelled with a specific molecular barcode, which can then be detected and counted using an automated fluorescence microscope

extract_protocol: RNA isolation was performed using an RNeasy® Mini Kit as per the manufacturers’ guidelines (all Qiagen – unless otherwise stated). Cells were lysed in a 1:1 solution of RLT buffer and 70% high-grade ethanol (Fisher Bioreagents) and mixed well with a needled syringe. Lysed cells were then transferred to an RNeasy® Mini spin column placed in a 2 ml collection tube and centrifuged at 8000 x g for 15 s. The spin column was then washed once with RW1 buffer, followed by two wash steps using RPE buffer, with subsequent centrifugation at 8000 x g for 15 – 120 s following the addition of each reagent. The resulting flow-through was discarded each time. Following washing, the spin column was placed in a new collection tube and 30 μl of RNase-free water was added directly to the spin column membrane in order to elute the RNA following centrifugation at 8000 x g for 1 min. The collected eluate was re-placed on the spin column membrane and centrifuged again to further increase the final concentration of the collected RNA. Purity was assessed using a NanoDrop™ spectrophotometer by measuring the ratio of absorbance at 260 nm versus 280 nm or 230 nm. Measured A260/A280 and A260/A230 ratios were typically ~2.0. Any RNA samples with A260/230 ratio below 2.0 were precipitated using 0.3 M sodium acetate solution (ThermoFisher) and isopropanol. RNA was diluted to 300 μl in RNase-free water before addition of sodium acetate. An equal volume of isopropanol was then added to the RNA solution, which was incubated overnight at -20°C. RNA was recovered by centrifugation at 14000 x g for 10 min at 4°C and the resulting pellet was washed twice in 70% ethanol. The final pellet was dried at RT before dissolving in RNase-free water. Subsequent measured A260/A230 ratios were typically improved to ≥ 2.0. Once purity was established, RNA was stored at -80°C until required for downstream analysis. Freeze-thaw cycles were avoided in order to prevent RNA degradation.

treatment_protocol: Isolated T cells were cultured in human plasma-like medium (HPLM; Gibco), unless stated otherwise, and seeded at a density of 1x10^6 cells per ml. Cell culture plates were coated overnight with 2 μg/ml anti-CD3 antibody (Biolegend) prior to T cell activation. T cells were co-stimulated with 20 μg/ml anti-CD28 (Biolegend). Cells were treated with 10 μM canagliflozin (Cambridge Bioscience), 10 μM dapagliflozin (Combi-Blocks) or dimethyl sulphoxide (DMSO) vehicle control (Merck). Plates were incubated at 37˚C in 5% CO2 for the desired amount of time. Following 3 h incubation, culture medium was supplemented with 10% dialysed FBS to prevent impaired T cell activation.

value: peripheral blood

value: naïve CD4+ T cell

value: vehicle


title: CRF423 canagliflozin-treated

description: CRF423 C

value: canagliflozin


title: CRF506 canagliflozin-treated

description: CRF506 C


title: CRF405 vehicle control

description: CRF405 V


title: Astrocytes, Untreated, 24h, 1


title: CRF506 vehicle control

description: CRF506 V


title: D1TA_shPten_2


title: RNA-Seq Astrocytes, Untreated, 1 week, 1


title: CRF405 canagliflozin-treated

description: CRF405 C


title: shPten_1


title: Astrocytes, TNF treated, 72h, 3


title: Astrocytes, TNF treated, 72h, 2


title: CRF360 vehicle control

description: CRF360 V


title: Control_3

source_name: Mouse embryonic fibroblasts_Control

value: Control


title: Astrocytes, TNF treated, 72h, 1


title: CRF360 canagliflozin-treated

description: CRF360 C


title: Astrocytes, Untreated, 72h, 3


title: CRF318 canaglilfozin-treated

description: CRF318 C

value: canaglilfozin


title: CRF119 vehicle control

description: CRF119 V


title: CRF318 vehicle control

description: CRF318 V


title: Control_1


title: Astrocytes, Untreated, 72h, 2


title: CRF506 dapagliflozin-treated

description: CRF506 D

value: naïve T cells

value: dapagliflozin


title: CRF119 canagliflozin-treated

description: CRF119 C


title: CRF532 dapagliflozin-treated

description: CRF532 D


title: CRF405 dapagliflozin-treated

description: CRF405 D


title: RPF_CFBE_R553X-CFTR_supp tRNA

description: Ribosome-protected fragments

data_processing:
Library strategy: Ribo-seq (ribosome profiling)
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using STAR (2.5.4b), parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1
Read counting using HTSeq, version 0.9.1
Genome_build: Homo sapiens Ensemble build GRCh38.p13
Genome_build: Mus musculus Ensemble build GRCm38
Supplementary_files_format_and_content: tab-delimited text files include unique read counts per gene per kilobase and million mapped reads RPKM for each sample

source_name: R553X-CFTR cotransfected with suppressor tRNA

growth_protocol: CFBE41o- cells were grown in Dulbecco´s Modified Essential Medium (DMEM). CFBE41o-cells were co-transfected in triplicate with 25 ng PTC-FLuc or WT-FLuc plasmids and 100 ng each tRNA variant using lipofectamine 3000 (Thermo Fisher Scientific)

extract_protocol:
The whole organs were pulverized in liquid nitrogen and lysed by grinding in 360 µL 10 mM Tris-HCl (pH 7.4) supplemented with 5 mM MgCl2, 100 mM KCL, 1% NP-40, 2mM DTT, 100 µg/mL cycloheximide topped with 40µL of 10% sodium deoxycholate. Lysate from each animal organ were used to produce an independent library. re flash frozen and immediately lysed by grinding in 10mM Tris-HCL pH 7.4, 5mM MgCl2, 100mM KCL, 1% NP-40, 2% sodium deoxycholate.The lysates from three animals each were pooled.
Isolation of mRNA-bound ribosome complexes, RNase I digestion-derived ribosome-protected fragments (RPFs), RNA-size selection and generation of the cDNA libraries was performed as described (Guo et al, 2010; doi: 10.1038/nature09267 )

treatment_protocol: Two mice were i.v. dosed with LUNAR1 co-formulated with 0.3 mg/kg R208X-aLuc mRNA and 0.6 mg/kg tS, and in two mice LUNAR2 co-formulated with 0.35 mg/kg tSA1T5::UGA suppressor with an anticodon to pair to UGA PTC with 0.35 mg/kg PTC-Cre mRNA (S69X-S82X) were i.t. administered. Six hours post treatment the mice were anesthetized and liver or lung, respectively, extracted and flash frozen. Mice treated with PBS for the same duration served as negative control.

value: CFBE 41o- cells

value: immortalized bronchial epithelial cells

value: suppressor tRNA contransfected


title: Astrocytes, Untreated, 1week, 4

value: Astrocyte

value: Untreated


title: Astrocytes, Untreated, 72h, 1


title: RPF_CFBE_WT_CFTR

description: Ribosome-protected fragments

source_name: WT CFTR

value: WT CFTR


title: CRF506 vehicle control

description: CRF506 V


title: CRF360 dapagliflozin-treated

description: CRF360 D