title: Limb cells, WT_124

value: limb cells


title: Limb cells, WT_123

status: Public on Oct 14 2022

type: SRA

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Raw sequencing reads was processed with Perl scripts to ensure the quality of data used in further analysis. We first removed the adaptor-polluted reads (reads containing more than 5 adapter-polluted bases) and the low-quality reads (reads with the number of phred Quality value less than 19 accounting for more than 15% of total bases). And then discarded reads with number of N bases accounting for more than 5 %. The obtained clean data was mapped to the mm10 genome release with bowtie2 using default parameters. Reads count for each gene in each sample was counted by HTSeq.
The reads were mapped to the mouse genome (mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Limb cells, WT

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: In general, embryonic experiments were performed on pooled sibling limbs of one litter (three to five limbs per pool). Embryos were genotyped and wild-type and Scx-/- mice were dissected and limbs were isolated. We finely chopped the tissue with small scissors in a drop of DMEM, and then digested the tissues in type I Collagenase 0.1% / Trypsin 0.05% (Life Technologies) diluted in low-glucose Dulbecco’s modified Eagle’s (L-DMEM) medium (Gibco) solution at 37°C for 10 min. Then, we let tissues to settle down and collected the supernatant in a fresh 50 ml tube, before adding 10-20% of fetal bovine serum to quench trypsin (on ice to stop collagenase). We repeated digestion steps for 4 times or more till all tissues are digested. The supernatants were then pooled. We filtered the pooled supernatants through 70μ cell filters (Falcon BD), and centrifuge for 10 min at 1600 rpm, before re-suspending the pellet in DMEM containing 2% serum, and kept cell suspension on ice until load on chip.

tag: age

tag: genotype

value: WT

tag: cell type


title: patient 4, day0, scRNA-seq

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

description:
C1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 and reference GRCh38-2020-A (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCh38-2020-A
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs were cryopreserved until ready to create library. PBMCs were quickly thawed at 37degrees celcius, washed to remove freezing media, and resuspended in PBS + 0.1% low endotoxin BSA to confirm viability of cells was >80%.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

tag: individual

value: patient 4

tag: disease state

value: PBMC

tag: treatment

value: PEG-IFN-lambda

tag: timepoint


title: patient 4, day3, scRNA-seq

description:
C2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: 2_WT_SD-HS_t90

city: Jena

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

country: Germany

institute: HKI Jena

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_A22_current_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.4.2). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_albicans_SC5314_A22_current_chromosomes.fasta
Supplementary files format and content: Raw.Counts.C.Albicans.Hyphae.csv, Comma seperated text file containing counts of all samples

organism: Candida albicans

source_name: Planktonic cells

growth_protocol: C. albicans were pre-grown overnight at 37°C in SD and used to set log-cultures in SD at OD600 0.3. Log-cultures were incubated at 37°C until OD600 of ~1 was reached. Cells were collected, washed with and resuspended in 1xYNB solution and used to set OD600 to 0.3 in the respective test medium and incubated at 37°C. Cells used for inoculation were also collected for t 0 min. After the indicated time test cultures were split and used for either metabolite or RNA extraction. All cultures were incubated in flasks with 180 pm shaking.

extract_protocol:
For total RNA isolation cells were resuspended in 440 µl AE buffer with 10% SDS and 440 µl of Acid-phenol:Chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed and incubated for 5 min at 65°C, frozen at -20°C for 30 min and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min centrifugation at 16000 g, the upper aqueous phase transferred and 1/10 of the volume sodium acetate (pH 5.3) and 1 volume of 2 propanol was added to precipitate the RNA for at least 30 min at -20°C. The supernatant was discarded after 10 min centrifugation at 12000 g, the RNA pellet washed twice with 80 % ethanol and finally solved in 300 µl nuclease free H2O. Quality and quantity of the RNA was assessed using 2100 Bioanalyzer (Agilent Technologies, California, USA) and Nanodrop (Thermo Fischer Scientific, Massachusetts, USA) measurements.
A total amount of 0.4 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA by mRNAusing poly-T oligo-attached magnetic beads. Fragmentation was carried out by Covaris sonication. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using dTTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality and quantity are assessed by Qubit and real-time PCR. Sequencing platform was Illumina Novaseq 6000 PE150.
Paired end RNA sequencing of cDNA fragments of preferentially 150~200 bp in length.

treatment_protocol: Cells were separated from test medium by centrifugation 2 min at 4000g and 4ºC. Cells were snap frozen in liquid nitrogen and stored at -80°C until further processing.

tag: strain

value: Strain

tag: genotype/variation

value: wild type

tag: media type

value: SD with 10% human serum

tag: time point

value: 90 min


title: Limb cells, WT_122


title: Limb cells, WT_121


title: 1_WT_SD-HS_t90


title: patient 3, day7, scRNA-seq

description:
B6
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 3

value: Placebo


title: Dendritic_cell_22_hrs_Don3

city: Nijmegen

first: Lea

last: Weiss

address: Geert Grooteplein Zuid 28, Dept Tumor Immunology, Route 278

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences, Radboudumc

data_processing:
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the mouse mm10 reference transcriptome using BWA MEM [Li and Durbin, 2009; PMID 20080505]. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Assembly: mm10
Supplementary files format and content: Text files with raw counts per gene

source_name: Spleen and lymph nodes

growth_protocol: CD8+ OT-I T lymphocytes were isolated from spleen and lymph nodes and cultured in RPMI medium (GibcoTM, 42401042) supplemented with 10% FBS, 2mM L-Glutamine, 0.5% Antibiotics/Antimycoticum and 50 µm beta-mercaptoethanol.

extract_protocol:
For mRNA sequencing, cells were stained for viability, CD8 expression and CD103 expression. Viable cells were sorted for CD8+ and CD103-. Sorted cells were lysed in 200 µl TRIzol (Thermo Fisher, 15596026) and stored at -80°C before sending to Single Cell Discoveries B.V.
Sequencing was performed using an adapted version of the CEL-seq protocol. In brief: Total RNA was extracted using the standard TRIzol protocol and used for library preparation and sequencing. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq.[42,43] In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight in vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).

treatment_protocol: CD8+ OT-I T lymphocytes (50,000 cells per 96 U bottom well) were stimulated with either 5ng/ml immunofilaments or 20,000 Flt-3Ligand dendritic cells pulsed with the SIITFEKL peptide.

tag: tissue

value: Spleen and lymph nodes

value: OT-1 aka C57BL/6-Tg(TcraTcrb)1100Mjb/Crl// Charles River

value: CD8+ OT-I T lymphocyte

tag: Sex

value: female

tag: time

value: 22 hr

value: Dendritic cell


title: Dendritic_cell_22_hrs_Don1


title: 4_ΔΔ_SD_t240

value: SD

value: 240 min


title: patient 6, day0, scRNA-seq

description:
D1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 6


title: IF-pMHC(SIIT)/IL-2_22_hrs_Don2


title: IF-pMHC(SIIT)/IL-2_22_hrs_Don3


title: CZ5837_1

city: Prague

first: Martin

last: Bezdicka

state: Czech Republic

address: V Uvalu 84

department: Department of Pediatrics

country: Czech Republic

institute: Second Faculty of Medicine and Motol University Hospital

data_processing:
Illumina BaseSpace Sequence Hub was used for basecalling.
Trimming using cutadapt.
Aligned against hg38 with the Gencode annotation release 38 (May 2021), performed along with gene counting by the STAR aligner with parameters mostly set as advised by the manufacturer of the Collibri library construction kit.
Gene counts provided by the STAR program.
The gene counts tables and the sample metadata were assembled into a DESeq2 DESeqDataSet object.
Assembly: hg38 with the Gencode annotation release 38 (May 2021).
Supplementary files format and content: raw gene counts per sample

source_name: Human podocytes with steroid-resistant nephrotic syndrome serum CZ5837

growth_protocol: The standard cultivation medium consisted of RPMI 1640 with 10 % FBS heat inactivated, 1 % insulin-transferrin-selenium (1 % penicillin-streptomycin only in undifferentiated state).

extract_protocol:
The cells were lysed and the RNA was harvested using Trizol reagent and the PureLink RNA Mini Kit.
Collibri™ 3´ mRNA Library Prep Kit (ThermoFisher Scientific, A38110096).

treatment_protocol: 10 %  human serum samples (from SSNS or SRNS patients) were incubated at 37°C in 5% CO2 for 72 hours in standard medium without FBS and ITS. There were three biological replicates for all samples.

value: Differentiated human immortalized podocytes

value: standard cultivation medium

tag: clinical group

value: steroid-resistant

tag: replicates

value: biological replicate 5837, technical replicate 1


title: IF-pMHC(SIIT)/IL-2_22_hrs_Don1


title: Limb cells, WT_120

value: WT

value: limb cells


title: Dendritic_cell_8_hrs_Don3

value: 8 hr


title: patient 3, day0, scRNA-seq

description:
B4
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 3

value: PBMC

value: Placebo


title: Limb cells, WT_11


title: Dendritic_cell_22_hrs_Don2

value: Spleen and lymph nodes

value: OT-1 aka C57BL/6-Tg(TcraTcrb)1100Mjb/Crl// Charles River

value: CD8+ OT-I T lymphocyte


title: 1_ΔΔ_SD_t240

value: Strain


title: Limb cells, WT_119


title: 2_ΔΔ_SD_t240

value: SD


title: Dendritic_cell_8_hrs_Don2

value: female

value: Dendritic cell


title: Limb cells, WT_118


title: 4_ΔΔ_SD_t90

value: 90 min


title: patient 2, day7, scRNA-seq

description:
B3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 2

value: PEG-IFN-lambda


title: Dendritic_cell_8_hrs_Don1


title: IF-pMHC(SIIT)/IL-2_8_hrs_Don3


title: 3_ΔΔ_SD_t90


title: IF-pMHC(SIIT)/IL-2_8_hrs_Don2


title: Limb cells, WT_117


title: Limb cells, WT_116


title: 2_ΔΔ_SD_t90


title: patient 3, day3, scRNA-seq

description:
B5
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: patient 1, day3, scRNA-seq

description:
A2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

value: patient 1


title: patient 2, day0, scRNA-seq

description:
B1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: 1_ΔΔ_SD_t90


title: IF-pMHC(SIIT)/IL-2_8_hrs_Don1


title: patient 1, day7, scRNA-seq

description:
A3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: patient 2, day3, scRNA-seq

description:
B2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt


title: 3_ΔΔ_SD_t240

value: 240 min


title: Limb cells, WT_114

value: WT

value: limb cells


title: 4_hgc1Δ_SD_t240


title: Limb cells, WT_115


title: Unstimulated_0_hrs_Don3

value: 0 hr

value: No treatment


title: Limb cells, WT_113


title: Unstimulated_0_hrs_Don1


title: 3_hgc1Δ_SD_t240


title: 2_hgc1Δ_SD_t240


title: 1_hgc1Δ_SD_t240


title: Limb cells, WT_111


title: Limb cells, WT_112


title: KP3_cells_siRNA_NEK7

city: Shenzhen

first: Jianhua

last: Qu

state: Guangdong

address: Lianhua Road 1120

institute: Peking University ShenZhen Hospital

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to human genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: cell line

value: human cells

value: NEK7 knockdown


title: KP3_cells_siRNA_NEK6

value: NEK6 knockdown


title: Limb cells, WT_10

tag: age


title: CFPAC_cells_siRNA_NEK7

source_name: CFPAC

value: CFPAC

tag: genotype


title: 4_hgc1Δ_SD_t90

value: Strain


title: 3_hgc1Δ_SD_t90

value: SD


title: Limb cells, WT_109

tag: cell type


title: CFPAC_cells_siRNA_NEK6


title: patient 1, day0, scRNA-seq

description:
A1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Metadata.txt

tag: individual

value: PBMC


title: Unstimulated_0_hrs_Don2

value: Spleen and lymph nodes

value: OT-1 aka C57BL/6-Tg(TcraTcrb)1100Mjb/Crl// Charles River

value: CD8+ OT-I T lymphocyte

value: female


title: Limb cells, WT_107


title: Limb cells, WT_106


title: Limb cells, WT_108


title: 2_WT_SD_t240

value: wild type


title: 4_WT_SD_t240

value: 240 min


title: CFPAC_cells_siRNA Control

value: WT


title: 3_WT_SD_t240


title: Limb cells, WT_104

value: limb cells


title: 1_hgc1Δ_SD_t90

value: 90 min


title: Limb cells, WT_105


title: 1_WT_SD_t240


title: 4_WT_SD_t90


title: KP3_cells_siRNA Control


title: Limb cells, WT_103


title: Limb cells, WT_110


title: 3_WT_SD_t90


title: Limb cells, WT_100


title: Limb cells, WT_102


title: 2_WT_SD_t90


title: 1_WT_SD_t90


title: Limb cells, WT_101


title: 4_ΔΔ_t0

value: 0 min


title: 2_hgc1Δ_SD_t90


title: 3_ΔΔ_t0


title: 2_ΔΔ_t0


title: 1_ΔΔ_t0


title: Saccharomyces cerevisiae-eaf1d (Swc4-13myc)-repeat2

city: Shanghai

first: Yue

last: Pan

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science, CAS

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description:
ChIP_eaf1d_ip.bw (Integrating repeat1 and repeat2 of eaf1d)
ChIP_eaf1d_peaks.narrowPeak (Integrating repeat1 and repeat2 of eaf1d)
eaf1d_vs_input_rDNA_log2.bw (Integrating repeat1 and repeat2 of eaf1d)

library_source: genomic

data_processing:
Paired-end sequencing reads were trimmed for adaptor and low-quality reads by fastp (version: 0.21.0).
Then, trimmed reads was aligned to the reference genome (Saccharomyces genome database: https://www.yeastgenome.org) using subcommand mem of BWA (version: 0.7.15-r1140) with default parameters.
Bam file was sorted and de-duplicated using the samtools (version: 1.4).
We used MACS2 (Version: 2 2.1.1.20160309) to call Swc4 ChIP–seq peaks with the qvalue < 0.05
GTF (gene transfer format) file for Saccharomyces cerevisiae was used to annotate the ChIP-seq peaks.
Assembly: S288C
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The yeast cells inoculated in to 50 ml YPD medium were grown to mid-log phase (0D600 ~0.6).

extract_protocol:
The yeast cell lysates were clarified from sonicated nuclei and Swc4-DNA complexes were isolated with antibody.
Sequencing library was constructed by The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, cat#E7645).

value: yeast cell

tag: chip antibody

value: c-Myc, Sigma-Aldrich, cat#M4439

value: eaf1d with SWC4-13MYC

tag: culture protocol

value: mid-log phase yeast cells, cultured at 30°C


title: Saccharomyces cerevisiae-wild-type (no tag)-repeat2

value: wild-type with no-tag


title: HeLa cells, Double_2

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
RNAseq samples were analyzed by NovaSeq 6000 instrument (Illumina).
The sequencing reads were aligned to the reference genome (hg38) using STAR (v2.5.3). Reads on each refSeq gene were counted with HTSeq (v0.6.0) using intersection-strict mode, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.1. After filtering out genes with a maximum count per million (CPM) across all samples less than 1, trimmed mean of M-values normalization (TMM) method and generalized linear models were used to compare gene expression data.
Genome_build: hg38
Supplementary_files_format_and_content: Summary txt file includes normalized CPM values.

source_name: HeLa cells

growth_protocol: HeLa cells were plated in 6-well plate (1.0×10^5 cells per well). After overnight culture, HeLa cells were transfected with miR-control 20nM (control), miR-128-3p 10nM + miR-control 10nM (miR-128), miR-148a-3p 10nM + miR-control 10nM (miR-148a), or miR-128-3p 10nM + miR-148a-3p 10nM (miR-128/148a) by lipofectamine RNAiMAX (Thermo Fisher Scientific).

extract_protocol:
48 hours after transfection, total RNA was extracted by miRNeasy Micro Kit.
Libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and Nextera XT DNA Library Prep Kit (Illumina) and were subjected to paired-end sequencing using NovaSeq 6000 instrument (Illumina).

treatment_protocol: Cells were directly subjected to RNA-seq analysis.

value: HeLa

tag: treatment

value: Double transfection of miR-128 and miR-148a mimic


title: 4_hgc1Δ_t0

tag: strain

value: Strain

value: SD


title: Saccharomyces cerevisiae-wild-type (no tag)-repeat1


title: Saccharomyces cerevisiae-swr1d (Swc4-13myc)-repeat1

description:
ChIP_swr1d_ip.bw (Integrating repeat1 and repeat2 of swr1d)
ChIP_swr1d_peaks.narrowPeak (Integrating repeat1 and repeat2 of swr1d)
swr1d_vs_input_rDNA_log2.bw (Integrating repeat1 and repeat2 of swr1d)

value: swr1d with SWC4-13MYC


title: Saccharomyces cerevisiae-swr1d (Swc4-13myc)-repeat2


title: HeLa cells, Double_1


title: Saccharomyces cerevisiae-eaf1d (Swc4-13myc)-repeat1


title: HeLa cells, Double_3


title: Saccharomyces cerevisiae-yaf9d (Swc4-13myc)-repeat2

description:
ChIP_yaf9d_ip.bw (Integrating repeat1 and repeat2 of yaf9d)
ChIP_yaf9d_peaks.narrowPeak (Integrating repeat1 and repeat2 of yaf9d)
yaf9d_vs_input_rDNA_log2.bw (Integrating repeat1 and repeat2 yaf9d)

value: yaf9d with SWC4-13MYC


title: 3_hgc1Δ_t0

tag: genotype/variation


title: Saccharomyces cerevisiae-yaf9d (Swc4-13myc)-repeat1


title: 2_hgc1Δ_t0

tag: media type


title: HeLa cells, miR148a_3

value: miR-148a mimic transfection


title: HeLa cells, miR148a_2


title: Saccharomyces cerevisiae-wild-type (Swc4-13myc)-repeat2

description:
ChIP_wt_ip.bw (Integrating repeat1 and repeat2 of wild-type)
ChIP_wt_peaks.narrowPeak (Integrating repeat1 and repeat2 of wild-type)
wt_vs_input_rDNA_log2.bw (Integrating repeat1 and repeat2 of wild-type)

value: wild-type with SWC4-13MYC


title: 1_hgc1Δ_t0

tag: time point


title: HeLa cells, miR128_3

value: miR-128 mimic transfection


title: 4_WT_t0

value: wild type


title: 3_WT_t0


title: HeLa cells, miR148a_1


title: FLAG_Foxf2_tongue_Input

city: Cincinnati

first: Jingyue

last: Xu

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

country: USA

institute: Cincinnati Children's Hospital

data_processing:
Raw FASTQ files were aligned to mm10 reference genome using Bowtie2 (2.4.1).
Sam files were converted to bam using samtools (1.7.1)
Peak calling was performed using the HOMER (Hypergeometric Optimization of Motif EnRichment) software (4.11.1).
The input sample were used as the control for calling peaks from the Foxf2-FLAG ChIP-seq data sets.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file was generated by Homer including the peak information

source_name: embryonic tongue cells

growth_protocol: We generated mice carrying 3xFLAG epitope-tagged endogenous Foxf2 protein using the CRISPR/Cas9-mediated genome editing technology. 75 tongue tissues were dissected from Foxf2FLAG/FLAG embryos at E12.5.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with anti-FLAG antibody.
Sequencing libraries were generated using ThruPLEX DNA sequencing kit (Takara).

tag: developmental stage

value: none input


title: HeLa cells, miR128_2


title: FLAG_Foxf2_tongue_ChIP_2

value: anti-FLAG


title: 2_WT_t0

value: 0 min


title: AS.PRLR.3

type: RNA

first: YingNa

last: Liao

address: No. 25, Lane 2200, Xietu Road, Shanghai

institute: Shanghai Cancer institute

description: MiRNA expression data from biological replicate 3 of AsPC-1 cells overexpressed PRLR.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) 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: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AsPC-1 cells, oe-PRLR, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PRLR overexpression cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: tissue

value: pancreas; Derived from metastatic site: ascites

value: oe-PRLR


title: 1_WT_t0


title: KO1

first: Ju

last: Qiu

address: 320 Yueyang Road

description: cells were isolated from steady state spleen.

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Quality filtered reads were mapped to mouse genome (mm10) using “HISAT2” (Galaxy Version 2.2.1).
Gene raw counts were analyzed by “FeatureCounts” (Galaxy Version 2.0.1) and genes were annotated by “annotateMyIDs” (Galaxy Version 3.12.0). Differential gene expression was analyzed by  edgeR (Galaxy Version 3.34.0).
Assembly: mm10
Supplementary files format and content: csv, raw counts of sequencing reads from replicates samples with tracking ID, gene short name.

source_name: SP Tregs

extract_protocol:
Cells were lysed in Trizol (Invitrogen) and total RNA was extracted.
Library construction and sequencing was performed by BGI Genomics, BGI-Wuhan. RNA were treated with DNase I and purified with magnetic beads with Oligo (dT). RNA were mixed with the fragmentation buffer and were fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. Suitable fragments were selected for the PCR amplification as templates. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used for quantification and qualification of the sample library. 150bp paired sequencing was performed using Illumina HiSeqTM4000.

value: spleen

value: Tregs

tag: cell markers

tag: mouse genotype


title: HeLa cells, Control_2

value: HeLa

value: miRNA control


title: H3K36me3-input

description: cells were isolated from steady state spleen

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Quality filtered reads were then mapped to mouse genome (mm10) by Bowtie2, and only uniquely mapped reads were saved.
Peak calling was done using MACS2 with an initial threshold q-value of 0.01 as cutoff based on input.
Identified peaks were merged with “bedtools Multiple Intersect” followed by “bedtools MergeBED” function
Raw counts based on BED file of merged peaks were extracted using bedtools MultiCovBed
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts of sequencing reads from samples with chromosome ID, chromosome start and end positions.

source_name: spleen Tregs

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated using the EpiShear™ Probe Sonicator (Active Motif, cat # 53051) with an EpiShear™ Cooled Sonication Platform (Active Motif, cat # 53080) and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking (overnight at 65°C) followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. Equal amount of chromatin (1µg) from the splenic or intestinal Tregs were used per immunoprecipitation (IP) reaction (H3K36me3 (Active Motif 61101).
Single-end 75nt sequencing was performed with Illumina NextSeq 500

treatment_protocol: Lymphocytes were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

value: H3K36me3 (Active Motif 61101)


title: KO2


title: HeLa cells, miR128_1


title: CTRL2


title: H3K36me3-spleen


title: AS.Ctrl.3

description: MiRNA expression data from biological replicate 3 of AsPC-1 cells overexpressed Ctrl.

source_name: AsPC-1 cells, oe-ctrl, replicate 3

value: control


title: AS.PRLR.1

description: MiRNA expression data from biological replicate 1 of AsPC-1 cells overexpressed PRLR.

source_name: AsPC-1 cells, oe-PRLR, replicate 1


title: H3K36me3-LI

description: cells were isolated from steady state large intestine

source_name: LI Tregs

value: large intestine


title: Saccharomyces cerevisiae-wild-type (Swc4-13myc)-repeat1

value: yeast cell

value: c-Myc, Sigma-Aldrich, cat#M4439

value: mid-log phase yeast cells, cultured at 30°C


title: CTRL1


title: AS.Ctrl.2

description: MiRNA expression data from biological replicate 2 of AsPC-1 cells overexpressed Ctrl.

source_name: AsPC-1 cells, oe-ctrl, replicate 2


title: AS.Ctrl.1

description: MiRNA expression data from biological replicate 1 of AsPC-1 cells overexpressed Ctrl.

source_name: AsPC-1 cells, oe-ctrl, replicate 1


title: s70-15-3_HNG33CCXX_L5

status: Public on Oct 13 2022

first: lianyu

last: lin

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

description: From isolate s70-15, Biological Replicate 3

data_processing:
An in-house Perl program was used to select clean reads by removing adaptor sequences, low quality sequences (sQ<=5) and reads with more than 10% N bases.
Sequencing reads adapters were trimmed by Trimmomatic and mapped to reference sequence with Tophat. Cufflinks and Cuffmerge were further used to extract all possible exon. Short reads were realigned to all exon sequence by Bowtie2, and expression abundance were calculated by RSEM with default parameters.
Assembly: 70-15 reference genome
Supplementary files format and content: Matrix table with TPM for every gene and every sample

organism: Pyricularia oryzae

source_name: hypha

growth_protocol: Magnaporthe oryzae strain MoRho3-CA/MoRho3-DN and 70-15 have been used in this study. The generation of MoRho3-CA/MoRho3-DN are descripted in previous study. The hyphae cultured at 26 °C using liquid complete medium (CM: 0.6% yeast extract, 0.6% casein hydrolysate, 1% sucrose, 1.5% agar) were harvested from 10-day-old samples. The leaves of 8-day-old barley (Hordeum vulgare cv. Gold Promise) and four-week-old rice seedlings (Oryza sativa L.) cultivar TP309 were inoculated with the hyphae suspension at 0.02% Tween solution. The plants were examined for disease symptoms at 7 days post inoculation (dpi).

extract_protocol:
Total RNA was extracted with the RNAprep pure Plant Kit (Tiangen, Beijing) according to the manufacturer’s instructions. RNA integrity and quantity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions
The cDNA library was sequenced on the Illumina sequencing platform (IlluminaHiSeq™ 2000) with 150 bp pair-end reads length and ~280 bp insert size

value: hypha

tag: isolate


title: s70-15-2_HNG33CCXX_L5

description: From isolate s70-15, Biological Replicate 2


title: s70-15-1_HNG33CCXX_L5

description: From isolate s70-15, Biological Replicate 1


title: CA-3_HNFMMCCXX_L2

description: From isolate CA, Biological Replicate 3

value: CA


title: CA-2_HNFMMCCXX_L2

description: From isolate CA, Biological Replicate 2


title: DN-2_HNFMMCCXX_L2

description: From isolate DN, Biological Replicate 2

value: DN


title: DN-3_HNFMMCCXX_L2

description: From isolate DN, Biological Replicate 3


title: AS.PRLR.2

description: MiRNA expression data from biological replicate 2 of AsPC-1 cells overexpressed PRLR.

source_name: AsPC-1 cells, oe-PRLR, replicate 2

tag: cell line


title: HeLa cells, Control_3


title: FLAG_Foxf2_tongue_ChIP_1

value: anti-FLAG


title: CA-1_HNFMMCCXX_L2

description: From isolate CA, Biological Replicate 1


title: Retina, Fbxl11-CKO, P7, rep4 [RNA-seq]

city: Tokyo

first: Toshiro

last: Iwagawa

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

data_processing:
Sequenced reads were mapped to the mouse genome (GENCODE GRCm38.p6) using HISAT2. Generated SAM files were converted to BAM files using SAMtools. Mapped fragments were counted using featureCounts, normalized and compared using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Excel files including count data for each Sample

source_name: retina

extract_protocol:
Total RNA was extracted from Fbxl11-CKO or control whole retinas at P7 using TRIzol LS Reagent.
The RNA-seq libraries were prepared using TruSeq Strand mRNA Sample Preparation Kit (Illumina, USA).

value: retina

tag: time


title: Retina, Fbxl11-CKO, P7, rep2 [RNA-seq]

tag: genotype


title: Retina, Fbxl11-CKO, P7, rep3 [RNA-seq]


title: HeLa cells, Control_1


title: Retina, WT, P7, rep3 [RNA-seq]

value: WT


title: Retina, WT, P7, rep2 [RNA-seq]


title: Retina, Fbxl11-CKO, P7, rep1 [RNA-seq]


title: Retina, WT, P7, rep1 [RNA-seq]


title: uninfected_3

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: RNA libraries

data_processing:
Sequenced libraries were processed with deepTools, using STAR , for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2.
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

molecule: polyA RNA

source_name: Small intestine

extract_protocol:
RNA was extracted using a Trizol based extraction and quantified using Qubit 2.0 (Thermo Fisher Scientific) following manufacturer instructions.
Libraries were prepared using illumina kits and sequenced with a HiSeq 2000 instrument.

value: Small intestine

value: healthy mouse

tag: library type

value: mRNA


title: infected_no_lesion_2

description: RNA libraries

value: Infected mouse healthy tissue


title: uninfected_4

description: RNA libraries


title: uninfected_2

description: RNA libraries


title: uninfected_5

description: RNA libraries


title: uninfected_1

description: RNA libraries


title: infected_no_lesion_4

description: RNA libraries


title: Retina, WT, P7, rep4 [RNA-seq]


title: infected_no_lesion_3

description: RNA libraries


title: infected_lesion_5

description: RNA libraries

value: Granuloma


title: infected_no_lesion_1

description: RNA libraries


title: infected_lesion_4

description: RNA libraries


title: DN-1_HNFMMCCXX_L2

description: From isolate DN, Biological Replicate 1


title: WTindark2_CGCAACS36L001R1_001

city: Merced

first: Clarissa

middle: Jane

last: Nobile

state: CA

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California, Merced

data_processing:
Bluebee data analysis
In-house RNAseq pipeline was used for trimming and removal of low-quality tails using bbmap suite
STAR aligner with modified ENCODE settings was used for alignment to SC5314 genome
HTSeq-count with kit specific options (FWD) was used for gene count reading
DESeq2 was used to identify the differentially expressed genes
Assembly: Candida albicans SC5314 assembly 21
Supplementary files format and content: gene counts

source_name: WT

growth_protocol: Strains were grown on standard chamydospore inducing conditions (on corn meal agar with tween 80 under coerslips and incubated at room temperature in dark)

extract_protocol:
RNA extraction was performed using Ribopure-Yeast RNA kit from Ambion
RNA-seq library was prepared using Lexogen’s quantseq 3' mRNA-Seq Library Prep Kit FWD as per Illumina user manual instructions


title: TF028indark2_CCTAAGS13L001R1_001

source_name: TF028 knockout

value: TF028 knockout


title: infected_lesion_1

description: RNA libraries


title: TF028indark1_ACCAGTS3L001R1_001


title: Q405_24_3

city: Kunming

first: yang

last: le

address: No.2 of Cuihubeilu

institute: Yunnan university

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Supplementary files format and content: HiSat2 and StringTie
Supplementary files format and content: xlsx file includes tpm value for each sample

organism: Orbilia oligospora

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

value: Fungal hyphae cells

tag: cell type

value: mutant strain

value: C. elegans induced


title: Q405_24_2


title: Q405_12_3


title: Q405_12_1


title: Q405_12_2


title: Q405_24_1


title: Q405_0_3


title: AO_24_3

value: wild type


title: WTindark1_GTTACCS35L001R1_001


title: Q405_0_2


title: Q405_0_1


title: Q405_6_1


title: AO_12_2


title: infected_lesion_3

description: RNA libraries


title: AO_24_2


title: Q405_6_3


title: Q405_6_2


title: AO_12_3


title: AO_12_1


title: infected_lesion_2

description: RNA libraries


title: AO_6_1


title: AO_6_3


title: AO_0_3


title: AO_0_1


title: AO_0_2


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.6 rep1

city: Beijing

first: Di

last: Zhang

address: No.5 YiHeYuan Road, Haidian District

institute: Peking University

data_processing:
Data processing including barcode splitting, linker trimming, and mapping were performed using Galaxy.
The processed reads were mapped to Escherichia coli genome escherichia_coli_k12_nc_000913_3 from the NCBI database with the BWA short read mapping algorithm.
To infer the ribosome A-site position, python package Plastid was used to align the 3’ end of reads to the stop and start codons, which are known to have higher ribosome densities.
The relative mRNA levels were also normalized to the total counts and gene length as reads per kilobase million (RPKM).
Genome_build: NC000913.3
Supplementary_files_format_and_content: Raw gene counts and RPKM values for every gene and every sample

organism: Escherichia coli

growth_protocol: Escherichia coli strain NCM3722 was grown in batch or continuous cultures. We utilized a 300mL volume chemostat (Sixfors, HT) with oxygen and pH probes to monitor the culture. The aeration rate was set at 4.5 l/h and pH was kept at 7.2 +/- 0.1.

extract_protocol:
The method of RNA extraction and ribosome profiling was described in detail previously (Li et al., 2018). After quantification of RNA concentration with NanoDrop, samples with 500µg RNA were digested with 750U MNase (10107921001, Roche) for 1 hour at 25˚C before being quenched with 6mM EGTA. The lysates were then layered onto a 10%-55% sucrose gradient and centrifuged. The monosome fraction was collected and snap frozen in liquid nitrogen. There were no observed polysome peaks, which indicated thoroughgoing digestion. The RNA was separated using hot phenol and size selected on 15% TBE-Urea PAGE gels run for 1 hour at 210V. Gels were stained with SYBR Gold and visualized using Dark Reader (Clare Chemical Research). Finally, for ribosome profiling, RNA fragments with size between 25-40 nt were extracted using isopropanol precipitation.
RNA fragments from footprints were dephosphorylated at the 3’ end by PNK (M0201, NEB). The repaired fragments were linked to the Universal miRNA Cloning Linker (S1315S, NEB), reverse transcribed (18080044, Thermo), and circularized (CL4111K, Epicentre). rRNA was subtracted from the circularized samples before PCR amplification (M0531L, NEB) and size selection. High quality PCR samples were checked by Bioanalyzer highly sensitive DNA chip.

treatment_protocol: For minimal glucose media, 40 mM MOPS media (M2120, Teknova) was utilized with glucose (0.4%, Sigma G8270), ammonia (9.5 mM NH4Cl, Sigma A9434) and phosphate (1.32 mM K2HPO4, Sigma P3786) added separately. For defined rich media, the minimal media is supplemented with 10x ACGU (M2103, Teknova) and 5X Supplement EZ (M2104, Teknova). For carbon- and nitrogen-limited media, glucose and ammonia concentrations were reduced by 5-fold (0.08% and 1.9mM respectively). Phosphorus-limited medium contains 0.132 mM K2HPO4.

tag: growth rate

value: Leucine limitation

tag: culture method

value: chemostat

tag: molecule subtype

value: ribosome protected mRNA


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.6 rep3

tag: strain

tag: treatment


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.6 rep2


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.1 rep3


title: AO_24_1


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.1 rep1


title: E. coli Ribo-seq - ΔleuB Leu-lim 0.1 rep2


title: AO_6_2


title: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep2

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep2

value: nitrogen limitation


title: Untreated_MMTV_Wnt1_scRNA-seq

city: New Orleans

first: James

middle: G

last: Jackson

state: LA

address: 1430 Tulane

institute: Tulane

data_processing:
Obtained sequencing data were processed through CellRanger
Data aligned to mouse genome (mm10)
Using Seurat package, quality control was performed to remove cells with more than 10% expression of mitochondrial genes, or cells that had fewer than 200 or greater than 7500 unique gene features.
Samples were normalized, and integrated
Genome_build: mm10
Supplementary_files_format_and_content: count matrix (csv)

source_name: Mammary tumor

growth_protocol: MMTV-Wnt1 tumor cells were transplanted into 6-8wk old female C57BL6/j wild-type mice, and allowed to grow until ~200mm^3 in volume

extract_protocol:
Single cell suspensions of mammary tumors were generated, assessed for viability, and transcriptomes generated using 10X Chromium single cell platform.
To generate scRNA-seq libraries, barcoded single-cell gel beads in emulsion were made and reverse transcribed according to manufacturer instructions (Chromium Single Cell 3' Reagents Kit, 10X Genomics).

treatment_protocol: One tumor was treated with 4mg/kg doxorubicin once daily for 5 total doses, and harvested 48h after final dose

tag: source cell type

value: MMTV-Wnt1 tumor cells

tag: host strain

value: none (untreated)


title: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep1

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep1


title: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep2

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep2


title: Doxo_rx_MMTV_Wnt1_scRNA-seq

value: 4mg/kg doxorubicin


title: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep3

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.6 rep3


title: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep1

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep1


title: SH1000 pEPSA5 3h/30min

city: Tampa

first: Lindsey

last: Shaw

address: 4202 E. Fowler Ave.

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform (version 11) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using RNA-Seq Analysis function with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization
Assembly: Normalized expression values and fold change comparisons were exported in excel format
Supplementary files format and content: Data was aligned to the NCTC 8325 reference genome (NC_007795.1)
Supplementary files format and content: Comparisons were carried out following quantile normalization via the Qiagen Bioinformatics experimental fold change feature.

organism: Staphylococcus aureus

source_name: bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. After which these cultures were used to seed fresh TSB at an OD600 of 0.05 Samples were then grown to an OD600 of 0.3 before being induced with xylose for 30 minutes, then 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

value: Vector control strain

tag: growth medium

value: TSB

tag: growth conditions

value: Xylose


title: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep3

source_name: E. coli Ribo-seq - ΔrplA N-lim 0.1 rep3


title: 73T

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

data_processing:
Cellranger pipeline was used here. Cellranger mkfastq was used for demultiplexing and generate fastq files and cellranger count was used to align the reads to Mmul10 and M33262.1 reference genomes.
M33262.1 was split and annotated into 5 regions as described in the manuscript.
Assembly: Mmul10
Assembly: M33262.1
Supplementary files format and content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

organism: Macaca mulatta

source_name: Rhesus macaque CD11b enriched brain microglia and macrophages

extract_protocol:
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the brain and cryopreserved. Isolates were immunomagnetically enriched for CD11b+ cells, and then flow cytometry sorted for CD11b positive, live events, and processed for scRNA.
scRNA10x Genomics Chromium GEM Chip and placed into Chromium Controller for library preparation. The prepared libraries  were sequenced using Illumina Nextseq550 sequencer for Sample 1 to sample 7 and Novaseq6000 fro sample 8 to sample 23.

tag: tissue

value: Enriched brain microglia and macrophages

value: morphine, SIV-latent virus


title: Bulk training high-fat diet rep4 [TH10.Tricep]

city: Boston

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

data_processing:
Six FASTQ files for each sample were concatenated for read de-duplication using unique molecular identifiers (UMIs).
We then ran Salmon 0.14.2 to quantify the number of unique reads for each transcript against Ensembl version 98 mouse transcripts.
The transcript level information was summarized to the gene-level using R package tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and log2CPM values for every gene and every sample

source_name: triceps

extract_protocol:
Total RNA was extracted at the Goodyear lab using an RNA extraction kit (Direct-zol™ RNA MiniPrep, Zymo Research). 10ng of total RNA quantified and quality assessed by Advanced Analytical Fragment Analyzer was used for library preparation on Tecan Evo150.
3′ DGE-custom primers 3V6NEXT-bmc#1-12 were added to a final concentration of 1 uM. to generate two subpools of 15 samples each. After addition of the oligonucleotides, Maxima H Minus RT was added per manufacturer’s recommendations with Template-Switching oligo 5V6NEXT followed by incubation at 42℃ for 90’ and inactivation at 80℃ for 10’. Following the template switching reaction, cDNA from 12 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 17 ul of water followed by digestion with Exonuclease I at 37℃ for 30 minutes, and inactivated at 80℃ for 20 minutes. Second strand synthesis and PCR amplification was done by adding the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer directly to the exonuclease reaction. Eight cycles of PCR were performed followed by clean up using regular SPRI beads at 0.6X, and eluted with 20ul of elution buffer (Qiagen). Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries were then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer in place of the normal N500 primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for sequencing using the Hiseq 2000 (Illumina, Inc) in 50bp single-end mode at the BioMicro Center at MIT.
3′ Digital Gene Expression (DGE) RNA-seq

treatment_protocol: Mice were separated into standard vs. high-fat diet groups (10% vs. 60% Kcal fat ad libitum, weeks 0-6) and each group was further separated into sedentary and training by voluntary wheel running (weeks 3-6). Tissue collection was done following a 6-hour fast and a 24-hour exercise wash-out done by locking of the wheels.

value: triceps

tag: age

value: 12-week old

value: 6-week high-fat-diet and 3-week training interventions


title: 80T


title: Bulk training high-fat diet rep5 [TH17.Tricep]


title: 75T


title: 78T


title: 83T

value: saline, SIV-latent virus


title: SH1000 pEPSA5::sigS 3h/30min

value: sigS overexpression strain


title: Bulk training high-fat diet rep2 [TH6.Tricep]


title: Bulk training high-fat diet rep3 [TH11.Tricep]


title: E. coli Ribo-seq - WT G 1.8 rep2

source_name: E. coli Ribo-seq - WT G 1.8 rep2

value: wild type

value: defined rich MOPS

value: batch culture


title: E. coli Ribo-seq - WT G 1.8 rep3

source_name: E. coli Ribo-seq - WT G 1.8 rep3

value: ribosome protected mRNA


title: 82T


title: 19EAT-07-19_S19

city: Corvallis

first: Andrey

last: Morgun

state: Oregon

address: Pharmacy Building, 1601 SW Jefferson Way

department: College of Pharmacy

institute: Oregon State University

data_processing:
Sequences were processed to remove the adapter, polyA, and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k = 13, ktrim = r, forcetrimleft = 12, useshortkmers = t, mink = 5, qtrim = r, trimq = 15, minlength = 20.
Reads were aligned to mouse genome and transcriptome (ENSEMBL NCBIM37) using Tophat (v. 2.1.1) with default parameters.
Number of reads per million were counted using HTSeq (v. 0.6.0).
Assembly: ENSEMBL NCBIM37
Supplementary files format and content: CSV file of relativized per million reads

source_name: EAT

growth_protocol: 7 weeks old, Specific Pathogen Free (SPF), C57BL/6 male mice were purchased from Jackson Laboratory (Bar Harbor, Maine) and housed in a controlled environment (12h daylight cycle) in groups of 4-5 per cage at the Laboratory Animal Resources Center (LARC) at Oregon State University (OSU), with ad libitum access to food and water. After one week of acclimatization, mice were either switched to a normal diet D12450K (ND) (4 kcal % lard and 0% sucrose) produced by Research Diets (New Brunswick, NJ).

extract_protocol:
RNA was extracted using an OMNI Bead Ruptor and 2.8-mm ceramic beads (OMNI International) followed by Qiashredder and an RNeasy Lipid Tissue Mini Kit (for epididymal fat) using Qiacube (Qiagen) automated extraction according to the manufacturer’s specifications with DNase treatment (RNase-Free DNase Set; Qiagen). Total RNA was quantified using QuantiT RNA Assay Kit (Thermo Fisher Scientific). Complementary DNA was prepared using qScript reverse transcription kit (QuantaBio).
RNA libraries were prepared with the QuantSeq 39mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.

treatment_protocol: Mice were gavaged with 10^9 CFU of O. valericigenes DSM 18026 in PBS for 4–5 wk every day.

tag: group

value: ND+Osci

value: Epididymal adipose tissue

tag: mouse id

tag: Sex

value: Male

tag: diet

value: Normal diet

value: Mice on normal diet, gavaged with 10^9 CFU Oscillibacter valericigenes


title: 20EAT-07-19_S20

tag: genotype


title: 77T


title: Bulk training high-fat diet rep1 [TH5.Tricep]


title: 18EAT-07-19_S18


title: E. coli Ribo-seq - WT M 0.9 rep3

source_name: E. coli Ribo-seq - WT M 0.9 rep3

value: glucose minimal


title: E. coli Ribo-seq - WT G 1.8 rep1

source_name: E. coli Ribo-seq - WT G 1.8 rep1


title: 15EAT-07-19_S15

value: ND+vehicle

value: Mice on normal diet


title: 17EAT-07-19_S17


title: Bulk sedentary high-fat diet rep4 [SH8.Tricep]

value: triceps

value: 6-week high-fat-diet and 3-week sedentary interventions


title: 14EAT-07-19_S14


title: E. coli Ribo-seq - WT M 0.9 rep2

source_name: E. coli Ribo-seq - WT M 0.9 rep2


title: E. coli Ribo-seq - WT M 0.9 rep1

source_name: E. coli Ribo-seq - WT M 0.9 rep1


title: 11EAT-07-19_S11


title: Bulk sedentary high-fat diet rep2 [SH4.Tricep]

value: 12-week old


title: 12EAT-07-19_S12


title: L646_WDD

data_processing:
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.
The sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
Then the reads were aligned to mouse genome and transcriptome (ENSEMBL NCBIM37) using Tophat (v2.1.1) with default parameters.
The number of reads per million for mouse liver genes were counted using HTSeq (v 0.6.0) 71 and quantile normalized.
Assembly: ENSEMBL NCBIM37
Supplementary files format and content: relativized per million reads

source_name: liver

growth_protocol: Briefly, male mice (B6:129S7-LdlrtmHer/j, stock# 002207) were purchased from Jackson Labs and were group housed (4 mice/cage) and maintained on a 12-hour light/dark cycle. Mice were acclimatized to the Oregon State University Linus Pauling science center vivarium for 2 weeks before proceeding with the experiments.

extract_protocol:
RNA was extracted from cell lysates using the RNeasy Mini Kit and subjected to a DNase treatment according to manufacturer's protocols (Qiagen) then stored at -80 ºC until further use.
mRNA libraries were prepared for sequencing with the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) HT for Illumina Sequencing platforms (Kit#k15.384) and sequenced on the Illumina NextSeq at Oregon State University.

treatment_protocol: Mice consumed the one of the following 5 diets, ad libitum for 16 weeks; each group consisted of 5-7 male mice. Purina chow 5001  was used as the Reference diet (RD). The RD group was kept on this diet for 30 weeks. The western diet (WD) was obtained from Research Diets (12709B) and used to induce NASH.  The WD group was separated into 2 groups: one group was maintained on a WD + olive oil diet for 8 weeks, with the other group was maintained on the WDD diet for 8 weeks.

value: WDD

value: Western diet (12709B) supplemented with DHA


title: 13EAT-07-19_S13


title: Bulk sedentary high-fat diet rep1 [SH3.Tricep]


title: L644_WDD


title: E. coli Ribo-seq - WT P-lim 0.6 rep3

source_name: E. coli Ribo-seq - WT P-lim 0.6 rep3

value: wild type

value: phosphate limitation

value: chemostat


title: E. coli Ribo-seq - WT P-lim 0.6 rep2

source_name: E. coli Ribo-seq - WT P-lim 0.6 rep2

value: ribosome protected mRNA


title: Bulk training standard (chow) diet rep5 [TC18.Tricep]

value: 6-week chow-diet and 3-week training interventions


title: E. coli Ribo-seq - WT P-lim 0.6 rep1

source_name: E. coli Ribo-seq - WT P-lim 0.6 rep1


title: L643_WDD


title: L642_WDD


title: L641_WDD


title: Bulk sedentary high-fat diet rep5 [SH12.Tricep]


title: Bulk training standard (chow) diet rep4 [TC14.Tricep]


title: 16EAT-07-19_S16

value: ND+Osci

value: Epididymal adipose tissue


title: Bulk sedentary high-fat diet rep3 [SH7.Tricep]


title: Bulk training standard (chow) diet rep3 [TC7.Tricep]


title: Bulk training standard (chow) diet rep2 [TC6.Tricep]


title: L637_WDO

value: Male

value: WDO

value: Western diet (12709B) supplemented with olive oil


title: E. coli Ribo-seq - WT P-lim 0.1 rep3

source_name: E. coli Ribo-seq - WT P-lim 0.1 rep3


title: L636_WDO


title: L647_WDD


title: E. coli Ribo-seq - WT P-lim 0.1 rep2

source_name: E. coli Ribo-seq - WT P-lim 0.1 rep2


title: L632_WDO


title: E. coli Ribo-seq - WT N-lim 0.6 rep2

source_name: E. coli Ribo-seq - WT N-lim 0.6 rep2

value: nitrogen limitation


title: Bulk training standard (chow) diet rep1 [TC1.Tricep]


title: L634_WDO


title: E. coli Ribo-seq - WT N-lim 0.6 rep3

source_name: E. coli Ribo-seq - WT N-lim 0.6 rep3


title: E. coli Ribo-seq - WT P-lim 0.1 rep1

source_name: E. coli Ribo-seq - WT P-lim 0.1 rep1


title: Bulk sedentary standard (chow) diet rep4 [SC11.Tricep]

source_name: triceps

value: 6-week chow-diet and 3-week sedentary interventions


title: L630_WDB

value: WDB

value: Western diet (12709B) baseline


title: L628_WDB


title: L640_WDD


title: E. coli Ribo-seq - WT N-lim 0.1 rep3

source_name: E. coli Ribo-seq - WT N-lim 0.1 rep3


title: L629_WDB


title: E. coli Ribo-seq - WT N-lim 0.6 rep1

source_name: E. coli Ribo-seq - WT N-lim 0.6 rep1


title: Bulk sedentary standard (chow) diet rep3 [SC8.Tricep]

value: triceps

value: 12-week old


title: L627_WDB


title: L639_WDO


title: Bulk sedentary standard (chow) diet rep2 [SC4.Tricep]


title: L620_RD

value: RD

value: Reference Diet (Purina Chow 5001)


title: L619_RD


title: L618_RD


title: Bulk sedentary standard (chow) diet rep1 [SC3.Tricep]


title: L633_WDO


title: E. coli Ribo-seq - WT N-lim 0.1 rep2

source_name: E. coli Ribo-seq - WT N-lim 0.1 rep2

value: wild type


title: L635_WDO


title: E. coli Ribo-seq - WT N-lim 0.1 rep1

source_name: E. coli Ribo-seq - WT N-lim 0.1 rep1

value: chemostat


title: Bulk sedentary standard (chow) diet rep5 [SC12.Tricep]


title: L631_WDB


title: L616_RD


title: L617_RD


title: E. coli Ribo-seq - WT C-lim 0.6 rep3

source_name: E. coli Ribo-seq - WT C-lim 0.6 rep3

value: carbon limitation

value: ribosome protected mRNA


title: Bulk training high-fat diet rep4 [TH10.vWAT]

source_name: visceral white adipose tissue

value: visceral white adipose tissue

value: 6-week high-fat-diet and 3-week training interventions


title: Bulk training high-fat diet rep5 [TH17.vWAT]


title: WDED_546

description: Western diet (12709B) supplemented with EPA&DHA

treatment_protocol: Mice consumed one of the following 5 diets, ad libitum for 16 weeks; each group consisted of 8 male mice. Purina chow 5001 was used as the Reference diet (RD). The western diet (WD) was obtained from Research Diets (12709B) and used to induce NASH. The WD was supplemented with olive oil (WDO), eicosapentaenoic acid (WD + EPA), docosahexaenoic acid (WD + DHA), or both EPA and EHA (WD + EPA + DHA). EPA and DHA were added to the diets to yield 2% of total calories; for the EPA + DHA, each was added to yield 1% of total calories, i.e. 2% total calories as C20-22 ω3 PUFA. OO was added to the WD to have a uniform level of fat energy in all the WDs.

value: Male

value: WDED


title: WDED_545


title: E. coli Ribo-seq - WT C-lim 0.6 rep2

source_name: E. coli Ribo-seq - WT C-lim 0.6 rep2


title: WDED_547

source_name: liver


title: WDED_548


title: E. coli Ribo-seq - WT C-lim 0.6 rep1

source_name: E. coli Ribo-seq - WT C-lim 0.6 rep1


title: WDED_542


title: Bulk training high-fat diet rep2 [TH6.vWAT]


title: WDED_543


title: Bulk training high-fat diet rep1 [TH5.vWAT]


title: WDED_544


title: E. coli Ribo-seq - WT C-lim 0.1 rep2

source_name: E. coli Ribo-seq - WT C-lim 0.1 rep2


title: WDD_540

description: Western diet (12709B) supplemented with DHA

value: WDD


title: E. coli Ribo-seq - WT C-lim 0.1 rep3

source_name: E. coli Ribo-seq - WT C-lim 0.1 rep3


title: Bulk sedentary high-fat diet rep5 [SH12.vWAT]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: WDED_541


title: WDD_539


title: E. coli Ribo-seq - WT C-lim 0.1 rep1

source_name: E. coli Ribo-seq - WT C-lim 0.1 rep1


title: Bulk sedentary high-fat diet rep4 [SH8.vWAT]


title: E. coli RNA-seq - ΔleuB Leu-lim 0.6 rep3

value: Leucine limitation

value: total mRNA


title: WDD_536


title: WDD_537


title: WDD_538


title: WDD_535


title: Bulk sedentary high-fat diet rep3 [SH7.vWAT]


title: Bulk training high-fat diet rep3 [TH11.vWAT]


title: E. coli RNA-seq - ΔleuB Leu-lim 0.6 rep2


title: WDE_532

description: Western diet (12709B) supplemented with EPA

value: WDE


title: E. coli RNA-seq - ΔleuB Leu-lim 0.6 rep1


title: Bulk sedentary high-fat diet rep1 [SH3.vWAT]


title: WDE_531


title: WDE_529


title: WDE_528


title: E. coli RNA-seq - ΔleuB Leu-lim 0.1 rep2


title: WDD_533


title: Bulk training standard (chow) diet rep4 [TC14.vWAT ]

value: 6-week chow-diet and 3-week training interventions


title: Bulk sedentary high-fat diet rep2 [SH4.vWAT]

value: 12-week old


title: WDE_527


title: E. coli RNA-seq - ΔleuB Leu-lim 0.1 rep1


title: Bulk training standard (chow) diet rep3 [TC7.vWAT]


title: WDE_525


title: E. coli RNA-seq - ΔrplA N-lim 0.6 rep3

source_name: E. coli RNA-seq - ΔrplA N-lim 0.6 rep3

value: nitrogen limitation


title: WDO_524

description: Western diet (12709B) supplemented with olive oil

value: WDO


title: WDO_522


title: WDE_526


title: Bulk training standard (chow) diet rep2 [TC6.vWAT]


title: Bulk training standard (chow) diet rep1 [TC1.vWAT]


title: Bulk training standard (chow) diet rep5 [TC18.vWAT]


title: E. coli RNA-seq - ΔleuB Leu-lim 0.1 rep3


title: WDO_523


title: E. coli RNA-seq - ΔrplA N-lim 0.6 rep1

source_name: E. coli RNA-seq - ΔrplA N-lim 0.6 rep1


title: E. coli RNA-seq - ΔrplA N-lim 0.6 rep2

source_name: E. coli RNA-seq - ΔrplA N-lim 0.6 rep2


title: WDO_520


title: WDO_521


title: E. coli RNA-seq - ΔrplA N-lim 0.1 rep3

source_name: E. coli RNA-seq - ΔrplA N-lim 0.1 rep3


title: WDE_530


title: WDO_519


title: WDO_518


title: Bulk sedentary standard (chow) diet rep4 [SC11.vWAT]

value: 6-week chow-diet and 3-week sedentary interventions


title: WDO_517


title: Bulk sedentary standard (chow) diet rep3 [SC8.vWAT]


title: E. coli RNA-seq - ΔrplA N-lim 0.1 rep2

source_name: E. coli RNA-seq - ΔrplA N-lim 0.1 rep2

value: chemostat


title: RD_516

description: Reference Diet (Purina Chow 5001)

value: Reference Diet


title: RD_515

description: Reference Diet (Purina Chow 5001)


title: RD_514

description: Reference Diet (Purina Chow 5001)


title: Bulk sedentary standard (chow) diet rep2 [SC4.vWAT]


title: Bulk sedentary standard (chow) diet rep5 [SC12.vWAT]


title: E. coli RNA-seq - WT G 1.8 rep3

source_name: E. coli RNA-seq - WT G 1.8 rep3

value: wild type

value: defined rich MOPS

value: batch culture


title: Bulk sedentary standard (chow) diet rep1 [SC3.vWAT]

value: visceral white adipose tissue


title: E. coli RNA-seq - WT G 1.8 rep2

source_name: E. coli RNA-seq - WT G 1.8 rep2


title: Bulk training high-fat diet rep5 [TH17.scWAT]

source_name: subcutaneous white adipose tissue

value: subcutaneous white adipose tissue

value: 6-week high-fat-diet and 3-week training interventions


title: RD_512

description: Reference Diet (Purina Chow 5001)

value: Male


title: RD_511

description: Reference Diet (Purina Chow 5001)


title: E. coli RNA-seq - WT G 1.8 rep1

source_name: E. coli RNA-seq - WT G 1.8 rep1


title: RD_509

description: Reference Diet (Purina Chow 5001)


title: Bulk training high-fat diet rep4 [TH10.scWAT]


title: RD_510

description: Reference Diet (Purina Chow 5001)


title: Bulk training high-fat diet rep2 [TH6.scWAT]


title: E. coli RNA-seq - WT M 0.9 rep3

source_name: E. coli RNA-seq - WT M 0.9 rep3

value: glucose minimal


title: Bulk training high-fat diet rep3 [TH11.scWAT]


title: E. coli RNA-seq - WT M 0.9 rep2

source_name: E. coli RNA-seq - WT M 0.9 rep2

value: total mRNA


title: iNKT1_Ctrl_rep3

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

description:
75 bp
KOvxWT.htseq.edgeR.txt

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with STAR v2.5.2.
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Assembly: mm10
Supplementary files format and content: normalized abundance measurements provided as edgeR output files

source_name: thymus

extract_protocol:
Total RNA was isolated using RNAseqy MicroKit (Qiage) according to the manufacturer's recommendations
Libraries were constructed using Nugen's Ovation Ultralow Library systems and were subsequently sugject to 76 cycles of NextSeq500 sequencing

value: thymus

tag: strain background

tag: cell type


title: iNKT1_cKO_rep3

description:
75 bp
KOvxWT.htseq.edgeR.txt


title: iNKT1_cKO_rep1

description:
75 bp
KOvxWT.htseq.edgeR.txt


title: iNKT1_cKO_rep2

description:
75 bp
KOvxWT.htseq.edgeR.txt


title: E. coli RNA-seq - ΔrplA N-lim 0.1 rep1

source_name: E. coli RNA-seq - ΔrplA N-lim 0.1 rep1

tag: growth rate

tag: culture method


title: RD_513

description: Reference Diet (Purina Chow 5001)

source_name: liver


title: E. coli RNA-seq - WT M 0.9 rep1

source_name: E. coli RNA-seq - WT M 0.9 rep1

tag: strain

tag: molecule subtype


title: RNA-P1-cKO-5

city: Dallas

first: Xurde

last: Menéndez Caravia

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3) (Langmead and Salzberg, 2012). STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene. DESeq2 R Bioconductor package (Gentleman et al., 2004; Anders et al., 2010) was used to normalize read counts and identify differentially expressed (DE) genes. KEGG (Kanehisa et al., 2017) pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: P1 whole heart

extract_protocol:
Flash-frozen cardiac samples were homogenized in 1 ml of TRIzol (Thermo Fisher Scientific, 15596026) in Precellys Evolution (3 cycles x 20 s at 6800 rpm). RNA as isolated using RNeasy Micro Kit (Qiagen, 74004) as per the provider’s instructions.
RNA-seq libraries (n=3 mice per genotype) were prepared using KAPA mRNA HyperPrep (Kapa Biosystems, kk8580) kit following manufacturer’s specifications.

value: Heart

value: P1 (postnatal day 1)

value: Lemd2 cKO (cardiac-specific deletion)


title: RNA-P1-cKO-6


title: E. coli RNA-seq - WT P-lim 0.6 rep3

source_name: E. coli RNA-seq - WT P-lim 0.6 rep3

tag: treatment

value: phosphate limitation


title: Bulk sedentary high-fat diet rep5 [SH12.scWAT]

value: 12-week old

value: 6-week high-fat-diet and 3-week sedentary interventions


title: E. coli RNA-seq - WT P-lim 0.6 rep2

source_name: E. coli RNA-seq - WT P-lim 0.6 rep2

value: chemostat


title: RNA-P1-floxed-3


title: RNA-P1-cKO-4


title: RNA-P1-floxed-2


title: iNKT1_Ctrl_rep2

description:
75 bp
KOvxWT.htseq.edgeR.txt


title: RNA-adult-KI/KI-6

source_name: Adult whole heart

value: 2 months

value: Lemd2 KI/KI (c.T38>G)


title: Bulk sedentary high-fat diet rep4 [SH8.scWAT]


title: E. coli RNA-seq - WT P-lim 0.1 rep3

source_name: E. coli RNA-seq - WT P-lim 0.1 rep3

value: wild type


title: RNA-P1-floxed-1


title: E. coli RNA-seq - WT P-lim 0.6 rep1

source_name: E. coli RNA-seq - WT P-lim 0.6 rep1


title: RNA-adult-KI/KI-4


title: Bulk sedentary high-fat diet rep3 [SH7.scWAT]


title: iNKT1_Ctrl_rep1

description:
75 bp
KOvxWT.htseq.edgeR.txt


title: Bulk sedentary high-fat diet rep2 [SH4.scWAT]


title: RNA-adult-KI/KI-5


title: Bulk training high-fat diet rep1 [TH5.scWAT]


title: Bulk sedentary high-fat diet rep1 [SH3.scWAT]


title: E. coli RNA-seq - WT P-lim 0.1 rep1

source_name: E. coli RNA-seq - WT P-lim 0.1 rep1


title: RNA-adult-WT-2

value: Lemd2 WT


title: RNA-adult-WT-3


title: Bulk training standard (chow) diet rep5 [TC18.scWAT]

value: subcutaneous white adipose tissue

value: 6-week chow-diet and 3-week training interventions


title: RNA-adult-WT-1


title: CnR_PolIIS2P_SH1sKO_1

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Library strategy: Cut&Run
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse assembly mm10 (GRCm38 release 99) using STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
Peaks were called comparing the respective treatment to IGG samples using Epic2 0.0.41 (Patten et al., Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis) for H4K20me1 and Macs2 2.1.1 (Zhang et al., Model-based Analysis of ChIP-Seq) for Pol II Ser2P.
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
To enable comparison of peaks in different samples, the resulting lists of significant peaks were overlapped and unified for each dataset separately (H4K20me1, Pol II Ser2P). Sample counts for union peaks were produced using bigWigAverageOverBed (UCSC Toolkit).
Reads mapping against Spike-in organism Drosophila melanogaster (BDGP6) were counted for each sample and used to normalize the matrices of union peak scores (Anders et al., Differential expression analysis for sequence count data).
Union peaks were annotated with the gene having the longest overlap based on reference data of Ensembl release 99.
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: Tab-delimited matrices with Spike-in normalized union peak counts.

source_name: Muscle satellite cell

extract_protocol:
Cleaved DNA fragments were released and extracted by phenol-chloroform. DNA fragments were further purified by magnetic carboxylated beads. S2 cell spike-in DNA was added.
Illumina sequencing libraries were generated using Low Input Library Prep Kit v2 (Takara) following the manufacturer’s instructions.

value: Muscle satellite cell

tag: antibody

value: Pol II Ser2P (Abcam ab5095)


title: CnR_PolIIS2P_SH1sKO_2


title: CnR_PolIIS2P_WT_2


title: E. coli RNA-seq - WT N-lim 0.6 rep3

source_name: E. coli RNA-seq - WT N-lim 0.6 rep3

value: nitrogen limitation

value: total mRNA


title: Bulk training standard (chow) diet rep4 [TC14.scWAT]

source_name: subcutaneous white adipose tissue


title: E. coli RNA-seq - WT N-lim 0.6 rep2

source_name: E. coli RNA-seq - WT N-lim 0.6 rep2


title: Bulk training standard (chow) diet rep3 [TC7.scWAT]


title: E. coli RNA-seq - WT N-lim 0.6 rep1

source_name: E. coli RNA-seq - WT N-lim 0.6 rep1


title: Bulk training standard (chow) diet rep2 [TC6.scWAT]


title: E. coli RNA-seq - WT P-lim 0.1 rep2

source_name: E. coli RNA-seq - WT P-lim 0.1 rep2


title: E. coli RNA-seq - WT N-lim 0.1 rep3

source_name: E. coli RNA-seq - WT N-lim 0.1 rep3


title: E. coli RNA-seq - WT N-lim 0.1 rep2

source_name: E. coli RNA-seq - WT N-lim 0.1 rep2


title: CnR_H4K20me1_SH1sKO_2

value: H4K20me1 (Abcam ab9051)


title: CnR_IGG_SH1sKO_1

value: IGG


title: DRIPseq_SH1sKO_3

data_processing:
Library strategy: DRIP-Seq
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse assembly mm10 (GRCm38 release 99) using STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
Peaks were called comparing the respective treatment to Input samples using Epic2 0.0.41 (Patten et al., Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
To enable comparison of peaks in different samples, the resulting lists of significant peaks were overlapped and unified. Sample counts for union peaks were produced using bigWigAverageOverBed (UCSC Toolkit).
Reads mapping against Spike-in organism Drosophila melanogaster (BDGP6) were counted for each sample and used to normalize the matrix of union peak scores (Anders et al., Differential expression analysis for sequence count data).
Union peaks were annotated with the gene having the longest overlap based on reference data of Ensembl release 99.
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: Tab-delimited matrix with Spike-in normalized union peak counts.

extract_protocol:
Genomic DNA from Ctrl and Suv420h1 mutant MuSCs was extracted by phenol/chloroform and sonicated. RNA:DNA hybrids were pulled down by S9.6 antibody. S2 cell spike-in DNA was added.
DNA libraries were synthesized from ssDNA using the Accel-NGS 1S DNA library kit


title: CnR_H4K20me1_WT_2


title: CnR_H4K20me1_WT_1


title: CnR_H4K20me1_SH1sKO_1


title: CnR_PolIIS2P_WT_1


title: E. coli RNA-seq - WT N-lim 0.1 rep1

source_name: E. coli RNA-seq - WT N-lim 0.1 rep1


title: DRIPseq_SH1sKO_2


title: Bulk sedentary standard (chow) diet rep4 [SC11.scWAT]

value: 6-week chow-diet and 3-week sedentary interventions


title: CnR_IGG_WT_1


title: Bulk sedentary standard (chow) diet rep3 [SC8.scWAT]


title: DRIPseq_WT_2


title: Bulk sedentary standard (chow) diet rep5 [SC12.scWAT]


title: DRIPseq_SH1sKO_1


title: E. coli RNA-seq - WT C-lim 0.6 rep3

source_name: E. coli RNA-seq - WT C-lim 0.6 rep3

value: carbon limitation


title: DRIPseq_WT_1


title: E. coli RNA-seq - WT C-lim 0.6 rep2

source_name: E. coli RNA-seq - WT C-lim 0.6 rep2


title: DRIPseq_Input_SH1sKO_1


title: DRIPseq_WT_3


title: DRIPseq_Input_WT_1


title: E. coli RNA-seq - WT C-lim 0.6 rep1

source_name: E. coli RNA-seq - WT C-lim 0.6 rep1


title: PROseq_SH1sKO_3

data_processing:
Library strategy: PRO-Seq
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse assembly mm10 (GRCm38 release vM15) using STAR 2.6.1d (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining one random alignment in case of multi-mapping reads.
Reads were deduplicated using Picard 2.18.16 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
Target features were produced by extracting all isoforms of protein_coding genes of Ensembl GRCm38 release vM15 with length >= 1000 nt and creating for each: 1) TSS region (start=TSS, stop=400 nt downstream of TSS), 2) body region (start=400 nt downstream of TSS, stop=TES).
Read counts for TSS/body features were created using bigWigAverageOverBed (UCSC Toolkit) and only counting reads from the correct strand.
Count matrices for TSS/body features were TPM normalized (sequencing depth, feature length) and combined.
All isoforms with an average TPM < 0.5 in either TSS or body features were removed.
One isoform was selected for each gene as the primary transcript based on the largest average TPM score on the TSS feature.
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: Tab-delimited matrix with TPM normalized counts of TSS/body features of isoforms as described above.

extract_protocol:
Fragmented biotin-labeled nascent RNA was isolated from permeabilized cells by streptavidin beads and phenol-chloroform extraction.
Fragmented nascent RNA was ligated with reverse 3' RNA adapter (5'p-GAUCGUCGGACUG-UAGAACUCUGAAC-/3'InvdT/), and biotin-labeled products were enriched by another round of streptavidin bead binding and extraction. For 5' end repair, the RNA products were successively treated with tobacco acid pyrophosphatase and polynucleotide kinase. 5' repaired RNA was ligated to reverse 5' RNA adaptor (5'-CCUUGGCACCCGAGAAUUCCA-3') before being further purified by the third round of streptavidin bead binding and extraction. RNA was reverse transcribed using 25 pmol Illumina RP1 primer (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3'). Final amplification was performed by NEBNext High-Fidelity 2x PCR Master Mix (NEB). Based on amplification curve 7-9 additional cycles were used after 5 initial cycles.


title: Bulk training standard (chow) diet rep1 [TC1.scWAT]

value: 12-week old


title: Bulk sedentary standard (chow) diet rep1 [SC3.scWAT]


title: PROseq_SH1sKO_2


title: PROseq_SH1sKO_1


title: E. coli RNA-seq - WT C-lim 0.1 rep3

source_name: E. coli RNA-seq - WT C-lim 0.1 rep3


title: PROseq_WT_3


title: PROseq_WT_1


title: PROseq_WT_2


title: E. coli RNA-seq - WT C-lim 0.1 rep2

source_name: E. coli RNA-seq - WT C-lim 0.1 rep2


title: Bulk sedentary standard (chow) diet rep2 [SC4.scWAT]


title: E. coli RNA-seq - WT C-lim 0.1 rep1

source_name: E. coli RNA-seq - WT C-lim 0.1 rep1


title: 83T_Caudate

source_name: Nuclei isolated from Rhesus macaque snap frozen caudate tissue

value: enriched caudate nuclei

value: saline, SIV-latent virus


title: 81T_WhiteMatter

source_name: Nuclei isolated from Rhesus macaque snap frozen frontal lobe white matter

value: enriched cwhite matter nuclei


title: Obp56h_KO male replicate 1

city: Greenwood

first: Heather

last: Flanagan-Steet

state: SC

address: 101 Gregor Mendel circle

institute: Greenwood Genetic Center

data_processing:
Custom pipeline- Mokashi et al, 2021, biorXiv; Johnstun et al, 2021, Molecular Biol Evolution
Assembly: Drosophila reference genome (D_mel_6.13)
Supplementary files format and content: counts file; txt

organism: Drosophila melanogaster

source_name: heads

extract_protocol:
Direct zol RNA mini kit (Zymo research)
Universal Plus Total RNA Seq kit with Custom AnyDeplete (Tecan, Männedorf, Switzerland)

value: heads

tag: gender

value: male

value: Obp56h null


title: CSB female replicate 2

value: female

value: Control i.e CSB


title: Obp56h_KO female replicate 2


title: CSB female replicate 1


title: Obp56h_KO female replicate 1


title: Obp56h_KO male replicate 2


title: 81T_Caudate


title: CSB male replicate 1


title: 79T_Caudate

value: morphine, SIV-latent virus


title: BTC40_LPS4_PGN40-7.8

description: BTC [49 ng/mL] + LPS [4 ng/mL]  + PGN treatment [40 ng/mL]

data_processing:
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.
The sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
The reads were aligned to the human genome and transcriptome (Gencode v40) using STAR v2.5.3a.
The number of reads per million for cells were counted using HTSeq (v 0.6.0)
Assembly: The human genome and transcriptome (Gencode v40) were used for assembly
Supplementary files format and content: text file of relativized per million reads

source_name: THP-1 cell line

tag: cell line

value: BTC+LPS+PGN

tag: replicate


title: 83T_WhiteMatter

tag: tissue


title: 78T_WhiteMatter


title: BTC40_LPS4_PGN40-7.4

tag: group


title: BTC40_LPS4_PGN40-7.5


title: 78T_Caudate


title: BTC40_LPS4_PGN40-7.1


title: CSB male replicate 2


title: 77T_Caudate


title: LPS4_PGN40-7.8

description: LPS [4 ng/mL] + PGN [40 ng/mL] treatment

value: LPS+PGN


title: WDD_534

source_name: liver

tag: mouse id

value: Male

value: WDD


title: 77T_WhiteMatter


title: LPS4_PGN40-7.5


title: LPS4_PGN40-7.6


title: LPS4_PGN40-7.4


title: LPS4_PGN40-7.1


title: 76T_WhiteMatter


title: BTC40-7.8

description: BTC treatment [40 ng/mL]

value: BTC


title: BTC40_LPS4_PGN40-7.6


title: BTC40-7.7

description: BTC treatment [40 ng/mL]


title: 76T_Caudate


title: BTC40-7.5

description: BTC treatment [40 ng/mL]


title: 75T_WhiteMatter


title: BTC40-7.1

description: BTC treatment [40 ng/mL]


title: BTC40-7.4

description: BTC treatment [40 ng/mL]


title: NTC-7.8

description: Control

value: NTC


title: BTC40-7.2

description: BTC treatment [40 ng/mL]


title: 74T_Caudate


title: NTC-7.6

description: Control


title: NTC-7.5

description: Control


title: 73T_WhiteMatter


title: BTC40-7.6

description: BTC treatment [40 ng/mL]


title: NTC-7.4

description: Control


title: NTC-7.1

description: Control


title: 74T_WhiteMatter


title: 29_Exp5_9_DHA+Veh

source_name: LX2 cell line

growth_protocol: LX2 cells were obtained from SL Friedman (Mount Sani Medical School) (46). LX2 cells are activated human hepatic stellate cells; they were maintained in DMEM with 10% FCS containing penicillin and streptomycin. Cells were plated onto 100 mm plastic petri dishes ∼100,000 cells/plate and treated with fatty acids (at 50 μM) in endotoxin-free BSA (at 20 μM) during the growth phase. Fatty acids [oleic acid (18:1 ω9) and DHA (22:6, ω3); Nu-Chek Prep] were used at 50 μM for 2- 48-hour cycle treatments.

treatment_protocol: After this pre-treatment, cells were trypsinized, washed in PBS, counted and plated at 3000 cells/well in a 96-well plate. Cells were fed DMEM with 1 % FCS without or with betacellulin (human recombinant betacellulin (BTC), R&D Systems) and with or without fatty acids at 50 After this pre-treatment, cells were trypsinized, washed in PBS, counted and plated at 3000 cells/well in a 96-well plate. Cells were fed DMEM with 1 % FCS without or with betacellulin (human recombinant betacellulin (BTC), R&D Systems) at 50 μM for 72 hrs. Cells were then seeded onto 6-well plates at 40,000 cells/well; and cells were treated with fatty acids for 96 hrsAfterward, media was removed, and cells were  treated without and with BTC at 20 ng/ml for 72 hrs.

value: DHA+Veh

tag: sample number

tag: cohort

value: DMEM and 1% FCS and DHA at 50 μM for 72 hours


title: 30_Exp5_10_DHA+BTC

value: DHA+BTC

value: DMEM and 1% FCS and DHA at 50 μM and 20 ng/mL BTC for 72 hours


title: 28_Exp5_6_OLA+BTC

value: OLA+BTC

value: DMEM and 1% FCS and OLA at 50 μM and 20 ng/mL BTC for 72 hours


title: 73T_Caudate

value: enriched caudate nuclei


title: 27_Exp5_5_OLA+Veh

value: OLA+Veh

value: DMEM and 1% FCS and OLA at 50 μM for 72 hours


title: C57BL/6, WD fed liver biopsy, 12weeks, non-responder4 [8-1]

city: seoul

first: Seung Min

last: Lee

state: 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Rep. of KOREA

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

country: South Korea

institute: hanyang university

data_processing:
Paired end sequencing reads of cDNA libraries (101bp) generated from a NovaSeq instrument were verified its sequence quality with FastQC v 0.11.7. For data preprocessing, low quality bases and adapter sequences in reads were trimmed using Trimmomatic v 0.38.
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0.
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes).
These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2. Because of its use of these efficient data structures and algorithms, HISAT generates spliced alignments several times faster than Bowtie and BWA widely used.
Assembly: mm10
Supplementary files format and content: read counts, FPKM values for each Sample

extract_protocol:
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).
RNA libraries for RNA-seq were prepared using the SMARTER mRNA-Seq library preparation kit according to the manufacturer's protocol.

value: liver

value: non-responders without therapeutic effect

tag: genotype

value: WT

value: Western diet fed with 12weeks


title: C57BL/6, WD fed liver biopsy, 12weeks, vehicle3 [10-1]


title: 26_Exp5_2_VEH+BTC

value: VEH+BTC

value: DMEM and 1% FCS and 20 ng/ML BTC for 72 hours


title: C57BL/6, WD fed liver biopsy, 12weeks, vehicle2 [7-1]


title: 24_Exp4_6_DHA+BTC


title: 23_Exp4_5_DHA+Veh


title: 22_Exp4_4_OLA+BTC


title: 21_Exp4_3_OLA+Veh


title: C57BL/6, WD fed liver biopsy, 12weeks, responder3 [6-3]

value: responders with therapeutic effect on OCA


title: 25_Exp5_1_VEH+Veh

value: VEH+Veh

value: DMEM and 1% FCS


title: C57BL/6, WD fed liver biopsy, 12weeks, non-responder3 [6-2]


title: 20_Exp4_2_Veh+BTC

value: Veh+BTC


title: 17_Exp3_5_DHA+Veh

value: DHA+Veh

value: DMEM and 1% FCS and DHA at 50 μM for 72 hours


title: C57BL/6, WD fed liver biopsy, 12weeks, responder2 [5-4]


title: P1083LO

type: genomic

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

data_processing: For all analyses, probes were removed in minfi if: they had a detection P-value<0.01; were cross-reactive; contained a SNP at the single base extension or CpG interrogation site at any MAF; were not present in a CpG context; were present on either sex chromosome. Given the cancer-related nature of some of the datasets analyzed, we also assessed probes in SeSAMe. Probes that failed under default parameters were also removed prior to analysis. For all analyses, DMRs were generated using DMRcate on beta values. A comparison of DMRs across conditions was then carried out by setting lambda=1000 and minimum CpGs=7.

label: Cy3, Cy5

source_name: Colon Organoid

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of distal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol: Genomic DNA was extracted using the Qiagen UCP DNA kit (Catalog No: 56204; Qiagen; Hilden, Germany) with few exceptions. For elution, a 5 minute final incubation of Buffer AUE was preferred to increase yield. Further, the elution step was carried out twice using two volumes of 25μl. DNA quality was assessed using gel electrophoresis to ensure that DNA was not heavily fragmented.

tag: Sex

value: M

tag: age

tag: smoking

value: Never

tag: phenotype

value: CTL


title: C57BL/6, WD fed liver biopsy, 12weeks, non-responder2 [4-3]

tag: strain


title: P1296LO

scan_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

value: F

value: Former


title: P1273LO

value: Current


title: C57BL/6, WD fed liver biopsy, 12weeks, responder1 [2-4]

value: liver


title: P1208LO


title: 18_Exp3_6_DHA+BTC

value: DHA+BTC

value: DMEM and 1% FCS and DHA at 50 μM and 20 ng/mL BTC for 72 hours


title: P1229LO


title: 15_Exp3_3_OLA+Veh

value: OLA+Veh

value: DMEM and 1% FCS and OLA at 50 μM for 72 hours


title: P1074LO


title: P1247LO


title: P1261LO

value: FAP


title: C57BL/6, WD fed liver biopsy, 12weeks, non-responder1 [2-2]

value: non-responders without therapeutic effect

value: WT

value: Western diet fed with 12weeks


title: P1262LO


title: P1284LO


title: 14_Exp3_2_Veh+BTC

value: Veh+BTC

value: DMEM and 1% FCS and 20 ng/ML BTC for 72 hours


title: P1103LO

value: M


title: 13_Exp3_1_Veh+Veh

value: Veh+Veh

value: DMEM and 1% FCS


title: C57BL/6, WD fed liver biopsy, 12weeks, vehicle1 [1-2]


title: P1269LO

value: F

value: Never

value: CTL


title: P1253LO


title: 11_Exp2_5_DHA+Veh

value: DHA+Veh

value: DMEM and 1% FCS and DHA at 50 μM for 72 hours


title: P1169LO


title: P1096LO


title: 10_Exp2_4_OLA+BTC

value: OLA+BTC

value: DMEM and 1% FCS and OLA at 50 μM and 20 ng/mL BTC for 72 hours


title: 9_Exp2_3_OLA+Veh

value: OLA+Veh

value: DMEM and 1% FCS and OLA at 50 μM for 72 hours


title: P1228LO

value: FAP


title: Retina, Fbxl11-CKO2, P1, H3K36me3

data_processing:
library strategy: CUT&Tag
The sequenced reads were mapped to mouse (GENCODE GRCm38.p6) and Escherichia coli (GenBank: CP053595.1) genomes with Bowtie2 to the genomes of mouse (GENCODE GRCm38.p6) and E. coli (GenBank: CP053595.1). The mapping results were converted to BAM and BED formats using SAMtools and scaled by the number of E. coli-derived reads using bedtools. Peak calling and peak annotation were performed using SEACR and ChIPseeker, respectively.
Assembly: GRCm38
Supplementary files format and content: bedgraph files. Reads were mappend on mouse genome, and then scaled with the number of reads mapped on E. coli genome.

source_name: retina

extract_protocol:
Control or Fbxl11-CKO retinal cells at P1 (1 x 105 cells/sample) were mixed with human colorectal cancer cell line SW480 (1 x 104 cells/sample), and resuspended in buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Nacalai Tesque), 1x Protease Inhibitor Cocktail) at 1 x 105 cells/100 μl. Concanavalin A magnetic beads (Bangs Laboratories, USA) were mixed with the cells in binding buffer  (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and rotated for 20 minutes at room temperature. Then, the cells were resuspended in 100 μl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Nacalai Tesque), 1x Protease Inhibitor Cocktail, 0.05% Digitonin (Millipore), 2 mM EDTA, and 0.1% bovine serum albumin) containing antibodies listed below at 10 μg/mL and rotated overnight at 4℃. The cells were washed and resuspended in 100 μl Dig-wash Buffer containing 10 μg/ml anti-rabbit IgG antibody (Rockland Immunochemicals, USA, 611-201-122), rotated for 1 hr at room temperature, and resuspended in Dig-300 Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 1x Protease Inhibitor Cocktail) containing 0.8 μl pAG-Tn5 adapter complex and rotated for 1 hr at room temperature. The cells were washed with Dig-300 Buffer three times, resuspended in 100 μl Tagmentation Buffer (Dig-300 Buffer containing 10 mM MgCl2), and incubated for 1 hr at 37℃. Then 2 μl of 10 mg/mL Proteinase K was added and further incubated at 37℃ for 30 min. DNA was purified by Phenol-Chloroform protocol and dissolved in 25 μl water.
The DNA was subjected to PCR (72℃ (5 mins) x 1, 98℃ (30 sec) x 1, 98℃ (10 sec)/ 63℃ (15 sec) x 17, 72℃ (1 min) x 1) using i5 and i7 primers and Q5 High-Fidelity 2x Master Mix (New England Biolabs, USA). The library was sequenced with Novaseq6000.

value: retina

tag: time

value: abcam, ab9050


title: 12_Exp2_6_DHA+BTC

value: DHA+BTC

tag: treatment

value: DMEM and 1% FCS and DHA at 50 μM and 20 ng/mL BTC for 72 hours


title: 7_Exp2_1_Veh+Veh


title: Retina, Fbxl11-CKO2, P1, IgG

tag: antibody

value: Cell Signaling, 2729S


title: 19_Exp4_1_Veh+Veh

value: Veh+Veh


title: P1055LO


title: 16_Exp3_4_OLA+BTC


title: 6_Exp1_6_DHA+BTC


title: P1236LO

value: M


title: 5_Exp1_5_DHA+Veh


title: 4_Exp1_4_OLA+BTC


title: P1164LO

value: F


title: 3_Exp1_3_OLA+Veh


title: P1151LO

value: Never


title: Retina, Fbxl11-CKO1, P1, IgG


title: P1210LO

value: CTL


title: P1291LO