title: D3_M2

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

description: Columns of processed data: A-I, general gene details; J-AA, raw counts; AB-AS, DESeq2 normalized counts; AT-BK, ComBat batch-corrected normalized counts; BL, DESeq2 baseMaean; BM-CV, groups of 6 columns for each pairwise comparison, first five are the DESeq2 results table, sixth column indicates non-significant (FALSE), significant (TRUE) or significant and passing fold-change filtering (THR).

data_processing:
Raw reads were processed with cutadapt, v3.4, using parameters -q 32,32 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -O 1 --match-read-wildcards -m 15; then filterred with fastq_quality_filter, v0.0.14 of the FASTX package, using parameters -q 20 -p 85.
Processed reads were aligned to the human genome with tophat, v2.1.1, using parameters -G genes.gtf -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 23 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-unstranded. Genes file was taken from Ensembl release 99.
Raw counts were obtained with htseq-count, v0.13.5, using parameters -s 'no'.
DESeq2, v1.30.0, was used for normalization and differential expression. Genes with less than 10 counts were filterred out prior to normalization. The donor of each sample was added as a batch factor to the statistical model and was used for batch-correction with the ComBat function of the sva package, v3.38.0. Significance threshold was taken as padj<0.05.
Assembly: GRCh38
Supplementary files format and content: An Excel file with a header line, followed by a line for each gene. Columns are as described for each sample.

source_name: Primary Macrophages

growth_protocol: Monocytes were cultured in complete RPMI (10% FBS, 1% penicillin/streptomycin, and 1% L-glutamine; Biological Industries) supplemented with 5% FBS, 1% non-essential amino acids, 1% sodium pyruvate, 0.0175 mM β-mercaptoethanol, and 50 ng/mL of M-CSF (R&D Systems, #216-MC-025) to generate macrophages. Macrophages were cultured for 7 additional days with media changes every 2 days.

extract_protocol:
RNA was isolated using the TRIzol™ protocol (invitrogen) according to the manufacturer’s instructions.
NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) was used with poly-A selection.

treatment_protocol: For the differentiation into M1-like macrophages, cells were incubated for 48 hours with IFNg (20ng/mL) and LPS (75ng/mL) and for M2-like macrophages IL13 (20ng/mL) and IL4 (20ng/mL) and with an additional media change for 24 hours. For the melanosome treatment, macrophages were cultured with melanosomes as isolated from the MNT1 melanoma cells, HaCat-keratinocytes, and primary fibroblasts.

tag: cell line

value: Primary Macrophages

value: Primary Monocytes Differentiated to Macrophages

value: Macrophages differentiated to M2-like with IL13 (20ng/mL) and IL4 (20ng/mL)_Donor 3


title: kidney, PND14, mCherry Glis3 KO, rep3

status: Public on Dec 31 2023

type: SRA

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

country: USA

institute: NIH/NIEHS

library_source: transcriptomic

data_processing:
Read pairs were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the unstranded PAX8-cre dataset and "-s2 -Sfr -p" for the reverse-stranded mCherry dataset.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand {Unstranded,Stranded} --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.

tag: tissue

value: kidney

tag: age

tag: genotype

value: mCherry Glis3 KO


title: GF4_Ctrl

city: seoul

first: Jimin

last: Cha

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each sample

source_name: Skin

growth_protocol: Not applicable

extract_protocol:
Skin fresh tissue was achieved, total skin RNA were prepared using RNeasy® Fibrous Tissue Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were generated using TruSeq RNA Sample Prep Kit v2(Illumina), and the samples were sequenced on HiSeq4000.

treatment_protocol: The mice were treated with ethanol or MC903 for 5 times daily.

value: Skin

tag: strain

tag: treatment

value: Ethanol

tag: group

value: germ-free


title: GF4_MC903


title: kidney, PND14, mCherry Glis3 KO, rep1


title: 4T1 48h_Pip4K2c rep 3_2 [MZ12]

city: New York

first: Lior

last: Zangi

address: 1470 Madison Ave

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were mapped with STAR aligner (v2.5.0) to the mouse reference genome mm10 with default parameters
Read counts were extracted with Cufflinks (v2.2.1)
Counts were normalized with the trimmed mean of M-values method (edgeR v3.42.4)
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM-normalized log2CPMs for each sample

source_name: 4T1 breast cancer

growth_protocol: The 4T1 breast cancer cell line (ATCC, #CRL-2539) was cultured in RPMI (Gibco, #72400-047) supplemented with 10% FBS and pen-strep.

extract_protocol:
RNA was isolated using Quick-RNA MiniPrep kit (Zymo Research, #R1055) according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using Kit following manufacturer's protocols

treatment_protocol: Cells were transfected with either Luc or Pip4K2c modRNA using Lipofectamine2000 (Invitrogen, #11668027) and collected 48h post transfection.

value: 4T1 breast cancer

tag: cell type

value: epithelial, mammary gland

tag: strain background

value: transfection with Pip4K2c modRNA


title: kidney, PND7, mCherry Glis3 KO, rep1


title: 4T1 48h_Pip4K2c rep 1_2 [MZ8]


title: 4T1 48h_Pip4K2c rep 1_1 [MZ7]


title: D2_M2

organism: Homo sapiens

value: Macrophages differentiated to M2-like with IL13 (20ng/mL) and IL4 (20ng/mL)_Donor 2


title: D2_M1

value: Macrophages differentiated to M1-like with LPS (75ng/mL) and IFNg (20ng/mL)_Donor 2


title: 4T1 48h_Pip4K2c rep 3_1 [MZ11]


title: GF1_MC903


title: SPF2_MC903

value: specific-pathogen free


title: 4T1 48h_Pip4K2c rep 2_2 [MZ10]


title: 4T1 48h_Luc rep 2_1 [MZ3]

value: transfection with Luciferase (Luc) modRNA


title: 4T1 48h_Luc rep 1_2 [MZ2]


title: D3_Fib

value: Macrophages cultured with Fibroblast-derived melanosomes_Donor 3


title: D1_M2

value: Macrophages differentiated to M2-like with IL13 (20ng/mL) and IL4 (20ng/mL)_Donor 1


title: inoculated ctrl 7

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

description:
none
group_ki_Differential_Expression.tsv
group_naive_Differential_Expression.tsv

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: GRCh38 V3.0.0

source_name: heart

extract_protocol:
Freshly isolated hearts from 16-week-old WT, Dsg2mut/mut and Dsg2mut/mut x Ccr2-/- mice (n=3 per group) were minced on ice with a razor blade, transferred to a 15 mL conical tube containing 3mL DMEM with 170uL collagenase IV (250U/mL final concentration), 35uL DNAse1 (60U/mL), and 75uL hyaluronidase (60U/mL), and incubated at 37 °C for 45 min with agitation. Thereafter, the digestion reaction was quenched with 5 mL of HBB buffer (2% FBS and 0.2% BSA in HBSS), passed through 40-µm filters into a 50 mL conical tube and transferred back into a 15 mL conical tube to obtain tighter pellets. Samples were then spun down at 4°C, 1200rpm for 5 min and the supernatant was discarded. Pellets were resuspended in 1 mL ACK Lysis buffer (Gibco A10492-01)  and incubated at room temperature for 5 min, followed by the addition of 9 mL DMEM and centrifugation (4°C, 5 min, 1200 rpm). Supernatant was discarded and the pellets were resuspended in 2 mL FACS buffer (2% FBS and 2mM EDTA in calcium/magnesium free PBS); centrifugation was repeated in above conditions and supernatant aspirated. The TotalSeq A 277 panel (BioLegend) antibody cocktail was resuspended in 100 µL of FACS buffer and added to each sample. The combined 100 µL were used to resuspend the pellet with the addition of 1 µL of DRAQ5 (5mM solution Thermo Fisher Scientific, 564907) and incubated on ice for 30 min. Solution was washed 3x with FACS buffer following same centrifugation as above and then resuspended in 300 µL of FACS buffer and 1 uL DAPI (BD Biosciences, 564907) and filtered into filter top FACS tubes. First singlets were gated and subsequent DRAQ5+/DAPI- events were collected in 300 µL cell resuspension buffer (0.04% BSA in PBS) – collected cells were centrifuged as above and resuspended in collection buffer to a target concentration of 1,000 cells/µL. Cells were counted on a hemocytometer before proceeding with the 10x protocol.  Sample preparation for single nuclei RNA-seq (snRNA-seq): Frozen hearts from 16-week-old WT, Dsg2mut/mut and Dsg2mut/mut x Ccr2-/- mice (n=3 per group) were minced with a razor blade and transferred into a 5 mL Dounce homogenizer containing 1–2 mL chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40 in nuclease-free water). Samples were homogenized gently using five passes without rotation, and then incubated on ice for 15 min. Lysate was gently passed through a 40-μm filter into 50-mL conical tube, followed by rinsing the filter once with 1 ml lysis buffer and transfer of lysate to a new 15-mL conical tube. Nuclei were then centrifuged at 500g for 5 min at 4°C, followed by resuspension in 1 mL Nuclei Wash Buffer (2% BSA and 0.2 U /µL RNase inhibitor in 1× PBS) and filtered through a 20-μm pluristrainer into a fresh 15-mL conical tube. Centrifugation was repeated according to the above parameters. Supernatant was then removed, and  nuclei were resuspended in 300 µL Nuclei Wash Buffer and transferred to a 5-mL tube for flow sorting. Then, 1 µl DRAQ5 (5 mM solution; Thermo Fisher, cat. no. 62251) was added, mixed gently and allowed to incubate for 5 min before sorting. DRAQ5+ nuclei were sorted into Nuclei Wash Buffer. Recovered nuclei were centrifuged again under the above parameters and were gently resuspended in Nuclei Wash Buffer to a target concentration of 1,000 nuclei/µL. Nuclei were counted on a hemocytometer.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: heart

value: MYH6-Cre (-) Rosa26-LSL-hACE2 (+/-)

value: intranasal inoculateion with SARS-CoV-2


title: 4T1 48h_Pip4K2c rep 2_1 [MZ9]


title: D3_M1

value: Primary Macrophages

value: Primary Monocytes Differentiated to Macrophages

value: Macrophages differentiated to M1-like with LPS (75ng/mL) and IFNg (20ng/mL)_Donor 3


title: SPF3_MC903

value: Skin


title: SPF3_Ctrl

value: Ethanol


title: SPF1_Ctrl


title: D1_M1

value: Macrophages differentiated to M1-like with LPS (75ng/mL) and IFNg (20ng/mL)_Donor 1


title: 4T1 48h_Luc rep 3_2 [MZ6]

value: 4T1 breast cancer

value: epithelial, mammary gland


title: 4T1 48h_Luc rep 2_2 [MZ4]


title: D2_Ker

value: Macrophages cultured with Keratinocyte-derived melanosomes_Donor 2


title: 4T1 48h_Luc rep 1_1 [MZ1]


title: SPF2_Ctrl


title: D2_Fib

value: Macrophages cultured with Fibroblast-derived melanosomes_Donor 2


title: inoculated ctrl 6


title: SPF1_MC903

value: specific-pathogen free


title: D1_Fib

value: Macrophages cultured with Fibroblast-derived melanosomes_Donor 1


title: GF1_Ctrl

value: germ-free


title: inoculated ctrl 5


title: D3_Ker

value: Macrophages cultured with Keratinocyte-derived melanosomes_Donor 3


title: inoculated ctrl 3

value: heart


title: naïve ctrl 1

value: MYH6-Cre (-) Rosa26-LSL-hACE2 (+/-)


title: inoculated ctrl 4

value: intranasal inoculateion with SARS-CoV-2


title: inoculated ctrl 2


title: Infected hACE2-KI 6

value: MYH6-Cre (+) Rosa26-LSL-hACE2 (+/-)


title: Infected hACE2-KI 7


title: GFP + 21 rep 3

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

country: France

institute: INSERM U1138

data_processing:
STAR : v2.7.6.a
STAR --runThreadN 24 --runMode genomeGenerate --genomeDir ./idx1 --genomeFastaFiles $fastaRef --sjdbOverhang 100 --limitSjdbInsertNsj 2050000 --genomeSAindexNbases 12 --sjdbGTFfile $gtfRef --runThreadN 24 --genomeDir ${PWD}/output/idx1/ --readFilesCommand zcat --readFilesIn $fqFile --outFileNamePrefix $fqID --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --sjdbGTFfile $gtfRef --alignIntronMin 10 --alignIntronMax 25000 --quantMode TranscriptomeSAM --twopassMode Basic
RSEM version 1.3.1
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_RSEM $resultats_RSEM
RStudio Server : v1.3.1093
DESeq2_1.26.0
bamCoverage -p 24 -v --outFileFormat "bigwig" --binSize 25 --normalizeUsingRPKM --ignoreDuplicates --minMappingQuality 30 --smoothLength 50 --bam $i --outFileName ${i}.bw
Assembly: Ensembl release 100
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: BigWIG

source_name: mouse ApcDHep hepatocytes

extract_protocol: RNAs were extracted by Trizol

treatment_protocol: RNA profiles from hepatocytes isolated from  Apclox/lox livers by perfusion with collagenase in three-month old mice injected with Ad5-Cre-GFP for 6, 15 and 21 days

tag: cell types

value: mouse  hepatocytes

value: Ad5-Cre-GFP 1,5x109 Vg


title: inoculated ctrl 1


title: GFP + 21 rep 2


title: naïve ctrl 4


title: GFP + 21 rep 1


title: D1_Ker

value: Primary Macrophages

value: Primary Monocytes Differentiated to Macrophages

value: Macrophages cultured with Keratinocyte-derived melanosomes_Donor 1


title: naïve ctrl 5


title: D3_MNT

value: Macrophages cultured with MNT1-derived melanosomes_Donor 3


title: D2_MNT

value: Macrophages cultured with MNT1-derived melanosomes_Donor 2


title: GFP + 15 rep 3


title: naïve ctrl 2


title: GFP + J6 rep 3


title: Infected hACE2-KI 5


title: D1_MNT

value: Macrophages cultured with MNT1-derived melanosomes_Donor 1


title: GFP + J6 rep 2


title: GFP + 15 rep 2


title: Infected hACE2-KI 3


title: Infected hACE2-KI 2


title: GFP + J6 rep 1


title: Infected hACE2-KI 4


title: D1_cnt

value: Naive macrophages_Donor 1


title: D3_cnt

value: Naive macrophages_Donor 3


title: Infected hACE2-KI 1


title: D2_cnt

value: Naive macrophages_Donor 2


title: WT-TAC 1

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

country: China

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAC

value: WT


title: usp13 ko-TAC 3

value: usp13 ko


title: WT-TAC 3


title: naïve ctrl 3

value: heart

value: MYH6-Cre (-) Rosa26-LSL-hACE2 (+/-)


title: usp13 ko-TAC 2


title: GFP -  rep 5

source_name: mouse wt hepatocytes


title: GFP - rep 6


title: testis-10% fat+fiber-NZO/HlLtJ-M (ORSAM9043)

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

molecule: polyA RNA

source_name: testis

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at sixteen weeks of age.

value: testis

tag: diet

value: 10% fat + fiber

value: NZO/HlLtJ

tag: Sex

value: Male


title: testis-10% fat+fiber-NZO/HlLtJ-M (ORSAM9044)

description: 100 bp paired-end to a targeted read depth of 30 million read pairs


title: WT-TAC 2


title: testis-10% fat+fiber-CAST/EiJ-M (ORSAM9041)

value: CAST/EiJ


title: testis-44% fat+fiber-CAST/EiJ-M (ORSAM9042)

value: 44% fat + fiber


title: MIBC35,High total immune cells

city: baltimore

first: yang

last: song

state: MD

address: 670 W. Baltimore St.

institute: university of maryland in baltimore

description: Cofactor Genomics ImmunoPrism assay

data_processing:
reads passed QC  are aligned to humann  reference hg38 using aligner STAR v.2.5.2a
read counts were estimated using htseq (1.0.0)
Differential expression analysis is done using DESeq2 (V 1.30.1)
Assembly: hg38
Supplementary files format and content: tab-delimited files included the raw counts for each sample.

source_name: muscle invasive bladder cancer biopsy

extract_protocol:
RNA-seq were extracted following the standard protocol by Cofactor Genomic
20 ng of RNA were used to prepare sequencing library following Cofactor Genomic protocols.

treatment_protocol: patients from two clinical trials with muscle-invasive bladder cancer (MIBC) were treated with Chemoradiation

value: muscle invasive bladder cancer biopsy

value: High total immune cells

value: chemoradiation


title: MIBC36,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC37,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells


title: MIBC34,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: GFP - rep 4

value: mouse  hepatocytes

value: Ad5-Cre-GFP 1,5x109 Vg


title: testis-44% fat+fiber-C57BL/6J-M (ORSAM9040)


title: testis-44% fat+fiber-C57BL/6J-M (ORSAM9039)


title: GFP - rep 3


title: GFP - rep 2


title: testis-10% fat+fiber-C57BL/6J-M (ORSAM9037)


title: usp13 ko-TAC 1

value: TAC


title: MIBC36,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC35,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: testis-44% fat+fiber-NZO/HlLtJ-M (ORSAM8218)

value: WT


title: testis-44% fat+fiber-NZO/HlLtJ-M (ORSAM8217)


title: MIBC33,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: AM, GMCSF, DON2

city: Rochester

first: Min

last: Wang

state: MN

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic

data_processing:
The RTA software (Illumina, version 2.5.2) was used for base-calling
Paired-end fastq files were mapped to the mouse mm10 reference genome using STAR version 2.6.0a.
Gene level counts were obtained using featureCounts from the Subread package version 1.4.6.
Different expression analysis was done using DESeq2 version 1.28.1.
Gene set enrichment analysis (GSEA) was performed using gene lists ranked by log2 fold change using the mouse gene set database from Enrichment Map.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: AM

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The RNA-Seq of the cDNA libraries was done using an Illumina HiSeq 4000 in conformity with the provider’s protocol with the HiSeq 3000/4000 PE Cluster Kit and Illumina cBot

value: AM

value: alveolar macrophages

value: GM-CSF stimulation and DON treatment

tag: time

value: Day 2


title: testis-44% fat+fiber-CAST/EiJ-M (ORSAM8214)

value: testis


title: MIBC32,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: AM, GMCSF, DON1


title: MIBC31,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: testis-10% fat+fiber-C57BL/6J-M (ORSAM8213)

value: 10% fat + fiber


title: testis-44% fat+fiber-C57BL/6J-M (ORSAM8212)

value: Male


title: testis-44% fat+fiber-NZO/HlLtJ-M (ORSAM7788)

value: NZO/HlLtJ


title: AM, GMCSF, Ctrl2

value: GM-CSF stimulation


title: MIBC30,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy


title: AM, GMCSF, Ctrl1


title: testis-44% fat+fiber-NZO/HlLtJ-M (ORSAM7787)

value: 44% fat + fiber


title: testis-10% fat+fiber-C57BL/6J-M (ORSAM9038)


title: testis-10% fat+fiber-NZO/HlLtJ-M (ORSAM7786)


title: AM, no-GMSCF2

value: no GM-CSF stimulation


title: testis-10% fat+fiber-NZO/HlLtJ-M (ORSAM7785)


title: MIBC34,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells

value: chemoradiation


title: testis-10% fat+fiber-CAST/EiJ-M (ORSAM8216)

value: CAST/EiJ


title: GFP - rep 1

value: mouse  hepatocytes

value: Ad5-Cre-GFP 1,5x109 Vg


title: testis-44% fat+fiber-CAST/EiJ-M (ORSAM7784)

value: WT


title: MIBC33,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: testis-10% fat+fiber-CAST/EiJ-M (ORSAM7783)


title: AM, no-GMSCF1

value: AM

value: alveolar macrophages


title: testis-44% fat+fiber-CAST/EiJ-M (ORSAM8215)


title: testis-44% fat+fiber-C57BL/6J-M (ORSAM7782)


title: testis-10% fat+fiber-C57BL/6J-M (ORSAM7781)


title: MIBC32,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: HL-1 Soluble Nuclear Extract rep3

city: Chicago

first: Johnathon

last: Hall

state: IL

address: 920 E 58th St

department: Molecular Genetics & Cell Biology

institute: University of Chicago

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_SNE3

data_processing:
Read alignment with Hisat2; fastq files were aligned to the mm10 reference genome with Hisat2 using standard options, followed by samtools sort function to generate sorted BAM files.
Reference gtf file generation with cat; gencode genes, gencode lincRNA, ERCC spike-in standards, and Tbx5-dependent ncRNA annotation files were concatenated using cat command to generate a reference gtf file.
Novel transcript detection with cufflinks and cuffmerge; for each sample, transcript GTF files were generated by running cufflinks: cufflinks -p16 -u -N -g bigannotation.gtf --library-type fr-firststrand -o CF_file filesorted.bam. Cuffmerge was used independently with CPE transcript GTF files and SNE transcript GTF files. Novel transcripts from the merged GTF files were detected by using Bedtools intersect, then these novel transcripts were concatenated onto the reference GTF file used in cufflinks to generate a complete transcriptome GTF file as a reference for next steps.
Gene expression analysis with cuffdiff; the complete reference GTF file with novel transcripts added was used with cuffdiff to calculate average FPKM values in the CPE and SNE of the three biological replicates. Linear regression analysis of the ERCC spike-in standard FPKM values was used to determine a scalar correction constant to calcualte corrected CPE FPKM values. Corrected CPE and SNE FPKM values were added together to calculate total FPKM. Corrected CPE FPKM values were divided by SNE FPKM to calculate fold chromatin-enrichment. The log10 values of total FPKM and fold chromatin-enrichment were calculated.
Associating gene_type with analyzed expression data; Unique "gene_id" and "gene_type" values were extracted from the complete reference GTF file using the awk, sort, and uniq commands. Gene_type data and analyzed gene expression data from the prior step were read into R. Dplyr inner_join was used to add a gene_type column to the analyzed gene expression data, which was saved as a CSV file.
Genome_build: mm10
Supplementary_files_format_and_content: The CSV file "cheRNA-seq-gene-expression-analysis.csv" is in comma separated value format, with column labels to identify genes, their expression levels, and degrees of chromatin-enrichment.

molecule: nuclear RNA

source_name: HL-1 cardiomyocyte cell line

growth_protocol: Cells were grown in Claycomb medium supplemented with 10% pre-screened FBS, L-glutamine, and norepinephrine

extract_protocol:
Nuclei were extracted by detergent lysis. Nuclear extracts were prepared by biochemical fractionation. ERCC spike-in standards were added to each nuclear fraction. RNA was extracted with TRIzol reagent.
rRNA was depleted with the Illumina Ribo-zero Gold kit. rRNA-depleted RNA was converted to cDNA for sequencing following the manufacturer's instructions for NEBNext Ultra II Directional kit.

value: cardiomyocyte

tag: fraction

value: soluble-nuclear RNA


title: MIBC28,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: MIBC31,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM8936) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8936

source_name: islets of Langerhans

extract_protocol:
KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA was isolated from pancreatic islets using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit.  Pancreatic islet libraries were sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs.

value: islets of Langerhans

value: Female


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM8939) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8939

value: 10% fat + fiber

value: NZO/HlLtJ

value: Male


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM8937) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8937

value: 44% fat + fiber


title: HL-1 Soluble Nuclear Extract rep1

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_SNE1


title: HL-1 Soluble Nuclear Extract rep2

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_SNE2


title: HL-1 Chromatin Pellet Extract rep3

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_CPE3

library_source: genomic

value: chromatin-enriched RNA


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8935) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8935


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8933) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8933


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8932) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8932


title: MIBC30,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy

value: Low total immune cells

value: chemoradiation


title: HL-1 Chromatin Pellet Extract rep2

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_CPE2


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8930) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8930


title: MIBC27,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: HL-1 Chromatin Pellet Extract rep1

description:
cheRNA-seq-gene-expression-analysis.csv
HL1_CPE1


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8931) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8931

value: CAST/EiJ


title: MIBC29,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: NPCI

city: La Jolla

first: Caroline

middle: R

last: McKeown

state: CA

address: 10550 N. Torrey Pines Rd., DNC-216

department: Dorris Neuroscience Center

institute: The Scripps Research Institute

data_processing:
Raw reads were quality-checked using FASTQC
Reads were aligned using STAR as well as TopHat2; no trimming was performed for STAR; Trimmomatic was used to trim for TopHat2
Alignments were quality-checked with SAMStat, and alignments with a MAPQ score > 20 were used for differentialy expression analysis
Reads were counted using HTSeq
Counts were normalized using the DESeq2 package
Genome_build: Xenbase v9.1
Supplementary_files_format_and_content: Series of matrix tables with DESeq2 normalized counts for alignments using STAR or Tophat2, by mRNA or CDS

organism: Xenopus laevis

source_name: stage 46 optic tectum

extract_protocol:
Brain regions were collected from stage 46 optic tectum and total RNA was extracted using the mirVana kit (Life Technologies, USA). DNase treatment was used to remove genomic DNA and was followed by clean-up using RNeasy mini kit (Qiagen, USA).
1µg of cDNA was sheared in microTube (Covaris) and then used for library preparation (KAPA Taq PCR kits). The next generation sequencing was done using HiSeq2000 platform (Illumina; RRID:SCR_020132) for single-end reads at size 100bp.

tag: visual stimulation

value: dark-exposed


title: MIBC29,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8926) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8926

value: WT


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8929) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8929


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM8938) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8938


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8928) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8928


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8927) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8927


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM8934) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8934


title: INIII

value: visual stimulation-exposed


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8925) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8925


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM8089) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8089


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM8090) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8090


title: GFP + 15 rep 1

value: mouse  hepatocytes

value: Ad5-Cre-GFP 1,5x109 Vg


title: INII


title: INI


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM8087) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8087


title: MIBC27,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC28,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: NPCIII


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8085) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8085


title: MIBC26,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC26,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM8084) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8084

value: islets of Langerhans


title: MIBC25,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8082) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8082

value: Female


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8081) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8081


title: MIBC24,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8080) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8080

value: 10% fat + fiber


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8079) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8079


title: MIBC24,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM8088) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8088

value: NZO/HlLtJ


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8078) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8078


title: MIBC25,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: Mahulata 48hrs drought stress

city: Cuttack

first: Koushik

last: Chakraborty

address: Bidyadharpur

country: India

institute: ICAR-National Rice Research Institute

data_processing:
the data was trimmed using trimmomatic
aligned with tophat2 using MSU6 as reference build
subsequent processing using cufflinks and cuffdiff
Genome_build: Oryza sativa subsp. Japonica reference genome (build MSU6.0)
Supplementary_files_format_and_content: xls files detailing the expressed genes and their annotation (in pairwise comparison as indicated in the file name)

organism: Oryza sativa

source_name: Leaf

extract_protocol:
Using the standard Trizol Method
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Early Vegetative Stage

value: 48hrs drought stress

value: leaf


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8077) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8077


title: Mahulata 96hrs drought stress

value: 96hrs drought stress


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM8086) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8086

value: Male


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8075) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8075

value: 44% fat + fiber


title: IR20 48hrs drought stress


title: MIBC22,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy

value: chemoradiation


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8076) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8076

value: WT


title: Mahulata 0hrs drought stress

value: 0hrs drought stress


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM8083) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8083

value: CAST/EiJ


title: NPCII

value: dark-exposed


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM7668) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7668


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM7664) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7664


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM7666) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7666


title: IR20 0hrs drought stress


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM7663) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7663


title: MIBC22,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells


title: IR20 96hrs drought stress


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM7662) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7662

value: islets of Langerhans


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM7661) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7661

value: Female


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM7660) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7660


title: MIBC23,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM7658) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7658


title: MIBC19,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC23,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC20,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM7655) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7655

value: 10% fat + fiber


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM7653) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7653


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM7654) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7654


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM7657) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7657


title: hypothalamus-44% fat+fiber-CAST/EiJ-F (ORSAM9463)

source_name: hypothalamus

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at fifteen weeks of age.

value: hypothalamus


title: MIBC21,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-CAST/EiJ-M (ORSAM9461)


title: MIBC16,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC21,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: Budding yeast, Rec8 ChIP, 8h in meiosis, rep2

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

data_processing:
An “in-lane” control spike in each lane of the flow-cell was performed accrding to Fasteris's precedure to estimate the error rate for sequences. These spiked control reads are mapped on the PhiX reference genome. Quality and statistics of raw reads were analyzed using FastQC (version 0.11.5).
Removal of Illumina adapters and trimming of raw sequence reads was done using Trimmomatic (version 0.36).
Processed reads (~2-8 Million reads per samples) were aligned to the S288c reference genome (version R64-1-1) using bowtie (version 2.3.0).
Samples having more than 75% alignment rate and aligned reads with more than 2 million reads were used for the downstream analysis and samples having an alignment rate less than 30% and less than 0.5 million reads were discarded from the analysis.
After analyzing the alignment statistics, conversion of the aligned file format (SAM) to its compressed file format (BAM), indexing and sorting was done using samtools (version 1.3.1).
The bedgraph files were generated from the BAM files for the input and IP samples using callpeak in MACS2 (version 2.2.7.1). The input signal was subtracted from the IP sample using bdgcmp in MACS2. The bedgraph files were converted to bigwig using bedGraphToBigWig in MACS2.
To identify the Rec8 peaks, only reads that are uniquely aligned were taken into account. Rec8 peaks with a p-value greater than 10-5 were filtered out. Peaks that were common from the two replicates from each sample were considered as the final Rec8 peaks.
Assembly: S288c
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Diploid colonies were inoculated in 5 ml YPD medium and grown for 24 h at 30°C to reach saturation. From the saturated YPD culture ~5 x 106 cells/ml were inoculated to liquid SPS (0.5% yeast extract, 1% peptone, and 0.67% yeast nitrogen base without amino acids, 1% potassium acetate, 0.05 M potassium biphthalate, and pH 5.5) medium and grown for 7 h at 30°C. This culture was used to inoculate 500 ml of liquid SPS at a cell density of ~3 x 105 cells/ml and grown for 12-16 h at 30°C until the cell density reached ~4 x 107 cells/ml. Cells were collected by centrifugation, washed twice with H2O, and re-suspended in 400 ml of sporulation (2% Potassium Acetate) medium at cell density ~4 x 107 cells/ml and incubated at 30°C with shaking.

extract_protocol:
From a synchronous meiotic culture, 50 ml of samples were collected at various time points and crosslinked using formaldehyde (1%) for 30 min. Cells were lysed using Beadbeater (Unigenetics). The cell extract was sonicated using Bioruptor (Diagenode) and the debris was removed by centrifugation. Protein A agarose beads were used to preclear the cell lysate from each sample. To the pre-cleared lysate, 2.5 μl Rec8 anti-serum and 7.5 mg of Protein-A agarose beads blocked with BSA were added. After incubation, the lysate was removed by centrifugation, and beads were washed to remove non-specific binding. The immunoprecipitated material was eluted from the beads and decrosslinked along with RNase A treatment. The DNA was purified following Proteinase K treatment using QIAGEN PCR purification kit.
ChIP-seq libraries were prepared using the illumina ChIP-Seq TruSeq kit from 20 ng of DNA as starting material for input and IP samples.

value: whole cell

tag: read length

value: 50 bp


title: hypothalamus-44% fat+fiber-C57BL/6J-M (ORSAM9462)


title: Budding yeast, Rec8 ChIP, 5h in meiosis, rep2


title: hypothalamus-10% fat+fiber-CAST/EiJ-F (ORSAM9464)


title: MIBC18,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-CAST/EiJ-M (ORSAM9460)


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM7656) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7656


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM7659) 2

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7659


title: MIBC20,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: Budding yeast, input, 5h in meiosis, rep2


title: hypothalamus-44% fat+fiber-CAST/EiJ-M (ORSAM9459)


title: hypothalamus-44% fat+fiber-CAST/EiJ-F (ORSAM9458)


title: hypothalamus-10% fat+fiber-CAST/EiJ-F (ORSAM9465)


title: MIBC17,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-M (ORSAM9455)

value: NZO/HlLtJ


title: MIBC15,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: Budding yeast, Rec8 ChIP, 5h in meiosis, rep1


title: MIBC19,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-M (ORSAM9456)

value: Male


title: Budding yeast, input, 5h in meiosis, rep1


title: MIBC14,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-C57BL/6J-M (ORSAM9452)

value: 44% fat + fiber


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-M (ORSAM9454)


title: Budding yeast, Rec8 ChIP, 8h in meiosis, rep1


title: MIBC17,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy


title: hypothalamus-44% fat+fiber-C57BL/6J-F (ORSAM9448)


title: hypothalamus-10% fat+fiber-C57BL/6J-M (ORSAM9450)


title: hypothalamus-10% fat+fiber-CAST/EiJ-F (ORSAM9449)


title: MIBC18,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: chemoradiation


title: MIBC13,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC16,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: tRNA-HySeq, Spt16_197 rep2

city: Hyderabad

first: Purnima

last: Bhargava

state: Telangana

address: Habsiguda X road

institute: CSIR-Centre for Cellular and Molecular Biology

data_processing:
Data was analyzed using Galaxy. Adapter sequences were clipped using NGS: QC and manipulation/Clip, specifying a minimum length of 25 nt, and enter a custom adapter sequence 5′-CTGTAGGCACCATCAAT-3′
Trimmed the adapter sequence using NGS: QC and Manipulation/Trim sequences
Mapped the sequences to a custom genome file consisting of all unique mature tRNA sequences in S. cerevisiae using Bowtie for illumina tool in Galaxy.
Count table was prepared using Idxstats in Samtools.
Genome_build: Custom genome file including all unique mature tRNA sequences in S. cerevisiae.

source_name: Spt16_197, Log-phase cells in the 1X YEP with 2% dextrose

growth_protocol: YM1729 and Spt16_197 strains were grown up to A600: 0.6-0.8 in YEP medium at 30°C

extract_protocol:
tRNA was hydroyzed and the fragments ranging 19-35 nt were selected for sequencing
Samples were processed using the protocol described in Ingolia, N.T., Brar, G.A., Rouskin, S., Mcgeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550.

tag: growth stage

tag: molecule subtype

value: size selected tRNA


title: tRNA-HySeq, WT rep2

source_name: YM1729, Log-phase cells in the 1X YEP with 2% dextrose


title: tRNA-HySeq, spt16-197 rep1

source_name: spt16-197, Log-phase cells in the 1X YEP with 2% dextrose

growth_protocol: YM1729 and spt16-197 strains were grown up to A600: 0.6-0.8 in YEP medium

extract_protocol:
tRNA was hydrolyzed and the fragments ranging 19-35 nt were selected for sequencing
Samples were processed using the protocol described in Ingolia, N.T., Brar, G.A., Rouskin, S., Mcgeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550.

value: Size selected tRNA


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-F (ORSAM9445)

tag: tissue

value: WT


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-M (ORSAM9444)

tag: genotype


title: hypothalamus-44% fat+fiber-C57BL/6J-F (ORSAM9453)

tag: strain


title: tRNA-HySeq, WT rep1

value: Log-phase cells in the 1X YEP with 2% dextrose


title: hypothalamus-10% fat+fiber-C57BL/6J-M (ORSAM9446)

tag: treatment


title: hypothalamus-44% fat+fiber-C57BL/6J-F (ORSAM9447)


title: MIBC14,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

tag: group


title: 4T1 48h_Luc rep 3_1 [MZ5]

source_name: 4T1 breast cancer

tag: cell line

value: 4T1 breast cancer

tag: cell type

value: epithelial, mammary gland

value: transfection with Luciferase (Luc) modRNA


title: MIBC12,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells


title: hypothalamus-10% fat+fiber-C57BL/6J-F (ORSAM9441)

value: 10% fat + fiber

value: Female


title: hypothalamus-10% fat+fiber-C57BL/6J-M (ORSAM9443)

value: hypothalamus


title: hypothalamus-10% fat+fiber-CAST/EiJ-M (ORSAM9439)

value: CAST/EiJ


title: hypothalamus-10% fat+fiber-C57BL/6J-F (ORSAM9440)


title: MIBC15,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: 2-4,female,control,anti-MLE,Rep1

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

institute: Brown University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT & RUN reads were trimmed using Trimmomatic v0.40 with default setting.
CUT & RUN reads were aligned to the UCSC dm6 genome using Bowtie version 2.4.4.
Peaks were called uing SEACR v1.3 with the significance cut-off q-value <=0.01
bigWig files were generated using deeptools bameCoverage. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size (reads per genome coverage, RPGC, normalization). stringent.bed files were generated using SEACR v1.3 with default settings.
Supplementary files format and content: dm6
Supplementary files format and content: bigWig, bed (stringent)

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Drosophila melanogaster fly stocks were maintained at 24℃ on standard corn flour sucrose media. Fly strains used: MTD-GAL4 (Bloomington, #31777), UAS-CLAMPRNAi[val22] (Bloomington, #57008), Meiotic drive fly stocks +; SD72/CyO and 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO (Bloomington, #64332). These were crossed to obtained female embryo of desired genotypes according to Rieder et al 2017.

extract_protocol:
The embryos were dechorionated in 6% bleaching solution, washed in cold 1XPBS and permeabilised using 0.05% Digitonin. pAMNase (700ng/ml) allowed to bind to antibody bound to MLE protein on chromatin. MNAse activity initiated by adding CaCl2 at 0℃ and after 30 minutes incubation allowed to stop by adding 2X RSTOP Buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/ml RNase, 40ug/ml glycogen, 10pg/ml yeast spike-in DNA). DNA fragment extracted and purified using Phenol:Chloroform extraction and 1ng of DNA used for making libraries.
Library prepared using Kapa hyper prep kit using manufacturer's protocol
Cut and Run sequencing, Paired end, 2X150bp illumina Hiseq

value: Embryo

tag: age

tag: chip antibody

value: rat anti-MLE (1:50, 6E11)


title: hypothalamus-10% fat+fiber-CAST/EiJ-M (ORSAM9438)

tag: diet

tag: Sex

value: Male


title: 0-2,female,clampRNAi,anti-MLE


title: hypothalamus-10% fat+fiber-CAST/EiJ-M (ORSAM9437)


title: 2-4,female,control,anti-MLE,Rep2


title: MIBC13,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy

value: chemoradiation


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-F (ORSAM9435)

value: 44% fat + fiber

value: NZO/HlLtJ


title: hypothalamus-10% fat+fiber-C57BL/6J-F (ORSAM9442)

value: WT


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-F (ORSAM9436)


title: MIBC11,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: 0-2,female,control,anti-MLE,Rep1


title: MIBC10,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: hypothalamus-44% fat+fiber-NZO/HlLtJ-F (ORSAM9434)


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-M (ORSAM9432)


title: 0-2,female,control,anti-MLERep2


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-M (ORSAM9433)


title: RRBS, Ctrl, K257

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

data_processing:
Sequencing was performed on Illumina HiSeq 2500 instrument with the 1x50 single-end sequencing mode.
Following an initial quality trimming, adapter sequences were removed from the raw reads using Trim Galore v0.6.10 (with Cutadapt v4.4) with parameters '--quality 20 --stringency 5 --length 35 --non_directional –rrbs'.
Bisulfite alignment to the GRCh38 reference genome and methylation calling was performed using Bismark v0.24.1 (with bowtie2 v2.3.5.1) with parameter '-N 1'. Alignment files were sorted with samtools v1.10.
Analysis of methylation data were performed using MethylKit v1.26.0 R package (with R v4.3.1). Bismark alignment data for CpG sites were read in and filtered using processBismarkAln() function with parameters 'read.context=CpG, mincov=10'.
Methylation data were filtered and normalized using filterByCoverage() function with parameters 'lo.count=10, hi.perc=99.9' and normalizeCoverage() function with parameter 'method=”median”'.
ALS vs Ctrl DMS (differentially methylated CpG sites) analysis was performed using the following functions: merging all sample data and filtering using unite() with the parameters 'min.per.group=4L, destrand=TRUE'; calculating differential methylation statistics using calculateDiffMeth() with default parameters'; DMS selection using getMethylDiff() with parameters 'difference=20, qvalue=0.01'.
ALS vs Ctrl DMR (differentially methylated regions) analysis was performed using the following functions: tiling the genome using tileMethylCounts() with parameters 'win.size=1000, step.size=1000, cov.bases=5'; merging all sample data and filtering using unite() with the parameters 'min.per.group=4L'; calculating differential methylation statistics using calculateDiffMeth() with default parameters; DMR selection using getMethylDiff() with parameters 'difference=20, qvalue=0.01'.
DMSs and DMRs were annotated with the overlapping genes (exon, intron, promoter, TSS) using the GRCh38.p13 annotation data.
Assembly: hg38
Supplementary files format and content: Raw CpG methylation data for each sample (txt)
Supplementary files format and content: DMS list with differential methylation statistics and annotation (tsv)
Supplementary files format and content: DMR list with differential methylation statistics and annotation (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.
The premium RRBS kit of Diagenode was employed to carry out the RRBS protocol including NGS library preparation, as described (Veillard, AC., Datlinger, P., Laczik, M. et al. Diagenode® Premium RRBS technology: cost-effective DNA methylation mapping with superior coverage. Nat Methods 13, i–ii (2016). https://doi.org/10.1038/nmeth.f.391). Briefly, 100 ng of DNA was fragmented by the MspI restriction enzyme, which cleaves DNA without regard to the cytosine methylation state. Following adaptor ligation and size selection by Ampure beads, we pooled up to 6 samples together. These pooled samples underwent bisulfite treatment, purification, and PCR amplification, according to the manufacturer’s recommendations. The final RRBS libraries were quantified using the Qubit dsDNA HS Assay from Life Technologies, and the library's size distribution profile was assessed using Agilent Bioanalyzer 2100 capillary electrophoresis.

value: blood

tag: patient code

tag: analysis group

value: Ctrl

value: female

tag: age (at_sampling)

tag: age (at_als_onset)

tag: disease

value: healthy

tag: symptoms


title: RRBS, Ctrl, K190

tag: tissue

value: male


title: hypothalamus-44% fat+fiber-C57BL/6J-M (ORSAM9451)

tag: genotype


title: MIBC9,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells


title: hypothalamus-44% fat+fiber-CAST/EiJ-F (ORSAM9457)

value: hypothalamus

tag: strain

value: Female


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-F (ORSAM9431)

value: 10% fat + fiber

tag: treatment


title: hypothalamus-10% fat+fiber-NZO/HlLtJ-F (ORSAM9430)


title: MIBC8,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

tag: group


title: liver-44% fat+fiber-NZO/HlLtJ-F (ORSAM8967)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8967

source_name: liver

value: liver


title: RRBS, Ctrl, K161


title: liver-10% fat+fiber-NZO/HlLtJ-M (ORSAM8968)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8968


title: RRBS, Ctrl, K128


title: liver-10% fat+fiber-NZO/HlLtJ-M (ORSAM8969)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8969


title: liver-44% fat+fiber-CAST/EiJ-M (ORSAM8965)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8965

value: CAST/EiJ


title: MIBC12,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: RRBS, Ctrl, K107


title: liver-44% fat+fiber-CAST/EiJ-F (ORSAM8963)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8963


title: MIBC7,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy


title: RRBS, Ctrl, K039


title: liver-44% fat+fiber-NZO/HlLtJ-F (ORSAM8966)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8966


title: MIBC11,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: chemoradiation


title: MIBC6,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: liver-10% fat+fiber-CAST/EiJ-F (ORSAM8962)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8962


title: liver-10% fat+fiber-CAST/EiJ-F (ORSAM8961)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8961


title: RRBS, ALS, ALS81

value: ALS

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


title: S_ME12

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse build mm9) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

source_name: Periapical lesion

growth_protocol: Mice were housed in light/temperature-controlled environment at the UT Health San Antonio with 2-5 animals per cage where food and water were available ad libitum. Breeding was completed withing our facility, and 8-12-week-old male mice were used for all experiments.

extract_protocol:
After tissue grinding and homogenization in RNA lysis buffer, total RNA was isolated from harvested periapical lesions using the RNAeasy Kit (Qiagen; Valencia, CA) according to the manufacturer’s recommendation. After quantification with Nanodrop (Thermo Scientific; Rockford, IL), RNA was stored at -80ºC.
Total RNA was used for RNA-Seq library preparation by following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. #, KR1151, KAPA Biosystems)

treatment_protocol: Apical periodontitis was modelled in mice by performing pulp exposure procedures and allowing infections to occur for either 0, 7, or 14 days. Briefly, an intraperitoneal injection of ketamine (75 mg/kg)/dexdomitor (1mg/kg) was given to anesthetize mice, as described previously (Austah et al. 2016). The mice were then mounted on a custom jaw retraction apparatus, and pulp exposures were created in all four first molars, and an intraperitoneal injection of Antisedan (1 mg/kg) was given to reverse the anesthesia for Day 7 and 14 mice. Day 0 mice were immediately euthanized via cervical dislocation following pulp exposure, and Day 7 and 14 mice were returned to the housing facility. At the appropriate time point, mice were briefly anesthetized with isoflurane and euthanized via cervical dislocation. Then the first molars were dissected, pooling 3-4 teeth per mouse, and immediately snap frozen in liquid nitrogen and stored at -80ºC.

value: Periapical lesion

tag: condition

value: 14d after pulp exposure, Nav1.8cre+/DTA+ strain


title: RRBS, ALS, ALS76

value: blood

value: lower and upper limb, bulbar not present


title: S_ME10


title: D14_ME


title: MIBC10,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: liver-44% fat+fiber-C57BL/6J-M (ORSAM8959)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8959

value: 44% fat + fiber

value: Male

value: WT


title: S_ME19

value: male

value: 7d after pulp exposure, Nav1.8cre+/DTA+ strain


title: MIBC8,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: liver-44% fat+fiber-C57BL/6J-M (ORSAM8960)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8960


title: liver-10% fat+fiber-C57BL/6J-M (ORSAM8958)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8958

value: 10% fat + fiber


title: MIBC9,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: MIBC5,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: Low total immune cells


title: RRBS, ALS, ALS69


title: RRBS, ALS, ALS74

value: female


title: liver-10% fat+fiber-C57BL/6J-M (ORSAM8957)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8957

value: liver


title: S_ME18


title: MIBC4,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy


title: S_ME17


title: RRBS, ALS, ALS61

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


title: liver-44% fat+fiber-C57BL/6J-F (ORSAM8956)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8956

value: Female


title: DRIP, ALS, K485

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 instrument (at the EMBL Genomics Core Facility, Heidelberg) in the 2x125 paired-end sequencing mode.
DRIP-seq reads were aligned to the GRCh38 reference sequence using bowtie2 v2.3.5.1 (default parameters).
Alignments were filtered using samtools v1.10 keeping only primary alignments of properly paired reads that had >30 mapping quality score. PCR and optical duplicates were also filtered out. (Parameters: samtools view -q30 -f3 -F3840.)
RPKM normalized coverage (bigwig) files have been generated with 100bp resolution using bamCoverage v3.5.1 (--normalizeUsing RPKM --binSize 100 --smoothLength 300).
Assembly: hg38
Supplementary files format and content: bigwig files (DRIP coverage)

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.
DNA-RNA Immunoprecipitation (DRIP) sequencing was started by blocking and coating magnetic beads (Dynal protein G). 2x50 μL of protein G beads were washed with 3x 1 ml of 5 mg/ml PBS/1mM EDTA/1% BSA solution using a MagnaRack. To the beads, we added 500 µl of 5 mg/ml PBS/1mM EDTA/1% BSA solution and 25 μg of the RNA-DNA hybrid-specific S9.6 monoclonal antibody. The mixture was incubated for 4 hours with rotation at 4°C in a cold room and then washed with 1 ml of PBS/1mM EDTA/1% BSA twice. For immunoprecipitation, we diluted each sample to 700 µl with ChIP lysis Buffer (50 mM Hepes/KOH pH 7,5, 0,14 M NaCl, 5 mM EDTA, 1% Triton X-100, 0,1 % Na-Deoxycholate). We mixed 200 μL of the sample with 500 μL of ChIP lysis Buffer and added 2 x 700 µl of this mixture to 50 µl of S9.6-coated beads. After incubating overnight at 4°C with rotation, we performed a series of washing steps using different buffers as described (Halász et al. 2017, PMID: 28341774). Finally, the DNA was eluted from the beads by adding 100 µl of IP Elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS), vortexing every 2 minutes, and incubating in a thermomixer for 15 minutes at 65°C. We then used a MagnaRack to separate the supernatant and pipetted it into a new low-binding tube. To further purify the DNA, we conducted a PCR clean-up using the NTB M&N kit, eluting the DNA in 3x 100 μL of H2O (pH >7). Before NGS library preparation, we performed further fragmentation through sonication in a 1.5 ml low-bind tube (300 μl sample) using a Bioruptor (Diagenode) with 2 x 4 cycles of 30 seconds ON/OFF at LOW settings. Finally, we concentrated the samples to 30 μL using a speed vacuum concentrator and measured the concentration using the Qubit dsDNA HS Assay Kit. NGS library preparation and sequencing was performed as described (Karányi et al. 2022, PMID: 36030240; Feró et al. 2023, PMID: 37286661) using the Illumina TruSeq ChIP Sample Preparation protocol.


title: S_ME16


title: MIBC7,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells

value: chemoradiation


title: liver-10% fat+fiber-CAST/EiJ-M (ORSAM8964)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8964

value: CAST/EiJ


title: MIBC3,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: RRBS, ALS, ALS75

value: blood

value: ALS


title: DRIP, ALS, K039


title: liver-44% fat+fiber-NZO/HlLtJ-M (ORSAM8122)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8122

value: 44% fat + fiber

value: NZO/HlLtJ


title: MIBC6,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: liver-44% fat+fiber-NZO/HlLtJ-M (ORSAM8121)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8121

value: Male

value: WT


title: MIBC5,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: S_ME15

value: Periapical lesion

value: male


title: S_ME14


title: DRIP, ALS, ALS76

value: lower and upper limb, bulbar not present


title: liver-10% fat+fiber-NZO/HlLtJ-F (ORSAM8120)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8120

value: 10% fat + fiber


title: DRIP, ALS, ALS81

value: female

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


title: MIBC2,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy

value: Low total immune cells


title: S_MC20

value: 14d after pulp exposure, cre-control strain


title: liver-10% fat+fiber-CAST/EiJ-M (ORSAM8118)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8118

value: liver


title: DRIP, ALS, ALS75


title: liver-10% fat+fiber-C57BL/6J-F (ORSAM8955)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8955

value: Female


title: liver-10% fat+fiber-NZO/HlLtJ-F (ORSAM8119)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8119


title: S_MC29

value: 7d after pulp exposure, cre-control strain


title: MIBC1,Low total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: chemoradiation


title: S_MC17


title: DRIP, ALS, ALS61

value: blood

value: ALS

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


title: liver-10% fat+fiber-CAST/EiJ-F (ORSAM8115)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8115

value: CAST/EiJ

value: WT


title: MIBC1,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: High total immune cells


title: S_MC27

value: Periapical lesion

value: male


title: liver-44% fat+fiber-CAST/EiJ-F (ORSAM8114)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8114

value: 44% fat + fiber


title: DRIP, ALS, ALS74

value: female

value: lower and upper limb, bulbar not present


title: MIBC4,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

value: muscle invasive bladder cancer biopsy


title: S_MC16

value: 14d after pulp exposure, cre-control strain


title: DRIP, ALS, ALS69

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


title: MeDIP_Normal Sample 2

city: Teliyarganj, Prayagraj

first: Priyanka

last: Gautam

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

institute: Motilal Nehru National Institute of Technology

data_processing:
Low quality sequences and adaptor sequences were trimmed using Trimmomatic [v0.35].
Alingment of trimmed sequences to GrCh37.were performed using BWA-Mem tool.
Further alignment files were converted into BAM file through samtools (V1.6).
For the analysis of methylated genomic region, differential expression analysis was performed using diffReps (v 1.55.6).
Supplementary files format and content: read counts

source_name: Normal Ovary Tissue

extract_protocol:
Genomic DNA was extracted using the proteinase K & phenol-chloroform method. The tissue samples (10-30mg) were homogenized in 2 ml of SET buffer followed by centrifugation. The supernatant was completely removed & the pellet was lysed with 1 ml lysis buffer and was subjected to Proteinase K digestion at 37 °C for 12h. The mixture was afterward treated with phenol: chloroform: isoamyl alcohol (25:24:1) and centrifuged at 25 °C. Next, DNA was precipitated with 1/30 volume of 3 M sodium acetate (pH 5.0) and two volumes of chilled absolute ethanol and washed with 70% ethanol. Finally, the DNA pellet was re-suspended in TE buffer and stored at 4°C for further use.
For MeDIP sequencing, sequencing librabries were prepared using MagMeDIP kit following manufacturer's protocol.

value: Normal Ovary Tissue

tag: tumor stage

value: Female

tag: histology

value: Normal


title: S_ME9


title: T24, shDLGAP5-1 (1)

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing: processed data for each sample

source_name: bladder

growth_protocol: T24 bladder cancer cells were maintained in RPM 1640 supplemented with 10% fetal bovine serum and antibiotics in humidified with 5% CO2 at 37 ℃

extract_protocol:
RNA was harvested using Magen's R4111-03 HiPure Mini Kit. 1.0 ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMRTER mRNA-seq Library Pre Kit following manufacturer’s protocols.

value: bladder

tag: cell line

tag: cell type

value: bladder cancer cells


title: MeDIP_Normal Sample 1

tag: age

tag: Sex


title: MIBC3,High total immune cells

description: Cofactor Genomics ImmunoPrism assay

source_name: muscle invasive bladder cancer biopsy

value: chemoradiation


title: S_MC24

value: 0hr/pre-exposure, cre-control strain


title: MIBC2,High total immune cells

description: Cofactor Genomics ImmunoPrism assay


title: DRIP, ALS, ALS62

value: blood

tag: patient code

value: ALS


title: S_MC28

value: Periapical lesion

value: 7d after pulp exposure, cre-control strain


title: liver-44% fat+fiber-CAST/EiJ-M (ORSAM8117)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8117

value: liver

tag: diet

value: 44% fat + fiber

value: CAST/EiJ

value: Male

value: WT


title: MeDIP_Tumor Sample 4

source_name: Cancerous Ovarian Tissue

value: Cancerous Ovarian Tissue

value: III

value: Serous


title: MeDIP_Benign Sample 1

source_name: Benign Ovary Tissue

value: Benign Ovary Tissue

value: I

value: Female

value: Benign


title: T24, shDLGAP5-1 (3)

value: bladder

value: bladder cancer cells


title: liver-10% fat+fiber-C57BL/6J-F (ORSAM8110)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8110

value: 10% fat + fiber


title: MeDIP_Normal Sample 3

value: Normal Ovary Tissue

value: Normal


title: liver-44% fat+fiber-C57BL/6J-M (ORSAM8111)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8111

value: liver


title: S_MC23

value: Periapical lesion

value: male

value: 0hr/pre-exposure, cre-control strain


title: T24, shDLGAP5-1 (2)


title: liver-10% fat+fiber-C57BL/6J-M (ORSAM8112)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8112

value: Male

value: WT


title: MeDIP_Tumor Sample 2

value: Cancerous Ovarian Tissue


title: liver-44% fat+fiber-CAST/EiJ-F (ORSAM8113)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8113

value: 44% fat + fiber

value: CAST/EiJ


title: S_MC26

value: 7d after pulp exposure, cre-control strain


title: S_MC25


title: SK-OV-3 cells, doxorubicin 300 nM + IN10018 3 μM treatment, 24 hours, rep2

city: Shanghai

first: Baoyuan

last: Zhang

state: Please Select

address: No.197,Rui Jin Er Road,Shanghai 200025 China

institute: Ruijin hospital

data_processing:
Tophat, cufflinks, and cuffdiff
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped to hg38 using Tophat
Read count extraction and normalization were performed using cufflinks and cuffdiff package
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: ovarian

extract_protocol:
Transcriptome profiling was performed to determine the mechanism of the observed clinical antitumor effects. In brief, the SK-OV-3 cells were treated with DMSO, 300 nM doxorubicin, 3 μM IN10018, and a combination of IN10018 and doxorubicin for 24 hours. The total mRNA was extracted for the RNA sequencing.
RNA was harvested using RNA iso plus reagent (Takara). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: ovarian

value: cancer cells

value: diploid

value: doxorubicin 300 nM + IN10018 3 μM


title: MeDIP_Tumor Sample 1

value: II

value: Female

value: Serous


title: liver-44% fat+fiber-C57BL/6J-F (ORSAM8107)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8107

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

value: liver


title: liver-44% fat+fiber-NZO/HlLtJ-M (ORSAM7700)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7700

value: NZO/HlLtJ


title: T24, shNC-1 (3)

value: bladder

value: bladder cancer cells


title: liver-44% fat+fiber-NZO/HlLtJ-M (ORSAM7699)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7699

value: Male


title: T24, shNC-1 (2)

value: WT


title: T24, shNC-1 (1)


title: liver-10% fat+fiber-NZO/HlLtJ-M (ORSAM7697)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7697

value: 10% fat + fiber


title: SK-OV-3 cells, IN10018 3 μM treatment, 24 hours, rep1


title: liver-10% fat+fiber-C57BL/6J-F (ORSAM8109)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8109


title: MeDIP_Tumor Sample 3

value: Cancerous Ovarian Tissue

value: IV


title: SK-OV-3 cells, doxorubicin 300 nM + IN10018 3 μM treatment, 24 hours, rep3


title: SK-OV-3 cells, doxorubicin 300 nM + IN10018 3 μM treatment, 24 hours, rep1


title: DHMC50

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

data_processing:
Quality control for raw single-end RNA-seq data was checked using FastQC v0.11.8
Reads were trimmed of polyA sequences and low-quality bases using Cutadapt v2.4
Reads were aligned to the human pre-mRNA genome GRCh38 with STAR v2.7.7a
Counts per gene were estimated using the htseq-count function in the HTseq software v0.11.2
Assembly: GRCh38
Supplementary files format and content: Count files in .csv file

source_name: brain

extract_protocol:
RNA was isolated following the RNeasy Plus kit
ibraries for bulk RNA-seq were prepared following the Takara Pico v3 low-input protocol

value: brain

tag: tumor type

value: non-tumor

value: F

tag: age at_diagnosis

value: untreated


title: DHMC51


title: liver-44% fat+fiber-CAST/EiJ-M (ORSAM8116)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8116

value: 44% fat + fiber

value: CAST/EiJ


title: liver-44% fat+fiber-C57BL/6J-F (ORSAM8108)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8108

value: Female


title: liver-44% fat+fiber-NZO/HlLtJ-F (ORSAM7696)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7696


title: DHMC36

source_name: brain tumor

value: brain tumor

value: Embryonal


title: Quadriceps, VDR, ChIP

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Alignment information for each read is stored in the BAM format.
Only reads that passed Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis; duplicate reads (“PCR duplicates”) were removed
Peak calling was performed using MACS2 (Zhang et al., Genome Biology 2008, 9:R137).
Motif analysis was performed on regions of 200 bp surrounding the summit of the top 2,500 peaks based on MACS2 p-values using HOMER (PMID: 20513432)
Assembly: hg38
Supplementary files format and content: BW

source_name: Skeletal muscle

extract_protocol:
Samples from the healthy limb and pre-surgery time point in the injured limb were not assessed due to insufficient chromatin to complete analysis consequent to low VDR expression in these samples. Briefly, crosslinked chromatin was incubated with 30 μL of VDR antibodies (sc-1008, Santa Cruz Biotechnology, Inc. Dallas, Texas) and immunoprecipitated. Purified DNA (20 μg) was prepared for sequencing using the ChIP-IT® ChIP-seq kit (Active Motif, Carlsbad, CA).
Libraries were sequenced on an Illumina NextSeq 500 (75-nt single-end). Reads were mapped to the GRCh38 genome using BWA with default settings

value: Skeletal muscle

value: 1 week post-ACLR

tag: chip antibody

value: sc-1008, Santa Cruz


title: SK-OV-3 cells, DMSO treatment, 24 hours, rep3

tag: tissue

value: ovarian

value: cancer cells

value: diploid

value: DMSO


title: liver-44% fat+fiber-NZO/HlLtJ-F (ORSAM7695)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7695

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

value: liver

value: NZO/HlLtJ

tag: genotype

value: WT


title: SK-OV-3 cells, doxorubicin 300 nM treatment, 24 hours, rep2

value: doxorubicin 300 nM


title: SK-OV-3 cells, IN10018 3 μM treatment, 24 hours, rep3


title: Quadriceps, input


title: liver-10% fat+fiber-NZO/HlLtJ-M (ORSAM7698)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7698

value: 10% fat + fiber

tag: strain

value: Male


title: liver-10% fat+fiber-NZO/HlLtJ-F (ORSAM7693)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7693

tag: treatment


title: SK-OV-3 cells, IN10018 3 μM treatment, 24 hours, rep2


title: DHMC32

value: Glioneuronal/Neuronal

value: M

value: untreated


title: liver-10% fat+fiber-CAST/EiJ-M (ORSAM7691)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7691

value: CAST/EiJ


title: SK-OV-3 cells, doxorubicin 300 nM treatment, 24 hours, rep3


title: DHMC34

value: brain tumor

value: Ependymoma

value: F


title: DHMC33

value: Embryonal


title: SK-OV-3 cells, DMSO treatment, 24 hours, rep2

value: ovarian

value: cancer cells


title: T5

city: Changsha

first: Pengfei

address: Xiangya Road 87

institute: Xiangya Hospital, Central South University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore and data quality was checked by FastQC (v0.11.2).
Clean reads were aligned to the referance genome using STAR.
Read count extraction and normalization were performed using using StringTie.
Differentially expression genes(DEGs) were determined by DEGseq2.
Assembly: GRCh38
Supplementary files format and content: mRNA_processed data.xlsx
Supplementary files format and content: circRNA_processed data.xlsx
Supplementary files format and content: lncRNA_processed_data.xls

source_name: nasal

extract_protocol:
The abstraction of total RNA was isolated from the frozen tissues by TRIzol (LifeTechnology,USA) following the manufacturer's instructions. The tissue samples were placed in 2ml RNA-free EP tube and ground with four 4mm steel balls in TissueLyser LT (QIAGEN, Dusseldorf, Germany). The purity and quality of the isolated RNA of each sample were assessed by measuring the OD260/280 ratio, with values ranging from 1.8-2.1 being considered acceptable.
RNA deep sequencing was carried out by Genergy (Shanghai,China), using a total of 2ug RNA to synthesize the first strand of cDNA, according to Promega GoScript’s protocol (Promega,USA). Strand-specific RNA-seq Libraries were generated with TruSeq® RNA LT Sample Prep Kit v2 (Illumina, CA, USA) following the guidelines. The Ribo-Zero Gold kit (Illumina, CA, USA) was used to remove rRNA, and the remaining RNA fragments was used to synthesize double-stranded cDNA. The double-stranded cDNA products were then end-repaired, added A-tailed and ligated to adaptors. Finally, PCR amplification was performed to enrich cDNA libraries, and the quality of libraries was controlled by Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technology, MA, USA). Sequencing was performed on an Illumina Hiseq 2500 instrument (Illumina, CA, USA) with the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, CA, USA).

value: nasal

tag: disease state

value: NPC


title: DHMC27


title: T4


title: T6


title: liver-10% fat+fiber-C57BL/6J-M (ORSAM7687)

city: Bar Harbor

first: Gary

address: 600 Main St

institute: The Jackson Laboratory

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7687

value: liver


title: liver-44% fat+fiber-CAST/EiJ-M (ORSAM7692)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7692

value: 44% fat + fiber

value: WT


title: SK-OV-3 cells, DMSO treatment, 24 hours, rep1

value: diploid

value: DMSO


title: T1


title: DHMC31

value: Astrocytoma


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-M (ORSAM9029)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9029

source_name: gastrocnemius muscle

value: gastrocnemius muscle

value: 10% fat + fiber

value: NZO/HlLtJ

value: Male


title: Control7

value: healthy


title: T7


title: gastrocnemius muscle-10% fat+fiber-NZO/HlLtJ-M (ORSAM9028)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9028


title: DHMC30

value: brain tumor

value: Ependymoma

value: M

value: untreated


title: liver-44% fat+fiber-C57BL/6J-F (ORSAM7686)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7686

value: Female


title: Control6

value: nasal


title: DHMC23

value: F


title: liver-10% fat+fiber-C57BL/6J-F (ORSAM7685)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7685

value: liver


title: Control5


title: DHMC25

value: Embryonal


title: DHMC29


title: DHMC28

value: Glioneuronal/Neuronal


title: Control4


title: DHMC26


title: T3

value: NPC


title: T2


title: liver-44% fat+fiber-CAST/EiJ-F (ORSAM7690)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7690

value: 44% fat + fiber

value: CAST/EiJ

value: WT


title: Control3


title: DHMC19


title: Control2


title: DHMC24


title: liver-44% fat+fiber-C57BL/6J-M (ORSAM7688)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM7688


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-F (ORSAM9026)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9026

value: gastrocnemius muscle

value: NZO/HlLtJ


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-M (ORSAM9024)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9024

value: 10% fat + fiber

value: Male


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-F (ORSAM9023)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9023


title: gastrocnemius muscle-44% fat+fiber-NZO/HlLtJ-F (ORSAM9027)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9027


title: DHMC22

value: brain tumor

value: Astrocytoma


title: 93 Whole Genome Bisulfite Sequencing 30X

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

data_processing:
Reads were trimmed with Trim Galore 0.6.6
Trimmed reads were aligned to UCSC hg19 and methylation at each base called with Bismark 0.23.0
Methylation call files were subsetted to bedGraph format and then converted to bigWig with UCSC bedGraphToBigWig
Assembly: UCSC hg19

source_name: Patient derived xenograft

growth_protocol: subcutaneous patient derived xenograft as detailed in PMID: 28156002

extract_protocol:
As detailed in PMID: 34312180, followed by bisulfite conversion
TruSeq

value: Patient derived xenograft

value: Bisulfite conversion


title: DHMC17

value: M

value: untreated


title: DHMC21

value: Ependymoma

value: F


title: 78 Whole Genome Bisulfite Sequencing 30X


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-F (ORSAM9021)

last: Churchill

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9021

value: Female


title: gastrocnemius muscle-44% fat+fiber-CAST/EiJ-M (ORSAM9025)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9025


title: gastrocnemius muscle-44% fat+fiber-C57BL/6J-M (ORSAM9020)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9020


title: DHMC20

value: Embryonal


title: 77 Whole Genome Bisulfite Sequencing 30X


title: Control1

value: nasal

value: healthy


title: DHMC18


title: gastrocnemius muscle-10% fat+fiber-CAST/EiJ-F (ORSAM9022)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9022

value: CAST/EiJ

value: WT


title: DHMC16

value: Glioneuronal/Neuronal


title: 208-1 Whole Genome Bisulfite Sequencing 30X


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-M (ORSAM9017)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9017

value: gastrocnemius muscle

value: 10% fat + fiber


title: DHMC12

value: brain tumor


title: DHMC13


title: 173-1 Whole Genome Bisulfite Sequencing 30X


title: DHMC15


title: Human Embryonic Kidney cells 293, clone 174

city: Fukuoka

first: Ikumi

last: Imamura

address: 2-3-1 Matsukadai Higashi-ku

department: Life sience

institute: Kyushu sangyo university

data_processing:
The libraries was subjected to sequencing using the DNBSEQ-G400 (MGISEQ-2000RS, MGI Tech) instrument.
The obtained reads were aligned using splitBarcode (https://github.com/MGI-tech-bioinformatics/splitBarcode).
The read data were downsized to 20 M read pairs using seqkit v0.13.0.
The adopter sequences were cleaned with cutadapt ver.2.10, the read data were mapped with HISAT v2.2.1.
The value of FPKMs (reads per kilobase of transcript per million reads mapped) of each gene was estimated with Cuffdiff v2.2.1.
The ratios of the FPKM values for each cell line to those for HEK293 cells were calculated, and then, the ratios of each genes were log2-transformed.
Assembly: hg19
Supplementary files format and content: FPKMs
Supplementary files format and content: The ratios of the FPKM values for each cell line to those for HEK293 cells were calculated, and then, the ratios of each genes were log2-transformed.

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
The DNA libraries for sequencing were constructed with Truseq Stranded mRNA Library Prep (Illumina,  San Diego, CA) and MGIEasy Universal Library Conversion Kit (MGI Tech, Shenzhen, PRC).

treatment_protocol: genome editing to introduce the vector into cells, 1.0 × 10^6 cells were pre-seeded and cultured at 37°C for 24 hr, and after the vector (1.2 μg) was introduced into the cells using a Lipofectamine 3000 Transfection kit (Thermo Fisher Scientific), the cells were cultured for 3 days.

value: Human Embryonic Kidney cells

value: partial KANK1-KO

value: genome editing


title: gastrocnemius muscle-10% fat+fiber-C57BL/6J-M (ORSAM9018)

description:
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM9018

value: Male


title: 176 Whole Genome Bisulfite Sequencing 30X

value: Patient derived xenograft

value: Bisulfite conversion


title: Human Embryonic Kidney cells 293, clone 114