title: CG_MEL3

city: henan

first: Xue

last: Yang

address: henan

institute: henan agricultrial university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: Nbv0.5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Nicotiana benthamiana

source_name: leaves

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves


title: CG_CK3

status: Public on Dec 30 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

value: CGMMV


title: WT1

value: WT


title: WT3


title: CG_MEL1


title: CG_MEL2


title: Patient T2-024

type: RNA

city: Annandale

first: Kathleen

last: Darcy

state: VA

address: 3289 Woodburn Road Suite 370

department: Gynecologic Cancer Center of Excellence

country: USA

institute: Henry M Jackson Foundation for the Advancement of Military Medicine

description: Gene expression data from EEC patients

hyb_protocol: Approximately 5 microgram of total RNA from each sample was labeled using the high yield transcript labeling kit (ENZO) and labeled RNAs were hybridized to U133A Plus 2.0 microarrays (Affymetrix Inc).

scan_protocol: Hybridized U133A Plus 2.0 microarrays (Affymetrix Inc) were washed and scanned according to the manufacturers specifications (Affymetrix Inc., 2001).

data_processing: Affymetrix hybridization-based microarray data were normalized using the RMA algorithm implemented in ‘simpleaffy’ Bioconductor package applied on raw CEL files, and only those probesets detected with expression levels >0 in at least 2/3 samples were retained for further analysis, respectively.

label: biotin

organism: Homo sapiens

source_name: Endometrial Cancer

label_protocol: One hundred ng of total RNA was amplified (Two-Cycle cDNA Synthesis Kit, Affymetrix Inc., Santa Clara, CA) from which biotinylated aRNA was prepared (Affymetrix Labeling Kit, Affymetrix Inc). Approximately 5 microgram of total RNA from each sample was labeled using the high yield transcript labeling kit (ENZO).

extract_protocol: Total RNA was isolated (RNeasy Micro Kit) and spectrophotometrically quantified (Nanodrop 1000, ThermoFischer Scientific, Inc., Wilmington, DE). The RNA Integrity Number (RIN, Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA) was utilized as a surrogate of RNA (and tissue specimen) integrity. Only those cases with a RIN > 5 were included in the transcriptomic analysis.  Cases were excluded if they had poor quality RNA (RIN<5) or a high GAPDH 3’:5’ ratio (>10).

treatment_protocol: Frozen primary tumors were embedded in optimal cutting temperature (OCT) compound and thin sections (8 micrometer) were cut and mounted on glass slides for pathology review.  A board-certified pathologist centrally reviewed hematoxylin and eosin stained sections, to select cases with at least 10% tumor cellularity, endometrioid histotype, and <=50% necrosis. Malignant epithelial cells were harvested from tissue specimens using laser microdissection (LMD) or macrodissection/scraping. When LMD was required, tissue sections were prepared on PEN membrane slides, crosslinked for 30 min using a UV crosslinker (Spectronics Corporation, Westbury, NY), stained in Mayer’s hematoxylin, air dried for 24 h, and underwent laser microdissection (LMD 6500, Leica Microsystems, Wetzlar, Germany) Malignant epithelial cells were collected into RLT Buffer (Qiagen, Valencia, CA) plus 1% ?-mercaptoethanol and stored at -80 °C.

tag: matastasis

value: No

tag: grade

value: Yes


title: CG_CK2


title: WT2


title: Patient T2-026

description: Gene expression data from EEC patients


title: Patient T2-027

description: Gene expression data from EEC patients


title: CG_CK1


title: DO_Mouse_Control_Liver-29

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description:
RNA sequencing using MiSeq
Liver-29

data_processing:
FastQC was run on all samples to ensure adequate per base sequence quality, per base N content, and adapter content. FastQC analysis detected adapter content at the end of the reads. Trim Galore version 0.4.4 was used to trim Illumina adapter sequence from the end of the reads. Any reads that were trimmed to less than 50 bp were removed.
FASTQ files of trimmed Illumina Tru-Seq RNA-Seq reads were aligned to the pooled transcriptome of all 8 DO founder strains (ftp://churchill-lab.jax.org/software/GBRS/) using Bowtie version 1.2.2  with the following parameters: -a -v 3 --best --strata. This configuration allows up to 3 mismatches and reports all alignments. After alignment, the total sequenced reads, total aligned reads, and alignment rate were calculated for each sample.
Genome_build: The Expectation Maximization algorithm for allele-specific expression (EMASE) was used to resolve the probable origin of multireads and estimate the gene abundance. This was implemented through the GBRS software using the EMASE model M4, which apportions multi-reads equally among genes, isoforms, and alleles. Multiway allele specificity was quantified for each sample using the “quantify” function in GBRS. Then the sample’s genome was reconstructed based upon gene-level transcripts per million signals in the 8 DO founder strains using GBRS “reconstruct” function and recommended settings. For each sample, the computationally reconstructed genome was then used (“quantify” function) to estimate the expression signal resulting in normalized diploid expression for each gene for each sample. Each gene was assigned a sample-specific founder genotype signifying the two founder strains for the diploid call.
Supplementary_files_format_and_content: total counts

organism: Mus musculus

source_name: Liver

growth_protocol: Male Diversity Outbred mice (Jackson Laboratory, Bar Harbor, ME) at 6 weeks of age were housed individually in polycarbonate cages with hardwood bedding (Northeastern Products Corporation, Warrensburg, NY) and a cotton fiber nestlet. Cages were maintained at a temperature between 20 and 25 ± 3 degrees C, relative humidity of 30-70%, and a 12-hour light-dark cycle. Animals were fed control diet (10 kcal % fat, D12450J/D12450JN; Research Diets, New Brunswick, NJ) ad libitum until start of the study. Reverse-osmosis treated tap water (City of Durham, NC) was provided to animals ad libitum throughout the study.

extract_protocol:
RNA was extracted from liver, muscle, and adipose samples collected from each animal at necropsy. Tissues (10 mg liver; 20 mg muscle; 60 mg adipose) were homogenized in the FastPrep 24-5G Homogenizer (MP Biomedicals, Irvine, CA) using Lysing Matrix D tubes. The RNA extractions were completed using the Maxwell RSC simplyRNA Tissue kit (Promega, Madison, WI).  Lysate pre-processing and cartridge preparation was done on the Promega Maxprep liquid handler and extractions were performed using the Promega Maxwell RSC48 instrument.  Sample concentrations were quantified  using the NanoDrop 8000 (Thermo Fisher Scientific) and RNA quality was checked on the Agilent 5200 Fragment Analyzer System (Agilent Technologies, Santa Clara, CA) using the Standard Sensitivity RNA kit (15NT). Samples with RQN ≥ 8 (muscle and liver) and RQN ≥ 7 (adipose) were used for sequencing.
RNA libraries were prepared using TrueSeq Stranded Total RNA LP kit (Illumina, San Diego, CA) using manufacturer protocols and 100 ng of RNA. Sequencing was conducted using the MiSeq system  (Illumina, San Diego, CA).

treatment_protocol: At study start animals were randomized and half of the mice (N=75) were placed on the High Fat diet (60 kcal %, D12492/D12492N; Research Diets, New Brunswick, NJ) for 14 weeks while the other half (N=75) continued receiving control diet ad libitum, except during designated fasting periods for measuring resting state glucose levels.

value: Liver

tag: Sex

value: male

tag: feed type

value: Control

tag: duration

tag: duration unit

value: weeks


title: DO_Mouse_Control_Liver-31

description:
RNA sequencing using MiSeq
Liver-31


title: Patient T2-025

description: Gene expression data from EEC patients


title: MDAMB231_M2

city: Heifei

first: Mingming

last: Wu

state: Anhui

address: inZhai Road Baohe District

institute: University of Science and Technology of China

data_processing:
SOAPnuke v1.5.2 software for reads filtration, Remove low-quality reads that containing joints, with unknown base N content greater than 5%,
The clean reads were mapped reference genome using HISAT2 v2.0.4
Bowtie2 v2.2.5 was used  to align Clean reads to the reference gene sequence
RSEM v1.2.8 was used to calculate the gene expression level of each sample
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file includes expression and FPKM values for each Sample

organism: Homo

growth_protocol: The MDA-MB-231 cell were cultured in 6-well plate for 48 hours

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

treatment_protocol: The cells were cultured with CM derived from parental MDA-MB-231 cell or BCSCs derived from mammospheres culture

tag: cell type

value: Breast cancer cells

tag: cell line

tag: treatment

value: Cultured with BCSC CM


title: MDAMB231_C3

value: Cultured with control CM


title: Patient T2-022

description: Gene expression data from EEC patients


title: MDAMB231_C2


title: Patient T2-023

description: Gene expression data from EEC patients


title: Patient T2-020

description: Gene expression data from EEC patients


title: MDAMB231_C1


title: MDAMB231_M3


title: Patient T2-019

description: Gene expression data from EEC patients


title: MDAMB231_M1


title: DO_Mouse_Control_Liver-28

description:
RNA sequencing using MiSeq
Liver-28


title: DO_Mouse_Control_Liver-27

description:
RNA sequencing using MiSeq
Liver-27


title: DO_Mouse_Control_Liver-26

description:
RNA sequencing using MiSeq
Liver-26


title: DO_Mouse_Control_Liver-25

description:
RNA sequencing using MiSeq
Liver-25


title: mycelia, H2BK131A-3

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (fragments per kilobaseof exon per million fragments mapped) for differential expression analysis.
Genome_build: pde_v1.0
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.txt

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in VMM medium with 2% glucose as carbon resource for 22 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 24 h. Total RNA was extracted for DGE analysis.

extract_protocol: Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.

tag: strain

value: Lysine mutation to alanine in H2B at position 131

tag: medium

value: Mandel’s medium with 2% glucose as carbon resource

tag: culture time

value: 24 h after transferring washed mycelia to the new medium

value: Fungal mycelia


title: Patient T2-018

description: Gene expression data from EEC patients


title: Patient T2-021

description: Gene expression data from EEC patients


title: mycelia, H2BK131A-2


title: Patient T2-017

description: Gene expression data from EEC patients


title: Patient T2-016

description: Gene expression data from EEC patients


title: Patient T2-015

description: Gene expression data from EEC patients


title: mycelia, H2BK131A-1


title: mycelia, H2BK123A-3

value: Lysine mutation to alanine in H2B at position 123


title: DO_Mouse_Control_Liver-23

description:
RNA sequencing using MiSeq
Liver-23


title: mycelia, H2BK123A-2


title: Patient T2-014

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-22

description:
RNA sequencing using MiSeq
Liver-22


title: mycelia, H2BK123A-1


title: peripheral blood plasma-Normal-J5

city: Hefei

first: Yichuan

last: Ding

address: No. 81 Meishan Road

institute: Anhui Medical University

description: Gene expression in healthy controls blood

hyb_protocol: 1μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 ×  Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization  buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the  gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for  17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and  scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.  Quantile normalization and subsequent data processing were performed using the R software limma  package.

source_name: peripheral blood plasma-Normal-J5

label_protocol: the enriched circular RNAs were amplified and transcribed  into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit;  Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and  specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

value: peripheral blood plasma

tag: gender

tag: age

tag: disease state

value: healthy


title: peripheral blood plasma-Normal-J9

source_name: peripheral blood plasma-Normal-J9

tag: tissue

value: female


title: mycelia, DlaeA-3

value: laeA deletion


title: mycelia, DlaeA-2


title: DO_Mouse_Control_Liver-21

description:
RNA sequencing using MiSeq
Liver-21


title: peripheral blood plasma-Normal-J3

source_name: peripheral blood plasma-Normal-J3


title: peripheral blood plasma-COPD-E

description: Gene expression in patients with very severe COPD blood

source_name: peripheral blood plasma-COPD-E

value: very severe COPD


title: peripheral blood plasma-COPD-D

source_name: peripheral blood plasma-COPD-D


title: peripheral blood plasma-COPD-C

source_name: peripheral blood plasma-COPD-C


title: Patient T2-013

description: Gene expression data from EEC patients

value: No

value: Yes


title: DO_Mouse_Control_Liver-24

description:
RNA sequencing using MiSeq
Liver-24

value: Liver

value: male

value: Control


title: Patient T2-012

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-20

description:
RNA sequencing using MiSeq
Liver-20

value: weeks


title: mycelia, WT-3

value: 114-2 (wild type)


title: mycelia, DlaeA-1


title: mycelia, WT-2


title: DO_Mouse_Control_Liver-19

description:
RNA sequencing using MiSeq
Liver-19


title: mycelia, WT-1

value: Mandel’s medium with 2 % glucose as carbon resource


title: DO_Mouse_Control_Liver-18

description:
RNA sequencing using MiSeq
Liver-18


title: Patient T2-011

description: Gene expression data from EEC patients


title: Sample 51 Rehyd 48h ST

city: Cape Town

first: Astrid

middle: Lillie

last: Radermacher

address: University Ave

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

data_processing:
The Tuxedo suite (Trapnell et al., 2014) was used for annotation and mapping to the reference genome for this species (Costa et al., 2017).
genome indexing was built by bowtie2
The reference transcriptome indexing and the alignment of the RNA-seq reads to the reference genome were performed by tophat
The transcriptome assembly of samples was performed by cufflink and the assembled transcriptome of different samples were merged by cuffmerge
Differential gene expression was performed using cuffdiff on FPKM (fragments per kilobase of exon per million mapped reads) gene expression data.
Genome_build: GCA_002076135.1
Supplementary_files_format_and_content: FPKM; fastq

organism: Xerophyta schlechteri

source_name: Xerophyta schlechteri leaf blade

extract_protocol:
Total RNA was extracted from hydrated, dehydrating (75%, 55%, 35%), desiccated (5% relative water content (RWC)) and rehydrated (48h – varying RWC values) leaf tissues of X.schlechteri. A modified extraction method was used, using Tri-reagent (Sigma-Aldrich Corporation, St. Louis, MO, USA) and the RNEasy mini-kit (Qiagen, Hilden, Germany). Samples held in storage at-80⁰C were transferred under liquid nitrogen into sterilized 2mL Eppendorff tubes containing three stainless steel bearings (pre-treated by soaking in chloroform and autoclaved twice along with the tubes). Before the tissue was allowed to thaw, 1mL cold Tri-reagent was pipetted into the tubes, ensuring that all tissue was completely submerged. The samples were maintained on ice until being transferred to an in-house homogenizer, where they were homogenized at room temperature for 12 minutes. The samples were placed on ice and 200µl chloroform was added to each tube. The samples were mixed by inversion and maintained on ice for 2 min. The tubes were then centrifuged at 13000g for 15 min at 4⁰C. The upper aqueous phase of each sample was transferred to the RNEasy mini-kit Shredder column and the manufacturer’s instructions for RNA extraction were followed with the following modifications: the RW1 buffer wash step was repeated with a volume of 200µl, the RPE buffer wash step was repeated twice and the RNA was eluted in RNase-free water pre-heated to 55⁰C after incubating for 10 min at room temperature. RNA integrity and quality were verified using a Bioanalyzer (Agilent technologies, USA).
Library preparation was conducted using the Illumina RNA-seq kit (San Diego, California) according to the manufacturer’s instructions.

tag: water content (nst)

value: Rehyd 48h

tag: senescence state

value: ST

value: leaf blade


title: Sample 50 Rehyd 48h PST

value: PST


title: Sample 48 Rehyd 48h ST


title: Sample 49 Rehyd 48h NST

value: NST


title: DO_Mouse_Control_Liver-17

description:
RNA sequencing using MiSeq
Liver-17


title: Sample 47 Rehyd 48h PST


title: Patient T2-009

description: Gene expression data from EEC patients

tag: matastasis

tag: grade


title: Sample 46 Rehyd 48h NST


title: DO_Mouse_Control_Liver-16

description:
RNA sequencing using MiSeq
Liver-16

tag: Sex

tag: feed type


title: DO_Mouse_Control_Liver-15

description:
RNA sequencing using MiSeq
Liver-15

tag: duration

tag: duration unit


title: Sample 44 Rehyd 48h PST


title: Sample 45 Rehyd 48h ST


title: Sample 43 Rehyd 48h NST


title: Patient T2-010

description: Gene expression data from EEC patients


title: Sample 42 <10% RWC ST


title: DO_Mouse_Control_Liver-14

description:
RNA sequencing using MiSeq
Liver-14


title: DO_Mouse_Control_Liver-13

description:
RNA sequencing using MiSeq
Liver-13


title: Sample 40 <10% RWC NST


title: Sample 41 <10% RWC PST


title: Sample 39 <10% RWC ST


title: Sample 38 <10% RWC PST


title: Sample 37 <10% RWC NST


title: Sample 36 <10% RWC ST


title: Sample 35 <10% RWC PST


title: DO_Mouse_Control_Liver-11

description:
RNA sequencing using MiSeq
Liver-11


title: Patient T2-007

description: Gene expression data from EEC patients


title: Sample 34 <10% RWC NST


title: Patient T2-006

description: Gene expression data from EEC patients


title: Patient T2-005

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-10

description:
RNA sequencing using MiSeq
Liver-10


title: DO_Mouse_Control_Liver-9

description:
RNA sequencing using MiSeq
Liver-9


title: Sample 32 35% RWC PST

value: 35% RWC


title: Sample 33 35% RWC ST


title: Sample 31 35% RWC NST


title: Patient T2-001

description: Gene expression data from EEC patients


title: Patient T2-003

description: Gene expression data from EEC patients


title: Sample 30 35% RWC ST


title: Patient T2-008

description: Gene expression data from EEC patients


title: Patient T2-004

description: Gene expression data from EEC patients


title: HBV-cccR08-6d-3_HBV_cccR08_6d

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Image analysis with Illumina RTA.
Base calling with Illumina bcl2fastq 2.17.
HBV genome and transcritpome analysis was performed with HBVouroboros v0.95.
Reads were mapped to human genome hg38 with Roche internal biokit pipeline.
Assembly: hg38
Supplementary files format and content: 20220925-HBVcccDNA-counts.gct: count matrix in GCT format
Supplementary files format and content: 20220925-HBVcccDNA-featureAnnotation.tsv: feature annotation in TSV format
Supplementary files format and content: 20220925-HBVcccDNA-sampleAnnotation.tsv: sample annotation in TSV format

source_name: Primary human hepatocytes

extract_protocol:
Cell were harvested 3h, 8h, or 24h after test compound addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C. For ribosomal RNA depletion the RiboZero magnetic Gold kit (Illumina) was used.
Quality of amplified libraries was accessed by capillary electrophoresis with a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified by quantitative PCR with a sequencing library quantification kit (KAPA iosystems) on a Roche Light Cycler 480. Multiplexed libraries with 1 % spiked in PhiX control were sequenced on a HiSeq2500 instrument for 50 cycles using version 4 chemistry reagents (Illumina).

tag: cell type

value: Primary human hepatocytes

tag: condition

value: HBV

tag: time

tag: replicate

tag: rin


title: HBV-DMSO-6d-3_HBV_DMSO_6d

tag: treatment

value: DMSO


title: HBV-cccR08-6d-4_HBV_cccR08_6d


title: HBV-DMSO-6d-4_HBV_DMSO_6d


title: DO_Mouse_Control_Liver-8-2

description:
RNA sequencing using MiSeq
Liver-8-2


title: DO_Mouse_Control_Liver-12

description:
RNA sequencing using MiSeq
Liver-12


title: Sample 29 35% RWC PST


title: Sample 28 35% RWC NST


title: Patient T2-002

description: Gene expression data from EEC patients

value: No


title: DO_Mouse_Control_Liver-7

description:
RNA sequencing using MiSeq
Liver-7


title: Sample 27 35% RWC ST


title: Sample 26 35% RWC PST


title: HBV-DMSO-6d-2_HBV_DMSO_6d


title: DO_Mouse_Control_Liver-6

description:
RNA sequencing using MiSeq
Liver-6


title: HBV-cccR07-6d-4_HBV_cccR07_6d


title: DO_Mouse_Control_Liver-4

description:
RNA sequencing using MiSeq
Liver-4


title: Sample 25 35% RWC NST


title: Sample 24 55% RWC ST

value: 55% RWC


title: DO_Mouse_Control_Liver-5

description:
RNA sequencing using MiSeq
Liver-5

value: Liver


title: Sample 21 55% RWC ST


title: Sample 23 55% RWC PST


title: Sample 20 55% RWC PST


title: DO_Mouse_Control_Liver-3

description:
RNA sequencing using MiSeq
Liver-3

value: male


title: Sample 19 55% RWC NST


title: DO_Mouse_Control_Liver-2

description:
RNA sequencing using MiSeq
Liver-2

value: Control


title: Sample 18 55% RWC ST


title: DMSO-6d-4_Mock_DMSO_6d

value: Mock


title: DO_Mouse_Control_Liver-1

description:
RNA sequencing using MiSeq
Liver-1

value: weeks


title: HBV-cccR07-6d-2_HBV_cccR07_6d


title: Sample 14 75% RWC PST

value: 75% RWC


title: DMSO-6d-2_Mock_DMSO_6d


title: DO_Mouse_High Fat_Fat-150

description:
RNA sequencing using MiSeq
Fat-150

source_name: Adipose

value: Adipose

value: High fat diet


title: Sample 16 55% RWC NST

value: leaf blade


title: Sample 13 75% RWC NST


title: DMSO-6d-3_Mock_DMSO_6d


title: HBV-cccR08-6d-2_HBV_cccR08_6d


title: Sample 12 75% RWC ST

value: ST


title: HBV-cccR07-6d-3_HBV_cccR07_6d


title: Sample 22 55% RWC NST

value: NST


title: DO_Mouse_High Fat_Fat-149

description:
RNA sequencing using MiSeq
Fat-149


title: cccR08-6d-4_Mock_cccR08_6d


title: Sample 11 75% RWC PST

value: PST


title: Sample 10 75% RWC NST


title: cccR08-6d-3_Mock_cccR08_6d

value: Primary human hepatocytes


title: DO_Mouse_High Fat_Fat-148

description:
RNA sequencing using MiSeq
Fat-148


title: cccR08-6d-2_Mock_cccR08_6d


title: Sample 8 75% RWC PST


title: DO_Mouse_High Fat_Fat-147

description:
RNA sequencing using MiSeq
Fat-147


title: Sample 7 75% RWC NST


title: Sample 9 75% RWC ST


title: Sample 6 FT ST

value: full turgor


title: Sample 5 FT NST


title: Sample 15 75% RWC ST


title: cccR07-6d-4_Mock_cccR07_6d


title: cccR07-6d-3_Mock_cccR07_6d


title: DO_Mouse_High Fat_Fat-146

description:
RNA sequencing using MiSeq
Fat-146


title: Sample 17 55% RWC PST


title: Sample 4 FT ST


title: Sample 2 FT ST


title: DO_Mouse_High Fat_Fat-145

description:
RNA sequencing using MiSeq
Fat-145


title: cccR07-6d-2_Mock_cccR07_6d


title: DO_Mouse_High Fat_Fat-144

description:
RNA sequencing using MiSeq
Fat-144


title: DO_Mouse_High Fat_Fat-143

description:
RNA sequencing using MiSeq
Fat-143


title: HBV-DMSO-3d-3_HBV_DMSO_3d

value: HBV

value: DMSO


title: Sample 1 FT NST


title: HBV-DMSO-3d-4_HBV_DMSO_3d


title: DO_Mouse_Control_Liver-30

description:
RNA sequencing using MiSeq
Liver-30


title: DO_Mouse_High Fat_Fat-142

description:
RNA sequencing using MiSeq
Fat-142


title: HBV-DMSO-3d-2_HBV_DMSO_3d


title: DO_Mouse_High Fat_Fat-141

description:
RNA sequencing using MiSeq
Fat-141


title: DO_Mouse_High Fat_Fat-140

description:
RNA sequencing using MiSeq
Fat-140


title: HBV-cccR08-3d-3_HBV_cccR08_3d


title: Sample 3 FT NST


title: HBV-cccR08-3d-2_HBV_cccR08_3d


title: DO_Mouse_High Fat_Fat-139

description:
RNA sequencing using MiSeq
Fat-139


title: DO_Mouse_High Fat_Fat-138

description:
RNA sequencing using MiSeq
Fat-138


title: HBV-cccR08-3d-1_HBV_cccR08_3d


title: DO_Mouse_High Fat_Fat-137

description:
RNA sequencing using MiSeq
Fat-137


title: HBV-cccR07-3d-3_HBV_cccR07_3d


title: HBV-cccR07-3d-4_HBV_cccR07_3d


title: DO_Mouse_High Fat_Fat-136

description:
RNA sequencing using MiSeq
Fat-136


title: Old, kidney, shNT, rep2

city: BEIJING

first: xiaojie

last: yu

state: China Mainland

address: NO.5 YIHEYUAN ROAD

institute: collage of life science

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq  reads with Trimmomatic (V0.39).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1).
HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene.
Assembly: mm10

source_name: kidney

growth_protocol: Mice were housed under standard conditions in a specific pathogen-free, temperature-controlled environment with a 12-h day/night cycle.

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer's instructions.
Libraries of RNA-seq were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissues were quickly frozen in liquid nitrogen and stored at -80 °C for RNA extraction.

value: kidney

tag: strain

tag: age

tag: genotype

value: WT

value: shNT


title: Old, kidney, shFOS, rep1

tag: tissue

value: shFOS


title: Old, kidney, shNT, rep1


title: Old, kidney, shFOS, rep3


title: Old, kidney, shNT, rep4


title: Old, kidney, shFOS, rep2


title: Old, kidney, shNT, rep3


title: MLP-29 HGF 6h replicate a

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina MurineRef8 V2 at 55°C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's GenomeStudio software.

data_processing: Data were normalized by Illumina's GenomeStudio software (v.1.9.0) with cubic spline normalization

label: Biotin

source_name: MLP-29 HGF 6h

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina Mouse8_V2 arrays

growth_protocol: MLP-29 are grown in DMEM with 10% bovine serum

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: For the expression analysis, MLP-29 cells were progressively starved for 1 week, and subsequently stimulated with HGF, or control medium, for 1, 6 and 24 hours in the presence of 2% bovine serum (BS; Sigma). The time-course stimulation was organized so that cells from all the experimental points could be lysed at the same time, to eliminate any possible variability due to culture conditions, cell density, time from the last passage, medium exhaustion. Stimulations were performed with recombinant HGF. The experiment was repeated twice, to generate biological replicates.

tag: cell line

value: mouse liver progenitor cells

tag: stimulated with

value: HGF for 6 hr


title: Old, kidney, shFOS, rep4


title: MLP-29 HGF 1h replicate a

source_name: MLP-29 HGF 1h

value: HGF for 1 hr


title: MLP-29 HGF 24h replicate b

source_name: MLP-29 HGF 24h

value: HGF for 24 hr


title: MLP-29 HGF 6h replicate b


title: MLP-29 CTRL replicate a

description: CTRL-a

source_name: MLP-29 CTRL

value: control medium (untreated Control)


title: MLP-29 HGF 1h replicate b


title: MLP-29 CTRL replicate b

description: CTRL-b


title: DO_Mouse_High Fat_Fat-135

description:
RNA sequencing using MiSeq
Fat-135

value: Adipose

value: male

value: High fat diet

value: weeks


title: HBV-cccR07-3d-2_HBV_cccR07_3d

value: Primary human hepatocytes


title: MLP-29 HGF 24h replicate a


title: Old, liver, shFOS, rep3

source_name: liver

value: liver


title: DMSO-3d-4_Mock_DMSO_3d

value: Mock


title: DO_Mouse_High Fat_Fat-134

description:
RNA sequencing using MiSeq
Fat-134


title: Old, liver, shFOS, rep1


title: Old, liver, shFOS, rep2


title: DMSO-3d-3_Mock_DMSO_3d

value: DMSO


title: DO_Mouse_High Fat_Fat-133

description:
RNA sequencing using MiSeq
Fat-133


title: Old, liver, shNT, rep4


title: Old, liver, shNT, rep2


title: DMSO-3d-2_Mock_DMSO_3d


title: Old, liver, shFOS, rep4


title: Old, liver, shNT, rep1


title: DO_Mouse_High Fat_Fat-131

description:
RNA sequencing using MiSeq
Fat-131


title: cccR08-3d-3_Mock_cccR08_3d


title: DO_Mouse_High Fat_Fat-132

description:
RNA sequencing using MiSeq
Fat-132


title: DO_Mouse_High Fat_Fat-129

description:
RNA sequencing using MiSeq
Fat-129


title: cccR08-3d-2_Mock_cccR08_3d


title: DO_Mouse_High Fat_Fat-130

description:
RNA sequencing using MiSeq
Fat-130


title: cccR07-3d-3_Mock_cccR07_3d


title: cccR08-3d-4_Mock_cccR08_3d


title: DO_Mouse_High Fat_Fat-127

description:
RNA sequencing using MiSeq
Fat-127


title: cccR07-3d-2_Mock_cccR07_3d


title: cccR07-3d-1_Mock_cccR07_3d


title: Olig1-7d-2

city: Shanghai

first: Xiuqing

last: Fu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong

department: School of Life Science and Technology (SLST)

institute: ShanghaiTech University

library_source: transcriptomic single cell

data_processing:
Quality distribution plot and base content distribution were generated by FASTQC.
HISAT2 software is used to align clean data to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include count values for each Sample.

molecule: polyA RNA

source_name: Retina ganglion cells

extract_protocol:
Collecting 10~15 single fluorescence-labeled RGCs into one tube by Unipick, we successfully obtained three batches of single-cell RNA-seq libraries that were quality-controlled by linear amplification of synthetic spike-in RNAs.
Whole transcriptome amplification in PCR tubes were performed following SMART-Seq® HT Kit protocol. Briefly, 10~20 picked cells (~0.2μl) were lysed in 10μl lysis buffer (with RNase Inhibitor). Next, samples were mixed well with 1μl 3’-SMART-Seq CDS Primer II A, and then incubated at 72°C for 3 minutes and immediately placed on ice for 2 minutes. Then, we incubated samples with 12.5μl One-Step Master Mix at 42°C for 90 minutes and amplified for 20 PCR cycles. The cells’ cDNA was purified by immobilization on AMPure XP beads and cDNA is eluted with 17μl Elution Buffer. After purification, 1μl the profile of the cDNA was evaluated using the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).

value: Retina ganglion cells

value: Male

value: Adult

value: AAV-Olig1 injection for 14 days and ONC for 7 days


title: Olig1-14d-2

value: WT

value: AAV-Olig1 injection for 14 days and ONC for 14 days


title: Olig1-14d-1


title: Olig1-7d-1


title: Olig1-7d-3


title: GFP-14d-1

value: AAV-GFP injection for 14 days and ONC for 14 days


title: Olig1-14d-3


title: GFP-7d-3

value: AAV-GFP injection for 14 days and ONC for 7 days


title: Old, liver, shNT, rep3

value: shNT


title: DO_Mouse_High Fat_Fat-126

description:
RNA sequencing using MiSeq
Fat-126

value: Adipose


title: HBV-DMSO-24h-3_HBV_DMSO_24h

value: HBV


title: GFP-14d-3


title: GFP-14d-2


title: DO_Mouse_High Fat_Fat-125

description:
RNA sequencing using MiSeq
Fat-125

value: male

value: High fat diet


title: DO_Mouse_High Fat_Fat-128

description:
RNA sequencing using MiSeq
Fat-128

value: weeks


title: HBV-DMSO-24h-2_HBV_DMSO_24h

value: Primary human hepatocytes


title: R3

source_name: spinal cord motor neuron

extract_protocol:
Collecting 10~15 single fluorescence-labeled spMNs into one tube by Unipick, we successfully obtained three batches of single-cell RNA-seq libraries (three of DiI+/DIO+ groups-R and three of control groups DiI-/DIO+-G) that were quality-controlled by linear amplification of synthetic spike-in RNAs.
Whole transcriptome amplification in PCR tubes were performed following SMART-Seq® HT Kit protocol. Briefly, 10~20 picked cells (~0.2μl) were lysed in 10μl lysis buffer (with RNase Inhibitor). Next, samples were mixed well with 1μl 3’-SMART-Seq CDS Primer II A, and then incubated at 72°C for 3 minutes and immediately placed on ice for 2 minutes. Then, we incubated samples with 12.5μl One-Step Master Mix at 42°C for 90 minutes and amplified for 20 PCR cycles. The cells’ cDNA was purified by immobilization on AMPure XP beads and cDNA is eluted with 17μl Elution Buffer. After purification, 1μl the profile of the cDNA was evaluated using the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).

value: spinal cord motor neuron

value: Sciatic nerve crush (DiO+/DiI+)

value: Day 6


title: DO_Mouse_High Fat_Fat-124

description:
RNA sequencing using MiSeq
Fat-124


title: R1


title: PD-005_del-phoB_Fed-batch_6h__1

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: ddb_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: ddb_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli BW25113

source_name: BW25113 del_phoB

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: BW25113 del_phoB

tag: culture type

value: fed-batch

value: 6 hour


title: HBV-DMSO-24h-1_HBV_DMSO_24h

value: DMSO


title: PD-003_del-phoB_Fed-batch_6h__2


title: DO_Mouse_High Fat_Fat-123

description:
RNA sequencing using MiSeq
Fat-123

tag: Sex


title: G3

value: WT

value: Sciatic nerve crush (DiO+/DiI-)


title: PD-003_del-phoB_Fed-batch_6h__1


title: HBV-cccR08-24h-4_HBV_cccR08_24h


title: GFP-7d-2

value: Retina ganglion cells

value: Male

value: Adult

value: AAV-GFP injection for 14 days and ONC for 7 days


title: G2


title: DO_Mouse_High Fat_Fat-121

description:
RNA sequencing using MiSeq
Fat-121

value: Adipose

value: male

tag: feed type


title: G1


title: DO_Mouse_High Fat_Fat-120

description:
RNA sequencing using MiSeq
Fat-120

value: High fat diet

tag: duration

value: weeks


title: HBV-cccR08-24h-2_HBV_cccR08_24h

value: Primary human hepatocytes

value: HBV


title: HBV-cccR08-24h-3_HBV_cccR08_24h


title: PD-003_del-phoB_Batch_9h__1

value: batch

value: 9 hour


title: DO_Mouse_High Fat_Fat-122

description:
RNA sequencing using MiSeq
Fat-122

tag: duration unit


title: heart,treatment,rep4 single

city: Beijing

first: cheng

last: qin

address: No.28 Fuxing Road

department: Department of Cardiology

institute: Chinese People's Liberation Army General Hospital and Medical School of Chinese People's Liberation Army

data_processing:
Samples were up-sequenced to obtain image files, which were transformed by the sequencing platform's own software to generate raw data (Raw Data) of FASTQ. The Raw Data of each sample were counted separately, including sample name, Q30, percentage of fuzzy bases, and Q20(%) and Q30(%).
The sequencing data contains some spliced, low-quality Reads, which can cause great interference to the subsequent information analysis, so the sequencing data need to be further filtered. The main criteria for data filtering include: 1. using Cutadapt to remove sequences with junction at the 3' end; 2. removing Reads with average quality score lower than Q20.
We evaluated the base quality of individual positions using the single-base quality distribution map of sequencing data. In general, the base quality of the 5' and 3' ends of the Reads is low, and the base quality of the middle part is high. Most of the sequences have a base quality above 20, which represents good sequencing quality
Filtered Reads were aligned to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ), an upgraded version of TopHat2. HISAT2 uses the improved BWT algorithm (Sirén et al. 2014) for faster and less resource intensive. For HISAT2 alignment, default parameters are used for non-strand-specific libraries, while strand-specific libraries require the library type to be specified (i.e. --rna-strandness RF for first and --rna-strandness FR for second). If the reference genome is selected appropriately and there is no contamination in the relevant experiments, the Mapping ratio of sequenced sequences will generally be higher than 70%.
Assembly: mm10

source_name: heart

extract_protocol:
RNA was harvested using Total RNA Extraction Reagent (Vazyme).1.5 ug of total RNA was used for the construction of sequencing libraries.
The ion interruption was used to break the RNA to a fragment of about 300bp in length. The fragment of 300bp in length was selected as the template, and the first strand of cDNA was synthesized using a 6-base random primer and reverse transcriptase, and the first strand cDNA was used as the template for the synthesis of the second strand cDNA.

value: heart

value: JWH133 10mg/kg i.p.for 3weeks


title: PD-003_del-phoB_Batch_9h__2

value: BW25113 del_phoB


title: HBV-cccR07-24h-3_HBV_cccR07_24h

tag: cell type


title: GFP-7d-1

value: WT


title: R2

value: spinal cord motor neuron

value: Sciatic nerve crush (DiO+/DiI+)

value: Day 6


title: DO_Mouse_High Fat_Fat-119

description:
RNA sequencing using MiSeq
Fat-119


title: heart,treatment,rep3 single


title: PD-005_del-phoB_Batch_6h__2

value: 6 hour


title: HBV-cccR07-24h-2_HBV_cccR07_24h

tag: condition


title: PD-005_del-phoB_Batch_6h__3

tag: time


title: heart,treatment,rep2 single


title: PD-005_del-phoB_Batch_6h__1


title: heart,treatment,rep1 single


title: HBV-cccR07-24h-1_HBV_cccR07_24h

tag: replicate


title: PD-004_del-kdpE_Fed-batch_15h__2

source_name: BW25113 del_kdpE

value: BW25113 del_kdpE

value: fed-batch

value: 15 hour


title: DO_Mouse_High Fat_Fat-117

description:
RNA sequencing using MiSeq
Fat-117

value: Adipose

value: male

value: High fat diet


title: DMSO-24h-4_Mock_DMSO_24h

value: Primary human hepatocytes

value: Mock

value: DMSO

tag: rin


title: DO_Mouse_High Fat_Fat-116

description:
RNA sequencing using MiSeq
Fat-116

value: weeks


title: heart,stress,rep4 single

value: heart


title: DMSO-24h-3_Mock_DMSO_24h

tag: treatment


title: heart,stress,rep3 single


title: PD-004_del-kdpE_Fed-batch_6h__2

tag: strain


title: PD-004_del-kdpE_Fed-batch_15h__1


title: cccR08-24h-4_Mock_cccR08_24h


title: DMSO-24h-2_Mock_DMSO_24h


title: heart,stress,rep2 single


title: DO_Mouse_High Fat_Fat-115

description:
RNA sequencing using MiSeq
Fat-115


title: heart,stress,rep1 single


title: DO_Mouse_High Fat_Fat-113

description:
RNA sequencing using MiSeq
Fat-113


title: PD-004_del-kdpE_Fed-batch_6h__1


title: DO_Mouse_High Fat_Fat-118

description:
RNA sequencing using MiSeq
Fat-118


title: DO_Mouse_High Fat_Fat-112

description:
RNA sequencing using MiSeq
Fat-112


title: PD-004_del-kdpE_Batch_6h__2

value: batch


title: heart,control,rep3 single


title: PD-004_del-kdpE_Batch_6h__1


title: DO_Mouse_High Fat_Fat-111

description:
RNA sequencing using MiSeq
Fat-111


title: cccR08-24h-2_Mock_cccR08_24h


title: cccR07-24h-4_Mock_cccR07_24h


title: heart,control,rep2 single


title: heart,control,rep1 single


title: PD-004_del-basS_Fed-batch_15h__1

source_name: BW25113 del_basS

value: BW25113 del_basS


title: DO_Mouse_High Fat_Fat-110

description:
RNA sequencing using MiSeq
Fat-110


title: cccR07-24h-3_Mock_cccR07_24h


title: DO_Mouse_High Fat_Fat-109

description:
RNA sequencing using MiSeq
Fat-109


title: DO_Mouse_High Fat_Fat-114

description:
RNA sequencing using MiSeq
Fat-114


title: heart,treatment,rep4 paired-end

value: JWH133 10mg/kg i.p.for 3weeks


title: DO_Mouse_High Fat_Fat-108

description:
RNA sequencing using MiSeq
Fat-108


title: PD-004_del-basS_Fed-batch_6h__2


title: PD-004_del-basS_Fed-batch_6h__1


title: heart,treatment,rep3 paired-end


title: cccR08-24h-3_Mock_cccR08_24h


title: cccR07-24h-2_Mock_cccR07_24h


title: heart,treatment,rep1 paired-end


title: HBV-DMSO-8h-3_HBV_DMSO_8h

value: HBV


title: HBV-DMSO-8h-2_HBV_DMSO_8h


title: DO_Mouse_High Fat_Fat-107

description:
RNA sequencing using MiSeq
Fat-107


title: heart,treatment,rep2 paired-end


title: PD-004_del-basS_Batch_6h__2


title: PD-004_del-basS_Batch_6h__1


title: DO_Mouse_High Fat_Fat-105

description:
RNA sequencing using MiSeq
Fat-105


title: DO_Mouse_High Fat_Fat-106

description:
RNA sequencing using MiSeq
Fat-106


title: heart,stress,rep4 paired-end


title: HBV-DMSO-8h-1_HBV_DMSO_8h


title: PD-003_BW25113_Fed-batch_21h__2

source_name: BW25113 wild-type

value: BW25113 wild-type

value: 21 hour


title: HBV-cccR08-8h-3_HBV_cccR08_8h


title: PD-004_del-basS_Fed-batch_15h__2


title: DO_Mouse_High Fat_Fat-104

description:
RNA sequencing using MiSeq
Fat-104


title: HBV-cccR08-8h-2_HBV_cccR08_8h


title: heart,stress,rep2 paired-end


title: PD-005_BW25113_Fed-batch_15h__2


title: heart,control,rep3 paired-end


title: HBV-cccR07-8h-2_HBV_cccR07_8h


title: HBV-cccR07-8h-3_HBV_cccR07_8h


title: heart,stress,rep1 paired-end


title: PD-005_BW25113_Fed-batch_15h__1


title: DO_Mouse_High Fat_Fat-103

description:
RNA sequencing using MiSeq
Fat-103


title: DO_Mouse_High Fat_Fat-101

description:
RNA sequencing using MiSeq
Fat-101


title: heart,stress,rep3 paired-end


title: PD-005_BW25113_Fed-batch_6h__1

value: 6 hour


title: DO_Mouse_High Fat_Fat-99

description:
RNA sequencing using MiSeq
Fat-99


title: DMSO-8h-2_Mock_DMSO_8h


title: Primary Macrophage, Chronic Hypoxia, rep 3

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GRCm38 - M. musculus
Supplementary_files_format_and_content: .txt file with normalized TPMs

source_name: Primary Macrophage, Chronic Hypoxia

growth_protocol: alpha-MEM + 10% FBS + 1% PSQ + 10% L929-conditioned media

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

treatment_protocol: Cells were cultured in standard oxygen (7 days), acute hypoxia (standard then 3h of 1% oxygen), or chronic hypoxia (7 days of 1% oxygen)

tag: growth protocol

value: in vitro cultured

value: chronic hypoxia

value: Primary macrophages


title: PD-003_BW25113_Fed-batch_6h__2

value: fed-batch


title: DO_Mouse_High Fat_Fat-102

description:
RNA sequencing using MiSeq
Fat-102

value: Adipose

value: male

value: High fat diet


title: DMSO-8h-3_Mock_DMSO_8h

value: Primary human hepatocytes

value: Mock

value: DMSO


title: DO_Mouse_High Fat_Fat-97

description:
RNA sequencing using MiSeq
Fat-97

value: weeks


title: PD-005_BW25113_Fed-batch_6h__2


title: heart,control,rep2 paired-end

value: heart


title: Primary Macrophage, Chronic Hypoxia, rep 2


title: HBV-cccR07-8h-1_HBV_cccR07_8h


title: DO_Mouse_High Fat_Fat-98

description:
RNA sequencing using MiSeq
Fat-98


title: DO_Mouse_High Fat_Fat-100

description:
RNA sequencing using MiSeq
Fat-100


title: PD-003_BW25113_Fed-batch_21h__1


title: DMSO-8h-1_Mock_DMSO_8h


title: DO_Mouse_High Fat_Fat-96

description:
RNA sequencing using MiSeq
Fat-96


title: PD-003_BW25113_Fed-batch_6h__1


title: HBV-cccR08-8h-1_HBV_cccR08_8h


title: Primary Macrophage, Chronic Hypoxia, rep 1


title: PD-005_BW25113_Fed-batch_6h__3


title: cccR08-8h-3_Mock_cccR08_8h


title: PD-003_BW25113_Batch_9h__2

value: batch

value: 9 hour


title: heart,control,rep1 paired-end


title: cccR08-8h-2_Mock_cccR08_8h


title: PD-003_BW25113_Batch_9h__1

value: BW25113 wild-type


title: DO_Mouse_High Fat_Fat-94

description:
RNA sequencing using MiSeq
Fat-94


title: Primary Macrophage, Acute Hypoxia, rep 2

source_name: Primary Macrophage, Acute Hypoxia

value: acute hypoxia


title: PD-005_BW25113_Batch_6h__2

value: 6 hour


title: cccR08-8h-1_Mock_cccR08_8h

source_name: Primary human hepatocytes


title: cccR07-8h-3_Mock_cccR07_8h


title: Primary Macrophage, Acute Hypoxia, rep 1

value: in vitro cultured


title: DO_Mouse_High Fat_Fat-92

description:
RNA sequencing using MiSeq
Fat-92

source_name: Adipose


title: Primary Macrophage, Standard, rep 2

source_name: Primary Macrophage, Standard

value: standard oxygen


title: PD-005_BW25113_Batch_6h__1


title: DO_Mouse_High Fat_Fat-93

description:
RNA sequencing using MiSeq
Fat-93


title: DO_Mouse_High Fat_Fat-91

description:
RNA sequencing using MiSeq
Fat-91


title: PD-009_del-tnaA_Fed-batch_15h__2

source_name: BW25113 del_tnaA

value: BW25113 del_tnaA

value: 15 hour


title: PD-009_del-tnaA_Fed-batch_15h__1

value: fed-batch


title: Primary Macrophage, Standard, rep 3

value: Primary macrophages


title: HBV-DMSO-3h-3_HBV_DMSO_3h

value: HBV


title: cccR07-8h-1_Mock_cccR07_8h

value: Primary human hepatocytes


title: Primary Macrophage, Standard, rep 1


title: DO_Mouse_High Fat_Fat-90

description:
RNA sequencing using MiSeq
Fat-90

value: Adipose

value: male

value: High fat diet


title: DO_Mouse_High Fat_Fat-89

description:
RNA sequencing using MiSeq
Fat-89

value: weeks


title: PD-009_del-tnaA_Fed-batch_6h__1


title: s_24h_3: PHx 24 h-3 sub-polysome

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.10.1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: The processed date is TPM calibrated according to RNA content of different fractions. The proportions of RNA in 0 h and 24 h polysome fractions are 0.452, 0.446, 0.473 and 0.338, 0.330, 0.359.

source_name: Liver

extract_protocol:
The Liver lysates were loaded onto the top of the sucrose density gradient and subjected to ultracentrifugation. The fractionations at different gradients were separated into 25 fractions with equal volume. RNA in each fraction was extracted using TRIzol LS reagent in accordance with the manufacturer's instructions. The RNA of the first 12 fractions were mixed and used as sub-polysome. The remaining 13 fractions were mixed and used as polysome.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: PHx 24 h

value: sub-polysome fraction


title: DO_Mouse_High Fat_Fat-95

description:
RNA sequencing using MiSeq
Fat-95


title: Primary Macrophage, Acute Hypoxia, rep 3

value: acute hypoxia


title: HBV-DMSO-3h-2_HBV_DMSO_3h

value: DMSO


title: s_24h_2: PHx 24 h-2 sub-polysome


title: DO_Mouse_High Fat_Fat-88

description:
RNA sequencing using MiSeq
Fat-88


title: PD-006_del-rpoS_Fed-batch_15h__2

source_name: BW25113 del_rpoS

value: BW25113 del_rpoS


title: DO_Mouse_High Fat_Fat-87

description:
RNA sequencing using MiSeq
Fat-87


title: cccR07-8h-2_Mock_cccR07_8h

value: Mock


title: s_24h_1: PHx 24 h-1 sub-polysome


title: DO_Mouse_High Fat_Fat-86

description:
RNA sequencing using MiSeq
Fat-86


title: PD-006_del-rpoS_Fed-batch_15h__1


title: HBV-cccR08-3h-3_HBV_cccR08_3h


title: HBV-cccR08-3h-2_HBV_cccR08_3h


title: s_0h_3: PHx 0 h-3 sub-polysome

value: PHx 0 h


title: DO_Mouse_High Fat_Fat-85

description:
RNA sequencing using MiSeq
Fat-85


title: PD-006_del-rpoS_Fed-batch_6h__3

value: 6 hour


title: s_0h_2: PHx 0 h-2 sub-polysome


title: PD-006_del-rpoS_Fed-batch_6h__2

value: fed-batch


title: s_0h_1: PHx 0 h-1 sub-polysome


title: DO_Mouse_High Fat_Fat-83

description:
RNA sequencing using MiSeq
Fat-83


title: HBV-cccR08-3h-1_HBV_cccR08_3h


title: HBV-cccR07-3h-3_HBV_cccR07_3h


title: DO_Mouse_High Fat_Fat-84

description:
RNA sequencing using MiSeq
Fat-84


title: HBV-cccR07-3h-2_HBV_cccR07_3h


title: PD-006_del-rpoS_Fed-batch_6h__1


title: PD-006_del-rpoS_Batch_9h__2

value: batch

value: 9 hour


title: PD-006_del-rpoS_Batch_9h__1


title: PD-009_del-tnaA_Batch_6h__1

value: BW25113 del_tnaA


title: DO_Mouse_High Fat_Fat-81

description:
RNA sequencing using MiSeq
Fat-81

value: Adipose


title: DO_Mouse_High Fat_Fat-82

description:
RNA sequencing using MiSeq
Fat-82

value: male


title: p_24h_1: PHx 24 h-1 polysome

value: polysome fraction


title: p_24h_3: PHx 24 h-3 polysome


title: HBV-DMSO-3h-1_HBV_DMSO_3h

value: Primary human hepatocytes

value: HBV


title: p_24h_2: PHx 24 h-2 polysome

value: Liver

value: PHx 24 h


title: DMSO-3h-3_Mock_DMSO_3h


title: HBV-cccR07-3h-1_HBV_cccR07_3h


title: DO_Mouse_High Fat_Fat-80

description:
RNA sequencing using MiSeq
Fat-80

value: High fat diet

value: weeks


title: p_0h_3: PHx 0 h-3 polysome


title: PD-009_del-luxS_Fed-batch_15h__1

source_name: BW25113 del_luxS

value: BW25113 del_luxS

value: 15 hour


title: DMSO-3h-2_Mock_DMSO_3h

value: Mock

value: DMSO


title: DO_Mouse_High Fat_Fat-79

description:
RNA sequencing using MiSeq
Fat-79


title: p_0h_2: PHx 0 h-2 polysome

value: PHx 0 h


title: DMSO-3h-1_Mock_DMSO_3h


title: p_0h_1: PHx 0 h-1 polysome


title: cccR08-3h-3_Mock_cccR08_3h


title: DO_Mouse_High Fat_Fat-78

description:
RNA sequencing using MiSeq
Fat-78


title: PD-009_del-luxS_Fed-batch_6h__1

value: fed-batch

value: 6 hour


title: DO_Mouse_High Fat_Fat-77

description:
RNA sequencing using MiSeq
Fat-77


title: PD-009_del-luxS_Fed-batch_6h__2


title: PD-009_del-luxS_Batch_6h__2

value: batch


title: PD-009_del-luxS_Batch_6h__1


title: Mier1 KO PHx 72 h 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.10.1
Genome_build: GRCm38.p5

extract_protocol:
Total RNA was extracted using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: AAV-Mier1 sgRNA

value: PHx 72 h


title: Mier1 KO PHx 72 h 1


title: DO_Mouse_High Fat_Fat-76

description:
RNA sequencing using MiSeq
Fat-76

value: Adipose

value: male


title: DO_Mouse_Control_Fat-75

description:
RNA sequencing using MiSeq
Fat-75

value: Control


title: PD-006_del-lsrR_Fed-batch_15h__3

source_name: BW25113 del_lsrR

value: BW25113 del_lsrR


title: Mier1 KO PHx 48 h 2

value: PHx 48 h


title: cccR07-3h-3_Mock_cccR07_3h

value: Primary human hepatocytes


title: DO_Mouse_Control_Fat-74

description:
RNA sequencing using MiSeq
Fat-74

value: weeks


title: Mier1 KO PHx 48 h 1


title: PD-009_del-luxS_Fed-batch_15h__2

value: BW25113 del_luxS

value: 15 hour


title: cccR07-3h-2_Mock_cccR07_3h

value: Mock


title: DO_Mouse_Control_Fat-73

description:
RNA sequencing using MiSeq
Fat-73


title: Mier1 KO PHx 36 h 2

value: PHx 36 h


title: PD-006_del-lsrR_Fed-batch_15h__1

value: fed-batch


title: DO_Mouse_Control_Fat-72

description:
RNA sequencing using MiSeq
Fat-72


title: skeletal muscle sample 24

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

description:
VL17_088
Total RNA-seq

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 pseudoaligned using kallisto v0.48.0 with default settings.
Assembly: gencode v37
Supplementary files format and content: Kallisto_raw_counts.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.

source_name: skeletal muscle

extract_protocol:
Qiagen RNeasy Mini Fibrous Tissue Kit was used to isolate RNA from 10 mg of frozen muscle tissue samples. Samples were homogenized using the TissueLyser II system with shaking twice for 2 min at 25 Hz. Total RNA samples were treated with DNase I using Turbo DNA-free Kit (Thermo Fisher Scientific) according to the kit guidelines. Only RNA samples with RIN>7 were included in the study. Samples were stored at -80 C until sequencing libraries were prepared.
Libraries for RNA sequencing were prepared from 100-300 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext rRNA Depletion Module (New England Biolabs). RNA libraries were sequenced on the Illumina HiSeq system with 250 cycles.

value: skeletal muscle

tag: age

tag: percent of fast fibers


title: Mier1 KO PHx 36 h 1

tag: tissue


title: PD-006_del-lsrR_Fed-batch_6h__2

value: 6 hour


title: Mier1 KO PHx 24 h 2

value: liver

value: PHx 24 h


title: cccR08-3h-2_Mock_cccR08_3h


title: cccR08-3h-1_Mock_cccR08_3h


title: skeletal muscle sample 23

description:
VL17_110
Total RNA-seq


title: Mier1 KO PHx 24 h 1

value: AAV-Mier1 sgRNA


title: cccR07-3h-1_Mock_cccR07_3h


title: DO_Mouse_Control_Fat-71

description:
RNA sequencing using MiSeq
Fat-71

value: Adipose


title: PD-006_del-lsrR_Fed-batch_6h__1


title: skeletal muscle sample 22

description:
VL17_090
Total RNA-seq


title: DO_Mouse_Control_Fat-70

description:
RNA sequencing using MiSeq
Fat-70

value: male


title: PD-006_del-lsrR_Batch_6h__2

value: batch


title: Mier1 KO PHx 0 h 2

value: PHx 0 h


title: PD-006_del-lsrR_Batch_6h__1

value: BW25113 del_lsrR


title: skeletal muscle sample 21

description:
VL17_079
Total RNA-seq


title: DO_Mouse_Control_Fat-69

description:
RNA sequencing using MiSeq
Fat-69

value: Control


title: DO_Mouse_Control_Fat-67

description:
RNA sequencing using MiSeq
Fat-67

value: weeks


title: PD-009_del-lsrK_Fed-batch_15h__3

source_name: BW25113 del_lsrK

value: BW25113 del_lsrK


title: PD-006_del-lsrR_Fed-batch_15h__2

value: 15 hour


title: Mier1 KO PHx 0 h 1


title: DO_Mouse_Control_Fat-68

description:
RNA sequencing using MiSeq
Fat-68


title: Control PHx 72 h 2

value: AAV-Cre

value: PHx 72 h


title: skeletal muscle sample 19

description:
VL17_094
Total RNA-seq


title: PD-009_del-lsrK_Fed-batch_15h__2

value: fed-batch


title: Control PHx 72 h 1


title: skeletal muscle sample 18

description:
VL17_093
Total RNA-seq

value: skeletal muscle


title: DO_Mouse_Control_Fat-66

description:
RNA sequencing using MiSeq
Fat-66


title: PD-009_del-lsrK_Fed-batch_15h__1


title: Control PHx 48 h 2

value: PHx 48 h


title: PD-009_del-lsrK_Fed-batch_6h__2

value: 6 hour


title: DO_Mouse_Control_Fat-64

description:
RNA sequencing using MiSeq
Fat-64


title: skeletal muscle sample 16

description:
VL17_169
Total RNA-seq


title: skeletal muscle sample 17

description:
VL17_036
Total RNA-seq


title: PD-009_del-lsrK_Fed-batch_6h__1


title: Control PHx 36 h 2

value: liver

value: PHx 36 h


title: PD-009_del-lsrK_Batch_6h__2


title: skeletal muscle sample 20

description:
VL17_056
Total RNA-seq


title: DO_Mouse_Control_Fat-62

description:
RNA sequencing using MiSeq
Fat-62

value: Adipose


title: Control PHx 36 h 1


title: DO_Mouse_Control_Fat-63

description:
RNA sequencing using MiSeq
Fat-63

value: male


title: PD-009_del-lsrK_Batch_6h__1

value: batch


title: DO_Mouse_Control_Fat-61

description:
RNA sequencing using MiSeq
Fat-61


title: DO_Mouse_Control_Fat-60

description:
RNA sequencing using MiSeq
Fat-60


title: PD-006_del-lsrB_Fed-batch_15h__2

source_name: BW25113 del_lsrB

value: BW25113 del_lsrB


title: PD-006_del-lsrB_Fed-batch_15h__1


title: Control PHx 24 h 1

value: PHx 24 h


title: Control PHx 24 h 2


title: DO_Mouse_Control_Fat-59

description:
RNA sequencing using MiSeq
Fat-59

value: Control


title: skeletal muscle sample 12

description:
VL17_145
Total RNA-seq


title: skeletal muscle sample 14

description:
VL17_130
Total RNA-seq


title: PD-006_del-lsrB_Fed-batch_6h__3


title: DO_Mouse_Control_Fat-65

description:
RNA sequencing using MiSeq
Fat-65

value: weeks


title: skeletal muscle sample 13

description:
VL17_029
Total RNA-seq


title: Control PHx 0 h 2

value: PHx 0 h


title: DO_Mouse_Control_Fat-58

description:
RNA sequencing using MiSeq
Fat-58


title: Control PHx 0 h 1


title: Control PHx 48 h 1


title: PD-006_del-lsrB_Fed-batch_6h__2


title: skeletal muscle sample 10

description:
VL17_042
Total RNA-seq


title: skeletal muscle sample 15

description:
VL17_152
Total RNA-seq


title: DO_Mouse_Control_Fat-57

description:
RNA sequencing using MiSeq
Fat-57


title: PD-006_del-lsrB_Fed-batch_6h__1


title: skeletal muscle sample 9

description:
VL17_119
Total RNA-seq


title: R_si_5d

city: Nanjing

first: Yuanjiao

state: China

address: Xianlin Road

institute: nanjing university of chinese medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: RAW264.7 were cultured in DMEM Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

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

value: monocyte/macrophage

tag: cell line

value: SFRS8 siRNA


title: R_WT_5d

value: negative control


title: DO_Mouse_Control_Fat-56

description:
RNA sequencing using MiSeq
Fat-56

extract_protocol:
RNA was extracted from liver, muscle, and adipose samples collected from each animal at necropsy. Tissues (10 mg liver; 20 mg muscle; 60 mg adipose) were homogenized in the FastPrep 24-5G Homogenizer (MP Biomedicals, Irvine, CA) using Lysing Matrix D tubes. The RNA extractions were completed using the Maxwell RSC simplyRNA Tissue kit (Promega, Madison, WI).  Lysate pre-processing and cartridge preparation was done on the Promega Maxprep liquid handler and extractions were performed using the Promega Maxwell RSC48 instrument.  Sample concentrations were quantified  using the NanoDrop 8000 (Thermo Fisher Scientific) and RNA quality was checked on the Agilent 5200 Fragment Analyzer System (Agilent Technologies, Santa Clara, CA) using the Standard Sensitivity RNA kit (15NT). Samples with RQN ≥ 8 (muscle and liver) and RQN ≥ 7 (adipose) were used for sequencing.
RNA libraries were prepared using TrueSeq Stranded Total RNA LP kit (Illumina, San Diego, CA) using manufacturer protocols and 100 ng of RNA. Sequencing was conducted using the MiSeq system  (Illumina, San Diego, CA).


title: PD-006_del-lsrB_Batch_6h__2

tag: culture type


title: skeletal muscle sample 8

description:
VL17_038
Total RNA-seq


title: skeletal muscle sample 7

description:
VL17_022
Total RNA-seq


title: DO_Mouse_Control_Fat-55

description:
RNA sequencing using MiSeq
Fat-55

tag: Sex


title: DO_Mouse_Control_Fat-54

description:
RNA sequencing using MiSeq
Fat-54

tag: feed type


title: PD-009_del-baeR_Fed-batch_18h__1

source_name: BW25113 del_baeR

value: BW25113 del_baeR

value: fed-batch

value: 18 hour


title: skeletal muscle sample 6

description:
VL17_072
Total RNA-seq

value: skeletal muscle


title: PD-006_del-lsrB_Batch_6h__1

value: 6 hour


title: DO_Mouse_Control_Fat-53

description:
RNA sequencing using MiSeq
Fat-53

tag: duration


title: PD-009_del-baeR_Fed-batch_12h__2

value: 12 hour


title: skeletal muscle sample 11

description:
VL17_103
Total RNA-seq


title: skeletal muscle sample 5

description:
VL17_064
Total RNA-seq


title: PD-009_del-baeR_Fed-batch_12h__1


title: Input-WT_LPS-6H-rep2

city: wuhan

first: Haojian

state: Hubei

address: Donghu Rd

department: Medical Research Institute

institute: Wuhan university

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using hisat2(version 2.1.0) default parameters
peaks were called using Macs2 with the following setting:q-value 0.01
deeptools were used to generate bigwig files
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using Bamcoverage; Scores represent RPKM

molecule: genomic DNA

source_name: BMDM

growth_protocol: PtipWT or PtipcKO mice were euthanized, and bone marrow were extracted for hindlimb femurs. Bone marrow cells were cultured for 7 days in DMEM supplemented with 10% FBS and 10ng/ml MCSF for 7 days on petri dishes to allow macrophage differentiation.

extract_protocol:
For histone ChIP-seq, lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with H3K4me1,H3K4me3 or H3K27Ac antibodies. For p300 and Hdac3 ChIP-seq, lysates were clarified from sonicated nuclei and p300-DNA or Hdac-DNA complexes were isolated with p300 or Hdac3 antibodies.
Illumina libraries were constructed using a modified custom paired-end protocol. In brief, samples were end-repaired (1*T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25 U T4 DNA polymerase, 0.75 U Klenow DNA polymerase and 7.5 U T4 polynucleotide kinase; 30 min at 21–25 C), A-tailed (1*NEB buffer 2, 0.4 mM dNTPs and 3.75 U of Klenow (exo-); 30 min at 37 C) and ligated (1*rapid DNA ligation buffer, 1 mM Illumina PE adapters and 1,600 U DNA ligase; 1–8 h at 21–25 C). Ligated fragments were amplified using indexed primers (Illumina) for 8–12 PCR cycles. DNA was purified with 1.8 volume KAPA DNA purification beads between each step.

treatment_protocol: Mouse bone marrow-derived macrophages were treated with LPS (100 ng/ml) for 0 or 6 hours.

value: BMDM

tag: antibody

value: Input

tag: genotype

value: PtipWT

tag: agent

value: LPS

tag: time point


title: Input-KO_LPS-6H-rep2

tag: cell type

value: PtipcKO


title: skeletal muscle sample 4

description:
VL17_059
Total RNA-seq


title: Input-WT_LPS-6H-rep1


title: Input-WT_0-rep2


title: Input-WT_0-rep1


title: PD-006_del-baeR_Fed-batch_12h__2

tag: time


title: skeletal muscle sample 3

description:
VL17_157
Total RNA-seq


title: DO_Mouse_Control_Fat-50

description:
RNA sequencing using MiSeq
Fat-50

data_processing:
FastQC was run on all samples to ensure adequate per base sequence quality, per base N content, and adapter content. FastQC analysis detected adapter content at the end of the reads. Trim Galore version 0.4.4 was used to trim Illumina adapter sequence from the end of the reads. Any reads that were trimmed to less than 50 bp were removed.
FASTQ files of trimmed Illumina Tru-Seq RNA-Seq reads were aligned to the pooled transcriptome of all 8 DO founder strains (ftp://churchill-lab.jax.org/software/GBRS/) using Bowtie version 1.2.2  with the following parameters: -a -v 3 --best --strata. This configuration allows up to 3 mismatches and reports all alignments. After alignment, the total sequenced reads, total aligned reads, and alignment rate were calculated for each sample.
Genome_build: The Expectation Maximization algorithm for allele-specific expression (EMASE) was used to resolve the probable origin of multireads and estimate the gene abundance. This was implemented through the GBRS software using the EMASE model M4, which apportions multi-reads equally among genes, isoforms, and alleles. Multiway allele specificity was quantified for each sample using the “quantify” function in GBRS. Then the sample’s genome was reconstructed based upon gene-level transcripts per million signals in the 8 DO founder strains using GBRS “reconstruct” function and recommended settings. For each sample, the computationally reconstructed genome was then used (“quantify” function) to estimate the expression signal resulting in normalized diploid expression for each gene for each sample. Each gene was assigned a sample-specific founder genotype signifying the two founder strains for the diploid call.
Supplementary_files_format_and_content: total counts

value: Adipose

value: male

value: Control

tag: duration unit


title: DO_Mouse_Control_Fat-52

description:
RNA sequencing using MiSeq
Fat-52

value: weeks


title: Input-KO_LPS-6H-rep1

tag: strain


title: PD-006_del-baeR_Fed-batch_12h__1


title: DO_Mouse_Control_Fat-48

description:
RNA sequencing using MiSeq
Fat-48


title: DO_Mouse_Control_Fat-49

description:
RNA sequencing using MiSeq
Fat-49


title: PD-009_del-baeR_Batch_12h__1

value: batch


title: SF-P13

city: Genova

first: Federica

last: Raggi

address: via genrolamo gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

description: Oligoarticular Juvenile Idiopathic Arthritis

data_processing:
Data processing, categorization, normalization, filtering, imputation and differential expression was carried out by PIPE-T galaxy tool.  Ct values falling within the range 14-32 were categorized as reliable values as recommended by the manufacturer guidelines. Global mean normalization was used to reduce any technical variability introduced in the data by the RT-qPCR experiments.    Only Exo-miR with at most 20% of missing values were retained for the analysis to reduce the bias introduced by imputation.  Mestdagh method was employed to assign a numeric expression value to missing values. The fold change and t test method was used to identify significant differentially expressed microRNA.
non-normalized data file reports raw Ct values. Ct value of 40 indicates a missing value. Normalized data file reports delta Ct values (Ct – sample mean expression ). NA value indicates a missing value.

label: Applied Biosystems Human TaqMan Low Density Array (TLDA, v2.0) (Card A)

source_name: Synovial fluid extracellular vesicles

label_protocol: EV-miR were analyzed by the TaqMan Array Card Technology. EV-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the Megaplex RT primers Human Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM  Pre-Amp primers Human Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiA 7 Real-Time PCR System.

extract_protocol: Extracellular vesicles (EV) isolation and RNA extraction from plasma and synovial fluid was performed with the exoRNeasy Serum/Plasma Midi kit (Qiagen Italia, Milano, Italy).

value: Synovial fluid extracellular vesicles

tag: disease state

tag: molecule subtype

value: microRNA


title: Input-KO_0-rep2


title: Input-KO_0-rep1


title: DO_Mouse_Control_Fat-47

first: Scott

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description:
RNA sequencing using MiSeq
Fat-47


title: P300-WT_LPS-6H-rep2


title: DO_Mouse_Control_Fat-51

description:
RNA sequencing using MiSeq
Fat-51


title: PD-006_del-baeR_Batch_12h__2

value: BW25113 del_baeR


title: DO_Mouse_Control_Fat-46

description:
RNA sequencing using MiSeq
Fat-46


title: SF-P11

value: Oligoarticular Juvenile Idiopathic Arthritis


title: SF-P12


title: P300-WT_LPS-6H-rep1


title: DO_Mouse_Control_Fat-44

description:
RNA sequencing using MiSeq
Fat-44


title: DO_Mouse_Control_Fat-45

description:
RNA sequencing using MiSeq
Fat-45


title: PD-009_del-arcA_Fed-batch_15h__2

source_name: BW25113 del_arcA

value: BW25113 del_arcA

value: fed-batch

value: 15 hour


title: P300-WT_0-rep2

value: BMDM


title: SF-P9


title: P300-WT_0-rep1


title: P300-KO_LPS-6H-rep2


title: SF-P8


title: DO_Mouse_Control_Fat-43

description:
RNA sequencing using MiSeq
Fat-43


title: skeletal muscle sample 2

description:
VL17_024
Total RNA-seq

value: skeletal muscle

tag: age

tag: percent of fast fibers


title: PD-009_del-baeR_Batch_12h__2

value: 12 hour


title: PD-009_del-arcA_Fed-batch_15h__1


title: skeletal muscle sample 1

description:
VL17_045
Total RNA-seq

tag: tissue


title: PD-009_del-arcA_Fed-batch_6h__2

tag: culture type

value: 6 hour


title: SF-P7


title: PD-009_del-arcA_Fed-batch_6h__1


title: P300-KO_LPS-6H-rep1

value: PtipcKO

value: LPS


title: P300-KO_0-rep2


title: SF-P6


title: DO_Mouse_Control_Fat-42

description:
RNA sequencing using MiSeq
Fat-42

value: Adipose

tag: Sex

value: male


title: PD-009_del-arcA_Batch_6h__2


title: DO_Mouse_Control_Fat-40

description:
RNA sequencing using MiSeq
Fat-40

tag: feed type

value: Control

value: weeks


title: P300-KO_0-rep1


title: PD-006_del-baeR_Batch_12h__1

value: batch


title: SF-P10

value: Synovial fluid extracellular vesicles

value: microRNA


title: PD-009_del-arcA_Batch_6h__1


title: Hdac3-WT_LPS-6H-rep2

value: PtipWT


title: PL-P13

source_name: Plasma extracellular vesicles

value: Plasma extracellular vesicles

value: Oligoarticular Juvenile Idiopathic Arthritis


title: PD-003_del-qseF_Fed-batch_21h__2

source_name: BW25113 del_qseF

value: BW25113 del_qseF

value: fed-batch

value: 21 hour


title: DO_Mouse_Control_Fat-38

description:
RNA sequencing using MiSeq
Fat-38

tag: duration


title: DO_Mouse_Control_Fat-39

description:
RNA sequencing using MiSeq
Fat-39


title: PL-P11


title: PL-P12


title: DO_Mouse_Control_Fat-36

description:
RNA sequencing using MiSeq
Fat-36


title: Hdac3-WT_0-rep2

value: BMDM

tag: antibody


title: Hdac3-WT_LPS-6H-rep1

tag: genotype


title: PD-003_del-qseF_Fed-batch_21h__1


title: PL-P10


title: DO_Mouse_Control_Fat-35

description:
RNA sequencing using MiSeq
Fat-35


title: PD-005_del-qseF_Fed-batch_15h__2

value: 15 hour


title: PD-005_del-qseF_Fed-batch_15h__1


title: Hdac3-WT_0-rep1


title: PL-P9


title: DO_Mouse_Control_Fat-41

description:
RNA sequencing using MiSeq
Fat-41


title: DO_Mouse_Control_Fat-34

description:
RNA sequencing using MiSeq
Fat-34


title: PD-005_del-qseF_Fed-batch_6h__3

value: 6 hour


title: PL-P8


title: DO_Mouse_Control_Fat-32

description:
RNA sequencing using MiSeq
Fat-32


title: PD-005_del-qseF_Fed-batch_6h__2


title: DO_Mouse_Control_Fat-33

description:
RNA sequencing using MiSeq
Fat-33


title: PL-P6


title: CTR 46

description: Healthy controls

value: healthy control


title: DO_Mouse_Control_Fat-31

description:
RNA sequencing using MiSeq
Fat-31

value: Adipose


title: Hdac3-KO_0-rep2

value: PtipcKO


title: Hdac3-KO_LPS-6H-rep1

tag: agent

value: LPS


title: PD-005_del-qseF_Fed-batch_6h__1


title: Hdac3-KO_0-rep1

tag: time point


title: PD-003_del-qseF_Fed-batch_6h__2


title: DO_Mouse_Control_Fat-30

description:
RNA sequencing using MiSeq
Fat-30

value: male

value: Control

value: weeks


title: H3K27ac-WT_LPS-6H-rep2

tag: cell type


title: CTR 41

description: Healthy controls

value: microRNA


title: PD-003_del-qseF_Fed-batch_6h__1

tag: time


title: CTR 39

description: Healthy controls


title: PD-003_del-qseF_Batch_6h__2

value: batch


title: H3K27ac-WT_LPS-6H-rep1

value: PtipWT


title: Hdac3-KO_LPS-6H-rep2


title: CTR 36

description: Healthy controls

value: Plasma extracellular vesicles


title: DO_Mouse_Control_Fat-28

description:
RNA sequencing using MiSeq
Fat-28

tag: duration unit


title: PL-P7

value: Oligoarticular Juvenile Idiopathic Arthritis


title: H3K27ac-WT_0-rep2

tag: strain


title: PD-003_del-qseF_Batch_6h__1

value: BW25113 del_qseF


title: CTR 30

description: Healthy controls

tag: disease state


title: DO_Mouse_Control_Fat-26

description:
RNA sequencing using MiSeq
Fat-26


title: DO_Mouse_Control_Fat-27

description:
RNA sequencing using MiSeq
Fat-27


title: H3K27ac-WT_0-rep1


title: CTR 13

description: Healthy controls

tag: molecule subtype


title: PD-005_del-qseF_Batch_6h__1


title: DO_Mouse_Control_Fat-25

description:
RNA sequencing using MiSeq
Fat-25


title: H3K27ac-KO_LPS-6H-rep2


title: DO_Mouse_Control_Fat-23

description:
RNA sequencing using MiSeq
Fat-23


title: PD-004_del-qseC_Fed-batch_15h__1

source_name: BW25113 del_qseC

value: BW25113 del_qseC

value: fed-batch


title: CTR 06

description: Healthy controls


title: H3K27ac-KO_0-rep2

value: BMDM


title: PD-004_del-qseC_Fed-batch_6h__2

value: 6 hour


title: DO_Mouse_Control_Fat-22

description:
RNA sequencing using MiSeq
Fat-22

source_name: Adipose


title: PD-004_del-qseC_Fed-batch_15h__2

value: 15 hour


title: H3K27ac-KO_0-rep1


title: PD-004_del-qseC_Fed-batch_6h__1


title: DO_Mouse_Control_Fat-21

description:
RNA sequencing using MiSeq
Fat-21

value: Adipose


title: H3K4me3-WT_LPS-6H-rep2


title: H3K27ac-KO_LPS-6H-rep1

value: PtipcKO


title: PD-005_del-qseF_Batch_6h__2


title: DO_Mouse_Control_Fat-19

description:
RNA sequencing using MiSeq
Fat-19


title: CTR 10

description: Healthy controls

value: healthy control


title: PD-004_del-qseC_Batch_6h__2


title: H3K4me3-WT_LPS-6H-rep1

value: LPS


title: H3K4me3-WT_0-rep2


title: DO_Mouse_Control_Fat-29

description:
RNA sequencing using MiSeq
Fat-29

value: male

value: Control


title: RNA (TET2bed) Rv-1928z+41BBL, Day 90 -3

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg38 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: Primary immune cells

extract_protocol:
Cell pellets were resuspended in RLT buffer and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN catalogue # 80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer EB. Phase separation in cells lysed in TRIzol Reagent (ThermoFisher catalogue # 15596018) was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Primary immune cells

tag: cell line

value: Primary T cells

value: TET2 KO

tag: treatment

value: CAR T cells isolated from mouse spleen (NSG) at day 90


title: RNA (TET2bed) Rv-1928z+41BBL, Day 90 -2

tag: tissue


title: RNA (WT) Rv-1928z+41BBL, Day 90 -3

value: WT


title: RNA (TET2bed) Rv-1928z+41BBL, Day 90 -1


title: PD-004_del-qseC_Batch_6h__1

tag: culture type

value: batch


title: DO_Mouse_Control_Fat-18

description:
RNA sequencing using MiSeq
Fat-18

tag: Sex

value: weeks


title: DO_Mouse_Control_Fat-17

description:
RNA sequencing using MiSeq
Fat-17

tag: feed type


title: H3K4me3-WT_0-rep1

value: PtipWT


title: RNA (WT) Rv-1928z+41BBL, Day 90 -2


title: PD-004_del-qseB_Fed-batch_15h__2

source_name: BW25113 del_qseB

value: BW25113 del_qseB

value: fed-batch


title: RNA (WT) Rv-1928z+41BBL, Day 90 -1


title: PD-004_del-qseB_Fed-batch_15h__1

value: 15 hour


title: DO_Mouse_Control_Fat-16

description:
RNA sequencing using MiSeq
Fat-16

value: Adipose

tag: duration


title: DO_Mouse_Control_Fat-15

description:
RNA sequencing using MiSeq
Fat-15


title: PD-004_del-qseB_Fed-batch_6h__2

value: 6 hour


title: PD-004_del-qseB_Fed-batch_6h__1


title: DO_Mouse_Control_Fat-20

description:
RNA sequencing using MiSeq
Fat-20


title: H3K4me3-KO_0-rep2

value: BMDM

tag: antibody

value: PtipcKO


title: H3K4me3-KO_LPS-6H-rep1

tag: genotype

value: LPS


title: H3K4me3-KO_0-rep1


title: DO_Mouse_Control_Fat-13

description:
RNA sequencing using MiSeq
Fat-13

value: male

value: Control


title: PD-004_del-qseB_Batch_6h__1


title: ATAC (TET2bed) Rv-1928z+41BBL, Day 90 -1

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg38 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp and the signal was then normalized to the size factor calculation in DESeq2 and created using the BEDTools suite.
Assembly: hg38
Supplementary files format and content: bigWig file with normalized read density

extract_protocol:
50,000 fresh T cells were washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalogue # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalogue # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalogue # M0541L). After evaluation by real-time PCR, 8 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalogue # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio.
Libraries were sequenced on a HiSeq4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 108 million paired reads were generated per sample.

value: Primary immune cells

value: Primary T cells


title: PD-003_del-phoB_Fed-batch_21h__2

source_name: BW25113 del_phoB

value: BW25113 del_phoB

value: 21 hour


title: ATAC (WT) Rv-1928z+41BBL, Day 90 -3

value: WT

value: CAR T cells isolated from mouse spleen (NSG) at day 90


title: H3K4me1-WT_LPS-6H-rep2

value: PtipWT

tag: agent


title: DO_Mouse_Control_Fat-12

description:
RNA sequencing using MiSeq
Fat-12

value: weeks


title: H3K4me3-KO_LPS-6H-rep2

tag: time point


title: DO_Mouse_Control_Fat-11

description:
RNA sequencing using MiSeq
Fat-11


title: PD-003_del-phoB_Fed-batch_21h__1

value: fed-batch


title: ATAC (WT) Rv-1928z+41BBL, Day 90 -2

tag: cell type


title: H3K4me1-WT_0-rep2


title: DO_Mouse_Control_Fat-10

description:
RNA sequencing using MiSeq
Fat-10


title: H3K4me1-WT_LPS-6H-rep1


title: PD-005_del-phoB_Fed-batch_15h__2

tag: time

value: 15 hour


title: H3K4me1-WT_0-rep1


title: DO_Mouse_Control_Fat-9

description:
RNA sequencing using MiSeq
Fat-9

value: Adipose

tag: duration unit


title: ATAC (TET2bed) Rv-1928z+41BBL, Day 90 -3

value: TET2 KO


title: ATAC (TET2bed) Rv-1928z+41BBL, Day 90 -2


title: DO_Mouse_Control_Fat-14

description:
RNA sequencing using MiSeq
Fat-14


title: H3K4me1-KO_LPS-6H-rep2

value: BMDM

tag: strain


title: PD-005_del-phoB_Fed-batch_6h__2

value: 6 hour


title: H3K4me1-KO_LPS-6H-rep1

value: PtipcKO

value: LPS


title: DO_Mouse_Control_Fat-8

description:
RNA sequencing using MiSeq
Fat-8

value: male

value: Control


title: DO_Mouse_Control_Fat-7

description:
RNA sequencing using MiSeq
Fat-7


title: Gastric cancer 8 [GC8]

city: Jinan

first: Ai

last: Li

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

institute: 山东大学

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 (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Gastric cancer

value: stomach; gastric tissue

value: untreated

tag: tissue subtype

value: Gastric cancer


title: H3K4me1-KO_0-rep2


title: Gastric cancer 9 [GC9]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: H3K4me1-KO_0-rep1


title: ATAC (WT) Rv-1928z+41BBL, Day 90 -1

value: Primary immune cells

value: Primary T cells

value: WT


title: DO_Mouse_Control_Fat-6

city: Durham

last: Auerbach

description:
RNA sequencing using MiSeq
Fat-6

value: weeks


title: Gastric cancer 7 [GC7]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Gastric cancer 6 [GC6]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: TAM-KO2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.1.0) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized  counts  each Sample

source_name: TAM

growth_protocol: MC38 cells were maintained in complete RPMI medium 1640 (Thermo Fisher), with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG) at 37°C/5% CO2. For induction of tumor, MC38 cells were injected subcutaneously into the flanks of mice (1×105 cells per injection in 100μl PBS). Male C57BL/6J mice of 6 to 8 weeks of age were used. Tumors were harvested at 3 weeks, and TAMs were isolated by FACS-sorting of CD45+CD11b+F4/80+ Ly6G- cells.

extract_protocol:
Total RNA of TAMs were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

value: tumor associated macrophages


title: TAM-KO3


title: Gastric cancer 4 [GC4]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: DO_Mouse_Control_Fat-5

description:
RNA sequencing using MiSeq
Fat-5


title: Gastric cancer 10 [GC10]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Gastric cancer 5 [GC5]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: PD-005_del-phoB_Fed-batch_15h__1

value: BW25113 del_phoB

value: fed-batch

value: 15 hour


title: TAM-KO1


title: Gastric cancer 3 [GC3]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: DO_Mouse_Control_Fat-2

description:
RNA sequencing using MiSeq
Fat-2

value: Adipose


title: TAM-W3

value: PtipWT


title: Gastric cancer 2 [GC2]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: DO_Mouse_Control_Fat-1

description:
RNA sequencing using MiSeq
Fat-1


title: TAM-W2


title: Gastric cancer 1 [GC1]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: DO_Mouse_Control_Fat-4

description:
RNA sequencing using MiSeq
Fat-4


title: TAM-W1


title: Intestinal metaplasia 10 [IM10]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

source_name: Intestinal metaplasia

value: Intestinal metaplasia


title: DO_Mouse_Control_Fat-3

description:
RNA sequencing using MiSeq
Fat-3


title: Intestinal metaplasia 9 [IM9]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Intestinal metaplasia 8 [IM8]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: BMDM-KO2-0

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.1.0) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts each Sample

extract_protocol:
BMDMs were collected after treated with LPS(100ng/ml) for 0 or 6 hours. Total RNA were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: BMDM

value: PtipcKO


title: BMDM-KO2-LPS-6H

value: LPS


title: T_M_6_R1

city: Lisbon

first: Vanessa

last: Azevedo

address: Campo Grande

department: Plant Biology Department

country: Portugal

institute: Biosystems & Integrative Sciences Institute

description: Gene Expression at 6hpi with water

hyb_protocol: Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C), using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Array images were analyzed using Agilent Feature Extraction software version 10.7.1.1 (Agilent Technologies, Santa Clara, CA). Default parameters (Protocol name_GE1_107_Sep09_grid name_028416_D_F_20100513) were used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as non-uniform outliers were excluded. To improve the resolution of the analysis, for the outliers, R Sincell workpakage was applied to obtain gProcessed Signals. GeneSpring MultiOmics Analysis version 14.9 (Agilent Technologies, Santa Clara, CA) was used. Data was normalised through a percentile shift of 75%, baseline median of all samples and different types of filters (expression, flag, data file and error - coefficient of variance <20%).

organism: Vitis vinifera

source_name: Tolerant, Mock, 6hpi, Replicate 1

growth_protocol: Grapevine cuttings were harvested, cut in similar sizes (with 2 buds per cutting) and partially immersed in a 30°C water bath within a 4°C chamber for 2 months. The cuttings were transferred to square plastic pots with a mixture of seedling substrate and perlite (3:1 v/v). Afterwards, the cuttings were placed in a greenhouse for 2 months with natural light conditions at a temperature between 5°C and 30°C.

extract_protocol: Total RNA was extracted from 0.1 g of leaves with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands).

treatment_protocol: On the adaxial side of the leaves of the different grapevine genotypes, P. viticola sporangia suspension (1.8x104 sporangia/ml) was sprayed on. As a control of the in vivo assay, plants were sprayed with water (mock inoculation).

value: N23/018 from cross population Red Globe x  Regal Seedless

value: Leaf

value: 6hpi with water


title: T_M_6_R3

description: Gene Expression at 6hpi with water

source_name: Tolerant, Mock, 6hpi, Replicate 3

label_protocol: Agilent Technologies, One-Color Microarray-based Gene expression Analyses, protocol version 6.9.1


title: T_M_6_R2

description: Gene Expression at 6hpi with water

source_name: Tolerant, Mock, 6hpi, Replicate 2


title: BMDM-KO1-LPS-6H


title: T_I_6_R3

description: Gene Expression at 6hpi with P. viticola

source_name: Tolerant, Inoculates, 6hpi, Replicate 3

value: 6hpi with P. viticola


title: T_M_24_R3

description: Gene Expression at 24hpi with water

source_name: Tolerant, Mock, 24hpi, Replicate 3

value: 24hpi with water


title: T_M_24_R2

description: Gene Expression at 24hpi with water

source_name: Tolerant, Mock, 24hpi, Replicate 2


title: Intestinal metaplasia 6 [IM6]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼

value: stomach; gastric tissue

value: untreated


title: T_M_24_R1

description: Gene Expression at 24hpi with water

source_name: Tolerant, Mock, 24hpi, Replicate 1


title: T_I_6_R2

source_name: Tolerant, Inoculates, 6hpi, Replicate 2


title: T_I_6_R1

source_name: Tolerant, Inoculates, 6hpi, Replicate 1


title: BMDM-KO1-0

source_name: BMDM


title: BMDM-WT2-LPS-6H


title: Intestinal metaplasia 4 [IM4]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: BMDM-WT2-0


title: BMDM-WT1-LPS-6H


title: T_I_24_R3

description: Gene Expression at 24hpi with P. viticola

source_name: Tolerant, Inoculates, 24hpi, Replicate 3

value: 24hpi with P. viticola


title: Intestinal metaplasia 7 [IM7]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: Intestinal metaplasia 3 [IM3]

address: 山东省济南市历下区文化西路44号山东大学趵突泉校区9号公寓楼


title: BMDM-WT1-0