title: MIDHiC_Brg1FV_mESC_6h_R1

value: Mouse Embryonic Stem Cell

tag: time


title: 123_963122-35

status: Public on Dec 31 2023

type: SRA

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

country: USA

institute: Benaroya Research Institute at Virginia Mason

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

tag: tissue

value: PBMC

tag: age

tag: Sex

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

tag: treatment

value: SCIT

tag: sts timepoint

value: PostChallenge


title: E4_S29

city: Freiburg i. Br.

first: Csaba

last: Jeney

state: Baden-Württemberg

address: Georges-Köhler-Allee 103

department: Department for Microsystems Engineering

country: Germany

institute: University of Freiburg

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the GRCh38 cDNA reference transcriptome from Ensembl using salmon v1.3.0, kallisto v0.46.1 as well as to GRCh38.p13 genome with STAR 2.7.5c in solo mode.
Transcript abundances (TPM) and count estimates were imported with the tximeta package for salmon and tximport for kallisto and summarized to genes using the summarizeToGene() statement. STAR alignment files were counted with featureCounts v2.0.3.
Cells with an alignment efficiency below 80 % were filtered out (salmon and kallisto). Cells with less than 60 % of uniquely mapped reads were filtered out (STAR). In both cases only cells with at least 1E+5 detected reads were considered.
Pseudo-bulk differential expression analysis (MCF7 vs BT-474) was performed with DESeq2 v1.32.0.
In order to evaluate transcriptomal similarity between cells analyzed on the miniaturized Smart-seq2 platform to published data (GSE151334), the datasets were combined, batch-corrected with BBKNN and projected into a two-dimensional space with SCANPY’s (v1.8.1) built-in UMAP function.
Assembly: GRCh38 cDNA reference transcriptome from Ensembl or GRCh38.p13 genome
Supplementary files format and content: DE analysis files contain DESeq2 output including ENSEMBL identifier, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj as column names
Supplementary files format and content: Raw count files contain the raw counts of each gene detected in the cell described

molecule: polyA RNA

source_name: Epithelial cell

growth_protocol: The cell lines were cultured in a cell culture incubator under a 5 % CO2 atmosphere at 37 °C. MCF7 cells were cultured in DMEM, BT-474 cells were cultured in DMEM/F12. Cells were harvested using trypsin.

extract_protocol: cDNA synthesis was perfromed using SMART-Seq Single Cell Kit (634472, Takara BIO). Library preparation was performed using Nextera XT DNA Library Preparation Kit (FC-131-1024, Illumina). Both at 1/10 of original reaction volumes. See associated manuscript for detailed information.

value: Mammary gland

tag: cell line

tag: cell type

value: breast cancer

value: untreated


title: Gene editing, RAG1 intron 1 sample1_N

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

description:
guide1_sample1_Peaks.bed
guide2_sample1_Peaks.bed

library_source: genomic

data_processing:
Elaborate using the GUIDE-seq pipeline
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample
Library strategy: Guide-Seq

molecule: genomic DNA

growth_protocol: Cells were cultured in RPMI 1640 medium (Corning) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Euroclone), 2mM L-glutamine (Euroclone) and 100U/I penicilin/streptomycin (Lonza)

extract_protocol:
Agencourt DNAdvance purification kit (Beckman Coulter cat. no. A48705)
Random sheraing of gDNA (500bp), end repairing/A-tailing, adapter ligation and nested PCRs

treatment_protocol: Edited cells were electroporated using SF Cell 4D-Nucleofector X Kit and Nucleofector 4D device and then cultured as descrived above

value: myelogenous leukemia cells

value: S.p. Cas9 + dsODN + gRNA#7


title: 116_970865-35

value: Female

value: Placebo


title: CES, ALS, ALS81

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

description: Sample=”ALS81” (ALS_CES_variant_list.tsv)

data_processing:
Sequencing was performed on Illumina MiSeq instrument with the 2x150 paired-end sequencing mode.
Read alignment and sequence variant analysis were performed using NextGENe Software version 2.4.2.3 (SoftGenetics, State College, PA). The reads were mapped against the human GRCh38 (hg38) reference genome. A variant was reported if at least 5 reads mapped to the variant position and at least 20% of the reads presented the variant.
Variants were annotated using the gnomAD v2.1.1 (GRCh38 LiftOver) database. The clinical interpretation of variants were extracted from the ClinVar (NCBI) database.
Analysis results of the samples were obtained from NextGENe as variant call format (vcf) files. Mutation reports (variant lists) were also exported as text tables (tsv) and then merged, sorted and formatted using R v4.3.0.
Assembly: hg38
Supplementary files format and content: variant call format (vcf) files
Supplementary files format and content: variant list (tsv)

source_name: blood

extract_protocol:
Genomic DNA extraction from whole blood. We prepared aliquots of 1 ml frozen whole blood sample from ALS and control patients and extracted 200 μL of it using the Macherey-Nagel™ NucleoSpin™ Tissue Kit according to the manufacturer's protocol.
CES (clinical exome sequencing) was performed by TruSight One Sequencing Panel Kit (Illumina, San Diego, CA) that covers coding regions of 4813 genes associated with human disease. Library preparation was done in accordance with the manufacturer’s instructions.
CES (clinical exome sequencing)

value: blood

tag: patient code

value: female

tag: age (at_sampling)

tag: age (at_als_onset)

tag: disease

value: ALS

tag: symptoms

value: classic (all 3 symptom groups), bulbar, lower and upper limb


title: Gene editing, RAG1 intron 1 sample3_N

description:
guide1_sample3_Peaks.bed
guide2_sample3_Peaks.bed

value: unedited


title: E6_S45

tag: tissue


title: E4_S125


title: 115_957447-35

tag: age

tag: Sex


title: E3_S21


title: Gene editing, RAG1 intron 1 sample1_P


title: MIDHiC_Brg1FV_mESC_3h_R1

city: La Jolla

first: Hanbin

last: Lu

state: CA

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

description:
ATAC_Brg1FV_mESC_3h_combined.hic
ATAC_Brg1FV_mESC_3h_combined.hic.mcool

data_processing:
Adaptors in pair-end (PE) sequencing reads were trimmed using Trimmomatic (Bolger et al., 2014). Trimmed PE reads were aligned to mm10 genome using HiC-Pro analysis pipeline (Servant et al., 2015). HiC-Pro performs ‘global’ and ‘local’ mapping. In the global mapping stage, full-length reads were first end-to-end aligned. Any unmapped reads will be split at the ligation sites (MID Hi-C ligation sites:  TTATAA, TTATNAG, CTNATNAG, CTNATAA) and the 5’ segment will be re-aligned in the local mapping stage. We denote this as one pass of iterative alignment. Instead of dumping the 3’ segment, we performed more passes of iterative alignment till no more segments of reads can be split or aligned. To obain the Hi-C valid interaction from a multi-fragment (>2) interaction read, we kept two farthest separated fragments as the representative validpair. The output validpairs were transformed to HIC (Rao et al., 2014) and COOL (Abdennur and Mirny, 2019) formats for downstream analysis. The contact maps were visualized by JUICEBOX (Durand et al., 2016b). To call HiCCUPS loops, we used the HiCCUPS subcommand in JUICER toolkit. For all other downstream analysis, we used COOLER and COOLTOOLS packages (Nora et al., 2020) to access Hi-C data stored in mcool file and analyze in python environment.
Genome_build: mm10
Supplementary files format and content: hic and mcool format
Library strategy: MID Hi-C

organism: Mus musculus

source_name: mESC

growth_protocol: E14TG2a mESCs were maintained in KnockOut DMEM (Thermo Fisher,10829018) medium, supplied with 15% FBS (R&D Systems, S10250H), 1mM MEM Non-Essential Amino Acids (Thermo Fisher, 11140-050), 2mM Glutamax (Thermo Fisher, 35050061), 100 U/mL Pen/Strep (Thermo Fisher, 15140122), 0.1 mM 2(β)-ME (Sigma, M-3148), and 1000 U/mL LIF (Cell Guidance Systems, GFM200) on 0.1% gelatin coated dishes at 37C with 5% CO2. Cells were passaged every two days. Medium was changed on a daily basis.

extract_protocol:
mESC cells were double crosslinked using formaldehyde (Fisher Scientific, 50-980-494) and DSG (ProteoChem, c1104-100mg) and aliquoted as described previously (Hsieh et al., 2020). One aliquot of fixed cells (~5 million) was washed in 1.4 mL low SDS buffer (50 mM pH 7.5 Tris-HCL, 10 mM NaCl, 0.1% SDS) with 1X Protease Inhibitor Cocktails (PICs; Roche, 11873580001). Incubate on ice for 15 min. Spin down the nuclei at 2500 rcf for 5 min at 4C. Remove supernatant and wash one more time in the low SDS buffer on ice. Then, resuspend nuclei in 1 mL digestion buffer (1X Cutsmart buffer, 1% Triton X-100, 1X PICs). Incubate at 37C for 20 min with gentle rotation. Add 250U MseI (NEB, R0525M) and 250U DdeI (NEB, R0175L) to digest nuclei at 37C for 6 hours or overnight with gentle rotation. After digestion, spin down the nuclei and resuspend in 1 mL fill-in reaction mix (1X CutSmart buffer, 1% Triton X-100, 66 uM dTTP, 66 uM dCTP, 66 uM dGTP, 66 uM dATP-Biotin (Jena Bioscience, JBS-NU-835-BIO14-L), 50 U Klenow DNA large polymerase I (NEB, M0210M), 1X PICs). Rotate at room temp for 90 min. Spin down nuclei and resuspend in 1 mL ligation mix (1X T4 DNA ligase buffer, 1% Triton X-100, 0.1 mg/mL BSA, 15 U T4 ligase (Life Technologies, 15224041), 1X PICs). Incubate at 14C overnight with gentle rotation. Next day, spin down the nuclei. The proximal ligated nuclei can be used for library preparation or proceeded to MID HiChIP.
Resuspend the proximal-ligated nuclei from MID Hi-C experiment in 300 uL ChIP elution buffer (1% SDS, 100 mM NaHCO3) and incubate at 65C overnight. Next day, add RnaseA and incubate at 37C for 45 min. Then, add Proteinase K and incubate at 55C for 2 hours. Purify DNA using Phenol:Chloroform:Isoamyl (PCI) method. Purified DNA can be stored in -80C till ready for library preparation. Before generating sequencing library, prepare Dynabeads MyOne Streptavidin T1 (Invitrogen, 65601) beads by washing 5 uL T1 beads twice in 600 ul Tween wash buffer (1X binding buffer, 0.05% Tween-20) at 55 C for 2 min. Reclaim the beads on magnetic stand and resuspend in 50 ul 2X binding buffer (2 M NaCl, 10 mM pH 7.5 Tris-HCl, 1 mM EDTA). The beads are ready for immobilizing biotin-labeled DNA. We used NEB fragmentase (NEB, M0348S) to fragment DNA. But sonication can be used to fulfill the same purpose. 50 ng to 500 ng DNA were treated with NEB fragmentase in 20 uL reaction volume, per manufacture instructed. Incubate the reaction at 37C for 9 to 13 min, optimized to generate 100 – 500bp fragment size. To stop the reaction, add 250 ul 2X binding buffer to the DNA fragmentation reaction and incubate at 55C for 15 min. Then, add 280 uL Zymo DNA elution buffer (Zymo Research, D3004-4-50) and 50 ul prepared T1 beads to the stopped reaction (total 600 ul). Rotate the beads and DNA mix at room temperature for 15 min. After that, reclaim the beads and wash twice in the Tween wash buffer as described above. The DNA-bound T1 beads were used for NEBNext Ultra II DNA Library Preparation (NEB, E7645S) per manufacture instruction with gentle taps during reactions to keep beads in suspension. We typically amplify 8-10 PCR cycles for library amplification. The library was then double-size selected using home-made SPRI beads to isolate fragments between 200 and 800 bp for next generation sequencing.

treatment_protocol: dTAG13 3hr

value: mESC

value: Mouse Embryonic Stem Cell

tag: genotype

tag: time

tag: antibody


title: 118_966648-31

value: PBMC

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

value: PreChallenge


title: CES, ALS, ALS75

description: Sample=”ALS75” (ALS_CES_variant_list.tsv)

value: male

value: lower and upper limb, bulbar not present


title: 114_957447-31

tag: visit number

tag: treatment

tag: sts timepoint


title: BAMS2 204361730135

type: genomic

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

description:
BAMS2
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

hyb_protocol: standard Illumina protocl

scan_protocol: standard Illumina protocl

data_processing: Raw IDAT files were processed using R package ChAMP. Probes with missing values are removed, samples with more than 10% of probes with a detection p-value of greater than 0.01, probes with a detection p-value of greater than 0.01 in at least one sample and probes for which 5% of samples have a bead count less than 3 are filtered out.  Probes targeting CpG sites that are near SNPs, belong to X/Y chromosomes, or align with multiple locations are filtered out

label: Cy3 and Cy5

source_name: Fibroblast

label_protocol: standard Illumina protocl

extract_protocol: Genomic DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel) from two different cell pellets for each sample. A minimum of 500ng was sent to Diagenode services for DNA methylation analysis

value: BAMS (bosma arhinia microphthalmia syndrome)

tag: sentrix id

tag: sentrix position


title: E3_S117

value: Mammary gland

tag: cell line

tag: cell type

value: breast cancer

value: untreated


title: 110_970809-35

tag: tissue

tag: age

value: Male

value: PostChallenge


title: E2_S13


title: CES, ALS, ALS69

description: Sample=”ALS69” (ALS_CES_variant_list.tsv)

value: blood

tag: patient code

tag: Sex

tag: age (at_sampling)

tag: age (at_als_onset)

tag: disease

tag: symptoms


title: F7_S54


title: MIDHiC_Brg1FV_mESC_0h_R1

description:
ATAC_Brg1FV_mESC_0h_combined.hic
ATAC_Brg1FV_mESC_0h_combined.hic.mcool

treatment_protocol: DMSO 0hr

tag: genotype

value: DMSO

tag: time

tag: antibody


title: CES, ALS, ALS74

description: Sample=”ALS74” (ALS_CES_variant_list.tsv)

value: female

value: ALS


title: 109_957477-35

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

tag: treatment

value: Placebo


title: CES, ALS, ALS62

description: Sample=”ALS62” (ALS_CES_variant_list.tsv)

tag: tissue

value: classic (all 3 symptom groups), bulbar, lower and upper limb


title: E2_S109

tag: cell line

tag: cell type


title: 108_966661-35

tag: age

tag: Sex

tag: sts timepoint


title: MIDHiC_Brg1FV_mESC_3h_R2

value: mESC

value: Mouse Embryonic Stem Cell


title: ATAC_Brg1FV_mESC_6h

data_processing:
Adaptors in pair-end (PE) sequencing reads were trimmed using Trimmomatic (Bolger et al., 2014). Trimmed PE reads were then aligned to mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with flags `--very-sensitive -I 10 -X 700 –dovetail`. Only mapped fragments with sizes between 0 to 200 BP were kept for further analysis. Peaks were called by MACS2 with flags `-g mm -f BEDPE -q 0.01 –SPMR –keep-dup auto`. Then, functionalities of deeptools (Ramírez et al., 2014) were used to analyze enrichment signals. Briefly, density tracks were generated by `bamCoverage` to be visualized in UCSC genome browser or by pyGenomeTracks (Lopez-Delisle et al., 2020). Clustering of peaks, based on H3K4me3, H3K27ac, and CTCF signal, and tornado plots were generated by `computeMatrix` and `plotHeatmap` to identify enhancers and promoters devoid of CTCF occupancies. Summarized signal profiles were generated by `plotProfile`. In addition, quantification of peaks was performed through counting the number of reads overlapping with peaks using PyRanges (Stovner and Sætrom, 2019). Homer (Heinz et al., 2010) was used to search enriched motifs within 200 BP from the peak centers.
Genome_build: mm10
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq samples were prepared using ATAC-seq kit from Active Motif (53150).
ATAC-seq samples were prepared using ATAC-seq kit from Active Motif (53150).

treatment_protocol: dTAG13 6hr


title: 107_966661-31

value: PBMC

value: PreChallenge


title: E12_S93


title: ATAC_Brg1FV_mESC_3h


title: E12_S189


title: CES, ALS, ALS61

description: Sample=”ALS61” (ALS_CES_variant_list.tsv)

tag: patient code

tag: age (at_sampling)

tag: age (at_als_onset)

tag: disease

tag: symptoms

value: classic (all 3 symptom groups), bulbar, lower and upper limb, pseudobulbar


title: 106_957477-31

tag: fastq total_reads

tag: percent aligned


title: ATAC_Brg1FV_mESC_0h

tag: genotype

tag: time

tag: antibody


title: E11_S85

tag: treatment


title: MIDHiC_Brg1FV_mESC_0h_R2


title: FOXC2

city: Shanghai

first: Bin

last: Li

address: Jinzun Road

country: China

institute: Shanghai jiaotong University

data_processing:
Libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website; Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence; Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HiPSC-derived cardiomyocytes

extract_protocol:
Total mRNAs were isolated from nTL- and sTL- hiPSC-derived cardiomyocytes using TRIZOL (Invitrogen) according to the directions. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit.
CDNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: HiPSC-derived cardiomyocytes

value: cardiomyocytes

value: FOXC1 overexpressed


title: FOXC3


title: CES, ALS, ALS76

description: Sample=”ALS76” (ALS_CES_variant_list.tsv)

value: lower and upper limb, bulbar not present


title: E11_S181

value: Mammary gland

tag: cell line

value: breast cancer

value: untreated


title: FOXC1

tag: cell type


title: 1892_WT

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: 10X scRNAseq

data_processing:
Space Ranger v3.1.0 to align reads to mouse reference genome (mm10)
Used Loupe Browser to filter Lgr5+ (median average expression > 0.5), Vil1+ (median average expression > 0.5), Klf4+ (median average expression > 1.5), Chga+ (median average expression > 1.0), and Dclk1+ (median average expression > 0.5) colonic IEC subset-containing spots
Differential gene expression analysis
Assembly: mm10
Supplementary files format and content: WT_metrics_summary.csv: Space Ranger pipeline output containing key metrics about the barcoding and sequencing process.
Supplementary files format and content: WT_barcodes.tsv.gz: Barcodes corresponding to column indices of the feature-barcode matrix
Supplementary files format and content: WT_features.tsv.gz: Features corresponding to row indices of the feature-barcode matrix
Supplementary files format and content: WT_matrix.mtx.gz: Feature-barcode matrix summarizing the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: IEC subset and Reg3 receptor genes_median normalized average expression values.xlsx: Median normalized average expression values of IEC-subset specific genes and Reg3 receptors among colonic IEC-subset containing spots
Supplementary files format and content: WT_Lgr5+_Vil1+_Klf4+_Chga+_Dclk1+.csv: Barcodes assigned to colonic IEC subset-containing spots
Library strategy: Spatial Transcriptomics

source_name: Entire colon

growth_protocol: Mouse was raised in a Specific Pathogen Free (SPF) facility on a normal diet.

extract_protocol:
Mouse colon sample was coiled into a “Swiss roll” and frozen immediately with chilled isopentane. The frozen tissue was then embedded into Optimal Cutting Temperature (OCT) compound. The intestinal tissue block was then processed by cryo-sectioning.
Tissue section was treated with permeabilization enzyme for 24 minutes, followed by reverse transcription and second strand synthesis  on the slide. The library construction was performed  per manufacturer’s instructions including fragmentation, end repair & A-tailing, post fragmentation end repair & A-tailing double sided size selection (SPRIselect), adaptor ligation, post ligation cleanup, sample Index PCR, and SPRIselect. The library size and quality was assessed using the Agilent TapeStation.
The library was ran on the NovaSeq S4 instrument following the manufacturer’s recommendations for 100 million reads.

treatment_protocol: No treatment. Female mouse at steady state was harvested at 8 weeks old.

tag: strain

value: Entire colon

tag: age

value: 8 weeks

value: Wildtype

value: Steady state


title: ATAC_Brg1FV_mESC_24h

treatment_protocol: dTAG13 24hr


title: E10_S77


title: E10_S173


title: vector-3

value: vector


title: DP-KO-3-Input

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
FastQC (Version 0.11.5) was used to identify features of the raw data that may indicate quality problems
Adaptor and low-quality reads were trimmed by trim galore (Version 0.6.5)
Reads were mapped to the mouse reference genome (mm10) with STAR (Version 2.6.0a). and post-processed with RSEM version 1.3.0. Default parameter settings were used for alignment
ExomePeak (Version 2.17.0) software was used for MeRIP peak calling
Motifs enriched in WT versus KO samples were identified by HOMER (Version 4.9.1) software
Assembly: mm10
Supplementary files format and content: txt and xls format. ExomePeak annotation results
Library strategy: m6A-LACE-seq and Merip-seq

source_name: thymocytes

extract_protocol:
RNA was isolated from iNKT cells or DP cells by using TRIzol reagent . Polyadenylated RNA was further enriched from total RNA using the Dynabeads mRNA. RNA samples were fragmented into ~150-nucleotide-long fragments with RNA Fragmentation Reagents Purification Kit
m6A-seq was performed with about 100 ng fragmented mRNA as previously described (Liu Y, et al., Cell Metabolism, 2021). m6A-LACE-seq was developed from m6A-seq with some modifications based on LACE-seq method for low-input samples as previously described (Su, R.et al., Nat Cell Biol., 2021)

value: thymocytes

value: DP (7AAD-CD1d-Tet-CD4+CD8+) cells

value: 6~8 weeks


title: DP-KO-3-m6A


title: 101_966717-31

value: PBMC

tag: Sex

value: Female

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT

tag: sts timepoint

value: PreChallenge


title: vector-2

value: HiPSC-derived cardiomyocytes

value: cardiomyocytes


title: DP-KO-2-m6A


title: E1_S5

value: Mammary gland


title: 100_963117-31

tag: fastq total_reads


title: 141_970801-35

tag: percent aligned

value: SCIT

value: PostChallenge


title: 99_958507-31


title: vector-1

tag: genotype


title: DP-KO-2-Input


title: E1_S101

value: breast cancer

value: untreated


title: 98_966717-35


title: DP-WT-3-m6A

value: WT


title: G2Y rep2

city: Zhoushan

first: Jianhua

last: Liu

address: 1 Zheda Road, Lin-cheng street

institute: Ocean College, Zhejiang University

description: transfer Glc-adapted cells to YE medium

data_processing:
Using FastQC v0.11.2 to check the qualities of sequenced reads
Sequenced Reads were removed adaptor-like sequences of 12-nts at the 5’-end and low quality nucleotide with different length at the 3’-end using Trimmomatic v0.32
The resulting sequences with minimal length of 50-nts were mapped to the reference genome P. aeruginosa PAO1 using Bowtie2 v2.2.6 with default parameters
Transcription levels were determined using rsem-calculate-expression to calculate TPM values (-p 6 --bowtie2 --paired-end)
Genome_build: P. aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Pseudomonas aeruginosa

source_name: whole cells

growth_protocol: All the bacterial cells were grown in MSM medium with either YE or glucose under 30 ℃.

extract_protocol:
Total RNA was extracted from sample cells using TRIzol Plus RNA Purification System  (Invitrogen-Life Technologies Co., Carlsbad, CA, USA) according to manufacturer’s  protocol, ribosomal RNA were removed prior to library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell samples prior to (0h) and after (48h) medium shift were collected by centrifugation at 4000 × g, cells were preserved in liquid nitrogen before extration.

tag: developmental stage

value: log phase

tag: culture medium

value: MSM with 2% YE


title: 96_958507-35

tag: treatment


title: G2Y rep1

description: transfer Glc-adapted cells to YE medium


title: D9_S164

tag: tissue


title: DP-WT-3-Input

value: thymocytes

tag: cell line


title: 104_963047-35

value: Male

value: Placebo


title: D9_S68

tag: cell type


title: GAD rep2

description: three times subculture in MSM with Glucose medium, named Glc-adapted

tag: strain

value: MSM with 2% Glucose


title: 105_963047-31

value: PBMC

tag: age


title: D8_S60


title: DP-WT-2-m6A

value: DP (7AAD-CD1d-Tet-CD4+CD8+) cells

value: 6~8 weeks


title: GAD rep1


title: 94_970841-31

tag: Sex

value: SLIT

value: PreChallenge


title: D7_S52

value: Mammary gland


title: 95_970841-35

tag: aligned counts_in_millions


title: Y2G rep2

description: transfer YE-adapted cells to Glu medium


title: 93_966691-31

tag: median cv_coverage


title: DP-WT-2-Input


title: Y2G rep1

description: transfer YE-adapted cells to Glu medium


title: iNKT-KO-3-input

value: iNKT (7AAD-CD1d-Tet+TCRbeta+) cells


title: 91_963052-31

tag: participant id


title: iNKT-KO-2-m6A


title: D7_S148


title: D6_S44


title: 92_958463-31

tag: visit number


title: YAD rep2

description: three times subculture in MSM with YE medium, named YE-adapted


title: YAD rep1


title: D6_S140


title: 89_963052-35

tag: sts timepoint

value: PostChallenge


title: D8_S156

value: breast cancer


title: iNKT-KO-2-input


title: 88_958463-35

tag: fastq total_reads


title: iNKT-KO-1-input


title: D5_S36

value: untreated


title: D5_S132


title: iNKT-KO-1-m6A


title: 90_966691-35

tag: percent aligned


title: 87_966658-35

value: Female

value: SCIT


title: D4_S124


title: 86_966658-31


title: iNKT-WT-3-m6A

tag: genotype

value: WT


title: iNKT-KO-3-m6A

value: thymocytes


title: 30_35_Control

type: RNA

city: Madrid

first: David

last: Menoyo

state: Madrid

address: Avenida Puerta de Hierro, 2-4

department: Producción Agraria

country: Spain

institute: Universidad Politécnica de Madrid

hyb_protocol: 3,8 µg of fragmented and labeled ss cDNA were hybridized to Applied BiosystemsTM GeneChipTM Chicken Gene 1.0 ST arrays for 16 h at 45° C and 60 rpm in an Applied BiosystemsTM GeneChipTM hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied BiosystemsTM GeneChipTM Fluidics Station FS450, and the fluorescent signals were measured with an Applied BiosystemsTM GeneChipTM GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied BiosystemsTM GeneChipTM Command Console v5.0 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Applied BiosystemsTM GeneChipTM Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated.

label: Biotin

organism: Gallus gallus

source_name: Liver Chicken Control

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: All animal care and experimental procedures were approved by the Ethics Commit-tee of the Universidad Politécnica de Madrid and are in compliance with the Spanish Guidelines for the Care and Use of Animals in Research (Permission no: 2021-001). A total of 560 1 d-old male Cobb 500 chickens were distributed among 35 floor pens with 16 birds each. Broiler chickens were fed experimental pelleted diets ad libitum across 2 feeding phases consisting of a starter phase from 1 to 21 d of age and grower phase from 22 to 39 d of age.

extract_protocol: Total RNA from frozen liver aliquots (15-20 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol and subsequently analyzed for quantity and quality using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz, Germany). The A260/A280 ratio and the average RNA concentration of total RNA samples were 1.86 ± 0.02 and 0.49 ± 0.03 µg/µL (n = 30), respectively. For microarray analysis, six liver total RNA samples/group were randomly selected. After checking RNA quality [RNA integrity number values and A260:A280 ratios were 6.76 ± 0.54 (mean ± SD) and 1.77 ± 0.10, respectively] as described [Gessner et al., 2017], RNA samples were processed at the at the Genomics Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de) following the Applied Biosystems GeneChip Whole Transcript (WT) PLUS Reagent Kit User Guide (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: The experiment was conducted with 5 treatments (HT0, HT7.5, HT15, HT22.5, and HT30) that consisted in 5 levels of supplemented vitamin E (0 to 40 mg/kg) with a difference of 10 mg/kg between diets. The vitamin E was substituted in these diets by HT (30 to 0 mg/kg) with a difference of 7.5 mg/kg between diets.

tag: breed

value: Cobb 500

value: male

tag: condition

value: Control

value: liver


title: D4_S28

tag: treatment


title: iNKT-WT-3-input

tag: tissue


title: D3_S20

tag: cell line


title: 85_970785-35

value: PBMC


title: iNKT-WT-2-input

tag: cell type

value: 6~8 weeks


title: 84_970785-31


title: 28_32_Control


title: iNKT-WT-2-m6A


title: 29_33_HT15

source_name: Liver Chicken HT15


title: 83_963042-31


title: 26_30_HT7-5

source_name: Liver Chicken HT7.5


title: 27_31_HT30

source_name: Liver Chicken HT30


title: iNKT-WT-1-m6A


title: D3_S116


title: iNKT-WT-1-input


title: D2_S108


title: 81_957436-35


title: D12_S92


title: D2_S12


title: 82_957436-31


title: 24_28_HT30


title: D12_S188


title: Skeletal 966-G M

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

source_name: skeletal

extract_protocol:
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.

treatment_protocol: Male and female mice of each CC founder strain were fed high fat high sugar 45% kcal fat plus 1360% kcal sucrose (Research Diets D19070208) or isocaloric control 10% kcal fat plus 0% kcal sucrose (Research Diets D19072203) diets for 9 weeks prior to tissue harvest and processing for ATAC-seq.

value: skeletal

tag: strain

value: PWK/PhJ

value: Skeletal Muscle - gastrocnemius muscle


title: 80_963042-35

tag: age


title: Skeletal 964-G F

value: A/J

tag: Sex

value: female


title: 79_970780-35

tag: aligned counts_in_millions

value: Placebo

value: PostChallenge


title: D11_S84

value: Mammary gland

value: breast cancer

value: untreated


title: 23_27_HT22-5

source_name: Liver Chicken HT22.5


title: 78_970780-31

value: Female

tag: median cv_coverage

value: PreChallenge


title: D11_S180


title: 77_966668-31

tag: participant id


title: 22_26_HT30

value: Cobb 500

value: male


title: D10_S76


title: 25_29_HT15

value: liver


title: Skeletal 962-G F


title: 76_957433-31

value: PBMC

tag: visit number


title: Skeletal 960-G M


title: Skeletal 963-G F


title: 20_24_Control

value: Control


title: D10_S172


title: Skeletal 967-G M

value: skeletal


title: 75_963081-31

tag: sts timepoint


title: D1_S4


title: 21_25_HT15


title: 18_22_HT7-5


title: 19_23_HT22-5


title: 73_957433-35

tag: fastq total_reads


title: 16_20_HT15


title: Skeletal 892-G M

value: WSB/EiJ


title: Skeletal 890-G M

value: Skeletal Muscle - gastrocnemius muscle


title: Skeletal 891-G M


title: C9_S67


title: 15_19_Control


title: 71_957471-31

value: Male

tag: percent aligned

value: SCIT


title: 14_18_HT15


title: C9_S163


title: 13_17_HT22-5


title: 68_966739-35


title: 69_966739-31


title: 17_21_HT30


title: Skeletal 887-G F

value: female


title: Skeletal 888-G F


title: C8_S59


title: C8_S155


title: Skeletal 886-G F


title: 74_963081-35

value: Placebo

value: PostChallenge


title: D1_S100

value: Mammary gland

value: breast cancer


title: 10_14_HT30


title: C7_S51

value: untreated


title: 11_15_Control


title: 67_970825-35


title: 66_970825-31

value: PreChallenge


title: Skeletal 889-G F


title: 09_12_HT22-5

value: Cobb 500


title: C6_S43


title: Skeletal 878-G M

value: male


title: 08_11_HT7-5_2

value: liver


title: 70_957471-35

value: PBMC


title: C6_S139


title: 12_16_HT7-5


title: 64_963029-31


title: Skeletal 877-G M


title: Skeletal 876-G M


title: 07_10_Control

value: Control


title: C5_S35


title: Skeletal 875-G M

value: skeletal


title: 06_9_HT7-5


title: C5_S131


title: C7_S147


title: 62_966660-31


title: 63_970813-31


title: Skeletal 885-G F

value: WSB/EiJ


title: C4_S27


title: 65_963029-35


title: 05_8_HT22-5


title: 61_970813-35


title: Skeletal 873-G F

value: Skeletal Muscle - gastrocnemius muscle


title: Skeletal 871-G F


title: 59_957449-35

value: Male


title: 04_7_HT30


title: Skeletal 804-G F


title: C3_S115


title: Skeletal 806-G F

value: A/J


title: 60_957449-31

value: SCIT


title: C3_S19


title: C2_S11


title: 57_966660-35


title: 03_6_HT7-5


title: Kidney Dehydrated rep5

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

description:
9-Rn5D_S10
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv

data_processing:
BBDuk adaptor trimming (tpe tbo) v39.01
Alignment of reads grouped by gene by Rsubread v2.12.3
featureCounts assignment of mapped reads to features v2.12.3
DESeq2 for differential expression analysis v1.36.0
Assembly: GCF_000001895.5 Rnor6.0
Supplementary files format and content: Tab delimited Raw counts file including all samples. featureCounts output
Supplementary files format and content: Differential gene expression output from DESeq2

organism: Rattus norvegicus

source_name: whole kidney

extract_protocol: Male Sprague-Dawley rats were killed by striking the cranium followed by decapitation between 10am and 12pm. Whole kidneys were dissected from each animal and placed on dry ice. Frozen tissue was added to a pre-cooled mortar containing a small volume of liquid nitrogen. The tissue was then ground to a fine powder using a pestle and the nitrogen allowed to evaporate. The powdered tissue was aliquoted, weighed, and stored at -80◦C. Cells were lysed by adding no more than 100mg/ml of Trizol (Qiazol 79306, Qiagen) to each powdered tissue sample, then vortexed for 2 minutes, then incubated on ice for 10 minutes. Lysed samples were spun at 12000xg for 10 minutes at 4◦C and the supernatant was transferred to a new tube. 1/5 volume of Chloroform (99.9%, 22711.244, VWR) was added to each sample and vortexed for 15 seconds until the solution looks like strawberry milkshake. Samples were then spun at 12000xg for 15 minutes at 4◦C. 250µl of the top RNA-containing aqueous phase was removed without contamination from the white interphase. RNA was extracted using Zymo Direct-Zol RNA miniprep (R2052, Zymo) as per manufacturer’s instructions.

treatment_protocol: 2 groups. Control = free acces to water. Dehydrated = 72 hour no access to water.

value: whole kidney

value: Sprague-Dawley

value: dehydrated


title: C4_S123

value: Mammary gland

value: breast cancer


title: Kidney Dehydrated rep2

description:
7-Rn2D_S8
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: C2_S107

value: untreated


title: Skeletal 802-G F

value: female


title: 01_2_HT15

value: Cobb 500

value: male


title: 56_963054-31

value: PBMC

value: PreChallenge


title: C12_S91


title: 55_957475-31


title: Skeletal 803-G F

value: skeletal


title: Skeletal 801-G F


title: 02_5_HT22-5

value: liver


title: C12_S187


title: Skeletal 800-G M

value: PWK/PhJ

value: Skeletal Muscle - gastrocnemius muscle


title: Kidney Dehydrated rep1

description:
6-Rn1D_S2
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv

value: Male


title: Kidney Dehydrated rep6

description:
5-Rn6C_S5
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: 54_966695-35

value: SCIT

value: PostChallenge


title: 58_963054-35


title: C11_S83


title: Kidney Dehydrated rep4

description:
8-Rn4D_S1
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv

value: whole kidney

value: Sprague-Dawley


title: C11_S179

value: Mammary gland


title: Kidney Control rep4

description:
3-Rn4C_S3
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv

value: control


title: 52_970781-35


title: Skeletal 797-G M


title: C10_S75

value: breast cancer

value: untreated


title: Kidney Control rep3

description:
2-Rn3C_S7
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: 51_963025-31


title: 53_970781-31


title: 50_966695-31


title: Skeletal 795-G F

value: female


title: C10_S171


title: Kidney Control rep2

description:
1-Rn2C_S4
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: C1_S99


title: Kidney Control rep6

description:
10-Rn6D_S6
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: 48_957475-35


title: Skeletal 796-G F


title: Skeletal 793-G F


title: C1_S3


title: Skeletal 798-G M

value: male


title: B9_S66


title: Kidney Control rep5

description:
4-Rn5C_S9
FeatureCountsRatKidneyRsubread.txt
RatKidney_DESeq2_Results.csv


title: Skeletal 2974-G M

value: WSB/EiJ


title: Skeletal 2553-G M

value: A/J


title: B9_S162


title: Non-diabetic Male control rep7

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description:
Non-diabetic_Male_control_7
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8)
151 bp reads were checked for quality using FastQC.
reads mapped with BWA-MEM, hg19
MACs peak-calling on reads with mapQ>=20
bedtools mutlicov for count matrix generation
Supplementary_files_format_and_content: Matrix of contig CpG methylation enrichment counts

source_name: white blood cells

extract_protocol:
purgene blood kit genomic DNA extraction
Methyl Miner enrichment
Illumina ChIP-seq library prep kit

value: white blood cells

tag: kidney complication


title: 47_966671-35

source_name: PBMC

value: PBMC

value: Placebo


title: Non-diabetic Male control rep5

description:
Non-diabetic_Male_control_5
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 794-G F

value: skeletal

value: PWK/PhJ

value: Skeletal Muscle - gastrocnemius muscle


title: Non-diabetic Male control rep6

description:
Non-diabetic_Male_control_6
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: Male


title: B8_S58

source_name: Epithelial cell


title: Skeletal 2292-G M

value: CAST/EiJ


title: 44_957450-31

value: PreChallenge


title: B8_S154

value: Mammary gland


title: Skeletal 2155-G F


title: Non-diabetic Male control rep3

description:
Non-diabetic_Male_control_3
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: control


title: 43_957450-35

value: PostChallenge


title: Non-diabetic Male control rep2

description:
Non-diabetic_Male_control_2
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1601-G M

value: NZO/HlLtJ


title: 42_963069-31


title: B7_S50

value: breast cancer

value: untreated


title: Skeletal 1389-G M

value: NOD/ShiLtJ

value: male


title: B6_S42


title: Skeletal 1388-G M


title: B7_S146


title: Non-diabetic Female control rep7

description:
Non-diabetic_Female_control_7
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: white blood cells

value: Female


title: 45_970872-35

value: PBMC

value: Placebo


title: Skeletal 1387-G M

value: skeletal


title: 41_963069-35


title: 40_966671-31


title: B6_S138


title: Non-diabetic Female control rep6

description:
Non-diabetic_Female_control_6
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: 39_963043-35


title: 38_966736-35


title: Non-diabetic Male control rep4

description:
Non-diabetic_Male_control_4
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Non-diabetic Female control rep5

description:
Non-diabetic_Female_control_5
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: B5_S34


title: Skeletal 1386-G F

value: Skeletal Muscle - gastrocnemius muscle

value: female


title: B5_S130


title: Skeletal 1385-G F


title: B4_S26


title: Non-diabetic Female control rep3

description:
Non-diabetic_Female_control_3
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: 37_966736-31

value: Male


title: 36_970869-35


title: Non-diabetic Male control rep1

description:
Non-diabetic_Male_control_1
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Non-diabetic Female control rep2

description:
Non-diabetic_Female_control_2
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: B4_S122


title: Skeletal 1382-G M


title: Skeletal 1381-G M


title: 33_963043-31

value: PreChallenge


title: B3_S114

value: Mammary gland


title: Diabetic Male No complication rep5

description:
Diabetic_Male_NC_5
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: No renal complication


title: Skeletal 1380-G M


title: B2_S106


title: 32_958460-35

value: PostChallenge


title: Skeletal 1379-G F


title: Non-diabetic Female control rep4

description:
Non-diabetic_Female_control_4
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: control


title: Diabetic Male No complication rep3

description:
Diabetic_Male_NC_3
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Diabetic Male No complication rep4

description:
Diabetic_Male_NC_4
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1377-G F


title: Skeletal 1378-G F


title: 31_958677-31

value: SCIT


title: Non-diabetic Female control rep1

description:
Non-diabetic_Female_control_1
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1384-G F


title: 34_958460-31


title: B12_S90

value: breast cancer

value: untreated


title: 30_966649-35


title: Skeletal 1375-G M

value: NZO/HlLtJ

value: male


title: Diabetic Male No complication rep1

description:
Diabetic_Male_NC_1
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: white blood cells


title: 35_970869-31

value: PBMC


title: Diabetic Male No complication rep2

description:
Diabetic_Male_NC_2
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: B3_S18


title: B11_S82


title: B2_S10


title: Skeletal 1374-G M


title: Diabetic Male macroalbuminuria rep6

description:
Diabetic_Male_macro_6
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: Renal Macroalbuminuria


title: 28_970847-35


title: 27_970847-31


title: Skeletal 1202-G M

value: skeletal


title: 26_963079-31


title: Diabetic Male macroalbuminuria rep2

description:
Diabetic_Male_macro_2
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: B10_S74


title: Skeletal 1373-G M

value: Skeletal Muscle - gastrocnemius muscle


title: B10_S170


title: Diabetic Male macroalbuminuria rep3

description:
Diabetic_Male_macro_3
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1197-G F

value: female


title: Diabetic Male end-stage renal disease rep3

description:
Diabetic_Male_ESRD_3
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt

value: Male

value: End-stage renal disease


title: 24_958677-35


title: Diabetic Male macroalbuminuria rep1

description:
Diabetic_Male_macro_1
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1201-G M


title: B12_S186

value: Mammary gland


title: B1_S98


title: 29_966649-31

value: PreChallenge


title: 25_963079-35

value: PostChallenge


title: B1_S2


title: Diabetic Male end-stage renal disease rep2

description:
Diabetic_Male_ESRD_2
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1185-G M

value: PWK/PhJ


title: Skeletal 1164-G M

value: WSB/EiJ


title: 23_966659-35

value: Placebo


title: A9_S65

value: breast cancer

value: untreated


title: Diabetic Male end-stage renal disease rep1

description:
Diabetic_Male_ESRD_1
FinnD_Male_CpG_metamacs_Q20_COUNT.mx.txt


title: B11_S178


title: 22_970792-31


title: A9_S161


title: Skeletal 1163-G M

value: male


title: Diabetic Female No complication rep5

description:
Diabetic_Female_NC_5
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: white blood cells

value: Female

value: No renal complication


title: A8_S57


title: Skeletal 1162-G M

value: skeletal


title: 19_963037-31

value: PBMC


title: A8_S153


title: Diabetic Female No complication rep4

description:
Diabetic_Female_NC_4
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: Skeletal 1160-G F

value: Skeletal Muscle - gastrocnemius muscle

value: female


title: Skeletal 1159-G M

value: CAST/EiJ


title: Diabetic Female No complication rep3

description:
Diabetic_Female_NC_3
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: Diabetic Female No complication rep2

description:
Diabetic_Female_NC_2
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: Diabetic Female No complication rep1

description:
Diabetic_Female_NC_1
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: 18_963037-35

value: Male


title: 16_970804-31

value: SLIT

value: PreChallenge


title: A7_S145

value: Mammary gland


title: Skeletal 1158-G M


title: Skeletal 1157-G M


title: Diabetic Female macroalbuminuria rep5

description:
Diabetic_Female_macro_5
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: Renal Macroalbuminuria


title: A7_S49


title: A6_S41


title: A6_S137


title: 15_966667-35

value: PostChallenge


title: Diabetic Female macroalbuminuria rep4

description:
Diabetic_Female_macro_4
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: 14_966667-31


title: Skeletal 1154-G M

value: A/J


title: A5_S33

value: breast cancer

value: untreated


title: Diabetic Female macroalbuminuria rep3

description:
Diabetic_Female_macro_3
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: white blood cells


title: 20_957430-31

value: Placebo


title: 13_970804-35


title: Skeletal 1153-G M

value: male


title: 17_966659-31


title: Skeletal 1147-G M

value: skeletal


title: A3_S113


title: 12_963028-35

value: PBMC


title: 9_963028-31


title: 10_958457-31


title: Diabetic Female macroalbuminuria rep2

description:
Diabetic_Female_macro_2
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: Female


title: 8_959051-35


title: Skeletal 1143-G M

value: NZO/HlLtJ

value: Skeletal Muscle - gastrocnemius muscle


title: Diabetic Female end-stage renal disease rep3

description:
Diabetic_Female_ESRD_3
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: End-stage renal disease


title: 7_966731-35

value: Male

value: SLIT


title: Diabetic Female end-stage renal disease rep4

description:
Diabetic_Female_ESRD_4
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt


title: A4_S25

value: Mammary gland


title: Diabetic Female macroalbuminuria rep1

description:
Diabetic_Female_macro_1
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: Renal Macroalbuminuria


title: Skeletal 1139-G F

value: female


title: IgG-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

data_processing:
*library strategy: CUT&Tag
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
For RNA-seq analysis, the RNA-seq data underwent initial quality assessment and adapter trimming utilizing Trim Galore (version 0.6.4_dev). Subsequently, the trimmed reads were aligned to the mm10 reference genome using STAR (version 2.7.2d). For the quantification of reads corresponding to genomic features, featureCounts (version 2.0.0) was employed.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage.
Supplementary files format and content: narrowPeak files were generated using MACS v2

growth_protocol: Mouse E14TG2a ESCs (a kind gift from M. Zhang’s laboratory, Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China) were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag was performed following the protocol provided by the Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen). A total of 50,000 cells were harvested and subjected to two rounds of washing using washing buffer (composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Protease inhibitor cocktail). Subsequently, the cells were incubated with activated Concanavalin A coated magnetic beads. To this, 0.5 μg of HA antibody was added and allowed to incubate on a rotating platform at 4 °C for a duration of 16 hours. Following this, 0.5 μL of Goat anti-Rabbit secondary antibody was introduced and incubated for an additional hour. After a thorough washing step, the cells were treated with pA/G-Tn5 transposase at 37°C for 1 hour. Subsequently, DNA extraction was carried out by DNA selection beads
Total RNA was harvested using Trizol reagent from 5*10^6 ESCs.
To amplify libraries, 16 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, 7 μL ddH2O, and 25 μL 2× Ultima Amplification Mix, and run the following cycling conditions with lid heat on: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of DNA selection beads (60 μL), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer.
RNA libraries were prepared for sequencing using standard

value: mouse embryonic stem cell

tag: genotype

value: Dek-KO; HA-Dek-WT over-expession

value: IgG CUT&Tag antibody


title: 5_963074-35

value: PostChallenge


title: A2_S105

value: breast cancer

value: untreated


title: IgG-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2


title: A12_S89


title: 11_958457-35


title: Skeletal 1140-G F

value: skeletal


title: A2_S9


title: A3_S17


title: Skeletal 1142-G M

value: male


title: A4_S121


title: Skeletal 1144-G F


title: Diabetic Female end-stage renal disease rep2

description:
Diabetic_Female_ESRD_2
FinnD_Female_CpG_metamacs_Q20_COUNT.mx.txt

value: white blood cells

value: Female


title: 49_963025-35

value: PBMC

value: SCIT


title: A5_S129


title: Skeletal 1138-G F

value: NZO/HlLtJ

value: Skeletal Muscle - gastrocnemius muscle


title: 4_959051-31

value: Male

value: SLIT

value: PreChallenge


title: A12_S185

value: Mammary gland


title: 3_963074-31


title: Skeletal 1136-G F

value: female


title: A11_S177


title: A11_S81


title: 2_970818-35


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 2

value: mouse embryonic stem cell

value: HA CUT&Tag antibody


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 1


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 2


title: A10_S73

value: breast cancer


title: 1_970818-31


title: Skeletal 1054-G M


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 2


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 1


title: Skeletal 1043-G M

value: A/J


title: A10_S169

value: untreated


title: Skeletal 1041-G F

value: skeletal


title: 966865-300_lib54706

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_nasal_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

source_name: Nasal Brush

value: Nasal Brush


title: A1_S97


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 1


title: 962974-300_lib54705


title: Skeletal 1037-G F

value: PWK/PhJ


title: 958654-300_lib54704


title: Skeletal 1141-G F


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 2


title: Skeletal 1137-G F


title: Skeletal 1035-G F


title: A1_S1


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 1


title: 966863-300_lib54702

value: Female


title: 962994-300_lib54701


title: HT1080 xenograft WT

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Cellranger mkfastq
Cellranger count
Data analyis using the R package Seurat
Genome_build: ENSEMBL GRCh38
Supplementary_files_format_and_content: Cellranger output files: Files containing cell barcodes, feature/gene names, raw gene counts for every gene and every sample

growth_protocol: For scaffold culture, tumor pieces retrieved from a myxoid liposarcoma patient-derived xenograft model were decellularized using detergent wash. The scaffolds were cut into small pieces and added to 48-well culture plates. 3x10^5 cells were added onto the scaffold in 0.5ml complete media and cultured for 21 days before harvesting for downstream analysis. Scaffold pieces were transferred to new wells with fresh media if cells were growing outside the scaffold area.

extract_protocol:
Live single cells were encapsulated in droplets prior to barcoding and reverse transcription.
Library construction was performed according to the 10x Genomics 3' solution protocol.
Single cell RNA-seq

value: Fibrosarcoma cells

tag: growth protocol

value: Xenograft


title: HT1080 xenograft FD


title: Skeletal 1034-G M

value: Skeletal Muscle - gastrocnemius muscle

value: male

tag: treatment


title: 959047-300_lib54700

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

tag: tissue

value: SLIT


title: Skeletal 1033-G M


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 2

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
For RNA-seq analysis, the RNA-seq data underwent initial quality assessment and adapter trimming utilizing Trim Galore (version 0.6.4_dev). Subsequently, the trimmed reads were aligned to the mm10 reference genome using STAR (version 2.7.2d). For the quantification of reads corresponding to genomic features, featureCounts (version 2.0.0) was employed.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage.
Supplementary files format and content: narrowPeak files were generated using MACS v2

tag: cell line


title: HT1080 scaffold FD

tag: cell type

value: Scaffold culture


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1

value: Dek-KO; HA-Dek-WT over-expession


title: HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2


title: Skeletal 1030-G M

tag: strain

value: CAST/EiJ


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 1

value: mouse embryonic stem cell


title: AIT118_lib54699

tag: age


title: HT1080 scaffold WT


title: Skeletal 1029-G M

tag: Sex


title: AIT115_lib54697

tag: aligned counts_in_millions


title: MS+NaCl+2,4-D

city: ISTANBUL

first: Haluk

last: Çelik

state: Vezneciler

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü

country: Turkey

institute: Istanbul University

data_processing:
Base calls performed using SOAPnuke (v1.5.2, https://github.com/BGI-flexlab/SOAPnuke), then stored in FASTQ format.
The clean reads were aligned using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts, v2.0.4, http://www.ccb.jhu.edu/software/hisat) and transcriptome assembly was set using StringTie software (v1.0.4, http://ccb.jhu.edu/software/stringtie) then compared to the reference annotation (the known genes of the A. thaliana genome) using the Cufflinks tools Cuffcompare (v2.2.1, http://cole-trapnell-lab.github.io/cufflinks).
The clean data were mapped to the unigene library using Bowtie2 (v2.2.5, http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml), then the expression level for  each gene from our data was measured using REM (v1.2.12,http://deweylab.biostat.wisc.edu/REM)..
FPKM (fragments per kilobase per million fragments mapped) for each unigene was calculated to determine the unigene  expression profiles. Genes with differential expression (DEG) between the two samples were identified via PossionDis, and the results were corrected for multiple testing with the Benjamini-Hochberg false discovery rate (FDR) of adjusted p-value ≤ 0.05, using the parameters FDR >= 2.00 and FDR <= 0.001 followed by their  hierarchical clustering.
Genome_build: TAIR 10.1
Supplementary_files_format_and_content: excell files, gene expression files

organism: Arabidopsis thaliana

source_name: A.thaliana root calli

growth_protocol: Wild type, Col-0, Arabidopsis thaliana seeds were surface sterilized with 70% ethanol and sown on Petri dishes filled with Murashige and Skoog basal medium (Murashige and Skoog, 1962), containing 3% (w/v) sucrose, solidified with 0.9% (w/v) agar and adjusted to pH 5.7. Petri dishes were incubated in a plant growth chamber under fluorescent light (16h light/8h dark light conditions) at 25°C for 5 days until germination.

extract_protocol:
The seedlings were transferred to test tubes filled with MS medium for the following weeks, and the 30-day-old plants were used for callus formation. Root explants (≈ 1 cm) were excised from the 30-day-old plants and surface sterilized. In sterile conditions, they were cut and placed into a fresh MS medium containing 0.5 mg/L of 2,4-dichlorophenoxyacetic acid (2,4-D), ensuring the cut end was in contact with the media. Callus cultures were continuously sub-cultured every 3 week  periods.
RNA isolation were carried out from the frozen calli of A. thaliana using TRIzol reagent (Invitrogen, USA). RNA integrity was assessed by agarose gel electrophoresis and RNA amount was measured by Nanodrop 2000 Spectrophotometer (Nanodrop Technologies, USA).
All RNA extracted from each group was pooled in an equimolar amount to create two sets of total RNA, one control and NaCl and 2,4-D treated, ready for cDNA library construction.Fragmentation of mRNA, cDNA library construction and sequencing were carried out by the Beijing Genomics Institute (BGI, Shenzhen, China). The libraries were constructed following the High-throughput Illumina sequencing library protocol, corresponding to three biological replicates from each group. After being checked for integrity, 40 µg of total RNA was used to purify the poly-A-containing mRNA molecules using poly-T oligo-attached magnetic beads. RNA was then sheared into small pieces using divalent cations under high temperature. Fragments of mRNA were used as a template to synthesize cDNA. A single ‘A’ base and subsequent adapter ligation were added before performing PCR. PCR products were quantified by Qubit, and samples were pooled to make a single strand DNA circle (ssDNA circle) to produce the final library. DNA nanoballs (DNBs) were generated from the ssDNA circle by rolling circle replication (RCR) to enhance fluorescent signals during the sequencing process. DNBs were read through on the BGISEQ-500 platform for the subsequent data analysis study.

treatment_protocol: Calli were transferred to MS medium containing only 100 mM NaCl and NaCl plus 0.5 mg/L 2,4-D. The calli were cultured for 4 weeks under fluorescent light (16 h  light/8 h dark illumination conditions) at 25°C.

value: root calli

value: 100 mM NaCl and 0.5 mg/L 2,4-Dichlorophenoxyacetic acid

value: 30 days old

value: wild type

tag: ecotype


title: Skeletal 1025-G F

value: skeletal

value: female


title: AIT116_lib54698

city: Seattle

first: Naresh

last: Doni Jayavelu

address: 1201 9th AVE

institute: Benaroya Research Institute at Virginia Mason

value: Nasal Brush

tag: median cv_coverage

tag: participant id


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 2


title: MS+NaCl

value: 100 mM NaCl


title: Skeletal 1024-G F


title: AIT114_lib54696

value: Female

tag: visit number


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 1


title: Skeletal 1021-G F


title: MS+2,4-D

value: 0.5 mg/L 2,4-Dichlorophenoxyacetic acid


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 2


title: AIT113_lib54695

tag: fastq total_reads


title: Skeletal 1020-G F

value: Skeletal Muscle - gastrocnemius muscle


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 2


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 1


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 1


title: Skeletal 1018-G M

value: male


title: AIT110_lib54692

tag: percent aligned


title: Skeletal 1016-G M


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2


title: MoS2_2

city: Shenzhen

first: Dan

last: Shi

address: Xueyuan Avenue 1098

institute: Shenzhen University General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
fastp v0.20.0 for quality control
HISAT2 version 2.1.0 for mapping reads to the grch38 genome
featureCounts v1.6.1 was used to count reads
Assembly: grch38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophages

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA of cells was extracted by TRIzol (Thermo Fisher Scientific, 15596026, USA,) and sent to the company (Novogene) to perform a standard RNA-sequencing procedure.
RNA-seq libraries were constructed using a NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA). The library preparations were sequenced on an Illumina Novaseq 6000 platform, and 150 bp paired-end reads were generated.

treatment_protocol: Cell treated with PBS or 6.25 μg/ml MoS2

value: macrophages

value: WT


title: MoS2_1


title: Control_3

value: PBS


title: Skeletal 1015-G M


title: AIT105_lib54689


title: Skeletal 1014-G F


title: Control_1


title: Control_2


title: RNA-seq of Dek_KO E14TG2a cells repeat 2

value: Dek-KO


title: Skeletal 1013-G F


title: MS

value: Untreated


title: AIT102_lib54688

value: Male


title: AIT107_lib54690


title: RNA-seq of Dek-KO E14TG2a cells repeat 1

value: mouse embryonic stem cell


title: AIT112_lib54694


title: MoS2_3


title: Skeletal 1012-G F


title: Skeletal 1019-G F

value: CAST/EiJ


title: cKO keratinocytes rep 2 RNA-Seq

first: Qirui

last: Wang

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: RNA-seq sample for cKO

data_processing:
The libraries were sequenced on an Illumina HiSeq 2500 platform and 150 bppaired-endreads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cKO Epidermis,P0

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) or Ribo-ZeroTM rRNA removal Kit (illumina). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA(by AxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
The libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The sequences were processed and analyzed by GENEWIZ.

value: cKO Epidermis,P0

value: epidermal keratinocytes


title: RNA-seq of parental E14TG2a cells repeat 2

value: Dek-WT


title: AIT111_lib54693

value: Nasal Brush


title: AIT100_lib54687


title: RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1

value: Dek-KO; HA-Dek-WT over-expession


title: cKO keratinocytes rep 1 RNA-Seq

description: RNA-seq sample for cKO


title: RNA-seq of parental E14TG2a cells repeat 1


title: AIT108_lib54691


title: AIT098_lib54686

value: Female


title: Liver 967-L M

source_name: liver

value: liver

value: PWK/PhJ

value: Liver - liver left lobe


title: AIT097_lib54685


title: NEIL2-KO ipsilateral biol rep 2 6h

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

data_processing:
Sequence reads were trimmed with TrimGalore, in single-end mode, clipping 10 bases at the 5’ of each read to remove sequencing bias, and filtering out all low-quality bases from reads (<30 Phred score).
Trimmed sequence reads were mapped to GRCm39/mm39 using HISAT2, with --dta in additional to default parameters.
Aligned sequence reads were sorted by coordinates and indexed using samtools.
Indexed sequence reads were annotated using featureCounts.
Read count normalization was performed with DESeq2.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample (normalization by median of ratios method).

source_name: hippocampus

extract_protocol:
Total RNA was isolated from homogenized mouse brain using Allprep DNA/RNA/Protein kit  (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were measured using a RNA Pico chip on an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: region

value: ipsilateral


title: Liver 966-L M

value: male


title: NEIL2-KO ipsilateral biol rep 2 3h

tag: genotype


title: Ctrl keratinocytes rep 1 RNA-Seq

description: RNA-seq sample for ctrl

source_name: Ctrl Epidermis,P0

value: Ctrl Epidermis,P0


title: NEIL2-KO ipsilateral biol rep 1 6h


title: Liver 964-L F

value: A/J

value: female


title: AIT095_lib54683


title: cKO keratinocytes  rep 1

description: Ribosome profiling sample for cKO

data_processing:
The libraries were sequenced on an Illumina HiSeq 2500 platform and 150 bppaired-endreads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: Ribosome profiling

extract_protocol:
Cells were washed with pre-chilled PBS (with 100 μg/ml cycloheximide, Sigma-Aldrich) and then harvested by centrifugation at 4 °C (500 g, 5 min). Cell pellet of each sample was resolved in pre-chilled lysis buffer (20 mM pH 7.4 Tris-HCl, 150 mM NaCl, 5 mM MgCl2, 0.1% NP-40, 1% Triton X-100, 1 mM DTT, 25 U/ml of RNase-free DNAse I, and 100 μg/ml cycloheximide). After 10 min of incubation on ice with periodic agitation, the lysate was centrifuged for 10 min (20,000 g at 4 °C), and the supernatant was collected.
The total RNA was isolated from 50 μl of the cell lysate using the Acid Phenol: chloroform extraction method and heat fragmented at 95°C for 25 min. The Ribosome protected RNA fragments (RPF) were obtained from 100 μl of the cell lysate treated with 60 U/A260 of RNase I, and further purified with Sephacryl S400 columns (GE Healthcare). Finally, the RPFs with the length of 25-35 nt were selected on a 15% Urea-Polyacrylamide gel. Next, the same procedure was followed to prepare the sequencing libraries from both the total RNA fragments and the RPFs. This includes 3’adaptor ligation, reverse transcription, circularization of the cDNA, and PCR amplification. The libraries were then sequenced on the Illumina HiSeq 2500 system with 50 cycles of single-end reading.


title: NEIL2-KO ipsilateral biol rep 1 3h


title: cKO keratinocytes rep 2

description: Ribosome profiling sample for cKO


title: Liver 963-L F


title: Skeletal 1011-G F

value: skeletal

value: Skeletal Muscle - gastrocnemius muscle


title: 966859-300_lib31124

value: Male

value: Placebo


title: Ctrl keratinocytes rep 2

description: Ribosome profiling sample for ctrl

value: epidermal keratinocytes


title: 962983-300_lib31123

value: Nasal Brush

value: SLIT


title: NEIL2-KO contralateral biol rep 2 6h

value: contralateral


title: NEIL2-KO contralateral biol rep 2 3h


title: Ctrl keratinocytes rep 1

description: Ribosome profiling sample for ctrl


title: Liver 960-L M

value: liver


title: Liver 962-L F


title: 966851-300_lib31121

value: SCIT


title: Ctrl keratinocytes rep 2 RNA-Seq

description: RNA-seq sample for ctrl


title: Liver 891-L M

value: WSB/EiJ

value: Liver - liver left lobe


title: NEIL2-KO contralateral biol rep 1 3h

value: hippocampus


title: Ctrl keratinocytes rep 2, input

description: MeRIP-seq sample for ctrl

data_processing:
Purified RNA was used for RNA-seq library generation with NEBNext Ultra II Directional RNA Library Prep.
Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.
Assembly: GRCm38
Supplementary files format and content: Methylated_RNA_sites
Library strategy: MeRIP-seq

extract_protocol:
Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (202003, Synaptic Systems, Germany) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours.
PolyA mRNA was enriched using GeneElute mRNA Miniprep Kit. MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure with slight modifications.

tag: fraction

value: input


title: AIT096_lib54684

tag: treatment


title: NEIL1-KO ipsilateral biol rep 2 6h

tag: tissue

value: ipsilateral


title: Ctrl keratinocytes rep 1, IP

description: MeRIP-seq sample for ctrl

value: Ctrl Epidermis,P0

tag: cell line

value: IP


title: 970452-300_lib31119


title: Liver 889-L F

tag: cell type

value: female


title: Ctrl keratinocytes rep 1, input

description: MeRIP-seq sample for ctrl


title: Liver 890-L M

tag: strain

value: male


title: 958671-300_lib31118

tag: age

value: Male


title: 962985-300_lib31120

tag: Sex


title: Liver 888-L F


title: NEIL1-KO ipsilateral biol rep 2 3h


title: NEIL1-KO ipsilateral biol rep 1 6h


title: AP_OCA4

city: Yangzhou

first: Guotao

last: Lu

address: 368 Hanjiang Middle Road, Yangzhou

institute: The Affiliated Hospital of Yangzhou University, Yangzhou University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were timmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit 0.05)
Timmed sequence reads were mapped to GrCM38m10 using CLC geromic benchwok (parameters- mismath cost 2 insertion cost 3 deleton cost 3 length fracion: 0.8 similarity ftaction- 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary pancreatic acinar cells

growth_protocol: Primary pancreatic acinar cells (PACs) were aintained in hepes suplemented with 2% fetal bovne serum (FBS) and antbiotics in humidfed atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was havested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: PACs injury was induced by adding 1 μM cholecystokinin octapeptide (CCK) for 6 h. Cells were incubated with increasing concentrations of OCA(2.5µM).

value: primary pancreatic acinar cells

value: WT


title: 970487-300_lib31117

value: Nasal Brush

value: Female

tag: aligned counts_in_millions

value: Placebo


title: 958662-300_lib31122

value: SLIT


title: Liver 892-L M

value: liver


title: 966835-300_lib31116


title: AP_OCA3


title: NEIL1-KO ipsilateral biol rep 1 3h


title: Ctrl keratinocytes rep 2, IP

description: MeRIP-seq sample for ctrl

value: epidermal keratinocytes


title: AP_OCA2


title: 962979-300_lib31115


title: NEIL2-KO contralateral biol rep 1 6h

value: contralateral


title: Liver 886-L F

value: WSB/EiJ

value: Liver - liver left lobe


title: NEIL1-KO contralateral biol rep 2 6h

value: hippocampus


title: Liver 887-L F


title: AP_OCA1


title: Liver 885-L F


title: NEIL1-KO contralateral biol rep 2 3h


title: 958484-300_lib31114


title: AP4


title: Liver 878-L M


title: NEIL1-KO contralateral biol rep 1 6h


title: 970442-300_lib31113


title: AP3


title: NEIL1-KO contralateral biol rep 1 3h


title: 966828-300_lib31112


title: AP2


title: WT ipsilateral biol rep 2 6h

value: ipsilateral


title: Liver 876-L M


title: 962993-300_lib31111


title: Liver 877-L M


title: Liver 875-L M


title: Day 5 immunization Tfh-4

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
Tfh1_imm_4_RNASeq
featureCount.txt

data_processing:
Sequencing adapters are removed with cutadpt with -m 35 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Trimmed reads are mapped to mouse reference genome mm10 and RefSeq annotation database using STAR with --outFilterMultimapNmax 3 --outSAMunmapped Within --outFilterMismatchNmax 2 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate -twopassMode Basic --quantMode GeneCounts --readFilesCommand zcat  --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Gene expression are generated with featureCount with parameters: -C --fracOverlap 1
Assembly: mm10
Supplementary files format and content: Tab delimited text file with gene expression values

source_name: Primary

growth_protocol: Sample groups: Group 1, infection-elicited non-Tfh cells, Group 2, infection-elicited Tfh cells, Group 3, immunization-elicited non-Tfh cells, Group 4, immunization-elicited Tfh cells

extract_protocol:
For infected recipient mice, on day 5 (not peak response, but the Tfh and non-Tfh cell fate are committed), isolate Tfh and non-Tfh cells from the spleen by cell FACS sorting.
RNA was harvested using the NucleoSpin RNA Columns of MACHEREY-NAGEL. 1.5-2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For immunized recipient mice, on day 5 (peak response), isolate Tfh and non Tfh cells from draining lymph nodes by cell FACS sorting.

value: Primary

value: Tfh

value: Immunization


title: 970478-300_lib31109

value: Male


title: Liver 873-L F

value: female


title: AP1

value: primary pancreatic acinar cells

value: WT


title: WT ipsilateral biol rep 1 3h


title: WT ipsilateral biol rep 2 3h


title: 966872-300_lib31108

value: Nasal Brush


title: Day 5 immunization Tfh-3

description:
Tfh1_imm_3_RNASeq
featureCount.txt


title: Day 5 immunization Tfh-2

description:
Tfh1_imm_2_RNASeq
featureCount.txt


title: WT ipsilateral biol rep 1 6h


title: 958477-300_lib31110

value: Female

value: Placebo


title: Liver 871-L F

value: liver


title: Liver 806-L F

value: A/J


title: 962986-300_lib31107


title: Liver 805-L F


title: WT contralateral biol rep 2 3h

value: contralateral


title: 970413-300_lib31105

value: SCIT


title: Liver 804-L F

value: Liver - liver left lobe


title: 966799-300_lib31104


title: Day 5 infection Tfh-4

description:
Tfh1_inf_4_RNASeq
featureCount.txt

value: Infection


title: WT contralateral biol rep 1 6h

value: hippocampus


title: Day 5 infection Tfh-3

description:
Tfh1_inf_3_RNASeq
featureCount.txt

value: Primary


title: WT contralateral biol rep 1 3h


title: Day 5 infection Tfh-2

description:
Tfh1_inf_2_RNASeq
featureCount.txt

value: Tfh


title: Liver 802-L F


title: mouse ovary, wildtype, RNA immunoprecipitated, biol rep3 [RIPWT_6]

city: San Francisco

first: Diana

middle: J

last: Laird

address: 35 Medical Center Way

institute: UCSF

description:
FoldEnrich_WT3
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls

data_processing:
quality control performed with FastQC (unkown version) and skewer (v0.1.126), this step performed by Novogene
aligned to genome with BWA (v0.7.12), step perfomed by Novogene
peak calling performed with MACS2 (v2.1.0, threshold q value = 0.05) step performed by Novogene
counts of fragments mapped normalized using DESeq2 (v1.26.0)
likelihod ratio test for significance used to compare gene enrichment between WT and KO samples
Assembly: Grcm38
Supplementary files format and content: csv, xls, txt. Peak calling and normalization, alignment counts, and foldenrichment counts (1 column per Inp/RIP sample pair)

source_name: E16.5 mouse ovary

extract_protocol:
5 pairs of ovaries homogenized in MCB buffer (150 mM KAc, 1% Triton X-100, 1% NP40, 50 mM HEPES at pH 7.4, 2 mM MgAc2, 10% glycerol, EDTA-free protease inhibitor, RNase inhibitor [Thermo Fisher Scientific, 10777019]), spun at max speed for 10 min. From each sample, 10% of the homogenate saved as in-put for western blotting, 10% saved as in-put for RNA extraction and sequencing.
Illumina library prep

treatment_protocol: FMR1 knockout and wildtype fetal E16.5 mouse ovaries

value: E16.5 mouse ovary

tag: rip antibody

value: FMRP ab17722

tag: molecule subtype

value: Immunoprecipitated RNA


title: mouse ovary, wildtype, RNA immunoprecipitated, biol rep2 [RIPWT_5]

description:
FoldEnrich_WT2
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls


title: mouse ovary, wildtype, RNA immunoprecipitated, biol rep1 [RIPWT_4]

description:
FoldEnrich_WT1
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls


title: 966829-300_lib31100

value: Male

tag: median cv_coverage

tag: participant id


title: Liver 801-L F

value: female


title: WT contralateral biol rep 2 6h

value: WT


title: 962997-300_lib31103

value: Nasal Brush

value: Female

tag: fastq total_reads

tag: visit number


title: Day 5 infection Tfh-1

description:
Tfh1_inf_1_RNASeq
featureCount.txt


title: Day 5 immunization Tfh-1

description:
Tfh1_imm_1_RNASeq
featureCount.txt

value: Immunization


title: 970482-300_lib31101

tag: percent aligned

value: Placebo


title: Day 5 immunization Th1-3

description:
Th1_imm_3_RNASeq
featureCount.txt

tag: genotype


title: Liver 798-L M

value: liver

value: PWK/PhJ

value: male


title: Liver 800-L M

value: Liver - liver left lobe


title: 962975-300_lib31099


title: 958433-300_lib31102

value: SCIT


title: mouse ovary, FMR1 knockout, RNA immunoprecipitated, biol rep3 [RIPKO_3]

description:
FoldEnrich_KO3
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls


title: Liver 797-L M


title: Day 5 immunization Th1-4

description:
Th1_imm_4_RNASeq
featureCount.txt

value: Primary


title: Liver 803-L F


title: 958670-300_lib31098


title: 970434-300_lib31097


title: Day 5 immunization Th1-1

description:
Th1_imm_1_RNASeq
featureCount.txt


title: Liver 795-L F


title: Day 5 infection Th1-4

description:
Th1_inf_4_RNASeq
featureCount.txt

value: Infection


title: 966855-300_lib31096


title: mouse ovary, wildtype, input, biol rep2 [InpWT_5]

description:
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls

value: E16.5 mouse ovary


title: Liver 794-L F


title: Day 5 infection Th1-2

description:
Th1_inf_2_RNASeq
featureCount.txt


title: mouse ovary, FMR1 knockout, input, biol rep3 [InpKO_3]


title: Liver 2974-L M

value: WSB/EiJ


title: mouse ovary, wildtype, input, biol rep1 [InpWT_4]


title: Day 5 infection Th1-1

description:
Th1_inf_1_RNASeq
featureCount.txt


title: 963004-300_lib31095


title: Liver 796-L F


title: Liver 2553-L M

value: A/J


title: 962934-300_lib31092


title: Day 5 immunization Th1-2

description:
Th1_imm_2_RNASeq
featureCount.txt


title: Liver 793-L F


title: mouse ovary, FMR1 knockout, input, biol rep2 [InpKO_2]


title: 970466-300_lib31094


title: mouse ovary, FMR1 knockout, RNA immunoprecipitated, biol rep1 [RIPKO_1]

description:
FoldEnrich_KO1
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls

value: FMRP ab17722

value: Immunoprecipitated RNA


title: mouse ovary, FMR1 knockout, input, biol rep1 [InpKO_1]


title: Liver 2292-L M

value: CAST/EiJ


title: mouse ovary, FMR1 knockout, RNA immunoprecipitated, biol rep2 [RIPKO_2]

description:
FoldEnrich_KO2
foldenrich_countdata.csv
KO_vs_WT_peak_compare_table.xls


title: 958655-300_lib31091

value: Nasal Brush


title: SetxKO testis, 18dpp, rep3

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using RSEM
Assembly: mm10
Supplementary files format and content: text files include TPM values for each sample

source_name: testis

extract_protocol:
Testicular cell samples were resuspended in QIAzol Lysis Reagent according to the manufacturer's instructions, and total RNAs were purified from homogenized cells using Qiagen RNeasy Mini Kit.
The mRNA sequencing libraries were prepared using the Illumina TruSeq methodology. mRNAs were purified from total RNA using biotin tagged poly dT oligonucleo- tides and streptavidin coated magnetic beads. The mRNAs were then fragmented and double stranded cDNA was generated by random priming.

value: testis

value: testicular cells

value: SetxKO


title: mouse ovary, wildtype, input, biol rep3 [InpWT_6]


title: 970410-300_lib31090

value: Male

value: Placebo


title: SetxKO testis, 18dpp, rep4


title: Liver 2155-L F

data_processing:
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track

value: liver

value: female


title: Day 5 infection Th1-3

description:
Th1_inf_3_RNASeq
featureCount.txt

value: WT


title: Liver 1601-L M

value: NZO/HlLtJ

value: Liver - liver left lobe

value: male


title: 966861-300_lib31093

value: Female


title: 966814-300_lib31089


title: SetxKO testis, 16dpp, rep4


title: SetxKO testis, 18dpp, rep1


title: gan1160

city: Chengdu

first: Linhao

last: Zhang

state: Sichuan

address: No. 37 Guoxue Lane

department: Gastroenterology

institute: West China Hospital, Sichuan University

description: 10X Genomics Chromium Controller

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

growth_protocol: Mice were provided ad libitum access to normal diet with a 12-hour light/dark cycle at room temperature with constant humidity.

extract_protocol:
Freshly collected liver cells from mice were washed with DPBS, diced and then extracted using Liver Dissociation Kit (mouse) with gentleMACS Dissociator from Miltenyi Biotec according to the manufacturer's instructions. Then the resuspended samples were sequentially applied to 70μm and 30μm strainer. The red blood cells were lysed with Red Blood Cell Lysis Solution. Then, after washing, the isolated liver cells were centrifuged with 50g for 30 seconds to remove most of hepatocytes. Next, cells in supernatant were washed and re-suspended in DPBS. A small portion of the cells were used for checking viability by staining with a Viability Dye. Finally, cells were washed in DPBS, centrifuged and resuspended in RPMI1640 medium with 5% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: A mouse model of liver fibrosis was established by intraperitoneal injection of thioacetamide (TAA) for 12 weeks, and 7.5 mg/kg celecoxib (C7.5) or 30 mg/kg celecoxib (C30) treatment was given orally by gavage started from 5th week of TAA injection to fibrotic mice.  Mice were allocated to the control group, TAA group, TAA+C7.5 and  TAA+C30 group with 1 in each according to the treatment. Hepatic nonparenchymal cells were isolated from one mouse for each group (control, TAA, TAA+C7.5, and TAA+C30 groups) and subjected to scRNA-seq.

value: Liver

value: 18-20 weeks old

value: Wild type

value: Thioacetamide+Celecoxib 7.5mg/kg


title: 962965-300_lib31088

value: Nasal Brush


title: gan1154

description: 10X Genomics Chromium Controller

value: Thioacetamide


title: Liver 1389-L M

extract_protocol:
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described  [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.

value: NOD/ShiLtJ


title: 970460-300_lib31087


title: SetxKO testis, 18dpp, rep2

value: testis

value: testicular cells

value: SetxKO