title: CML LSC from BL/6 (WT) rep2

description: CML LSC isolated from bone marrow of BL/6 (WT) rep2

value: post natal week 8


title: Whole Embryo - Solvent Violet 47 - 23µM - R2

status: Public on Feb 07 2021

type: SRA

city: Vicksburg

first: Natalia

last: Garcia-Reyero

state: MS

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

country: USA

institute: U.S. Army Corps of Engineers

description:
1637-NV-1_5-AGCGATAG-GGCTCTGA_S271
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

library_source: transcriptomic

data_processing:
fastq files were trimmed with Trim Galore v.0.6.5
trimmedreads were quantified using Salmon v.1.1.0 with default settings for paired-end reads in selective alignment mode and aligned against version 97 of the danio rerio reference genome GRCz11
Salmon output was summarized to genes using tximport v.1.1.4.2 in R. Ensembl gene ids were called from the org.Dr.eg.db v. 3.10.0 package in R.
Normalization factors were calculated using calcNormFactors in edgeR
Differentially expressed genes (>=1.5 fold and < 0.05 FDR) were identified by quasi-likelihood negative binomial generalized linear model with edgeR v.3.28.1.
Genome_build: version 97 of zebrafish reference genome GRCz11
Supplementary_files_format_and_content: raw counts for all samples from tximport are in rawcounts.txt. Dye-specific txt files contain log2 counts per million (CPM) values for each sample
rawcounts.txt: raw counts from salmon, read by tximport
DisperseRed9_log2cpm.txt: log2 cpms for disperse red 9 samples
DisperseBlue14_log2cpm.txt: log2 cpms for disperse blue 14 samples
SolventViolet47_log2cpm.txt: log2 cpms for solvent violet 47 samples
SolventRed169_log2cpm.txt: log2 cpms for solvent red 169 samples
SolventYellow33_log2cpm.txt: log2 cpms for solvent yellow 33 samples

molecule: total RNA

organism: Danio rerio

source_name: Whole Embryo - Solvent Violet 47 - 23µM

growth_protocol: Adult 5D zebrafish begin spawning at 7am, and embryos are collected within the first two hours of spawning. The most healthy, fertilized embryos are selected for dechorionation. They were then loaded into 96-well round bottom plates filled with 100uL of embryo media, and the Bioprinter was used to add chemicals to make their final concentrations

extract_protocol:
Direct-zol RNA miniprep kit (Zymo research)
RNASeq libraries were prepared using 200 ng of total RNA and the NEBNext® Ultra™ II RNA Library Prep  (NEB, Cat: E7765S) per manufacturer’s instructions, with mRNA enriched via poly-A-selection using oligoDT beads.

treatment_protocol: Embryos were collected for RNA isolation at 48hpf to and to evade the eventual death of the embryos and to assess embryos during a time when significant gene changes may be occurring due to chemical exposure

tag: strain

value: SPF 5-D

tag: treatment

value: Solvent Violet 47

tag: concentration


title: naive LSK from CD93-/- (KO) rep2

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: naïve LSK isolated from bone marrow of CD93-/- (KO) rep2

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.15 and analyzed using ArrayStar software v.15 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

organism: Mus musculus

source_name: LSK cells

extract_protocol:
Total RNA was extracted from FACS-purified bone marrow BL/6 (WT) or CD93-/- (KO) LSKs and BL/6 (WT) or CD93-/- (KO) LSCs using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified BL/6 and CD93-/- LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 recipients (BL/6 and CD93-/- CML). Upon CML development, LSCs from BL/6 and CD93-/- CML mice were isolated. Naïve LSKs from BL/6 (WT) or CD93-/- (KO) mice were used as controls.

tag: tissue

value: Bone marrow

tag: cell type

value: Bone marrow derived LSKs

tag: age

tag: genotype

tag: disease state

value: naive


title: Whole Embryo - Solvent Red 169 - 50µM - R1

description:
1637-NV-1_6-AGCGATAG-TAATCTTA_S272
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 50µM

value: Solvent Red 169


title: brain, Control rep 5

city: Houston

first: Jian

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FastQC was used to check the read quality
HiSAT2 2.1.0 was used to map the reads to mouse genome (mm10) with transcription annotations (GENCODE vM8 basic).
featureCounts was used to count the gene level reads numbers.
DESeq2 was used to do the differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: edgeR result in Excel format

source_name: brain

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The Rosa26-CreERT2;QkLoxP/LoxP (Qk-Rosa26-iCKO) mice and littermate controls were injected with tamoxifen at postnatal day 1 and their brains were collected at postnatal day 7.

value: brain

value: WT


title: Whole Embryo - Disperse Red 9 - 25µM - R4

description:
1637-NV-1_3-AGCGATAG-CAGGACGT_S269
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 25µM

value: Disperse Red 9


title: brain, Control rep 3


title: Whole Embryo - Disperse Blue 14 - 314µM - R2

description:
1637-NV-1_4-AGCGATAG-CCTATCCT_S270
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 314µM

value: Disperse Blue 14


title: brain, Qk-Rosa26-iCKO rep 2


title: naive LSK from CD93-/- (KO) rep1

description: naïve LSK isolated from bone marrow of CD93-/- (KO) rep1


title: CML LSC from BL/6 (WT) rep1

description: CML LSC isolated from bone marrow of BL/6 (WT) rep1

source_name: CML LSC cells

value: Bone marrow derived LSCs

value: CML


title: Whole Embryo - Disperse Blue 14 - 133µM - R2

description:
1637-NV-1_2-AGCGATAG-ATAGAGGC_S268
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 133µM


title: brain, Control rep 2


title: brain, Control rep 4


title: brain, Control rep2

data_processing:
FastQC was used to check the read quality
HiSAT2 2.1.0 was used to map the reads to mouse genome (mm10) with transcription annotations (GENCODE vM8 basic).
featureCounts was used to count the gene level reads numbers.
DESeq2 was used to do the differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 result in Excel format.

treatment_protocol: The Plp-CreERT2;QkLoxP/LoxP (Qk-Plp-iCKO) mice and littermate controls were injected with tamoxifen at postnatal day 7 and day 8 and their brains were collected at postnatal day 30.


title: Whole Embryo - Solvent Red 169 - 1µM - R1

description:
1637-NV-1_1-AGCGATAG-AGGCGAAG_S267
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 1µM


title: brain, Qk-Rosa26-iCKO rep 3


title: brain, Control rep1


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation - rep1

type: RNA

city: Puławy

first: Paweł

last: Mirosław

address: 57, Partyzantow Avenue

department: Department of Virology

country: Poland

institute: NATIONAL VETERINARY RESEARCH INSTITUTE

description: Infected cell line compared to uninfected cell line after 72h incubation. Biological replication 1. Sample 1.

hyb_protocol: Following fragmentation, 100 µl of solution with fragmented cRNA were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 17 h at 65C. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent SureScan Dx Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: Agilent Feature Extraction Software (version 12.0.3.1) was used for background subtraction and Linear Lowess normalization.

organism: Bos taurus

source_name: bovine kidney cell line

label_protocol: The synthesis of labeled cRNA was carried out using the Low Input Quick Amp Labeling Kit (Agilent Technologies). The reaction mixture contained 0.75 µL of nuclease-free water, 3.2 µL of 5x reaction buffer, 0.6 µL of 0.1 M DTT, 1 µL of NTP mix, 0.21 µL of T7 RNA polymerase, 0.24 µL of Cyanine 3 or Cyanine 5, and 10 µL of cDNA.

growth_protocol: Madin-darby bovine kidney cells (MDBK, ATCC) were cultured in Minimum Essential Medium Eagle (MEM-E, Sigma) containing 10 % foetal calf serum (Gibco) and 1% of antibiotics (Sigma).

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Mini kit following the supplied protocol. The Low Input Quick Amp Labeling Kit (Agilent Technologies) was used for cDNA synthesis at 40°C for 2h.

treatment_protocol: MDBK cells were infected with BVDV strain NADL. RNA were isolated at 24 or 72 hours post-infection. At the same time, RNA was isolated from uninfected cells.

tag: cell line

value: MDBK

tag: virus strain infection

value: Uninfected

tag: incubation time

value: NADL


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation - rep3

description: Infected cell line compared to uninfected cell line after 72h incubation. Biological replication 2. Sample 1.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation - rep2

description: Infected cell line compared to uninfected cell line after 72h incubation. Biological replication 1. Sample 2.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation - rep4

description: Infected cell line compared to uninfected cell line after 72h incubation. Biological replication 2. Sample 2.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation - rep3

description: Infected cell line compared to uninfected cell line after 24h incubation. Biological replication 2. Sample 1.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation - rep2

description: Infected cell line compared to uninfected cell line after 24h incubation. Biological replication 1. Sample 2


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation - rep1

description: Infected cell line compared to uninfected cell line after 24h incubation. Biological replication 1. Sample 1


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation - rep4

description: Infected cell line compared to uninfected cell line after 24h incubation. Biological replication 2. Sample 2.


title: brain, Control rep 1


title: Huh7.5 rep2

city: Guangzhou

first: jinqian

last: li

address: Sun Yat-sen University

country: China

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using 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 (RPKM) 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.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.isoforms.FPKM.txt: Tab-delimited text files include read counts and FPKM values.

organism: Homo sapiens

source_name: Hepatoma carcinoma cell line

extract_protocol:
Huh7.5 cells were infected in duplicate with 1b Con1cc virus. At peak infection (>80% cells were HCV positive, day 7 post infection), total RNA was isolated using TRIzol LS. 1 ug of total RNA was use for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Hepatoma carcinoma cell line


title: Ly6Chi monocytes 14d injury 3

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
Mouse macrophage GRCm38 FASTA and GTF files were downloaded from Ensembl release 98.  The reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0.
Mouse monocyte GRCm38 FASTA and GTF files were downloaded from Ensembl release 100.  The reference database was created using STAR version 2.7.3a with splice junctions optimized for 150 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0.
Counts were filtered to remove features with zero counts or less than 5 reads
PCA analysis and differential gene expression analysis was performed using hciR package, using DESeq2 (version 1.28.1).
Genome_build: mm10, M_musculus_Dec_2011, GRCm38
Supplementary_files_format_and_content: txt file with counts

source_name: lung primary cells

growth_protocol: all animals were eutanized according to IACUC protocol. Lungs were lavaged with ice cold saline solution. This was followed by  perfusion through the heart with saline. Lungs were then incubated in collagenase D for 30 min (37C, 5%CO2), followed by single cell suspension through a 70um strainer.Red blood cells were lyzed, cell counted and cells resuspended in staining buffer for flow cytometric staining and cell sorting. Cells were sorted directly in RLT buffer and frozen until all samples were collected for sequencing.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
Libraries  prepared using the NEBNext Ultra RNA Library Prep Kit for Illumin.  mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR.

treatment_protocol: Single oral gavage treatment with tamoxifen excises neomycin cassette and boosts mutant SPC mutant expression

value: 14d injury

value: monocytes

value: SP-CI73T mutant

value: tamoxifen


title: naive LSK from BL/6 (WT) rep2

description: naïve LSK isolated from bone marrow of BL/6 (WT) rep2

value: Bone marrow

value: Bone marrow derived LSKs

value: post natal week 8


title: MM360

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.33 with arguments -threads 10 input.1.fastq.gz input.2.fastq.gz output.1.trimmed.fastq.gz output.1U.trimmed.fastq.gz output.2.trimmed.fastq.gz output.2U.trimmed.fastq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30
Trimmed and high quality reads were aligned using STAR v2.4.2a on index created using mm10 genome assembly and Encode M19 annotation. Software parameters are as follows STAR --runThreadN 10 --runMode alignReads --genomeDir mm10 --genomeLoad LoadAndKeep --readFilesCommand zcat --outFilterIntronMoti fs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 80000000000 --outFileNamePrefix output.STAR. --readFilesIn output.1.trimmed.fastq.gz output.2.trimmed.fastq.gz
Genome_build: mm10
Supplementary_files_format_and_content: exons.counts.tsv a table containing read counts overlapping exons summarized using featureCounts v1.6.4
Supplementary_files_format_and_content: fold_change_table.tsv a table containing methylated cytosine sites and fold change between comparisons

source_name: adult mouse brain

growth_protocol: They were maintained on a 12-h light/dark cycle and given ad libitum access to food and water. Mutant mice were caged with their wild-type littermates

extract_protocol:
Total RNA was isolated from mouse hypothalami using Qiazol lysis reagent followed by purification with the RNeasy Mini kit (Qiagen) according to manufacturer protocol. Genomic DNA contamination was removed with the DNA-free kit (Ambion) and remaining DNA-free RNA was tested for purity using PCR for genomic locus. Total RNA was tested on the 2100 Bioanalyzer (Agilent Technologies) to ensure a RIN quality higher than 9, and quantified using Nanodrop.
Ribosomal RNA was depleted using the RiboErasemodule (Roche)followed by library preparation using KAPA RNA HyperPrep Kit(Roche)
The libraries were sequenced as 50bp pair-end readsusing Nova-seq Illumina platform.

value: hypothalamus

value: 7 weeks


title: MCF7 replicate 2

city: Boston

first: Songlei

last: Liu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

data_processing:
A human genome reference index was built by STAR 2.5.2b using genome primary assembly (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/GRCh38.primary_assembly.genome.fa.gz) and annotation file (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/gencode.v27.primary_assembly.annotation.gtf.gz) from GENCODE.
Read alignment and quantification were performed using STAR -quantMode GeneCounts.
Genome_build: GRCh38 GENCODE release 27
Supplementary_files_format_and_content: Text file with reads per gene counts from STAR -quantMode GeneCounts

molecule: polyA RNA

source_name: MCF7 cells

extract_protocol:
Cells cultured in 6-well plates were treated with 600 µl TRIzol (ThermoFisher, 15596018) directly on plate. The solution was used for total RNA extraction using Direct-zol RNA MiniPrep Kit (Zymo Research, R2050). RNA amount was quantified using Qubit RNA HS Assay Kit (ThermoFisher, Q32852) and RNA integrity was checked by the presence of 18S and 28S bands on a 2% E-Gel EX Agarose Gel (ThermoFisher, G402002).
1 µg RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) following manufacturer’s instruction on combined usage with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Library QC and sequencing was performed by the Biopolymers Facility at Harvard Medical School.
Stranded poly(A) RNA-seq

value: Mammary gland, breast

value: MCF7 cells

value: Epithelial


title: MM464

value: 6 weeks

value: KO


title: Ly6Chi monocytes 3d injury 4

value: 3d injury


title: Con1cc infected rep2

value: HCV genotype 1b (strain Con1) infection


title: Con1cc infected rep1

value: Hepatoma carcinoma cell line


title: MCF7 replicate 1


title: MM363


title: Ly6Chi monocytes 3d injury 1


title: Ly6Chi monocytes 3d injury 2


title: MM180


title: MBD764


title: Ly6Chi monocytes 14d injury 1

value: 14d injury


title: endometrial epithelial organoids derived from an unidentified healthy donor 3

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The base quality trimming was performed using fqtrim (v 0.9.4) for phred 30 and minimum read length of 20.
Reference mapping was performed using hisat2 (v 2.0.3).
Counted mapped reads to genes with featureCounts and Ensembl  annotation
edgeR-robust DE analysis with genes filtered at rowSum >1
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts for each gene

source_name: endometrial epithelial cells donor3

growth_protocol: primary human endometrial epithelial cells were cultured in matrigel domes under conventional organoid expansion medium, and variations thereof, for 10 days

extract_protocol:
organoid cells were pelleted and resuspended in 1 ml trizol reagent (invitrogen) and stored at -80. thereafter, tubes were thawed on ice, vigourously vortexed (~2 min) to homogenize before the addition of 200 ul chloroform per tube. tubes were vigourously vortexed and contents passed through 5prime heavy-gel phase-lock tubes (andwin scientific) by centrifugation (14,000 x g for 7 min at 4 degrees c). the supernatant was processed according to the direct-zol rna extraction protocol (zymo research) according to manufacturer instructions.
Libraries were prepared using an Illumina TruSeq mRNA kit (Illumina Inc.).

treatment_protocol: conventional organoid expansion medium (4 days) before n2 supplement replacement with estradiol (2 days) followed by initial culture medium lacking n2 and estradiol (4 days)

tag: culture stage

value: cells isolated from endometrial organoid cultures at their 7th in vitro passage

value: endometrial epithelial cells


title: brain, Qk-Rosa26-iCKO rep 1

value: brain


title: Ly6Chi monocytes control4

value: control

value: monocytes

value: SP-CI73T mutant

value: untreated


title: MBD765

value: hypothalamus

value: WT


title: brain, Qk-Plp-iCKO rep2


title: Ly6Chi monocytes 14d injury 4

value: tamoxifen


title: naive LSK from BL/6 (WT) rep1

description: naïve LSK isolated from bone marrow of BL/6 (WT)

value: Bone marrow

value: Bone marrow derived LSKs

value: post natal week 8

value: naive


title: MBD756

value: 7 weeks


title: brain, Qk-Plp-iCKO rep1


title: S012

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

data_processing:
Basecalling perormed by RTA.
Demultiplexing performed by Bcl2fastq.
Alignment, tagging, gene and transcript counting performed CellRanger.
Aggregation performed by CellRanger.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) cell information (Info.txt)

source_name: Primary liver cancer single-cell

extract_protocol: Single cells prepared from biopsies were captured following the 10x Genomics Single Cell 3’ Reagent Kit v2 user guide. Briefly, single cells were washed and re-suspended in PBS supplemented with 0.04% BSA. Cell numbers was adjusted to 1,200 cells/ul based on cell concentration and viability. Cell suspension was then partitioned into Gel Beads-in-emulsion (GEMs) together with a pool of ~3,500,000 10x Barcodes to index each cell’s transcriptome when they are dissolved during reverse transcription (GEM-RT). First-strand cDNA was purified from the post GEM-RT reaction mixture after GEM generation and barcoding. Purified first-strand cDNA was used as template of 14 cycles of PCR, and PCR products were cleaned up using SPRIselect size selection beads. The cDNA concentration was assessed with a Bioanalyzer (Agilent Technologies). cDNA libraries were prepared following the 10x Genomics Single Cell 3’ Reagent Kit v2 user guide with necessary modifications to the PCR cycles according to the recovered cDNA concentration.

tag: cancer type

value: Hepatocellular carcinoma


title: MBD762

value: 6 weeks


title: Ly6Chi monocytes control2


title: MM362


title: MM361


title: Ly6Chi monocytes 14d injury 2

value: 14d injury


title: S009


title: MBD755


title: PGP1 fibroblasts replicate 2

source_name: PGP1 fibroblasts

value: Skin

value: Fibroblast


title: SigF+CD11b- alveolar macrophages 14d injury 2

value: alveolar macrophages


title: SigF+CD11b- alveolar macrophages 14d injury 1


title: Ly6Chi monocytes 3d injury 3

value: 3d injury

value: monocytes


title: PGP1 fibroblasts replicate 1


title: MM181

value: KO


title: MBD746

value: hypothalamus

value: 12 weeks


title: Huh7.5 rep1

value: Hepatoma carcinoma cell line

value: Uninfected


title: endometrial epithelial organoids derived from an unidentified healthy donor 2

source_name: endometrial epithelial cells donor2

value: cells isolated from endometrial organoid cultures at their 9th in vitro passage

value: endometrial epithelial cells


title: SigF+CD11b- alveolar macrophages 3d injury 3

value: SP-CI73T mutant

value: tamoxifen


title: S006

value: Hepatocellular carcinoma


title: endometrial epithelial organoids derived from an unidentified healthy donor 1

source_name: endometrial epithelial cells donor1

value: cells isolated from endometrial organoid cultures at their 12th in vitro passage


title: MBD763

value: 6 weeks

value: WT


title: S005


title: MBD743


title: S013


title: Ly6Chi monocytes control3

value: control

value: untreated


title: MBD731

value: 15 weeks


title: S011


title: S004


title: Ly6Chi monocytes control1

value: monocytes


title: SigF+CD11b- alveolar macrophages control3

value: alveolar macrophages


title: Sox2_ChIPseq_day3_induction_OSKM

first: Chen

last: yanpu

state: guangdong

address: Kaiyuan No. 190, Luogang district

department: drug discovery pipelines

institute: Guangzhou Institute of Biomedicine and Health

description:
Sox2 binding
sox2_in_oct4_rmdup_sort.bed

library_source: genomic

data_processing:
ChIP-seq reads were mapped to mouse genome (mm10) using Bowtie2 with the alignment parameter settings ‘end-to-end’ and ‘very-sensitive’. Samtools was used to filter for reads with mapping quality > 30 (samtools view q=30) and duplicated reads were removed using samtools rmdup to account for PCR bias.
Peaks were called in MACS2 software with options callpeak, mfold of 6, 60 and bandwidth of 300 (Zhang et al., 2008) with input control.
HOMER peak calling, first the tag directories were created for individual read.sam files with makeTagDirectory and then for peak calling the following command was used, findPeaks ChIPtagDir -style factor -o HOMERpeaks/peaks.txt -i tagDir_input -gsize 2726933925 -F 0 -L 0 -C 0. Called peaks were converted from text to bed format using pos2bed.pl option.
Dfilter peak calling was done using following command run_dfilter.sh -d=ChIP.bed -c=input.bed -f=bed -pe -o= dfilterpeaks.bed -ks=10 -lpval=6 -tagsize=250 -nonzero –refine.
Summits with distances <500 bp were merged using bedtools merge (Quinlan and Hall, 2010) and the midpoint of the merged region was kept. A unique ID with individual TF name was provided to each peak.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using genomeCoverageBed and bedGraphToBigWig

molecule: genomic DNA

source_name: reprogramming intermediate after 3days of induction

growth_protocol: OG2 MEF cells (60-70 x 10^6 cells per sample) P3 were transduced with ePOU/SKM and Oct4/SKM cocktails twice respectively, and cultured in mES medium with 50μg/ml VC, then collect cells were collected after 3 day3 of cuturing.

extract_protocol:
Cells were resuspended in PBS at a density of 5 x 10^5/ml and then chemically crosslinked by the addition of 1% formaldehyde for 10 min at room temperature with gentle rotation. Crosslinking was stopped by the addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with 10 ml cold PBS and lysed in 10 ml lysis Buffer 1 (150 mM NaCl, 0.5% NP40; 1 mM EDTA, 10% glycerol, 0.25% triton-X100) freshly added complete proteinase inhibitor cocktail in 15 ml tubes at 4 °C for 10 min with gentle rocking. The lysate was centrifuged for 10 min at 1350 x g at 4°C. The supernatant was discarded and the pellet was resuspended in 10 ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor) incubated at 4°C for 10min. The procedure was repeated using 10 ml lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, protease inhibitor) and 10 min rocking at RT. Nuclei were collected by centrifugation and washed twice with sonication buffer (10 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, protease inhibitor) and finally suspended in sonication buffer. Samples were sonicated using a Covaris S220 machine with settings to obtain DNA fragments with a length from 300 to 400 bp using microTUBEs (130 μl) for 5 cycles of 30 sec ON and 60 sec OFF using default settings recommended for microTUBEs. 1/10th volume of 10% Triton-X100 was added and the lysate was centrifuged at high speed (20,000 x g for 10 min at 4°C). 1/10th of the supernatant was stored as input control. ChIP was performed using the IP-Star compacted automated system (Diagenode) using 6 μg ChIP-grade Oct4 (Santa Cruz; # Sc-8628X) and Sox2 (Santa Cruz; #sc-17320X) antibodies with 80 μl protein G Dynabeads with IPure 8 samples 200 μl protocol. The coupling time for beads and antibody was 5 hours followed by incubation with lysate for 15 hours at 4°C. Automated wash steps of 10 minutes at 4°C were performed in the following order: low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), LiCl buffer (500 mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Na-deoxycholate), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse‐crosslinked by overnight incubation at 65°C. Samples were treated with RNaseA (0.2 mg/ml final concentration) at 37°C for 2h followed by proteinase K (0.2 g/ml final conc.) at 55°C for 3 hours. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1) and phase separated using heavy phaselock tubes by centrifugation at 10000 rpm for 10 min at RT and precipitated with 100% ethanol with 20μg/μl glycogen as co-precipitant. The precipitate was washed with 80% ethanol and finally eluted in 20ul water. DNA concentration was determined using Qubit dsDNA HS assay kit (Thermo Fisher Scientific; #Q32851).
The libraries were generated using the Trueseq Nano DNA Lib prep kit (Illumina)

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct6 promoter with transduced reprogramming factors

tag: transgene

value: Oct4, Sox2, Klf4, cMyc

tag: chip antibody

value: anti-Sox2, Santa Cruz(Sc-17320X)


title: MBD761

value: hypothalamus


title: S003


title: MBD732


title: S010

value: Intrahepatic cholangiocarcinoma


title: SigF+CD11b- alveolar macrophages 14d injury 3

value: 14d injury


title: S008


title: S007


title: SigF+CD11b- alveolar macrophages control1

value: SP-CI73T mutant


title: MBD725


title: MBD745

value: 12 weeks


title: MBD744


title: Input_DNA_day3_ePOUSKM

description:
input
input_ePOU_rmdup_sort.bed

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct9 promoter with transduced reprogramming factors

value: ePOU, Sox2, Klf4, cMyc

value: no


title: SigF+CD11b- alveolar macrophages 3d injury 2

value: 3d injury

value: tamoxifen


title: Input_DNA_day3_OSKM

description:
input
input_oct4_rmdup_sort.bed

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct8 promoter with transduced reprogramming factors


title: SigF+CD11b- alveolar macrophages 3d injury 1


title: Sox2_ChIPseq_day3_induction_ePOUSKM

description:
Sox2 binding
sox2_in_ePOU_rmdup_sort.bed

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct7 promoter with transduced reprogramming factors


title: sc_YBrain1_S1

status: Public on Feb 06 2021

city: newberry

first: Shane

middle: A

last: Evans

state: Florida

address: 22806 West Newberry Road

department: Bio Med

institute: Brown University

description: aligned to mm10 cell ranger 2.1.0

data_processing:
Aligned with cell ranger
Read into Seurat Version 3.1.4
Data combined using SC-Transform, DE analysis and clustering done on the RNA-assay.
Genome_build: mm10 for single cell and pre-mRNA mm10 for single nucleus. Pre-mRNA build was created accorindg to 10x genomics website sintructions
Supplementary_files_format_and_content: gz compressed tar files of cell ranger outputs and bam files.

source_name: hippocampus

extract_protocol:
MACS brain dissociation kit for single cell and PURE Nuclei Lysis Buffer with sucrose gradient for single nucleus
10x V2 chemistry for single cell and 10x VDJ chemistry for single nucleus
Droplet Based RNA-sequencing 10x chemistry

value: 4 months

tag: single cell or nucleus

value: single cell

tag: male of female

value: F

tag: 10x chemistry

value: 3 prime V2

tag: mouse id

value: SC Young Mouse 1 and 2

tag: sequencing runs


title: sn_Obrain3

description: aligned to pre-mRNA mm10 cell ranger 3

value: 24 months

value: single nucleus

value: 5 prime VDJ

value: SN Old Mouse 3 and 4


title: sc_OBrain1_S1

description: aligned to mm10 cell ranger 2.1.0

value: SC Old Mouse 1 and 2


title: vector -1 [re-used]

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

description:
V-1_S13_L003
This is duplicated sample record of GSM3629723 for the convenient retrieval of the complete raw data from SRA

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 2500 for Samples 1-5 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the zebrafish genome using STAR (v2.5) RNA-seq aligner with the following parameter “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to genes using featureCounts (from subread v1.5.1) with the following parameters: for Samples 1-5:  “-s 1 –Q 10”, for Samples 6-11, "-p -Q 10".
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw counts

growth_protocol: zebrafish embryos were grow to 3 day post fertilization in embryonic media

extract_protocol:
tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing.
mRNA sequencing library were constructed withSMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.).

treatment_protocol: transgenic zebrafish lines were used to produce embryos. For miR-99 target discovery, transgenic lines expressing miR-99 or a vector control together with a GFP reporter were used.

tag: genotype/variation

value: overexpressing vector

value: neutrophils


title: miR-99-3

description:
99-3_S21_L003
processed data file: rawCounts_miR99.xlsx

value: overexpressing miR-99

tag: cell type


title: sc_Ybrain3_S1

description: aligned to mm10 cell ranger 2.1.0

tag: age

value: SC Young Mouse 3 and 4


title: MBD726

tag: tissue

value: hypothalamus

value: 15 weeks

tag: genotype

value: WT


title: S002

value: Hepatocellular carcinoma


title: Oct4_ChIPseq_day3_induction_ePOUSKM

description:
Oct4 binding
ePOU_rmdup_sort.bed

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct5 promoter with transduced reprogramming factors

value: ePOU, Sox2, Klf4, cMyc

value: anti-Oct4, Santa Cruz(Sc-8628X)


title: SigF+CD11b- alveolar macrophages control2

tag: treatment

value: control

value: alveolar macrophages

tag: strain

value: SP-CI73T mutant

value: untreated


title: Oct4_ChIPseq_day3_induction_OSKM

description:
Oct4 binding
oct4_rmdup_sort.bed

value: mouse embryonic fibroblast (MEF) with GFP transgene driven Oct4 promoter with transduced reprogramming factors

value: Oct4, Sox2, Klf4, cMyc


title: FFPE pituitary tumor_CD [982_16]

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

data_processing:
Unmapped bam files were converted into fastq files with a bamToFastq script from bedtools.
Read mapping to known human miRNAs (according to miRBase release 22) and reads quantification were performed using miRDeep2.14.
Data normalization and differential expression analysis were performed using DESeq2.
Filtration for low-expression miRNAs and miRNAs genes with less than five sequencing reads in at least half of the samples were excluded.
Genome_build: hg18
Supplementary_files_format_and_content: CSV file containg sequencing reads for all of the samples.

source_name: FFPE pituitary tumor_CD

extract_protocol:
RecoverAllTM Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, Waltham, MA, USA)
Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific)

tag: subject status

value: CD

tag: usp8 (1 – mutation; 0 – wild type)

tag: tissue/sample type

value: pituitary tumor sample fixed in formaline

tag: molecule subtype

value: miRNA


title: SigF+CD11b- alveolar macrophages control4


title: miR-99-1

description:
99-1_S19_L003
processed data file: rawCounts_miR99.xlsx

value: overexpressing miR-99

value: neutrophils


title: FFPE pituitary tumor_SCA [9453_15]

source_name: FFPE pituitary tumor_SCA

value: SCA


title: S001

tag: cancer type


title: sn_YBrain1

description: aligned to pre-mRNA mm10 cell ranger 3

value: 4 months

tag: single cell or nucleus

value: single nucleus

value: F

value: 5 prime VDJ

value: SN Young Mouse 1 and 2


title: FFPE pituitary tumor_CD [789_17]


title: sn_Ybrain3

description: aligned to pre-mRNA mm10 cell ranger 3

tag: male of female

value: SN Young Mouse 3 and 4


title: sn_OBrain1

description: aligned to pre-mRNA mm10 cell ranger 3

value: 24 months

tag: 10x chemistry

value: SN Old Mouse 1 and 2


title: sc_Obrain3_S1

description: aligned to mm10 cell ranger 2.1.0

value: single cell

value: 3 prime V2

tag: mouse id

value: SC Old Mouse 3 and 4


title: FFPE pituitary tumor_CD [6917_14]

value: CD


title: FFPE pituitary tumor_CD [6305_17]

value: pituitary tumor sample fixed in formaline


title: FFPE pituitary tumor_CD [6647_17]

value: miRNA


title: vector -3 [re-used]

description:
V-3_S15_L003
This is duplicated sample record of GSM3629725 for the convenient retrieval of the complete raw data from SRA

value: overexpressing vector


title: miR-99-2

description:
99-2_S20_L003
processed data file: rawCounts_miR99.xlsx

value: overexpressing miR-99

value: neutrophils


title: KD_Nap1l2_0d_1

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to Mus_musculus whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

growth_protocol: C3H10T/2 cell was cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGI protocols

treatment_protocol: Non-target control and knockdown Nap1l2 C3H10T1/2 cells with or without osteogenesis induction for 7days

value: embryo

value: knockdown Nap1l2

tag: cell line


title: Ctrl_0d_1

value: Non-target control


title: FFPE pituitary tumor_CD [8324_15]


title: KD_Nap1l2_7d_2

value: knockdown Nap1l2 C3H10T1/2 cells with osteogenesis induction for 7days before harvest


title: FFPE pituitary tumor_SCA [3855_13]

value: SCA


title: FFPE pituitary tumor_CD [9438_15]


title: KD_Nap1l2_0d_2


title: FFPE pituitary tumor_CD [5389_16]


title: KD_Nap1l2_7d_1


title: FFPE pituitary tumor_CD [7337_1_1_16]


title: Ctrl_7d_2

value: osteogenesis induction for 7days


title: Ctrl_7d_1


title: Ctrl_0d_2


title: FFPE pituitary tumor_CD [17226_1_1_15]


title: FFPE pituitary tumor_SCA [17540_15]


title: FFPE pituitary tumor_CD [17225_15]


title: FFPE pituitary tumor_CD [17_14544]


title: FFPE pituitary tumor_SCA [2538_12]


title: FFPE pituitary tumor_CD [19289_1_1_14]


title: 239 Oral

type: other

city: Philadelphia

first: Erle

middle: S

last: Robertson

state: Pennsylvania

address: 3610 Hamilton Walk Johnson Pavilion

department: Department of Otorhinolaryngology

institute: University of Pennsylvania

hyb_protocol: For each PathoChIP array, a Cy3 labeled specimen and a Cy5 labeled reference were combined and hybridized together in constant rotation at 65°C for 12 hours. The slides were then washed and scanned for visualization using an Agilent SureScan G4900DA array scanner.

scan_protocol: Agilent SureScan G4900DA array scanner was used to scan the microarrays.

data_processing:
Agilent Feature Extraction software was used for extraction of the raw green and red signal data from the microarray images captured by the G400DA scanner.
A scale factor, which was inferred from HRP, was set as 0.3 to control the effect from red to green signal. Specifically, we multiply the log2 red signal by the scale factor to get the normalized background signal which was then subtracted from the log2 green signal to get the final normalized data. The normalized value of a probe is called hybridization signal intensity (HSI) which indicates the abundance of the species of the probe in the tested sample.

molecule: other

source_name: Oral tissue

label_protocol: 1μg of the amplified products from the patient and reference genomes were labelled separately with Cy3 and Cy5, respectively (SureTag labeling kit, Agilent Technologies, Santa Clara, CA). All labeled controls and experimental specimens were purified and hybridized to the PathoChIP microarrays

growth_protocol: Reference sample NR52285 was obtained from BEI resource ATCC and 15 patients samples (oropharyngeal and nasopharyngeal swabs) were obtained from Hospital of University of Pennsylvania, eluted in viral transport media (VTM), then heat inactivated at 56°C for 30 minutes prior to transfer to the laboratory where the DNA and RNA were extracted.

extract_protocol: The swab samples and the blank control samples were were micro-centrifuged at 4°C at 15,000rpms for 20 minutes which will collect all cells, virions and other microbial agents eluted in the VTM. The pelleted samples were then resuspended for simultaneous DNA and RNA extraction (AllPrep DNA/RNA FFPE Kit, Qiagen, Hilden, Germany). The quality of extracted nucleic acids was determined by A260/280 measurements. WTA were performed using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma-Aldrich, St. Louis, MO) for each specimen using extracted DNA and RNA.Reference control human DNA and RNA was extracted from the human B cell line, BJAB (obtained from ATCC, Manassas, VA)

value: Oral tissue

tag: gender

value: Male

tag: molecule

value: RNA and DNA

source_name: BJAB

value: BJAB


title: FFPE pituitary tumor_CD [18843_15]


title: 239 Nasal

source_name: Nasal tissue

value: Nasal tissue

tag: age


title: 230 Nasal

tag: tissue


title: 237 Oral

value: Female


title: FFPE pituitary tumor_CD [17_14373]

value: CD

value: pituitary tumor sample fixed in formaline


title: 230 Oral


title: 238 Oral


title: D7_DMSO_B3

city: Singapore

first: Choon Kiat

last: Lim

state: Singapore

address: 14 Medical Drive

department: Medicine

country: Singapore

institute: National University of Singapore

data_processing:
Transcript abundance were quantified with Kallisto v0.43.1 with default settings. Index were generated from GENCODE M13 (GRCm38.p5) fasta file
Expression at transcript level were transformed into length corrected gene expression with tximport
Differential expression analysis was carried out with DESeq2
Genome_build: GENCODE M13 (GRCm38.p5)
Supplementary_files_format_and_content: Differential expression analysis

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were transduced with retroviruses encoding GHMT trasncription factors and grew in StemPro-34 SFM

extract_protocol:
RNA was extracted with Zymo's Direct-zol RNA Miniprep Kit according to manufacturer's protocol
Libraries were constructed with Illumina's TruSeq RNA Library Prep Kit according to manufacturer's protocol

treatment_protocol: Ethanol, DMSO, I-CBP112 or C646 were added to the cells for 7 days and medium was refreshed every 3-4 days

value: Embryo

tag: cell type

value: Fibroblasts

value: 1% DMSO


title: 237 Nasal


title: 245 Nasal/Oral

source_name: Nasal and Oral tissue

value: Nasal and Oral tissue


title: 238 Nasal


title: D7_C646_B3

tag: treatment


title: FFPE pituitary tumor_SCA [17623_16]

value: miRNA


title: FFPE pituitary tumor_CD [18827_15]


title: FFPE pituitary tumor_SCA [17_6307]


title: FFPE pituitary tumor_SCA [19899_15]


title: FFPE pituitary tumor_CD [17_12764]


title: FFPE pituitary tumor_SCA [17_12553]


title: FFPE pituitary tumor_SCA [17_14385]


title: FFPE pituitary tumor_CD [17_11143]


title: FFPE pituitary tumor_SCA [3853_13]


title: D7_DMSO_B2

tag: strain


title: 242 Nasal/Oral


title: 240 Nasal/Oral


title: 247 Nasal/Oral


title: 244 Nasal/Oral


title: 0234 Oral/Nasal

source_name: Oral and Nasal tissue

value: Oral and Nasal tissue


title: FFPE pituitary tumor_CD [16300_1_1_16]

tag: subject status


title: intestinal_organoids_sgc1

city: Shanghai

first: Tang

last: peiyuan

address: Xietu road

institute: Fudan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm9

source_name: intestinal organoids

extract_protocol:
Total RNA from organoids treated with SGC-CBP30 or vehicle was extracted at 36 hours post 8Gy irradiation. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequencing to each sample.

value: intestine

value: 8-12 weeks

tag: genotype

value: wild type


title: intestinal_organoids_sgc2


title: intestinal_organoids_con2

value: vehicle


title: D7_C646_B2


title: FFPE pituitary tumor_SCA [17_14278]

value: SCA

tag: usp8 (1 – mutation; 0 – wild type)

tag: tissue/sample type


title: 242 Oral

value: Oral tissue

value: RNA and DNA


title: 240 Nasal

value: Nasal tissue

value: BJAB


title: 0228 Oral/Nasal

value: Female


title: D7_ICBP112_B3

value: 5 uM I-CBP112


title: D7_ICBP112_B2

value: Embryo


title: 0227 Oral

value: Male


title: FFPE pituitary tumor_CD [16_16294_1_1]

value: CD

value: pituitary tumor sample fixed in formaline

tag: molecule subtype


title: FFPE pituitary tumor_CD [16_15011_1]

value: miRNA


title: D7_Ethanol_B3

value: Fibroblasts

value: 0.1% ethanol


title: Triplets: 70S

city: Camperdown

first: Zac

last: Chatterton

state: Australia

address: 97 Mallet St, ME30K

department: Brain and Mind Centre

country: Australia

institute: The University of Sydney

description:
genomic DNA
Triplets

data_processing:
Paired-end 50bp reads were trimmed to 26bp using fastqutils truncate function for combined analysis with paired-end 26bp reads. Fastq files were processed using cutadapt to trim poor-quality reads (< Q30). A targeted bisulfite reference genome was generated using bismark command bismark_genome_preparation for the fasta file that includes all 35 assay targets and Lambda genome. Trimmed paired-end reads were then mapped to the targeted bisulfite reference genome using bismark (--bowtie2 --non_directional). Stacked DNA methylation calls and coverage ((.CX_report.txt files)  were obtained using bismark_methylation_extractor (-p --comprehensive --merge_non_CpG --cytosine_report --CX).
Count matrix files were produced from raw.fastq files using methylK (https://github.com/zchatt/methylK) (threshold=0.5  read_length=26 signal2noise=5000).

source_name: Triplets

extract_protocol:
Triplets: Dorsolateral prefrontal cortex (DLPFC) and ventral white matter (VWM) were dissected from post-mortem frozen brain tissues from subjects with no diagnosis of any neurodegenerative disease at time of death. Neuronal nuclei were isolated from the DLPFC dissections using methods previously described (Jiang, Matevossian et al. 2008). Briefly, frozen sections of the DLPFC (~100mg) from each subject were homogenized on ice, cells were lysed using a cell lysis buffer, and nuclei were isolated by high-speed centrifugation through a sucrose buffer. Nuclei were immunostained using the Alexa-Fluor conjugated anti-NeuN antibody (Abcam, ab190195) and isolated by FACS (BD FACS-Aria).
Cell-free DNA extraction from plasma or serum was performed using the Analytik Jena PME free-circulating DNA Extraction Kit (845-IR-0003050) using the SE/SBS system only. Bisulfite Conversions were performed using the MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV50).
Libaries were constructed using the Nextera transposase (Tn5) enzyme supplied within Illumina Nextera® DNA Sample Preparation Kit (FC-121-1031).

value: DLPFC

tag: sample name

value: NeuN+

tag: training days

tag: disease state

tag: follow-up months


title: Triplets: 62S

description:
genomic DNA
Triplets


title: 0235 Oral/Nasal

value: Oral and Nasal tissue

tag: cell line


title: D7_Ethanol_B2


title: FFPE pituitary tumor_SCA [16_17015]

value: SCA


title: HIV-1 293T C-siD_Splicing

city: CHAPEL HILL

first: Ann

middle: Lynette

last: Emery

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina At Chapel Hill

data_processing:
separate the 4 primer pair sets into separate files and filter out bad reads
process each primer pair file set using in-house ruby programs from Swanstrom lab (available on request) to measure HIV-1 splicing events
Supplementary_files_format_and_content: splicing events

extract_protocol: Primer ID tagged Illumina paired end sequencing

tag: agent

value: HIV-1 NL4-3

tag: sirna

value: siRNA (siD)

tag: technique

value: splicing assays


title: FFPE pituitary tumor_CD [15644_16]


title: HIV-1 293T CplusD_Splicing

value: overexpressed YTHDC1 (plusD)


title: 242 Nasal

tag: tissue

value: Nasal tissue

tag: gender

value: Female

tag: age

tag: molecule

value: RNA and DNA

value: BJAB


title: 0233 Oral

value: Oral tissue


title: 0232 Nasal

value: Male


title: HIV-1 293T BplusD_Splicing


title: 0233 Nasal


title: 0227 Nasal


title: NR-52285 0.00001ng

type: mixed

organism: Severe acute respiratory syndrome coronavirus 2

source_name: SARS-COV-2 RNA

tag: source

value: Purchased from BEI resource (NR-52285)

value: Total RNA


title: 0232 Oral


title: Triplets: 50S

description:
genomic DNA
Triplets

tag: cell type


title: Triplets: 4S

description:
genomic DNA
Triplets


title: intestinal_organoids_con1

tag: strain

value: intestine

value: 8-12 weeks

tag: genotype

value: wild type

tag: treatment

value: vehicle


title: Triplets: 55S

description:
genomic DNA
Triplets

value: DLPFC

tag: sample name

value: NeuN+


title: HIV-1 293T C-siC_Splicing

value: HIV-1 NL4-3

value: control (siC)


title: HIV-1 293T A-siD_Splicing

value: siRNA (siD)

value: splicing assays


title: FFPE pituitary tumor_SCA [13441_16]

tag: subject status

value: SCA

tag: usp8 (1 – mutation; 0 – wild type)

tag: tissue/sample type

value: pituitary tumor sample fixed in formaline

tag: molecule subtype

value: miRNA


title: HIV-1 293T B-siD_Splicing

tag: agent


title: FFPE pituitary tumor_SCA [12280_13]


title: Triplets: 45S

description:
genomic DNA
Triplets

tag: training days

tag: disease state

tag: follow-up months


title: FFPE pituitary tumor_SCA [1327_16]


title: NR-52285 0.001ng

tag: cell line

value: BJAB

value: RNA and DNA


title: Triplets: 8S

description:
genomic DNA
Triplets

tag: tissue


title: HIV-1 293T B-siC_Splicing

tag: sirna

tag: technique


title: Triplets: 4B

description:
genomic DNA
Triplets

tag: cell type

value: NeuN-


title: NR-52285 0.0001ng

tag: source

value: Purchased from BEI resource (NR-52285)

tag: molecule

value: Total RNA


title: FFPE pituitary tumor_SCA [12693_12]


title: HIV-1 293T AplusD_Splicing

value: overexpressed YTHDC1 (plusD)


title: Triplets: 47S

description:
genomic DNA
Triplets


title: FFPE pituitary tumor_SCA [1250_15]


title: 10x72

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Trunk region of mouse embryo at embryonic day E13.5, excluding the skin, liver and intestine

data_processing:
Sequenced bcl files were converted to fastq files with cellranger 3.0.1
The sequenced 10X libraries from 3 samples were mapped to mm10 mouse genome and assigned to droplets with Cell Ranger software (version 3.0.1) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: h5 datasets with raw gene expression counts

source_name: Mouse embryo - trunk region

extract_protocol:
At embryonic day (E)13.5, mouse embryos were eviscerated, and the trunk region of the embryo was dissected from the skin, liver and intestine. The dissociation of cells was the same as for human fetal cells. Single EGFP+ cells were sorted on a BD Influx FACS equipped with a 140 µm nozzle and a cooling unit with a sample temperature of 4°C and collected into cold HBSS buffer. Collected cells were pelleted and subjected to RNA sequencing library preparation.
On the day of 10x Chromium library preparation the cells were brought to +4°C and centrifuged at 1000 rcf for 10 min at 4°C. Supernatant was carefully removed and 500 uL of rehydration buffer (1X DPBS (Gibco 14190144) containing 1.0% BSA (Sigma, B4287) and 0.5U/?l RNAse Out (ThermoFisher Scientific, 10777019) was added to cell pellet, re-suspended and centrifuged at 1000 rcf for 10 min at 4°C. The wash with rehydration buffer was repeated one more time, after which cells were counted. If a lot of debris was observed during cell count the cell suspension was subjected for FACS to remove debris. After cell count or FACS cells were pelleted again and re-suspended in rehydration buffer to get 700-1200 cells/ul but no less than 50 uL. Library preparation was done in accordance with 10x Genomics Chromium Single Cell 3’ (v3) aiming at recovering 5000-8000 cells at Illumina Novaseq with the help of Eukaryotic Single Cell Genomic Facility, SciLifeLab, Stockholm, Sweden.

treatment_protocol: A lentiviral transfer plasmid was generated by exchanging the PGK1 promoter from LV-GFP57 with a stronger EF1a promoter, and inserting a 30 bp variable sequence into the 3' UTR of GFP (resulting in a library of >5 million unique transcribed barcodes). Lentiviral particles were produced by KI VirusTech at high titer virus (>10^9 TU/ml). Female CD-1 mice age 2-5 month were housed in animal facilities at Karolinska Institute, Sweden. Experimental female mice was placed in time controlled pregnancy and at embryonic day (E) 8.25 (range of injection time 5AM-7:30AM) 46 nl of lentiviral particles was injected into the amniotic fluid using ultrasound-guided nano-injection, as described previously for E9.5 injection. Injection at E8.25 targets skin and neural plate before neurulation, allowing tracing of neural crest derivatives from neural plate to final destinations.

tag: developmental stage, weeks


title: Breachers: 3E04-1-P

description:
genomic DNA
Breachers

source_name: Breachers

extract_protocol:
Breachers: In collaboration with the Walter Reed Army Institute of Research, to investigate the effects of repeated blast wave exposure in explosive entry personnel (Breachers), serum samples were taken from 12 breachers following training days 1,7,8 and 9. Additionally, genomic DNA was extracted from whole blood collected on training days 1 and 10.
Cell-free DNA extraction from plasma or serum was performed using the Analytik Jena PME free-circulating DNA Extraction Kit (845-IR-0003050) using the SE/SBS system only. Bisulfite Conversions were performed using the MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV50).
Libaries were constructed using the Nextera transposase (Tn5) enzyme supplied within Illumina Nextera® DNA Sample Preparation Kit (FC-121-1031).

value: PBMC

tag: sample name


title: FFPE pituitary tumor_SCA [11434_13]

tag: subject status


title: Breachers: 3F04-01-P

description:
genomic DNA
Breachers


title: Triplets: 70B

description:
genomic DNA
Triplets


title: Breachers: 3X01-1-P

description:
genomic DNA
Breachers


title: FFPE pituitary tumor_CD [11141_17]

value: CD

tag: usp8 (1 – mutation; 0 – wild type)


title: HIV-1 293T A-siC_Splicing


title: Breachers: 3F02-01-P

description:
genomic DNA
Breachers


title: Breachers: 3D05-01-P

description:
genomic DNA
Breachers


title: FFPE pituitary tumor_CD [1081_15]

tag: tissue/sample type


title: Breachers: 3E02-01-P

description:
genomic DNA
Breachers


title: FFPE pituitary tumor_SCA [11963_15]

tag: molecule subtype


title: 10x71


title: Triplets: 1B

description:
genomic DNA
Triplets

value: DLPFC


title: Triplets: 13S (2)

description:
genomic DNA
Triplets

value: NeuN+


title: FFPE pituitary tumor_CD [10613_17]


title: 10x70


title: NR-52285 0.1ng


title: Triplets: 10S (2)

description:
genomic DNA
Triplets


title: NR-52285 1ng


title: Breachers: 3C01-1-P

description:
genomic DNA
Breachers


title: Isolated single nuclei from 7 pooled hippocampi of 9-month old P301S/LDLR mice

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.1.0)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.1.0)
barcode processing, Cell Ranger Single Cell Software Suite (v2.1.0)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.1.0)
alignment, Cell Ranger Single Cell Software Suite (v2.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Hippocampi tissue

extract_protocol:
Frozen hippocampi from 7-8 mice of the same genotype were pooled as a single sample. Tissue was homogenized with a Dounce homogenizer in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.005% NP-40 in nuclease free water), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 ℃. Nuclei were washed and filtered twice with Nuclei Wash Buffer (1x PBS with 1.0% BSA and 0.2 U/uL RNasin Ribonuclease Inhibitors (Promega)). Nuclei pellets were resuspended in 500 μl Nuclei Wash Buffer, and mixed with 900 µl Sucrose Cushion Buffer (2.7 mL Nuclei PURE 2M Sucrose Cushion Solution (Sigma-Aldrich, Cat# S9308) + 300 uL Nuclei PURE Sucrose Cushion Solution (Sigma-Aldrich, Cat# S9058)). The 1,400 μl mixture was carefully layered on top of 500 μl Sucrose Cushion Buffer, and centrifuged at 13,000g for 45 min at 4 ℃ to separate the nuclei from cell debris. The nuclei pellet was resuspended in Nuclei Wash Buffer and filtered through a 40-μm FlowMi Cell Strainer (Sigma-Aldrich, Cat# BAH136800040).
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ Reagent Kits as per manufacturer’s instructions (10x Genomics). The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: strain

tag: mouse genotype

value: nuclei of hippocampi


title: FFPE pituitary tumor_CD [10610_17]


title: Isolated single nuclei from 7 pooled hippocampi of 9-month old P301S/EKO mice


title: NR-52285 0.01ng


title: Breachers: 3A05-1-P

description:
genomic DNA
Breachers

tag: training days

tag: disease state


title: Isolated single nuclei from 7 pooled hippocampi of 9-month old EKO mice

value: EKO


title: FFPE pituitary tumor_CD [10447_16]


title: Breachers: 3A04-01-P

description:
genomic DNA
Breachers

tag: follow-up months


title: FFPE pituitary tumor_CD [1_949_15]


title: Breachers: 3D04-1-P

description:
genomic DNA
Breachers

tag: tissue


title: Breachers: 3X01-08-02

description:
cell-free DNA
Breachers
NeuN_cfDNAounts_aggnorm.txt
Cerebellum_cfDNAounts_aggnorm.txt

value: Plasma


title: Isolated single nuclei from 7 pooled hippocampi of 9-month old LDLR mice

value: LDLR


title: BJAB 20ng

source_name: blank control

value: blank control

tag: cell line


title: T2D_Dementia: A2382

description:
cell-free DNA
T2D_Dementia
NeuN_cfDNAounts_aggnorm.txt
Cerebellum_cfDNAounts_aggnorm.txt

extract_protocol:
T2D_Dementia: As part of the Israel Diabetes and Cognitive Decline (IDCD) study whole blood was collected from subjects within serum tubes and stored on ice for a maximum of 6 hours before laboratory processing. The blood tubes were centrifuged (10 minutes, 1,500 rpm) at room temperature. Serum was then pipetted from top and stored at -80C. All subjects were diagnosed with Type 2 diabetes.
Cell-free DNA extraction from plasma or serum was performed using the Analytik Jena PME free-circulating DNA Extraction Kit (845-IR-0003050) using the SE/SBS system only. Bisulfite Conversions were performed using the MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV50).
Libaries were constructed using the Nextera transposase (Tn5) enzyme supplied within Illumina Nextera® DNA Sample Preparation Kit (FC-121-1031).

value: Serum

value: control

value: baseline


title: DNAse_seq-B6xCAST-mESC-BS02277A

city: New York

first: Matthew

middle: T

last: Maurano

state: NY

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

data_processing:
Trimmed to remove low-quality sequence or adapter contamination using the trimmomatic tool (Parameters: TOPHRED33 ILLUMINACLIP: TruSeq3-PE2.fa:2:5:5:1:true MAXINFO:27:0.95 TRAILING:20 MINLEN:27')
Reads were mapped with Burrows-Wheeler Aligner to the mouse reference assembly and the strain-specific genome (Parameters: bwa aln -n 0.04 -l 32 -t 2 -Y)
Alignments were post-processed with a custom Python script using pysam to retain only properly-paired or single-end reads mapping  uniquely to the autosomes and chrX with a mapping quality of at least 20. Paired end reads were required to have an inferred template length of less than 500 bp.
Duplicate reads were flagged on a per-library basis using Samblaster
Mapped tags were converted to BED format using awk and bedops
DNase I hypersensitive sites were identified using hotspot2
Transcript counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: bed.gz file containing DHS hotspots
Supplementary_files_format_and_content: bigWig files indicate DHS density

source_name: mESC

extract_protocol:
Whole liver (all lobes), both kidneys and all lobes of the lungs were rapidly dissected from sacrificed mice. Tissues were minced in 2 mm square pieces and resuspended in 5 mL of homogenization buffer per tissue. Nuclei were released using 5-10 strokes in a Dounce homogenizer with a loose-fitting type-A pestle and the resulting homogenate was filtered through a 120µm filter. Marrow was obtained from femurs of 8 week old female mice. B cells were isolated using an AutoMACS (Miltenyi Biotech) to deplete CD43 and Mac-1/CD11b markers. Nuclei were extracted by resuspending cells in buffer A supplemented with 0.015% detergent (IGEPAL-CA630) (Sigma) and incubating for 5-10 minutes on ice.
Fresh nuclei were digested with DNase I for 3 minutes. Fragments <250 bp were recovered by sucrose ultracentrifugation, end-repaired and ligated with adapters compatible with the Illumina sequencing platform. Libraries were amplified using minimal PCR cycles based on a trial qPCR amplification. Total RNA was isolated using the mirVana miRNA Isolation Kit with phenol (AM1560). Spike-in controls were mixed in (Ambion-ERCC Mix, Cat no. 4456740) and Illumina sequencing libraries were made using the RNA TruSeq Stranded total RNA (Illumina).

value: mESC


title: Breachers: 3A03-01-P

description:
genomic DNA
Breachers


title: Isolated single nuclei from 7 pooled hippocampi of 9-month old WT mice

value: WT


title: Breachers: 3X01-09-02


title: FFPE pituitary tumor_SCA [10611_17]

value: SCA

value: pituitary tumor sample fixed in formaline

value: miRNA


title: Breachers: 3X01-07-02


title: mouse-human-complete-mixing

city: Pasadena

first: Mary

middle: Villanueva

last: Arrastia

state: CA

address: 1200 E California Blvd

department: Chemistry and Chemical Engineering

institute: California Institute of Technology

data_processing:
Library strategy: single-cell SPRITE
Basecalls performed using STAR 2.6.1 using the following parameters: --outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterIntronMotifs None --alignIntronMax 50000 --alignMatesGapMax 1000 --genomeLoad NoSharedMemory --outReadsUnmapped Fastx --alignIntronMin 80 --alignSJDBoverhangMin 5 --sjdbOverhang 100 --limitOutSJcollapsed 10000000 --limitIObufferSize=300000000
SAMtools 1.9 was applied to filter mapped reads, and only uniquely mapped reads (-q 255) were kept.
Alignments that had overlapped a masked region as denoted by Repeatmasker (UCSC, milliDiv < 140) were removed using bedtools (version 2.25.0)
Finally, reads that were aligned to a non-unique region of the genome were removed by excluding alignments that mapped to regions by the ComputeGenomeMask program (read length = 35 nt)
After these filtration steps, all BAM files that corresponded to the same sample but contained different Illumina primers at sequencing were pooled together before cluster identification
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Other (clusters file - all DNA fragments that are tagged with the same 4 barcodes are grouped together by barcode name)

organism:
Homo sapiens
Mus musculus

source_name: mouse embryonic stem cells + human embryonic kidney cells

growth_protocol: Mouse embryonic stem (ES) cell lines were cultured in serum-free 2i/LIF medium and maintained at an exponential growth phase as previously described (Engreitz et al., 2014). HEK293T, a female human embryonic kidney cell line transformed with the SV40 large T antigen was obtained from ATCC (#CRL-1573) and cultured in complete media consisting of DMEM (#11965092, GIBCO, Life Technologies; Carlsbad, CA) supplemented with 10% FBS (Seradigm Premium Grade HI FBS, VWR), 1X penicillin-streptomycin (GIBCO, Life Technologies), 1X MEM non-essential amino acids (GIBCO, Life Technologies), 1 mM sodium pyruvate (GIBCO, Life Technologies) and maintained at 37°C under 5% CO2. For maintenance, 800,000 cells were seeded into 10 mL of complete media every 3-4 d in 10-cm plates.

extract_protocol:
mESC + HEK nuclei (mixed in the same solution) were isolated and permeabilized. In-nuclei restriction digest occurred followed by in-nuclei dA-tailing. 4 rounds of in-nuclei barcoding were performed to uniquely label DNA complexes inside individual nuclei with a cell-specific barcode. Sonication was done to lyse nuclei, and 3 round of DNA-complex barcoding was done to preserve spatial DNA information. After barcoding, DNA complexes were reverse crosslinked and DNA was purified for PCR.
Crosslinked (with 1% formaldehyde, 2mM disuccinimidyl glutarate) chromatin was first digested in-nuclei with HpyCH4V restriction enzyme. DNA complexes in-nuclei were then ligated with a cell-specific DNA barcode by split-and-pooling over a 96 well-plate (where each well contains a unique DNA barcode) over 4 rounds. Nuclei & DNA complexes are then reverse crosslinked, DNA is purified and amplified using Illumina-standard primers. Library is cleaned up by running on a 1% agarose gel, cutting the library between 300-1000 bp, and purifying the library using Zymo's gel clean-up columns. The library is then sequenced with paired-end sequencing.

treatment_protocol: mESCs + HEK were crosslinked together in suspension with 1% formaldehyde and 2 mM disuccinimidyl glutarate

value: Mouse embryonic stem cell line bsps

value: human embryonic kidney cell line HEK293T


title: Isolated single nuclei from 8 pooled hippocampi of 9-month old P301S mice


title: Triplets: 10B (2)

description:
genomic DNA
Triplets

value: DLPFC

value: NeuN-


title: Triplets: 36S

description:
genomic DNA
Triplets

value: NeuN+


title: DNAse_seq-B6xCAST-mESC-BS02283A


title: C9KO rep_2

city: WuHan

first: yang

last: wei

state: HuBei

address: 169#Donghu Nan road, Wuchang Disrict, Wuhan city

department: Medical Research Institute

institute: WuHan university

description:
C9KOB
DSSAOM_9WTvs9KO_compare.txt

data_processing:
Illumina Hiseq X Ten platform for sequencing with 150-bp paired-end reads strategy (Novogene).
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev).
All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read.
Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Genome_build: Mus_musculus_Ensemble_94
Supplementary_files_format_and_content: Tab-delimited text files with FPKM for every gene and every sample.

source_name: Colorectal tumor

extract_protocol:
Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days. The colons were flushed with PBS to clear feces and slit open longitudinally. The distal colon tissues (0.5 cm in length, about 0.5 cm away from the anus) were washed in PBS and homogenized in 2 ml TRIzol (Invitrogen). Colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were AOM/DSS colorectal tumor model. The colorectal tumors were flushed with PBS to clear feces and homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colons

tag: genotype


title: Triplets: 1S

description:
genomic DNA
Triplets

tag: cell type


title: C9KO rep_1

description:
C9KOA
DSSAOM_9WTvs9KO_compare.txt


title: DNAse_seq-B6xCAST-mESC-CTCF-BS03752A

tag: chip antibody

value: CTCF


title: Breachers: 3A02-1-P

description:
genomic DNA
Breachers

value: PBMC


title: Triplets: 13S

description:
genomic DNA
Triplets


title: Breachers: 3F04-08-02

value: Plasma


title: Triplets: 13B

description:
genomic DNA
Triplets


title: PBMCs, RTP 9

city: Hefei

first: Dongyao

state: Anhui

address: No.96, JinZhai Road Baohe District

institute: University of Science and Technology of China

description: ExpressionProfile.txt, column P-29A

data_processing:
Illumina Casava1.7 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 (RPKM) 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.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
PBMC were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Female

tag: age

value: Blood

value: retesting-positive (RTP)

tag: previous severity

value: moderate


title: PBMCs, RTP 10

description: ExpressionProfile.txt, column P-30A


title: Triplets: 10S

description:
genomic DNA
Triplets

tag: sample name


title: PBMCs, RTP 7

description: ExpressionProfile.txt, column P-20A

value: Male


title: Breachers: 3F02-07-02


title: PBMCs, RTP 8

description: ExpressionProfile.txt, column P-25A


title: Triplets: 10B

description:
genomic DNA
Triplets


title: C5KO rep_1

description:
C5KOA
DSSAOM_5WTvs5KO_compare.txt


title: C5KO rep_2

description:
C5KOB
DSSAOM_5WTvs5KO_compare.txt


title: C9WT rep_1

description:
C9WTA
DSSAOM_9WTvs9KO_compare.txt


title: PBMCs, RTP 6

description: ExpressionProfile.txt, column P-19A


title: C9WT rep_2

description:
C9WTB
DSSAOM_9WTvs9KO_compare.txt


title: Breachers: 3F04-09-02


title: Breachers: 3E04-09-02


title: Breachers: 3E04-08-02


title: PBMCs, RTP 5

description: ExpressionProfile.txt, column P-17A


title: NR-52285 0.000001ng

tag: source

value: Purchased from BEI resource (NR-52285)

tag: molecule

value: Total RNA

value: BJAB

value: RNA and DNA


title: C5WT rep_2

description:
C5WTB
DSSAOM_5WTvs5KO_compare.txt


title: Breachers: 3X01-01-02


title: PBMCs, RTP 4

description: ExpressionProfile.txt, column P-15A


title: Breachers: 3F02-09-02


title: Breachers: 3F04-01-02


title: Breachers: 3E04-01-02


title: PBMCs, RTP 3

description: ExpressionProfile.txt, column P-11A


title: Breachers: 3E02-08-02


title: P9KO rep_2

description:
P9KOB
COLITIS_compare.txt

source_name: Colitis


title: Breachers: 3F02-08-02


title: P9KO rep_1

description:
P9KOA
COLITIS_compare.txt


title: PBMCs, RTP 2

description: ExpressionProfile.txt, column P-10A


title: Breachers: 3F02-01-02


title: PBMCs, RTP 1

description: ExpressionProfile.txt, column P-9A


title: P9WT rep_1

description:
P9WTA
COLITIS_compare.txt


title: PBMCs, Convalescent 6

description: ExpressionProfile.txt, column R6

value: convalescent


title: P9WT rep_2

description:
P9WTC
COLITIS_compare.txt


title: Breachers: 3D04-09-02


title: Breachers: 3E02-07-02


title: Breachers: 3E02-09-02


title: PBMCs, Convalescent 5

description: ExpressionProfile.txt, column R5


title: Breachers: 3E02-01-02


title: Breachers: 3D05-09-02


title: P5KO rep_2

description:
P5KOB
COLITIS_compare.txt


title: C5WT rep_1

description:
C5WTA
DSSAOM_5WTvs5KO_compare.txt


title: Breachers: 3F04-07-02


title: P5KO rep_3

description:
P5KOC
COLITIS_compare.txt


title: Breachers: 3D04-07-02


title: Breachers: 3E04-07-02


title: PBMCs, Convalescent 4

description: ExpressionProfile.txt, column R4


title: Breachers: 3D04-08-02


title: Breachers: 3D04-01-02


title: Breachers: 3D05-08-02


title: P5KO rep_1

description:
P5KOA
COLITIS_compare.txt


title: PBMCs, Convalescent 3

description: ExpressionProfile.txt, column R3


title: P5WT rep_2

description:
P5WTB
COLITIS_compare.txt


title: Breachers: 3C01-08-02


title: PBMCs, Convalescent 2

description: ExpressionProfile.txt, column R2


title: Breachers: 3C01-07-02


title: Breachers: 3D05-01-02


title: PBMCs, Convalescent 1

description: ExpressionProfile.txt, column R1


title: Breachers: 3A04-09-02


title: Breachers: 3C01-01-02


title: Breachers: 3A04-08-02


title: PBMCs, Healthy 10

description: ExpressionProfile.txt, column H9

value: healthy


title: Breachers: 3A05-09-02


title: P5WT rep_1

description:
P5WTA
COLITIS_compare.txt


title: PBMCs, Healthy 9

description: ExpressionProfile.txt, column H8


title: Breachers: 3A05-08-02


title: PBMCs, Healthy 7

description: ExpressionProfile.txt, column H6


title: PBMCs, Healthy 8

description: ExpressionProfile.txt, column H7


title: Breachers: 3A04-01-02


title: Breachers: 3A04-07-02


title: 745_R1_001

city: NY

first: Yoshinobu

last: Nakayama

address: 160 Convent Ave

institute: City College of New York

data_processing:
The trimmed reads were mapped to the mus musculus GRCm38 reference genome available on ENSEMBL using STAR ultrafast universal RNA-seq aligner.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The differential expression analysis was performed by DESeq2
The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample

source_name: heart

growth_protocol: In vivo tissues

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep kit, according to the manufacturer’s instructions.

treatment_protocol: MerCreMer, 4-hydroxytamoxifen treatment

tag: background strain

value: conditional knock-in

tag: txnip status

value: Txnip C247S mutant


title: Breachers: 3C01-09-02


title: Breachers: 3A05-07-02


title: Breachers: 3A03-09-02


title: Breachers: 3A05-01-02


title: P5WT rep_3

description:
P5WTC
COLITIS_compare.txt

value: Colons

tag: strain


title: Breachers: 3D05-07-02

tag: training days


title: PBMCs, Healthy 5

last: Wang

description: ExpressionProfile.txt, column H4

tag: disease state


title: PBMCs, Healthy 4

description: ExpressionProfile.txt, column H13


title: Breachers: 3A03-01-02

tag: follow-up months


title: Breachers: 3A03-08-02

tag: tissue


title: 762_R1_001

value: wild-type

value: Txnip WT


title: 747_R1_001


title: 758_R1_001


title: 744_R1_001


title: Breachers: 3A03-07-02

value: Plasma


title: Breachers: 3A02-08-02


title: PBMCs, Healthy 3

description: ExpressionProfile.txt, column H12

value: Female

value: PBMC


title: Breachers: 3A02-09-02


title: PBMCs, Healthy 2

description: ExpressionProfile.txt, column H11

value: Blood


title: WT-C3H10T1-2-H3K14ac

data_processing:
Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the Mus musculus (mm10) genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.0 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: bigwig files were generated using macs2; Scores represent an average read coverage
Supplementary_files_format_and_content: narrowpeak files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD503-02). Briefly, TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55℃. The tagged DNA fragments can be further amplified with two pairs of primers N5 (N5XX) / N7 (N7XX) and P5 / P7 (PCR Primer Mix, PPM).  After adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

treatment_protocol: C3H10T/2 cells were infected with lentivirus carrying Nap1l2 shRNA.

value: embryo

tag: treatment

value: Non-target control

tag: cell line


title: Breachers: 3A02-07-02

tag: cell type


title: PBMCs, Healthy 6

description: ExpressionProfile.txt, column H5


title: PBMCs, Healthy 1

description: ExpressionProfile.txt, column H10

value: Male


title: HCC8

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Illumina bcl2fastq conversion software used for basecalling.
reads were aligned using the STAR (2.5.2b) software.
raw read counts were obtained using htseq-count (HTSeq-0.6.1p12)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from tissues #3, #4, #7 and #8 using TRI-reagent (Molecular Research Center), treated with TURBO DNase (Fisher) and subjected to RNA-seq analysis
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (A cat#FC-122-2101, B cat#FC122-2102)

tag: tissue sample

value: liver (HCC)

tag: chronic infection

value: HBV


title: HCC4


title: Liver7

value: liver (non-malignant)


title: sh-Nap1L2-C3H10T1-2-Input

tag: chip antibody

value: Knockdown Nap1l2


title: WT-C3H10T1-2-Input


title: Breachers: 3A02-01-02


title: Liver3


title: 759_R1_001

tag: genotype


title: MELA31_rep1 T2

status: Public on Feb 05 2021

city: Modena

first: Andrea

last: Cossarizza

state: Modena

address: Via Campi 287

country: Italy

institute: University of Modena and Reggio Emilia

data_processing:
Fastq generation, alignment to the human genome and gene quantification were performed with Generate FASTQ v 1.0.0 and SureCell RNA Single-Cell v 1.1.0 respectively.
The UMI count matrix was used for downstream analysis with Seurat v3 and Monocle2 R packages.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with UMI counts for every gene and every cell

source_name: Peripheral blood mononuclear cell

extract_protocol:
Cryopreserved PBMC were thawed in R10 supplemented with 20 μg/ml DNase I from bovine pancreas (Sigma-Aldrich). After washing with phosphate buffer saline (PBS), cells were stained with the Red Live Dead Fixable Viability kit (ThermoFisher) for 15 min at room temperature. PBMC were washed with PBS and stained with mAb anti-CD3-PE and -CD8-FITC (Biolegend). Viable CD3+, CD8+ T cells were sorted by using eS3 sorter. Cell sorting was performed with 96-99% purity. Cell suspension were then visualized and counted with trypan blue using Bio-Rad T20 Automated Cell Counter to get a precise estimation of total number of sorted cells and of cells concentration. Cells were then pelletted and resuspended in the appropriate volume of cold 1X PBS + 0.1% BSA until reached the final concentration of 3000 cells/μl. Afterwards we loaded about 54.000 cells of each sample into one cartrige of the ddseq system.
Following capture and lysis, cDNA was synthesized and amplified for 15 cycles following the Illumina® Bio-Rad® SureCellTM WTA 3′Library Prep for Peripheral Blood Mononuclear Cells (PBMC) protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following Illumina® Bio-Rad® instruction for read generation, reaching at least 50000 reads as mean reads per cell.

tag: time-point

tag: donor

value: Melanoma patients

value: Not-Responders

value: CD8 T lymphocytes

value: Pembrolizumab


title: MELA31_rep3 T2


title: MELA31_rep4 T2


title: MELA31_rep2 T2


title: MELA30_rep1 T2

value: Nivolumab


title: MELA29_rep4 T2

value: Responders


title: MELA30_rep3 T2


title: MELA29_rep3 T2


title: MELA29_rep2 T2


title: MELA30_rep4 T2


title: MELA30_rep2 T2


title: MELA29_rep1 T2


title: sh-Nap1L2-C3H10T1-2-H3K14ac


title: MELA28_rep4 T2


title: MELA28_rep3 T2


title: MELA28_rep1 T2


title: MELA26_rep1 T2


title: MELA25_rep2 T2


title: MELA25_rep1 T2


title: MELA26_rep2 T2


title: MELA23_rep3 T2


title: MELA20_rep3 T2


title: MELA21_rep4 T2


title: MELA20_rep1 T2


title: MELA23_rep4 T2


title: MELA20_rep2 T2


title: MELA23_rep2 T2


title: MELA21_rep1 T2


title: MELA17_rep4 T2


title: MELA17_rep2 T2


title: MELA16_rep3 T2


title: MELA20_rep4 T2


title: MELA16_rep2 T2


title: MELA13_rep4 T2


title: MELA17_rep1 T2


title: MELA17_rep3 T2


title: MELA11_rep4 T2


title: MELA16_rep1 T2


title: MELA13_rep1 T2


title: MELA13_rep2 T2


title: MELA11_rep2 T2


title: MELA11_rep3 T2


title: MELA11_rep1 T2


title: MELA10_rep4 T2


title: MELA7_rep3 T2


title: MELA10_rep2 T2


title: MELA7_rep1 T2


title: MELA5_rep3 T2


title: MELA5_rep2 T2


title: MELA10_rep1 T2


title: MELA10_rep3 T2


title: MELA7_rep4 T2


title: MELA31_rep4 T1


title: MELA3_rep2 T2


title: MELA5_rep1 T2


title: MELA31_rep2 T1


title: MELA30_rep2 T1


title: MELA31_rep3 T1


title: MELA29_rep4 T1


title: MELA31_rep1 T1


title: MELA29_rep2 T1


title: MELA29_rep1 T1


title: MELA28_rep1 T1


title: MELA28_rep2 T1


title: MELA27_rep1 T1


title: MELA30_rep3 T1


title: MELA28_rep3 T1


title: MELA26_rep3 T1


title: MELA27_rep2 T1


title: MELA25_rep3 T1


title: MELA29_rep3 T1


title: MELA25_rep2 T1


title: MELA7_rep2 T2


title: MELA24_rep3 T1


title: MELA25_rep1 T1


title: MELA25_rep4 T1


title: MELA24_rep1 T1


title: MELA28_rep4 T1


title: MELA20_rep4 T1


title: MELA26_rep1 T1


title: MELA20_rep3 T1


title: MELA17_rep1 T1


title: MELA16_rep4 T1


title: MELA24_rep4 T1


title: MELA17_rep4 T1


title: MELA3_rep1 T2


title: MELA16_rep3 T1


title: MELA20_rep2 T1


title: MELA20_rep1 T1


title: MELA17_rep2 T1


title: MELA24_rep2 T1


title: MELA17_rep3 T1


title: S67_Individual24_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

description:
S67
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

data_processing:
See https://github.com/brucemoran/rdl_RNAseq for full reproducible pipeline.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rdl_RNAseq.sleuthObject.Rdata: sleuth object containing raw counts, filtered transcript and gene level counts and scaled values (TPM, scaled reads per base).
Supplementary_files_format_and_content: rdl_RNAseq.sleuthObject.obs_raw.tsv: Tab-separated text file containing TPM.

organism: Rattus norvegicus

source_name: Endometrium

growth_protocol: Rats were age-matched and housed in spacious ventilated cages with hard floors in groups of 3-4 rats. They had 24 hour access to ad-lib food and water. Enrichment, in the form of cardboard and Perspex tunnels were provided in all cages. Ample saw dust was used as bedding and this was changed, along with the cage on a weekly basis. Weekly weights and food intakes were recorded prospectively and all animals were inspected daily for any welfare concerns. All animals were formally scored weekly using the rat grimace scale with any welfare concerns immediately reported to the departmental vet (DV). Animal handling training provided by the BMF staff as well as the professional qualification TEARAP were both mandatory requirements prior to commencing this study. High fat diet with 60%kCal fat, 20%kCal carbohydrate and 20%kCal protein was sourced from Research Diets, NJ, USA and was used as diet in the HFD, LG and DRG groups respectively. This calorie rich research diet, D12492, was chosen as it has an established safety and efficacy in causing diet-induced-obesity in research rats. Normal chow with 3%kCal fat content was used as the chosen diet in the NCD group as it is generally accepted as the standard diet for research rats. The normal chow was sourced from Tekland Global Diets, WI, USA. Rats in the validation study and the LG group of rats from the intervention study were fed ‘ad lib’ amounts of their respective diets from their cage hoppers and had access to the food 24 hours a day. As stated, rats in the DRG had ‘ad lib’ access to HFD from 3 to 12 months of age and restricted access to HFD from 12 to 15 months of age in order to achieve the desired amount of weight loss.

extract_protocol:
RNA was isolated from normal and endometrial tumour tissue using EZ-RNA Total RNA Isolation Kit according to the manufacturer’s protocol (Omega Bio-Tek). RNA quantity and quality were determined using a Nanodrop spectrophotometer ND-1000 (Nanodrop Technologies, DE, USA), and Agilent Bioanalyzer 2100 (Agilent Technologies, UK).
Next-generation sequencing libraries were prepared using the NeoPrep Automated Library Prep System and Illumina TruSeq stranded mRNA library prep kit using the manufacturer's instructions (Illumina, San Diego, CA, USA).
After quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific- 7 bp adapters and sequenced at 2 x 75bp paired end read length using an Illumina NextSeq 500 sequencer.

treatment_protocol: Victoza, the tradename for Liraglutide was sourced from the college pharmacy. Liraglutide is a long acting GLP-1 agonist developed by NovoNordisk, which shares 97% homology with GLP-1 and has a circulating half-life of 10-14 hours. Liraglutide was approved for use in type 2 diabetes in Europe in 2009 and the USA in 2010 and is administered as a once daily subcutaneous injection either as a monotherapy or in combination with other antidiabetic agents in humans. In this context it was used as a monotherapy with the sole aim of inducing weight loss. It is commercially available as a pre-made solution in a calibrated 3ml syringe in a concentration of 6mg/ml. Liraglutide was dose-titrated daily over an eight-day period commencing at a dose of .01mg/kg/day to 0.24mg/kg/rat/day. Water intake was monitored twice daily in the two days prior to commencing injections in order to ascertain the average daily water intake per rat. Sub-cutaneous injection sites were altered daily in order to avoid injection site inflammation or ulceration. The sites used included the scruff of the neck, both flanks and the abdomen. Injections were given between 0600 and 1100 am in order to facilitate proper monitoring of water intake. Twice daily intake of water was monitored until adypsia was out-ruled and maintenance dose liraglutide was reached which was typically for 10 days. The rats also had daily welfare scores using the ‘rat grimace scale’ during this period until the maintenance dose of liraglutide had been reached and fears regarding adypsia had ceased (Appendix 6). Rats showing signs of adypsia were given a bolus injection of 4mls of normal saline and subjected to twice daily welfare scores. Any rat scoring greater than or equal to five on the welfare score card was subjected to a review by the departmental vet. At 12 months of age this group of rats were subjected to the intervention of weight loss via diet restriction. Having previously had ad lib access to HFD this group of rats now had rationed access to food each morning (between 1000-1200) in order to achieve the desired weight loss. The estimated daily intake of food per rat was calculated in the month leading up to the commencement of diet restriction. This daily intake was slowly tapered down over a four-week period in order to achieve the desired weight loss. The weight loss was then maintained for the remainder of the study. In order to accurately and safely achieve this weight loss each rat was individually housed for meal times and given the required amount of time to consume its meal. This avoided the emergence of a ‘dominant’ or ‘runt’ rat in each cage. Once the food had been consumed by each rat they were then returned to group housing where there was no access to food but ad lib access to water. The rats were scored daily for the duration of this intervention using the rat grimace scale. Any rat scoring greater than or equal to five on the welfare score card was subjected to a review by the departmental vet.

tag: individual

value: BDII/Han

value: Normal endometrium

tag: diet

value: HFD

tag: intervention

value: LIR

tag: batch


title: MELA16_rep1 T1

value: Blood


title: MELA13_rep4 T1


title: S66_Individual24_TissueTumour_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S66
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

tag: strain

value: Endometrial tumor


title: MELA13_rep1 T1

tag: disease state


title: MELA13_rep2 T1


title: MELA12_rep2 T1


title: MELA12_rep1 T1


title: MELA23_rep1 T1


title: MELA11_rep2 T1


title: MELA11_rep3 T1


title: S60_Individual19_TissueTumour_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S60
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S59_Individual17_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S59
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA13_rep3 T1


title: S58_Individual16_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S58
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S65_Individual23_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S65
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S62_Individual19_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S62
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA11_rep4 T1


title: S55_Individual20_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S55
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S56_Individual21_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S56
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S57_Individual14_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S57
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA11_rep1 T1


title: S63_Individual19_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S63
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA10_rep1 T1


title: S64_Individual20_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S64
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA16_rep2 T1


title: MELA7_rep4 T1


title: MELA7_rep3 T1


title: S52_Individual17_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATddhE

description:
S52
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: NO


title: MELA12_rep3 T1


title: S61_Individual19_TissueTumour_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S61
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA7_rep1 T1


title: S54_Individual19_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

description:
S54
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA7_rep2 T1


title: S51_Individual16_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATddhE

description:
S51
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S49_Individual14_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S49
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: RES