title: Raw.Sm_Str_HFlow_rb6_BAm

city: BUFFALO

first: Kerry

middle: E

last: Poppenberg

state: NY

address: 875 Ellicott St

institute: University at Buffalo

description:
Rabbit
SM8
counts_matrix.txt

data_processing:
For all data, per-cycle base-call (BCL) files generated by the NextSeq were converted to per-read FASTQ files using bcl2fastq v.2.20.0.422 using default parameters.
The quality of the sequencing was reviewed using FastQC v.0.11.5. Detection of potential contamination was done using FastQ Screen v.0.11.1. FastQC and FastQ Screen quality reports were summarized using MultiQC v.1.5.
No adapter sequences were detected, so no trimming was performed. Sequencing reads were aligned to rabbit genome, oryCun2, using STAR aligner50 Only uniquely mapped reads were retained for downstream analysis.
Read counts were measured according to Ensembl gene annotation. Sequence alignments were compressed and sorted into binary alignment map (BAM) files using samtools v.1.9. Counting of mapped reads for genomic features was performed using Subread featureCounts v.1.6.2 using the parameters -s 2, -g gene_id, - t exon, -Q 60 -C, the annotation file specified with the -a parameter was the Ensembl reference OryCun2.0 (GCA_000003625.1).
Aggregate quality control data (i.e. alignment statistics and feature assignment statistics) were again summarized using MultiQC.
Genome_build: Ensembl reference OryCun2.0 (GCA_000003625.1).
Supplementary_files_format_and_content: counts_matrix.txt: Tab-delimited matrix file includes raw counts for all samples.

organism: Oryctolagus cuniculus

source_name: Basilar artery media

extract_protocol:
Immediately following euthanasia, animals were perfused with 1 U/mL heparin in 0.9% saline solution for 10 minutes. Then, the brain was removed, and the most posterior cerebral arteries, from the vertebral arteries to the posterior cerebral arteries and superior cerebellar arteries, were surgically excised. The BA with the BT and short portions of the downstream branches was placed in optimal cutting temperature compound and flash frozen in liquid nitrogen. Longitudinal sections of the BA and coronal sections through the BT were cut at 8 µm thickness, adhered to nuclease-free Foil Membrane Slides for use with the Leica laser microdissection system and stored at -80oC until laser microdissection. Immediately prior to microdissection, sections were fixed for 2 min with ice-cold 70% ethanol, washed twice for 60 sec with ice-cold RNase-free water to remove residual embedding media, and dehydrated by one 2-minute wash in 95% ethanol and two 2-minute washes in 100% ethanol, then air dried for one hour in a vacuum desiccator at room temperature. Dehydrated sections were micro-dissected on a Leica LMD6000 system (Leica Microsystems): ~10 um wide strips were cut from the intimal layer (containing ECs) and separate strips were cut through the full thickness of the remaining medial layer (containing VSMCs). Intimal and medial tissue fragments from the BA and from a region extending ~100 µm distally from the apex of the BT were collected separately into dry microfuge tubes and held at -80 degrees C until RNA extraction. To increase RNA yield, tissue from ~10 sections were combined for each sample.
Total RNA was extracted and amplified from each sample tube using SMART-Seq v4 Ultra Low Input RNA Kits (Takara Bio). To check the quality of extraction and amplification, an aliquot of the end product was examined by electrophoresis using an Agilent 2100 BioAnalyzer RNA 6000 Pico Chip (Agilent, Las Vegas, NV). RNA samples to be sequenced had concentrations of 3.5-40 ng/µl and a broad molecular-weight distribution spanning 100-6000 bp and peaking at 800-2000 bp.
cDNA libraries were prepared using Nextera DNA Library Preparation Kits (Illumina, San Diego, CA) and subjected to 75-cycle, single-read sequencing on an Illumina NextSeq500.

tag: breed

value: New Zealand white

tag: Sex

value: Female

tag: vessel

value: Basilar artery

value: Media

tag: flow

value: High

tag: rabbit


title: Mettl3PolII1_Rep2

status: Public on Jul 28 2021

type: SRA

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

country: Germany

institute: University of Mainz

description: Pol II ChIP from S2R+ cells depleted for Mettl3

library_source: genomic

data_processing:
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila.
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: dm6 (Drosophila melanogaster)
Supplementary_files_format_and_content: Ctrl_HA.bw: Replicate averaged, input normalized bigwig file of Control HA
Supplementary_files_format_and_content: Ctrl_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with LacZ depletion
Supplementary_files_format_and_content: Ctrl_KD_Ser2P.bw : Replicate averaged, input normalized bigwig file for Ser2P with LacZ depletion
Supplementary_files_format_and_content: Mettl14_HA_UCSC.bw : Replicate averaged, input normalized bigwig file of Mettl14HA
Supplementary_files_format_and_content: Mettl14_KD_PolII_ave.bw: Replicate averaged, input normalized bigwig file for Pol II with Mettl14 depletion
Supplementary_files_format_and_content: Mettl14_KD_Ser2P_ave.bw : Replicate averaged, input normalized bigwig file for Ser2P with Mettl14 depletion
Supplementary_files_format_and_content: Mettl3_HA.bw: Replicate averaged, input normalized bigwig file of Mettl3 HA
Supplementary_files_format_and_content: Mettl3_HA_Ime4KD.bw : Replicate averaged, input normalized bigwig file of Mettl3 HA, with Mettl3 depletion
Supplementary_files_format_and_content: Mettl3_HA_RNaseT1.bw: Replicate averaged, input normalized bigwig file of Mettl3 HA, with RNAseT1 treatment
Supplementary_files_format_and_content: Mettl3_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with Mettl3 depletion
Supplementary_files_format_and_content: Mettl3_KD_Ser2P.bw: Replicate averaged, input normalized bigwig file for Ser2P with Mettl3 depletion
Supplementary_files_format_and_content: Ythdc1_HA.bw: Replicate averaged, input normalized bigwig file of Ythdc1 HA
Supplementary_files_format_and_content: Ythdc1_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with Ythdc1 depletion
Supplementary_files_format_and_content: fl2d_HA.bw: Replicate averaged, input normalized bigwig file of fl2d HA
Supplementary_files_format_and_content: fl2d_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with fl2d depletion
Supplementary_files_format_and_content: fl2d_KD_Ser2P.bw: Replicate averaged, input normalized bigwig file for Ser2P with fl2d depletion

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: cell culture

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4ºC. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4ºC.
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol
NebNext UltraII

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated two times and cells were harvested 5 days after the first treatment.

tag: antibody

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11

tag: cell type

value: Embryonic

tag: cell line

value: S2R+ Cells


title: 36454-P1-FC

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the Mmul_8.0.1 genome sequence using STAR-2.5.2b with --quantMode GeneCounts --outSAMtype None and all other paramters default
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: tab-delimited text files (STAR output) include transcript raw count values for each sample

molecule: total RNA

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from PBMC using RNEasy Mini kit reagents on a QIAcube instrument
cDNA libraries were constructed from 300 ng total RNA using Lexogen QuantSeq 3' FWD and sequenced on an Illumina HiSeq 4000 acquiring single-strand 65-bp reads (targeting > 10M reads/sample).

value: SIP-Isolated

tag: tissue

value: Peripheral blood mononuclear cells


title: 36391-P2-D13

value: SIP-JuvenilePartnered


title: Mettl3PolII1_Rep1


title: HCT116-CD276KO_4

city: Biberach (Riss)

first: Sibel

last: Durlanik

address: Birkendorferstr. 65

department: Cancer Immunology & Immune Modulation

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in [ https://pubmed.ncbi.nlm.nih.gov/32180900/ ]): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner [https://doi.org/10.1093/bioinformatics/bts635] allowing for soft clipping of adapter sequences. For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) [ https://pubmed.ncbi.nlm.nih.gov/21816040/ ] and featureCounts (v1.5.1) [ https://pubmed.ncbi.nlm.nih.gov/24227677/ ]. Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) [ https://pubmed.ncbi.nlm.nih.gov/27769170/ ] at the respective steps.   Finally, differential expression analysis was performed on the human mapped counts derived from featureCount using limma/voom [https://pubmed.ncbi.nlm.nih.gov/25605792/ , https://pubmed.ncbi.nlm.nih.gov/24485249/ ].
Genome_build: Homo sapiens (human) genome hg38/GRCh38
Supplementary_files_format_and_content: tpm.txt contains expression levels (tpm) in tab-separated format.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HCT116 colon cancer cells (ATCC, CCL-247) were propagated and maintained in McCoy’s 5A (Modified) medium (16600082, Gibco) with 10% FCS supplement.

extract_protocol:
RNA isolation and quality control   HCT116WT and HCT116CD276KO cells were cultured and maintained in different culture flasks for further propagation. Five biological replicates were used per group for a total of 10 samples. 1x106 cells per sample were collected, centrifuged, washed two times with PBS. After removal of supernatant completely, cell pellets were immediately frozen at -80C until further use. Total RNA extraction for Next-Generation Sequencing from cell pellets lysed in RLT plus buffer were performed by using the AllPrep DNA/RNA Mini Kit (80224, Qiagen) according to the company’s protocol. An on-column DNA digestion was performed and the final elution volume was 30 µL.  Total RNA was quantitatively and qualitatively assessed using the fluorescence-based RNA Broad Range Qubit Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 30 ng/µL while RIN were all >8.5.
Whole Transcriptome Sequencing  10 HCT116-derived RNA samples were normalized and 200 ng of input was used for library construction using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) upstream and the NEXNext Multiplex Oligos for Illumina (E7600) downstream (all New England Biolabs). Sequencing libraries were quantified, normalized, pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered with the HiSeq 3000/4000 SR Cluster Kit on a cBot; and sequenced on a HiSeq 4000 Sequencing System (Illumina) with dual index, single read at 50 bp length (Read parameters: Rd1: 51 Rd2: 8, Rd3: 8), reaching an average depth of 40 million Pass-Filter reads per sample (11.1% CV).

treatment_protocol: Crispr-Cas9 gene editing for HCT116 cells   Neon Transfection System (MPK1096 Invitrogen) was utilized to deliver the Cas9 (A36499, Invitrogen) - ribonuclear proteins (RNP) complex including guiding RNA against CD276 (A35533 -CRISPR806748_SGM, Invitrogen) or scrambled gRNA (A35526, Invitrogen) as control into the cell according to the company’s protocol with following modification.   HCT116 cells were treated with accutase (A6964, Sigma Aldrich) to detach and washed with PBS. For each transfection, 5x104 cells were electroporated with RNP complex (240 ng gRNA + 1.25 µg Cas9) in 10 µl reaction buffer with following setting on Neon: 1530V, 20ms, 1 pulse. After electroporation, cells were seeded in 24-well culture plate (142475, ThermoFisher) in McCoy’s 5A (modified) medium with 10% FCS supplement and cultured for 4 days. CD276 expression on the cell surface was analyzed by flow cytometry.

tag: genotype

tag: replicate


title: 36454-P1-D2


title: Raw.Sm_Str_NFlow_rb3_BAm

description:
Rabbit
SM5
counts_matrix.txt

value: Normal


title: Raw.Sm_Str_NFlow_rb4_BAm

description:
Rabbit
SM6
counts_matrix.txt


title: 36391-P2-D8


title: Mettl3_KD_Ser2P_Rep1

description: Ser2P ChIP from S2R+ cells depleted for Mettl3

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: 36454-P2-D2


title: Mettl3_KD_Ser2P_Rep2


title: RNA seq ko3

city: Cincinnati

first: Zhaowei

last: Tu

address: 3333 Burnet Ave

institute: Cincinnati Children's Medical Center

data_processing:
Sequencing reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1. The trimmed reads were aligned to the Mus musculus reference genome version GRCm38/mm10 with the program STAR v2.6.1e for RNA-seq and with BOWTIE v2.3.4.1 for ATAC-seq and CUT&RUN-seq experiments. Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
For RNA seq, Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database. Read counting was done with the program feature Counts v1.6.2 from the Rsubread package. Raw counts were normalized as transcripts per million (TPM). Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0.
For ATAC seq, Peaks were called with MACS2 v2.1.2 using the --broad option. ATAC genomic regions among all samples were obtained by merging called peaks at 50% overlap using BEDtools v2.27.0 and in-house programs. This was done at two levels using, between replicates and between treatments. In the former, we require peaks to be present in all biological replicates, meaning a peak observed in one replicate has to have a peak present in all other replicates at the 50% cutoff. On the latter, we keep all peaks from different treatments (merging the peaks in common at 50%). The resulting set of peaks, originally in BED format, were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.6.2 (Rsubread package). Each feature in the GTF file has the value "peak" on the second column.
For Cut & Run, reads with an aligned length between 0 and 280bp were selected for peak calling. The cutoff was chosen to include the first peak in the histogram of read lengths between aligned read pairs. Aligned length is defined as the distance in base-pairs from beginning of alignment in read1 to end of alignment in read2. Peak calling was done with the program MACS v2.1.2 using the narrow peaks mode (default). CUT&RUN genomic regions were obtained using the same method used in the analysis of ATAC-seq data. Resulting peaks, originally in BED format, were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.6.2 (Rsubread package).
Genome_build: mm10
Supplementary_files_format_and_content: TPM expression files for RNA seq data and BigWig for ATAC seq and Cut&Run data.

organism: Mus musculus

source_name: LSK

growth_protocol: The cells were sorted from mice with different genotypes and directly used for prepareing libraries.

extract_protocol:
Trizol was used for RNA seq extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols, ATAC seq library was based on Illumina Tagment DNA Enzyme and Buffer Kit. Cut&Run was followed as published online protocols
RNA-Seq, ATAC seq and Cut &Run libraries werer prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina from New England Biolabs

treatment_protocol: pI;pC was injected to induce deletion in the mice. Cells were sorted for use without any culture or other treatment

tag: strain

tag: harvest condition

value: 6 days post deletion


title: RNA seq LSK pKO2


title: RNA seq LSK pKO1


title: RNA seq ko2


title: 36391-P2-D2


title: Mettl3HAT1_Rep2

description: HA ChIP of Mettl3 from S2R+ cells transfected HA tagged Mettl3 with RNAseT1 treatment

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417


title: RNA seq wt3

value: WT


title: Raw.Sm_Bif_HFlow_rb6_BTm

description:
Rabbit
SM4
counts_matrix.txt

source_name: Basilar terminus media

value: Basilar terminus


title: Raw.Sm_Bif_NFlow_rb4_BTm

description:
Rabbit
SM2
counts_matrix.txt

value: New Zealand white


title: Raw.Sm_Bif_HFlow_rb5_BTm

description:
Rabbit
SM3
counts_matrix.txt

value: Female


title: RNA seq ko1


title: Mettl3HAChIP_Rep2

description: HA ChIP of Mettl14 from S2R+ cells transfected HA tagged Mettl3


title: Raw.Endo_Str_HFlow_rb6_Bai

description:
Rabbit
Endo8
counts_matrix.txt

source_name: Basilar artery intima

value: Basilar artery

value: Intima


title: RNA seq wt1


title: Mettl3KD1_Mettl3HAChIP

description: HA ChIP of Mettl3 from S2R+ cells transfected HA tagged Mettl3 with Mettl3 depletion


title: RNA seq pko3


title: 36391-P2-FC


title: Raw.Endo_Str_NFlow_rb4_Bai

description:
Rabbit
Endo6
counts_matrix.txt


title: Raw.Sm_Bif_NFlow_rb3_BTm

description:
Rabbit
SM1
counts_matrix.txt

value: Media


title: Raw.Sm_Str_HFlow_rb5_BAm

description:
Rabbit
SM7
counts_matrix.txt

value: High


title: Mettl3HAT1_Rep1

value: Embryonic


title: RNA seq wt2


title: SINVB2: Total(suckling BALB/c 3dpi)

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Road

country: China

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Supplementary_files_format_and_content: mapping results

source_name: hindlimb muscle

extract_protocol:
Total RNA was extracted from mice hindlimb muscle tissue or 293T cells using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

value: BALB/c

tag: treatment

value: SINVB2 virus


title: 36391-P1-D8

value: SIP-Isolated

value: Peripheral blood mononuclear cells


title: 36391-P1-D2


title: SINV: Total(suckling BALB/c 3dpi)

value: SINV virus


title: 36175-P2-D2

value: SIP-JuvenilePartnered


title: Raw.Endo_Str_HFlow_rb5_Bai

description:
Rabbit
Endo7
counts_matrix.txt


title: NoV∆B2: suckling C57BL/6 Lgp2-/- 4dpi

value: NoV∆B2 virus


title: Mettl3HAInput

description: Input control

value: Input Sample HA

value: S2R+ Cells


title: 36175-P2-FC


title: Mettl3HAChIP_Rep1

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417


title: fl2d_KD_Ser2P_Rep1

description: Ser2P ChIP from S2R+ cells depleted for fl2d

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: 36391-P1-FC


title: fl2dPolII1_Rep2

description: Pol II ChIP from S2R+ cells depleted for fl2d

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11


title: 36175-P2-D13


title: Raw.Endo_Bif_NFlow_rb3_Bti

description:
Rabbit
Endo1
counts_matrix.txt

source_name: Basilar terminus intima

value: New Zealand white

value: Female

value: Basilar terminus

value: Normal


title: Raw.Endo_Bif_HFlow_rb5_Bti

description:
Rabbit
Endo3
counts_matrix.txt

value: Intima

value: High


title: SINVmB2: Total(suckling BALB/c 3dpi)

value: BALB/c

value: WT

value: SINVmB2 virus


title: 36391-P1-D13

value: SIP-Isolated

value: Peripheral blood mononuclear cells


title: 36175-P1-D8


title: VSV12h-IP

city: Jinan

first: Li

last: Qi

address: School of Basic Medical Science,Shandong University,Wenhua West Road,No 44,Jinan City,Shandong 250000,China

department: School of Basic Medical Science

institute: Shandong University

data_processing:
Basecalls performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Mouse genome (MM10) using BOWTIE software (V2.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files

source_name: primary peritoneal macrophages

growth_protocol: Mouse primary peritoneal macrophages were cultured at 37°C under 5% CO2 in endotoxin-free DMEM supplemented with 10% fetal bovine serum (Invitrogen-Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
10 ng of DNA samples were prepared for Illumina sequencing as the following steps: 1) DNA samples were blunt-ended; 2) A dA base was added to the 3' end of each strand; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Size selection of ~200-1500bp  enriched product using AMPure XP beads. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina HiSeq 4000 following the HiSeq 3000/4000 SBS Kit (300 cycles) protocol.

treatment_protocol: One replicate was VSV treated for 12 hours.

value: primary peritoneal macrophages

value: Treated with VSV for 12h

tag: chip antibody

value: KAP1(abcam, ab22553)


title: Raw.Endo_Str_NFlow_rb3_Bai

description:
Rabbit
Endo5
counts_matrix.txt

value: Basilar artery


title: fl2dPolII1_Rep1

value: Embryonic

value: S2R+ Cells


title: 36175-P2-D8

value: SIP-JuvenilePartnered


title: VSV12h-input


title: NoV: Ago-IP(suckling C57BL/6 7dpi)

value: NoV virus


title: Raw.Endo_Bif_NFlow_rb4_Bti

description:
Rabbit
Endo2
counts_matrix.txt

value: New Zealand white

value: Female

value: Basilar terminus


title: fl2dHAInput

description: Input control

value: Input Sample HA


title: 0-IP

value: Untreated


title: NoV: B2-IP(suckling C57BL/6 7dpi)

value: WT


title: 36175-P1-D13


title: NoV: suckling C57BL/6 7dpi


title: 47 NASH6 explant liver

city: Philadelphia

first: Tobias

last: Raabe

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were filtered to retain only high quality reads. In addition, ribosomal reads and repeats were eliminated by alignment to a generic set of ribosomal/repeat sequences. Remaining reads were processed with RNA-Seq Unified Mapper (RUM) (Grant et al, Bioinformatics, 2011)
Following RUM alignments to human genome (build hg19) and known transcripts (RefSeq, UCSC, ENSEMBL, etc), a feature-level quantitation (transcript, exon, and intron) was output as a result
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts per transcript annotated with gene symbol and RefSeq accession

source_name: NASH6 male  liver explant

growth_protocol: Up to 150µL of matrix can be pooled per 15mL tube. After removing the organoids from the culture using a 1ml pipet tip, we added ~3mL of ice cold basal medium per 50µL of matrix and let the cells stand on ice 5-10 min. After centrifugation at 1600rpm 3min (Sorvall RT 6000D centrifuge) and removal of the top layer of basal medium the pellet was resuspended in 1ml of basal medium and pipetted up and down ~15 times with a 10ml pipettip mounted on a 1ml pipet tip, which yeils a mix of single cells and clumps of ~2-10 cells, which increases cell survival after splitting and obviates the need for using Y-27632 for routine splitting.  After centrifugation at 1600rpm 3min the supernatant was carefully removed and the desired volume of matrix (50-60µL drops per well and seeded onto 24 well suspension plates. After incubating ~10min at 37Co, the drops were overlaid with pre-warmed expansion medium + Y-27632 (Basal media, + 1x B-27 supplement without vitamin A, 1mM NAC, 10mM Nicotinamide, 10% R-spondin conditioned medium, 1x N2 supplement, 100ng/mL FGF-10, 25ng/mL HGF, 25ng/mL human EGF, 10nM leu15 Gastrin, 10µM Forskolin, 5µM A83-01) according to (9,10) after incubation. For this study, unless otherwise noted, organoids were expanded for 5-6 passages before differentiation, one additional passage for dedifferentiation, and in the case of a second differentiation stage, a second additional passage. Times between splits varied from ~4-8 days depending on the organoid line.

extract_protocol:
Harvest of RNA was done  with TRIZol (Life Technologies, 15596026). Differentiation medium was removed from the well and 500µL of TRIZol was added directly above the basement matrix droplet. The droplet was gently scraped from the surface and resuspended in the TRIZol by pipetting 10 times in a P1000. Samples were transfered to sterile eppendorf tubes and flash frozen on dry ice before being stored at -80 oC. For frozen explant liver from NASH patients 5 and 6, a sterilized mortar and pestle was used to grind about 200 mg of the tissue under liquid nitrogen. 500µl TRIZOL was added to the sample, pipetted vigorously and then refrozen at -80 oC. RNA was isolated using a slightly modified version of the Qiagen RNeasy Mini Kit with on Column DNase Digestion kit protocol. Samples were thawed at room temperature and 100µL of chloroform added. Tubes were inverted and spun for 20 minutes at 13,000rpm at 4oC in a Heraeus, biofuge fresco tabletop centrifuge. The aqueous upper phase was then transferred to a new RNase free Eppendorf tube for purification beginning at the addition of an equal volume of 70% ETOH to each sample (directly following tissue or cell lysis/homogenization). Additionally, RNeasy Mini columns were capped, wrapped in parafilm, and heated at 50 oC for 10 minutes immediately preceding elution in 40µL of RNase free water. RNA concentration was measured using the Take3 trio microspot plate and BioTek plate reader. RNA integrity was assessed by visualizing the ribosomal RNA bands through 0.8% agarose gel electrophoresis.
Library Preparation: NEBNext Ultra II Directional RNA Library Prep Kit (catalog# E7765) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog# E7490), and NEBNext Multiplex Oligos for Illumina (catalog# E6609) were applied for the creation of cDNA libraries according to manufacturer’s instructions with no deviations. The Aligent Bioanalyzer High Sensitivity DNA chip (#i5067-4626) was used to asses quality of the liraries. The KAPA Biosystems qPCR kit was purchased from ROCHE (cat# 07960336001) and used for library qunatitation. All completed libraries were run  as a single pool on an Illumina HiSeq 4000 analyzer by the UPenn Next Generation Sequencing Core (NGSC), except the libraries for 2D organoids and biliary organoids which were run in a separate pool on an Illumina NovaSeq 6000 sequencer by the NGSC.

treatment_protocol: Expanding organoids were differentiated in1 well of a  24well plate by supplementing the expansion medium with BMP-7 for approximately 2-3 days before switching to complete differentiation medium. Hepatic organoids were considered differentiated and ready for RNA isolation after 11-14 days in differentiation medium. For ductal dedifferentiation, hepatic organoids were split into fresh basement matrix, overlayed with expansion medium containing  Y-27632  and cultured for at least one week before routine passaging. For redifferentiation  dedifferentiated expanded organoid cultures were subjected to the same differentiation procedure that was used for the first differentiation.

tag: disease state

value: cirrhotic NASH human liver

value: male

value: NASH explant liver

tag: differentiation status

value: direct RNA isolation from liver

tag: rna isolation method

value: total RNA isolated by TRIZOL procedure


title: ADMDHT3

city: Houston

first: Robert

middle: L

last: Satcher

state: TX

address: 1515 Holcombe

department: Orthopaedic Oncology

institute: MD Anderson Cancer Center

description:
Expression_Gene ADMDHT_vs_DHT.xlsx
Expression_Gene ADMDHT_vs_ADM.xlsx

data_processing:
Agilent 2100 Bioanalyzer was used for assessment of the quality of sequencing library.Raw data files in FASTQ format were generated from the Illumina sequencer
Sequence quality was examined using the FastQC.
After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered less than 20 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with Hisat 2 software
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM

source_name: M2-10B4 cells

growth_protocol: Confluent cultures of M2-10B4 cells were changed into adipocyte differentiation medium (ADM) containing 10% charcoal-stripped serum (CSS) supplemented with insulin (2 μg/mL), dexamethasone (1 μM), and rosiglitazone (2 μM) (Sigma-Aldrich) in phenol red -free RPMI (Sigma R7509), added with L-glutamine to 2 mM and Hepes to 25 mM.  ADM was changed every third day.

extract_protocol:
Cells were harvest at day 9. RNA was purified with Trizol and Rneasy mini kit with RNase free DNase treatment.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT)  magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

treatment_protocol: DHT (10nM) treatment changed every 3rd day along with fresh medium change  for a total of 9 days.

tag: background strain

value: C57BL/6J X C3H/HeJ

value: DHT-treated in adipogenic medium


title: Raw.Endo_Bif_HFlow_rb6_Bti

description:
Rabbit
Endo4
counts_matrix.txt

tag: breed

tag: Sex

tag: vessel

value: Intima

value: High


title: fl2dHAChIP_Rep2

description: HA ChIP of Mettl14 from S2R+ cells transfected HA tagged fl2d

tag: antibody

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417

value: Embryonic

value: S2R+ Cells


title: 0-input

tag: cell type

value: primary peritoneal macrophages

value: KAP1(abcam, ab22553)


title: 46 NASH6 explant liver


title: fl2dHAChIP_Rep1

tag: cell line


title: fl2d_KD_Ser2P_Rep2

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: B16-R2-2

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
50bp single-end sequenced reads were analyzed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat-2.0.10, using Bowtie 1.0.0  and Samtools 0.1.1.9, allowing two mismatches and 20 multihits. Differential expression was calculated with DESeq2, using the human NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml. GSEAPreranked was used to perform gene set enrichment analysis of the described gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.1) were finally considered.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: FPKMs obtained with Cuffnorm

source_name: Dr. Michael Detmar and Dr. Steven Proulx (ETH Zurich, Switzerland)

growth_protocol: All melanoma cell lines were grown in high glucose DMEM (Lonza #D6429) supplemented with 10% fetal bovine serum (Hyclone #SH30071.03IH), 2 mM glutamine and 20 μg/ml gentamicin (Sigma #G1272).

extract_protocol:
Total RNA was isolated from cells or xenografts using the RNeasy Mini Kit (Qiagen #74106).
Total RNA was isolated from cells or xenografts using the RNeasy Mini Kit (Qiagen #74106). The quantity and quality of the extracted RNA was assessed using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific) and Agilent 2100 Bioanalyzer. RNA sequencing (RNA-seq) was performed by the CNIO Genomics Unit. 1 μg of total RNA from each sample was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced using the Illumina HiSeq2500 platform by following manufacturer's protocols.

treatment_protocol: No treatment

value: Mouse melanoma cell line, derived from a lymph node metastasis

value: No treatment


title: NoV: suckling C57BL/6 4dpi

value: WT

value: NoV virus


title: 45 NASH5 explant liver

source_name: NASH5 female  liver explant

value: cirrhotic NASH human liver

value: female

value: NASH explant liver


title: CtrlPolII1_Rep2

description: Pol II ChIP from S2R+ cells depleted for LacZ

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11


title: CtrlHAInput

description: Input control

value: Input Sample HA


title: NoV∆B2: suckling C57BL/6 7dpi

value: NoV∆B2 virus


title: 44 NASH5 explant liver

value: direct RNA isolation from liver

value: total RNA isolated by TRIZOL procedure


title: 36175-P1-FC

value: SIP-Isolated

tag: tissue

value: Peripheral blood mononuclear cells


title: CtrlPolII1_Rep1

value: Embryonic

value: S2R+ Cells


title: Ctrl_KD_Ser2P_Rep1

description: Ser2P ChIP from S2R+ cells depleted for LacZ

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: B16-R2L-2

value: Mouse melanoma cell line, from a lung metastasis derived from a lymph node metastasis


title: CtrlHAChIP_Rep1

description: HA ChIP from S2R+ cells transfected with HA-Control

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417


title: Ctrl_KD_Ser2P_Rep2


title: B16-R2L-1

value: No treatment


title: Mettl14PolII1_Rep2

description: Pol II ChIP from S2R+ cells depleted for Mettl14


title: ADMDHT1

value: C57BL/6J X C3H/HeJ

value: DHT-treated in adipogenic medium


title: ADM1

description:
Expression_Gene ADM_vs_Ctrl.xlsx
Expression_Gene ADMDHT_vs_ADM.xlsx

value: untreated in adipogenic medium


title: 36175-P1-D2


title: ADNDHT2


title: B16-R2-1

value: Mouse melanoma cell line, derived from a lymph node metastasis


title: CtrlHAChIP_Rep2


title: DHT3

description:
Expression_Gene DHT_vs_Ctrl.xlsx
Expression_Gene ADMDHT_vs_DHT.xlsx

value: DHT-treated in regular medium


title: 48 NASH6 explant liver

value: cirrhotic NASH human liver

value: male

value: NASH explant liver


title: ADM3


title: B16-F1-1

source_name: American Type Culture Collection (ATCC)

value: Mouse melanoma cell line, low metastatic potential


title: 33 AC p5

source_name: AC alcoholic cirrhosis  female liver explant

value: alcoholic cirrhosis  human liver

value: female

value: hepatic organoids

value: 12d hepatic differentiation of biliary organoids

value: total RNA isolated by TRIZOL procedure


title: 32 AC p5


title: ADM2


title: C2

description:
Expression_Gene DHT_vs_Ctrl.xlsx
Expression_Gene ADM_vs_Ctrl.xlsx

value: untreated in regular medium


title: Mettl14HAChIP_Rep1

description: HA ChIP of Mettl14 from S2R+ cells transfected HA tagged Mettl14

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417

value: Embryonic

value: S2R+ Cells


title: 21 CF p5

source_name: CF cystic fibropsis female liver explant

value: cystic fibropsis human liver


title: 31 AC p5


title: 43 NASH5 explant liver

value: direct RNA isolation from liver


title: B16-F1-2

value: No treatment


title: Mettl14PolII1_Rep1

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11


title: 20 CF p5


title: C1

value: C57BL/6J X C3H/HeJ


title: CUTO44

type: genomic

city: AURORA

last: Doebele

state: CO

department: Medical Oncology

institute: University of Colorado-AMC

description: Infinium HumanCytoSNP-850K v2.1 BeadChips

hyb_protocol: The resuspended, fragmented DNA sample was denature at 95C for 20mins, cooled for 30mins and then loaded onto a prepared BeadChip and place in the Hyb Chamber for 24hr hybrization at 48C. The BeadChip was wash with PB1 to prep it for Xstain and single-base extension follow by Bead Chip staining.  Finally, the BeadChip was washed with PB1 and coated with XC4/ethanol mix.  BeadChip was dried till scanning.

scan_protocol: The dried BeadChip was imaged using the iScan Reader according to illumina protocol

data_processing: Genomic DNA extracted from patient-derived LUAD cell line was genotyped using Infinium HumanCytoSNP-850K-12 v2.1 BeadChips (Illumina).

label: A-DNP, C-Bio

source_name: Patient-derived lung adenocarcinoma cell line

label_protocol: The MSA1 plate was prepared according to Illuminia protocol. 200ng of gDNA was added to the wells and denatured with 4ul of 0.1NaOH for 10mins at room temperature(RT). 68ul of random primer mix and 75ulmulti-sample ampification master mix was added to the well.  The plate was place in the Illumina Hyb oven for 24hours at 37C for uniform amplification.  The sample then underwent enzymatic DNA fragmentation for 1 hour at 37C followed by DNA precipitation with 100% isopropanol and PM1 solution followed by air drying the MSA1 plate for 1 hour.  Prior to hybridization, the dry sample was resuspended in RA1 buffer

growth_protocol: CUTO44 cell line were cultured in RPMI-1640 with 10%FBS and grown on a 10cm TC Dish.  When 100% confluency was reach, cells were trypsinized and spun down as cell pellet

extract_protocol: Genomic DNA was isolated using a BioRobot M48 Workstation with MagAttract technology (Qiagen)

treatment_protocol: No treatement were done on cell pellet

tag: gender

value: Liver

value: Lung adenocarcinoma


title: Mettl14_KD_Ser2P_Rep2

description: Ser2P ChIP from S2R+ cells depleted for Mettl14

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: 42 NASH6 p6

value: cirrhotic NASH human liver

value: male


title: 41 NASH6 p6

value: hepatic organoids


title: 19 CF p5

value: female

value: 12d hepatic differentiation of biliary organoids


title: IFNg- Tfh

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample

source_name: Tfh cell

extract_protocol:
total RNA were extracted using RNeasy Plus Mini Kit (Qiagen, Cat No. 74134)
Library were constructed using SMARTer® Ultra® Low Input RNA for Illumina® Sequencing kit (Clontech Laboratories, Cat No. 010616)

treatment_protocol: PMA 50ng/ml and ionomycin 500ng/ml treated sorted Tfh cells for 2h and then harvested and extracted the total RNA

value: Draining lymph nodes

value: Tfh cell, IFNg-

tag: model

value: H1N1 PR8 influenza infection


title: PDR

city: Bejing

first: Chao

last: Ye

address: No. 5, Haiyangcang, Dongcheng District, Beijing

department: Dongzhimen Hospital

institute: Beijing University of Chinese Medicine

data_processing:
Sequencing libraries were generated using NEBNext® Ultra 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 using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ 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 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in 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 was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.
After filtering, reference genome and gene model annotation files were downloaded from a genome website browser (NCBI/UCSC/Ensembl). Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. Bowtie was used for a BWT (Burrows–Wheeler Transformer) algorithm for mapping reads to the genome and Tophat can generate a database of splice junctions based on the gene model annotation file and thus achieve a better mapping result than other non-splice mapping tools.
For the quantification of gene expression level, HTSeq V0.6.1 was used to count the read numbers mapped for each gene. The RPKM of each gene was calculated based on the gene read counts mapped to this gene. A differential expression analysis was performed using the DESeq R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Macrophages

extract_protocol:
Total RNAs of macrophages were extracted in accordance with the manual of TRIzol®(Life Technologies, Inc., Gaithersburg, MD). Preparation of library and sequencing of transcriptome were carried out using Illumina Novoseq6000 (Novogene Bioinformatics Technology Co., Ltd., Beijing,China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Macrophages

tag: age

value: post natal day 6 weeks

tag: genotype

value: ApoE-/-

tag: sample group

value: Phlegm-Dampness Retention (PDR) syndrome

tag: strain background


title: Mettl14HAInput

description: Input control

source_name: cell culture

value: Input Sample HA

value: Embryonic

value: S2R+ Cells


title: DHT2

value: C57BL/6J X C3H/HeJ

tag: treatment

value: DHT-treated in regular medium


title: C3

value: untreated in regular medium


title: Mettl14_KD_Ser2P_Rep1

value: Ser2P (Abcam Cat No-ab5095) Lot No GR193165


title: DHT1


title: Mettl14HAChIP_Rep2

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417


title: ESS-Tfh rep3

tag: strain

value: Tfh cell

value: Experimental Sjogren syndrome


title: 40 NASH6 p6

tag: disease state

value: cirrhotic NASH human liver

value: male

value: hepatic organoids

tag: differentiation status

value: 12d hepatic differentiation of biliary organoids

tag: rna isolation method

value: total RNA isolated by TRIZOL procedure


title: IFNg+ Tfh

value: Draining lymph nodes

value: Tfh cell, IFNg+

value: H1N1 PR8 influenza infection


title: Bone marrow stromal cells-GCA 2

city: changsha

first: CHANGJUN

last: LI

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

description: Sample 5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow stromal cells-GCA

growth_protocol: bone marrow cells from tibiae and femurs of mice were collected and FACS sorted for BMSCs (Sca-1+ CD29+ CD45− CD11b−). BMSCs were then cultured in 6/12-well plates with α-MEM containing 10% fetal bovine serum.

extract_protocol:
After removing culture medium, RNA was harvested using Trizol reagent.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

treatment_protocol: BMSCs were treated with rGCA (50nM ) or PBS for three days.

value: Primary Bone marrow stromal cells

value: GCA


title: SEA-Tfh

value: SEA immunization


title: ESS-Tfh rep1


title: Bone marrow stromal cells-GCA 1

description: Sample 4


title: 38 NASH5 p5

source_name: NASH5 female liver explant

tag: Sex

value: female


title: SKYD

value: Macrophages

value: post natal day 6 weeks

value: ApoE-/-

value: Spleen and Kidney Yang Deficiency (SKYD) syndrome


title: 34 NASH4 p5

source_name: NASH4 male  liver explant


title: Bone marrow stromal cells-PBS 3

description: Sample 3

source_name: Bone marrow stromal cells-PBS

value: PBS


title: 35 NASH4 p5

value: cirrhotic NASH human liver


title: 39 NASH5 p5


title: ESS-Tfh rep2

value: Tfh cell

value: Experimental Sjogren syndrome


title: Bone marrow stromal cells-GCA 3

description: Sample 6


title: 36 NASH4 p5

value: male

value: hepatic organoids

value: 12d hepatic differentiation of biliary organoids


title: FLU-Tfh rep2

value: Draining lymph nodes


title: Bone marrow stromal cells-PBS 2

description: Sample 2


title: 30 NASH3 p5

source_name: NASH3 male  liver explant

value: total RNA isolated by TRIZOL procedure


title: Bone marrow stromal cells-PBS 1

description: Sample 1

value: Primary Bone marrow stromal cells


title: 37 NASH5 p5


title: PP-Tfh rep3

value: Peyer's patches

value: Steady status


title: PP-Tfh rep2


title: iMPCs

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

data_processing:
sequenced reads were aligned to the mm10 reference genome using CellRanger version 3.0.2.
The filtered reads assigned to cell barcodes were analyzed with the R package Seurat, version 4.0.0 (Hao, 2020). In an initial quality control step, all cells with less than 300 genes expressed were removed, as well as all genes expressed in less than 10 cells (in CreateSeuratObject function). In a second step, only cells with less than 20% percentage mitochondria expression were retained.
The data was normalized using SCTransform (Hafemeister and Satija, 2019) and decomposed using PCA.
UMAP (McInnes, 2020)  embeddings were then computed using the first 30 dimensions as input. Based on the UMAP embedding, further quality control was performed by removing clusters of contaminating cells (identified by differential expression and relevant marker genes of contaminating populations) and of poor-quality cells (identified as outliers by number of genes expressed or percentage mitochondria).
Genome_build: mm10
Supplementary_files_format_and_content: text files containing SCT-normalized expression values (the 'data' slot in the Seurat object) for each analyzed cell after QC.

growth_protocol: MEFs harboring Rosa-rtTA, Col1a1-tetO-MyoD and Pax7-nGFP were isolated from E13.5 embryos and were maintained in DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO) and 10% Fetal Bovine Serum (HyClone). For dedifferentiation into iMPCs, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech), 5μM Forskolin (Sigma), 5μM RepSox (Sigma), 3μM GSK3β inhibitor CHIR99021 (Tocris) and 2μg/ml Doxycycline (Sigma). For transdifferentiation into myotubes, MEFs were maintained in knockout DMEM (GIBCO) containing 1X glutaMAX (GIBCO), 1X MEM non essential Amino Acid Solution (GIBCO), 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO), 0.1% β-mercaptoethanol (GIBCO), 10% KnockOut Serum Replacement (GIBCO), 10% Fetal Bovine Serum (HyClone), 10ng/ml basic FGF (Peprotech) and 2μg/ml Doxycycline (Sigma). Hypoxia experiments were performed in 5% O2 level. Freshly isolated satellite cells (fSCs) were isolated from adult Pax7-nGFP mice (10-12 weeks). Cultured satellite cells (cSCs) were maintained in F10 (GIBCO) with 20% Horse Serum (GIBCO), 1X glutaMAX (GIBCO) and 100 U/ml penicillin, 100 μg/mL streptomycin (GIBCO). 5ng/ml basic FGF (Sigma) was daily added. For differentiating cSCs, cSCs were cultured in 2% horse serum differentiation medium for 2 days.

extract_protocol:
Cells (1000 cells/μl) were resuspended with PBS and were loaded into Chromium 10x system.
scRNA-seq libraries were generated from approximately 5000 cells per sample using Chromium 10x instrument with version 3.0 kit.
single cell RNA-sequencing

value: E13.5 embryo

value: Muscle progenitor cells derived from MEFs

value: overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 10 days, Pax7-nGFP sorted by FACS


title: FLU-Tfh rep1

value: H1N1 PR8 influenza infection


title: PP-Tfh rep1


title: 29 NASH3 p5


title: MEF_DoxFRG_Day4

value: Muscle progenitor cells/Myocytes/Myotubes derived from MEFs

value: overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 4 days


title: 28 NASH3 p5

value: cirrhotic NASH human liver


title: MEF_Dox_Day4

value: Myocytes/Myotubes derived from MEFs

value: overexpressing MyoD for 4 days


title: 27 NASH2 p5

source_name: NASH 2 male  liver explant

value: male


title: MEF_DoxFRG_Day8

value: overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 8 days


title: KLH-Tfh rep3

value: Tfh cell

value: KLH immunization


title: 25 NASH2 p5

value: hepatic organoids

value: 12d hepatic differentiation of biliary organoids

value: total RNA isolated by TRIZOL procedure


title: KLH-Tfh rep2

value: Draining lymph nodes


title: KLH-Tfh rep1


title: 24 NASH1 p6

source_name: NASH1 male liver explant


title: ATAC-seq_P11_1

city: St. Louis

first: Guoyan

last: Zhao

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

data_processing:
ATAC-seq Integrative Analysis Package (AIAP) was used for sequence quality assurance, mapping, peak calling, and downstream differential open chromatin analysis.
Genome_build: Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6)
Supplementary_files_format_and_content: BED format with peak positions called by MACS2 and bigWig format showing peak signals

organism: Rattus norvegicus

source_name: Retinal Ganglion Cell

extract_protocol: After isolation, 300,000 RGCs were centrifugued and resuspended in Neurobasal/B27+ medium and 10% DMSO, to quick frozen at -80 °C. Samples were processed by UCSD Center of Epigenomic Technologies using their proprietary assay for Transposase-Accessible Chromatin coupled with high-throughput sequencing (ATAC-seq).

value: postnatal P11 day

value: retina

value: Retinal Ganglion Cells


title: 23 NASH1 p6


title: MEF_Day0

value: E13.5 embryo

value: Mouse embryonic fibroblasts (MEFs)

value: cultured in MEF medium for 2 days


title: MEF_Dox_Day2

value: overexpressing MyoD for 2 days


title: diff_cSCs

source_name: skeletal muscle tissue

value: Skeletal muscles (8-10 weeks age of mice)

value: muscle stem cells cultured in vitro for 2 days with horse serum

value: cultured in satellite cell medium for 4 days then cultured in differentiating medium for 2 days


title: MEF_DoxFRG_Day2

value: Muscle progenitor cells/Myocytes/Myotubes derived from MEFs

value: overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 2 days


title: ATAC-seq_E21_2

value: embryonic E21 day


title: expanded_cSCs

value: muscle stem cells cultured in vitro for 6 days

value: cultured in satellite cell medium for 6 days


title: ATAC-seq_E21_1


title: 26 NASH2 p5

value: cirrhotic NASH human liver

value: male

value: hepatic organoids

value: 12d hepatic differentiation of biliary organoids

value: total RNA isolated by TRIZOL procedure


title: 9-Control

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
PE50 reads were quality checked with package FastQC, then trimmed using Trimgalore (with default settings). Trimmed reads were mapped to murine genome annotation (mm10) using STAR with default settings. .
Mapped reads were then counted using RsubRead.  Normalization and log2 transformation was done with edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing log2 normalized counts per million (log2cpm) per sample

source_name: heart tissue

growth_protocol: Wild-type mice (C57BL/6, age 8-10 weeks) were obtained from Janvier Lab (S.A.S., St. Berthevin Cedex, France). Only male mice were used throughout this study.

extract_protocol:
RNA was extracted from heart tissues (comprising the infarcted and surrounding tissue) using RNeasy Mini Kit (QIAGEN, Germany) and RNA concentration was measured using nanodrop (2000C, Peq lab, Germany). The quality and integrity of RNA were controlled with an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols.

treatment_protocol: Mice received fXai (Rivaroxaban; 3 mg/kg) or fIIai (Dabigatran;10 mg/kg) for 7 days. Mice were sacrificed at the end of study period and heart samples were isolated and RNAseq was performed.

value: heart

value: Untreated


title: 22 NASH1 p6


title: 15 MLD p5

source_name: MLD healthy male  liver,  living donor

value: healthy human liver


title: ATAC-seq_P11_2

value: postnatal P11 day

value: retina

value: Retinal Ganglion Cells


title: PA4 PDX tumors- JQ1+gem

city: Birmingham

first: Karina

last: Yoon

address: 1670 University Blvd VH241

institute: University of Alabama at Birmingham

description:
PA4_JQ_gem_S4
PA4-PA16-VC_JQ_gem-RPKM-counts-processed-files.txt

data_processing:
Raw data in fastq format were processed using Trimmonomatic tool to remove adapter sequences.
Aligning was done with the HISTA2 algorithm.
PCR replicates were removed using SAMtools, the resulting BAM or SAM files used to quantitate expression level using Partek Genomics Suite.
Normalization of reads per kilobase of transcripts per million mapped reads (RPKM) was performed before statistical analysis to quantitate fold-changes of specific gens and P values.
Candidate genes having fold changes > 2 between groups underwent additional pathway analysis using Ingenuity Pathway Abalysis (IPA).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PA4-PA16-VC_JQ_gem-RPKM-counts-processed-files.txt: Tab-delimited text file includes RPKM values for each sample.

source_name: PDX tumors

extract_protocol:
Total RNA was isolated from snap frozen tumor tissue specimens using TRIzol-chloroform extraction. RNA was processed for sequencing using the RNeasy Mini Kit (Qiagen, Germantown, MA, USA). Purified RNA concentration and quality were determined by ND-1000 spectrophotometer using NanoDrop 3.0.1 software.
RNA libraries were prepared for sequencing using standard Illumina protocol.

treatment_protocol: We administered vehicle (saline followed by 10% DMSO in 10% β-cyclodextrin), or the combination (gemcitabine 100 mg/kg weekly followed by 50 mg/kg JQ1 daily) by intraperitoneal injection for 21 days. Twenty-four hours following final treatment mice were euthanized, tumor tissue harvested snap frozen in liquid nitrogen for further analysis.

value: Human tumors grown in mice

value: JQ1 + gemcitabine

tag: tumor type

value: pancreatic cancer


title: PA4 PDX tumors- vehicle control

description:
PA4_VC_S1
PA4-PA16-VC_JQ_gem-RPKM-counts-processed-files.txt

value: Vehicle


title: PA16 PDX tumors- vehicle control

description:
PA16_VC_S5
PA4-PA16-VC_JQ_gem-RPKM-counts-processed-files.txt


title: 14 MLD p5


title: TNJ92 mutant CdCl2 treated 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of data was performed using FastQC package
Reads were aligned to Aspergillus nidulans (FGSC A4) genome using hisat2 (version 2.1.0)
Differential gene expression testing was performed using DESeq2 (version 1.20.0)
Genome_build: Genome: http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current/A_nidulans_FGSC_A4_version_s10-m04-r12_chromosomes.fasta.gz; Genome features file (GFF): http://www.aspergillusgenome.org/download/gff/A_nidulans_FGSC_A4/A_nidulans_FGSC_A4_version_s10-m04-r12_features_with_chromosome_sequences.gff.gz
Supplementary_files_format_and_content: Excel file containing the following collumns for each sample: Gene ID, Count, Transcript length, RPKM

organism: Aspergillus nidulans

source_name: fungal mycelia

growth_protocol: Strains were maintained on Barratt’s minimal medium agar plates (Barratt et al. 1965) and conidia collected freshly from plates incubated at 37 °C for 6 d were used in all experiments. For submerged cultivation 100 ml aliquots of Barratt’s minimal broth supplemented with 5 g/l yeast extract (in 500 ml Erlenmeyer flasks) were inoculated with 50,000,000 conidia and were incubated for 16 h at 37 °C and at 3.7 Hz shaking frequency. Some of the cultures were treated with CdCl2 (0.2 mmol/l final concentration) and all the cultures were further incubated at 37 °C and at 3.7 Hz shaking frequency for 0.5 h.

extract_protocol:
Total RNA was isolated from lyophilized mycelia using TRISOL reagent (Chomczynski 1993). RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: CdCl2 was added to the 16 h cultures at 0.2 mmol/l final concentration. Samples were taken at 0.5 h after the treatment.

value: TNJ92 (DatfA)

tag: culturing condition

value: CdCl2 treated


title: 8-Control


title: TNJ92 mutant CdCl2 treated 2


title: 15-RIVA

value: Rivai:Rivaroxaban (fXai)


title: 13 MLD p5

value: male

tag: cell type


title: PA16 PDX tumors- JQ1+gem

description:
PA16_JQ_gem_S8
PA4-PA16-VC_JQ_gem-RPKM-counts-processed-files.txt


title: 12 FLD after second differentiation  final p8

source_name: FDD healthy female  liver,  living donor

value: female

value: hepatic organoids


title: MOLM13_NMNAT1_sg_rep 2

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were aligned to hg38 genome assembly using STAR aligner.
Differentially expressed genes were identified using DeSeq2.
Promoter motif analysis was done using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: csv files

source_name: AML

growth_protocol: MOLM13 leukemia cells was cultured in RPMI1640 supplemented with 10% FBS and 1% Pen/Strep in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
NMNAT1 WT or KO MOLM13 cells were sorted into Trizol and RNA purified according to the manufacturer's instructions. DNase I-treated RNA samples were purified using the QIAGEN MinElute kit before cDNA was made and amplified with a SMART-Seq2 kit.
The cDNA was fragmented and barcoded for sequencing using a Nextera XT kit.

treatment_protocol: MOLM13 cells were transduced with Cas9 lentivirus and performed blasticidin selection (10 mg/ml) 3 days after transduction to select for Cas9-expressing cells. After selection, the Cas9-expressing MOLM13 cells were single-cell sorted into 96-well plates and expanded. Cas9 functionality in MOLM13 cells was confirmed with Cas9 reporter lentiviral vectors (Addgene #67979 and #67980). Then, the Cas9-expressing MOLM13 cellls were transduced with sgRNA lentivirus targeting NMNAT1 or negative control, and sorted into Trizol at 4 days post transduction.

value: Blood

value: acute myeloid leukemia

tag: sgrna


title: 12-Dabi

tag: tissue

value: heart

value: Dabi:Dabigatran (fIIai)


title: MOLM13_NMNAT1_sg_rep 1


title: TNJ92 mutant untreated 3

value: untreated


title: 10-Dabi


title: TNJ92 mutant untreated 2


title: MOLM13_Negtive_control _rep 2

value: negative control


title: TNJ92 mutant untreated 1


title: MOLM13_Negtive_control _rep 1


title: Sham_007

treatment_protocol: Wild-type mice (C57BL/6, age 8-10 weeks) received fXai (3 mg/kg) or fIIai (10 mg/kg) for 7 days and aPC (1 mg/kg) 30 minutes prior  to myocardial IRI surgery. Myocardial ischemia reperfusion was induced by LAD ligation for 90 min followed by 24 h of reperfusion. Drugs treatment was reinitiated 2 h post-surgery and continued for 24 h. Mice were sacrificed at the end of study period and heart samples including infarcted part were isolated and RNAseq was performed.

value: sham


title: THS30 strain CdCl2 treated 3

value: THS30 (reference)


title: 11 FLD after second differentiation  final p8

value: healthy human liver

value: 12d hepatic differentiation of biliary organoids

value: total RNA isolated by TRIZOL procedure


title: Sham_006


title: 8 FLD p5


title: 231-KO

city: Seoul

first: Han-Teo

last: Lee

address: Daehakro 103, Jongro

department: College of Medicine

country: South Korea

institute: Hong-Duk Youn

data_processing:
The raw image data was transformed by base calling into sequence data and stored in FASTQ format. The reads were trimmed for adaptor sequences, low-quality sequences using ngsShoRT and aligned to the human genome (GRCh37/hg19 genome assembly) using STAR (v2.4.0.1) with the default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Chromosome name, start site, end site and data valure were indicated in four column

source_name: Breast cancer cell line

growth_protocol: Human breast carcinoma cell line MDA-MB-231 were cultured in Dulbecco’s modified eagle medium (DMEM) with 10% (v/v) fetal bovine serum (FBS) and penicillin–streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Using TRIzol RNA isolation reagent (Life Technologies, Carlsbad, CA), total mRNA was isolated. RNA integrity was confirmed using an Agilent RNA 6000 Pico kit (Agilent, Santa Clara, CA).
Isolated RNA was used to prepare an mRNA sequencing library using TruSeq Stranded mRNA sample preparation kit (Illumina, San Diego, CA).

tag: cell line


title: 9 FLD p5


title: 10 FLD after second differentiation  final p8


title: Sham_003


title: 7 FLD p5


title: 231-Mock

value: wild type


title: 14-RIVA


title: THS30 strain CdCl2 treated 2

value: CdCl2 treated


title: 6 FDD after second differentiation final p8

source_name: FDD healthy female  liver,  deceased donor


title: 5 FDD after second differentiation final p8


title: HEK293T_900U_RNaseI

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description:
Ribosome profiling
processed data file: HEK293T_supplementary_count_table.txt

data_processing:
Library strategy: Ribo-Seq
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13.
Processed yeast reads were mapped to tRNA, rRNA, snRNA and snoRNA; reads from human samples were mapped to rRNA using bowtie version 1.2.1.1.
Residual reads were uniquely mapped to non-dubious ORFs (hg38; SacCer3; C_albicans_SC5314_version_A22;Pombe_ASM294v2) extended by 18 nt into the UTRs.
Genome_build: hg38 (GRCh38); SacCer3 (R64); C_albicans_SC5314_version_A22 (ASM18296v3); Pombe_ASM294v2 (ASM294v2)
Supplementary_files_format_and_content: *_count_table.txt: Tab-delimited text files include raw counts for each sample.

source_name: Human embryonic kidney cells

growth_protocol: HEK 293T cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C. Yeast cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4–0.5) at 30C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
For HEK 293T cells, total RNA is extracted using phenol:chloroform method. For yeast, total RNA is extracted using the hot-acid-phenol method.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: (+/+) samples are pre-treated with CHX and lyzed in buffer containing CHX; (-/+) samples are lyzed in buffer containing CHX WITHOUT CHX pre-treatment; (-/-) samples are lyzed without CHX pre-treatment in buffer devoid of CHX.

value: HEK 293T

value: Embryonic kidney cell line

value: 900U RNaseI


title: HEK293T_700U_RNaseI

value: 700U RNaseI


title: TNJ92 mutant CdCl2 treated 1

value: TNJ92 (DatfA)


title: Riva-318

value: Rivai:Rivaroxaban (fXai)


title: THS30 strain untreated 2


title: THS30 strain untreated 3


title: HEK293T_500U_RNaseI

value: 500U RNaseI


title: Riva-313

value: heart


title: 4 FDD after second differentiation final p8

value: female

value: hepatic organoids


title: 3 FDD p5

source_name: FDD healthy female  liver, deceased donor


title: THS30 strain untreated 1

value: untreated


title: HEK293T_300U_RNaseI

value: 300U RNaseI


title: Bovine intestinal organoids P5

city: Wanju-gun

first: Bo Ram

state: Jeollabuk-do

address: 1500, Kongjwipatjwi-ro, Iseo-myeon

department: Animal Biotechnology & Environment

institute: National Institute of Animal Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Bos taurus whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: Bos taurus (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Bos taurus

source_name: Bovine intestinal organoids P5

growth_protocol: Small intestinal crypts were isolated from jejunum of healthy Hanwoo (> 24 month old), sequentially embedded in Matrigel and cultivated in Intesticult medium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Bovine intestinal organoids P5

tag: passages

value: Hanwoo cow


title: 2 FDD p5

value: healthy human liver

value: 12d hepatic differentiation of biliary organoids

value: total RNA isolated by TRIZOL procedure


title: HEK293T_2min_200ugCHX

value: HEK 293T

value: 2min 200ug CHX


title: THS30 strain CdCl2 treated 1

value: THS30 (reference)

value: CdCl2 treated


title: Riva-319


title: 1 FDD p5


title: Cont_19


title: Dabi-202

value: Dabi:Dabigatran (fIIai)


title: HEK293T_5min_100ugCHX

value: Embryonic kidney cell line

value: 5min 100ug CHX


title: Dabi-203

value: heart


title: hMSC stretched ATAC rep1

city: Hefei

first: Ran

last: Zhang

address: No.96 Jinzhai road

institute: University of Science and Technology of China

data_processing:
ATAC-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120
Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M.
peaks were called using Genrich version 0.5 with the following setting: -v -j
bedGraph files were generated using  homer version 4.9
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: narrowpeak files of peaks

source_name: mesenchymal stem cells

growth_protocol: hMSCs were cultured in ncMission Basal Medium (RP02010-01, Nuwacell) supplemented with ncMission 25 × Supplement (RP020210-02, Nuwacell). Culture dishes were kept at 37◦C in a humidified incubator with 5% CO2.

extract_protocol: Tn5 digest cells and then PCR for sequencing

treatment_protocol: hMSCs were subjected to uniaxial cyclic stretching for 48 hr at 1Hz of 8% magnitude

value: umbilical cord

value: mesenchymal stem cells

value: stretched (1Hz,8%)


title: Bovine muscle

source_name: Bovine muscle

value: Bovine muscle

value: Tissue


title: Bovine intestinal organoids P10

source_name: Bovine intestinal organoids P10

value: Bovine intestinal organoids P10

value: Hanwoo cow


title: Bovine Intesine

source_name: Bovine Intesine

value: Bovine Intesine


title: hMSC stretched ATAC rep2


title: HEK293T_1min_200ugCHX

value: 1min 200ug CHX


title: HEK293T_2min_100ugCHX

value: HEK 293T

value: 2min 100ug CHX


title: hMSC unstretched ATAC rep2

value: unstretched


title: Dabi-204


title: aPC-793

value: activated protein c


title: Cont_18

value: untreated


title: Raw_D3_1

city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

data_processing:
Alignemnt was conducted by hisat2
Alignment result was processed with SAMtools
Reads count was conducted by stringtie
Differencial analysis was conducted by deseq2
Genome_build: ASM19595v2
Supplementary_files_format_and_content: txt contained read count corresponding to every sample

organism: Mycobacterium tuberculosis H37Ra

source_name: Intracellular H37Ra in Raw 264.7 cells 3 d.p.i sample 1

growth_protocol: M.tb H37Ra were cultured to OD600=0.5

extract_protocol:
Infected cells were lysed with 30 mL of GTC buffer at day 3 postinfection and centrifuged for 20 min at 5,000 g to pellet bacteria. The bacterial pellets were resuspended in 1 mL of GTC and centrifuged for 2 min at 15,000 g. The bacterial pellets were disturbed in 1mL of Trizol reagent by vortex for 10 min.
The mRNAs were reverse-transcripted to cDNA and converted into double-stranded cDNA molecules. Following end-repair and dA-tailing, the paried-end sequencing adaptors were ligated to the ends of the cDNA fragments, and then subjected to library amplification and purification.

treatment_protocol: Raw 264.7 cells and bEnd.3 cells were infected with M.tb (MOI=10) for 6 h at 37°C in 5% CO2

tag: host cell

value: Raw 264.7 cells


title: HEK293T_minus_minus_2

description:
Ribosome profiling
processed data file: HEK293T_count_table.txt

value: Embryonic kidney cell line

value: Not pre-treated with CHX, not lyzed in buffer containing CHX


title: Raw_D3_2

source_name: Intracellular H37Ra in Raw 264.7 cells 3 d.p.i sample 2


title: HEK293T_minus_minus_3


title: HC4

city: Hangzhou

first: xiaochan

last: chen

address: No.88 Jiefang Road

institute: The second Affliated Hospital of Zhejiang University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Tophat v2.1.0 [1] to map the cleaned reads to the GRCh38 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff.The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) [3,4]. The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and Reads counts for each Sample .

source_name: Heathy control

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat# 217004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Venous blood samples were get from healthy controls and pSS. Human PBMCs were isolated using a Ficoll method based on the density difference between PBMCs and other components in the blood.

tag: subject status

value: Heathy control

value: Peripheral Blood

value: PBMCs


title: bEnd.3_D3_2

source_name: Intracellular H37Ra in bEnd.3 cells 3 d.p.i sample 2

value: bEnd.3 cells


title: bEnd.3_D3_1

source_name: Intracellular H37Ra in bEnd.3 cells 3 d.p.i sample 1


title: HC3


title: hMSC unstretched ATAC rep1

value: umbilical cord

value: mesenchymal stem cells


title: aPC-791

source_name: heart tissue

value: heart


title: HEK293T_minus_plus_3

value: Not pre-treated with CHX, lyzed in buffer containing CHX


title: aPC-792


title: HEK293T_minus_plus_2


title: circScmh1-3

city: Nanjing

first: Li

last: Yang

state: Jiangsu

address: Dingjiaqiao 87

department: Pharmacology

institute: Southeast University

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: primary neuron

growth_protocol: Primary neurons from C57BL/6J mice were isolated from embryonic day 14 (E14) mouse cortex. Neurons at 10 days  were used in this study.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: Neurons were transduced with Vector or circScmh1 lentivirus.

value: cortex

tag: time

value: cultured day 10


title: differentiation DM2

city: Nanning

first: Ruimen

address: NO.100 University Road,Xi xiang tang

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The RPKM（expected number of Reads Per Kilobase of transcript sequence per Millions base pairs sequenced）value was used to estimate the expression levels of mRNAs and lncRNAs.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bubalus bubalis

source_name: muscle stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). 3 μg RNA per sample was used as the initial material for RNA sample preparation. PolyA-Seq libraries were prepared following the described protocol at RiboBio (Guangzhou, China) in accordance to the manufacturer’s instructions. The identification of mRNAs and lncRNAs were carried out with reference to RiboBio's technical methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: Muscle-derived stem cells

value: Muscle

tag: group

value: differentiation


title: HEK293T_minus_plus_1

value: HEK 293T

tag: treatment


title: circScmh1-2

tag: strain


title: Cont_17

first: Robert

value: untreated


title: differentiation DM3


title: differentiation DM1


title: PSS4

source_name: pSS patient

value: Primary Sjögren’s syndrome (pSS) patient


title: circScmh1-1


title: HEK293T_plus_plus_3

value: Embryonic kidney cell line

value: Pre-treated with CHX, lyzed in buffer containing CHX


title: PSS3

value: Peripheral Blood


title: proliferation GM3

value: proliferation


title: Vector-3


title: HEK293T_plus_plus_2


title: HEK293T_minus_minus_1

value: Not pre-treated with CHX, not lyzed in buffer containing CHX


title: proliferation GM2


title: Vector-2


title: HEK293T_plus_plus_1


title: PSS1

value: PBMCs


title: PSS2


title: Vector-1


title: HC2

value: Heathy control


title: HC1


title: proliferation GM1


title: Ovaries

status: Public on Jul 27 2021

city: Orenburg

first: Alexander

middle: S

last: Balkin

address: 11 Pionerskaya st.

country: Russia

institute: Institute for Cellular and Intracellular Symbiosis

description: total RNA enriched with qtc transcripts by RACE

data_processing:
Library strategy: RACE-seq
Demultiplexed reads were filtered according to minimum quality (Q=8) and length (l=500) using Nanofilt.
Clean reads were mapped onto Drosophila melanogaster transcriptome (BDGP6.28 ensembl release 102) with minimap2 in splice mode.
The number of reads per transcript were evaluated with salmon.
Differential gene expression analysis provided by edgeR.
Genome_build: BDGP6.32 (GCA_000001215.4)
Supplementary_files_format_and_content: Tabular file include Drosophila melanogaster transcipts coverage values, evaluated with salmon.

source_name: ovaries

growth_protocol: Flies were reared on the standard growth medium (agar, semolina, yeast, sugar, raisins) in 100 x 25 mm vials with 5 to 10 ml of food at a constant temperature of 25±1°С and 12-hour day light.

extract_protocol:
A line of wild type flies Oregon R was used for transcripts analysis. Flies have been collected on 5-7 day after hatching and frozen with liquid nitrogen before heads were separated from the bodies by vigorous shaking. The eyes were separated with tweezers while the heads were frozen. Testes and heads were isolated in PBS from males on 5-7 days after hatching using small tweezers. The samples were cooled at –80°C prior to using.. tal RNA was isolated with TRI Reagent (Molecular Research Center, Inc.) according to the manufacturer's instructions. The quality of the RNAs were monitored using the Agilent 2100 Bioanalyser (Agilent) and Agilent RNA 6000 Pico Kit (Agilent). The extracted RNA was quantified with an Implen NanoPhotometer (Implen, Germany) and Qubit 4 Fluorimeter (Invitrogen). DNA impurities were removed by using DNA-free™ Kit (Invitrogen) as recommended by the manufacturer.  Total RNA was used for cDNA production.
Double-stranded cDNA was obtained from total RNA by using cDNA mint kit (Evrogen) according to the manufacturer instructions. The cDNA for 3’- and 5’-terminal fragments of qtc transcripts was obtained by single rounds of amplification with the Q5 High- Fidelity 2X Master Mix (NEB, UK) by using the MINT RACE primer set (Evrogen) and specially designed gene-specific primers.

value: Oregon R

value: Ovaries

value: female


title: S_male

source_name: salivary glands, male

treatment_protocol: Flies have been collected on 5-7 day after hatching and frozen with liquid nitrogen before heads were separated from the bodies by vigorous shaking. The eyes were separated with tweezers while the heads were frozen. Testes and heads were isolated in PBS from males on 5-7 days after hatching using small tweezers. The samples were cooled at –80°C prior to using.

value: salivary glands

value: male


title: S_female

source_name: salivary glands, female


title: Testes

source_name: testes

value: Testes


title: E_male

source_name: eyes, male

value: eyes


title: H_female

source_name: heads, female

value: heads


title: H_male

source_name: heads, male


title: CHEQ-seq Enhancer tiling B MM099 cDNA rep 1

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
processed data file:
CHEQ-seq_Enhancer_tiling_B_processed.tsv

data_processing:
Library strategy: CHEQ-seq
Enhancer - barcode assignment files are processed with a custom script. Enhancers and barcodes are separated with cutadapt. Enhancers are mapped to the human hg19 genome using minimap.
Raw cDNA and plasmid reads are first processed with a custom script to extract and count each barcode before associating them to the corresponding enhancer based on the enhancer - bc assignment list.
Enhancer activity from MPRA assay is estimated via a custom R script. Enhancers are first filtered based on the number of BCs identified in the sequencing reads. Thresholds of 5 (for the H3K37ac library and enhancer tiling library), 10 (for ATAC-seq library) or 20 (for the SOX-MITF combinations library) BCs per enhancer are selected based on the complexity of the library and the sequencing saturation of the enhancer - BC assignment samples. For the remaining enhancers, BC counts are aggregated per enhancer and then a count per million (CPM) normalisation is applied. Plasmid (input) and cDNA (output) samples are merged by keeping only enhancers remaining in both samples after filtering. Input normalisation is done by dividing CPM normalised cDNA counts by CPM normalised plasmid counts resulting in a FC value. For libraries with shuffled sequences, a basal expression normalisation is further applied by dividing the FC value of the enhancer by the median FC value of the shuffled sequences. For CHEQ-seq SOX10-KD library, enhancer activity from cDNA and plasmid barcode counts is performed with DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: Enhancer to barcode assignment lists are tables containing two columns: Enhancer name; barcode associated to that enhancer. Enhancer activity matrices are table containing: Enhancer name; Enhancer class; Enhancer activity Fold Change (one column per cell line). DEseq2 result table contains the following columns: Enhancer name; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj; enhancer class.
CHEQ-seq_5p_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_Intron_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_ATAC_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-A_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-B_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_SOX10-KD_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_SOX-MITF_combinations_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_5p_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq 5' H3K27ac
CHEQ-seq_Intron_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq Intron H3K27ac
CHEQ-seq_ATAC_processed.tsv: Enhancer activity matrix for CHEQ-seq ATAC
STARR-seq_ATAC_processed.tsv: Enhancer activity matrix for STARR-seq ATAC
CHEQ-seq_Enhancer_tiling_A_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling A
CHEQ-seq_Enhancer_tiling_B_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling B
CHEQ-seq_SOX10-KD_processed.tsv: DEseq2 result table for CHEQ-seq SOX10-KD
CHEQ-seq_SOX-MITF_combinations_processed.tsv: Enhancer activity matrix for CHEQ-seq SOX - MITF combinations

source_name: Melanoma cell line

growth_protocol: Melanoma cell lines were cultured with Ham's F-10 nutrient mix + 10% FBS + 0.5% penicillin/streptomycin in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). DNA was extracted with a plasmid extraction protocol from Qiagen.
Plasmid libraries, extracted plasmids and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.

tag: molecule subtype

value: mRNA


title: CHEQ-seq Enhancer tiling B MM029 cDNA rep 1


title: CHEQ-seq Enhancer tiling B MM057 plasmid

value: Plasmid


title: CHEQ-seq Enhancer tiling B MM087 cDNA rep 1


title: CHEQ-seq Enhancer tiling B MM001 plasmid


title: CHEQ-seq Enhancer tiling B MM001 cDNA rep 1


title: CHEQ-seq Enhancer tiling B MM057 cDNA rep 1


title: MAS resolution macrophages, biological replicate 2

type: RNA

city: Cincinnati

first: Denny

middle: Kan

last: Gao

state: OH

address: 3333 Burnet Avenue

department: Rheumatology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: For each sample, 3 ug of fragmented cDNA was hybridized to Mouse Clariom S Arrays (Thermo Fisher Scientific). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create the .chp files.

label: biotin

source_name: Alveolar macrophages from MAS resolution (day 30)

label_protocol: The GeneChip 3' IVT Pico Reagent Kit (Thermo Fisher Scientific) was used to create biotin-labeled double-stranded cDNA targets.

growth_protocol: Female C57BL/6J mice 6 weeks of age were purchased from the Jackson Laboratory and stored at CCHMC.

extract_protocol: Total RNA was extracted using the Trizol protocol.

treatment_protocol: Mice were given PBS or CpG 1826 injection 5 times over a 10-day period. BAL obtained on day 10 (control and acute MAS) or day 30 (MAS resolution). Alveolar macrophages purified by adherence.

value: alveolar macrophages

tag: age

value: 6 weeks

value: alveolar macrophages in MAS resolution


title: E_female

source_name: eyes, female

tag: Sex


title: MAS resolution macrophages, biological replicate 4


title: MAS resolution macrophages, biological replicate 1


title: CHEQ-seq Enhancer tiling A MM029 plasmid rep 1

description:
processed data file:
CHEQ-seq_Enhancer_tiling_A_processed.tsv


title: CHEQ-seq Enhancer tiling A MM029 cDNA rep 1


title: CHEQ-seq Enhancer tiling A MM057 cDNA rep 1


title: MAS resolution macrophages, biological replicate 3


title: Acute MAS macrophages, biological replicate 1

source_name: Alveolar macrophages from acute MAS (day 10)

value: alveolar macrophages in acute MAS


title: Control macrophages, biological replicate 3

source_name: Alveolar macrophages from control (PBS) treatment

value: control alveolar macrophages


title: Acute MAS macrophages, biological replicate 3


title: Control macrophages, biological replicate 4


title: 32804L_10uM_MDV_S22_R1_001.fastq

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Basecalls were performed using Illumina software
The quality and number of reads for each sample were assessed with FastQC v0.11.3.
Adaptors were trimmed from reads, and low-quality bases, with Phred scores < 28, were trimmed from ends of reads, using Trimgalore v0.4.4 . Trimmed reads of <20 nucleotides were discarded.
Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using TopHat v2.1.1 allowing for up to two mismatches. Reads not uniquely aligned to the genome were discarded.
HTSeq-count v0.6.1 was used with the union model to assign uniquely aligned reads to Ensembl Hg38.86-annotated genes. Data were normalized across libraries by the trimmed mean of M-values (TMM) normalization method, implemented in R v3.5.0, using Bioconductor v3.6 EdgeR v3.20.9 package. Only genes expressed at a count-per-million above 0.5 for at least 18 out of 36 samples were analysed for evidence of differential gene expression. Differentially expressed genes were identified using the quasi-likelihood negative binomial generalized log-linear model implemented in EdgeR and were defined as having an FDR adjusted P value of < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing EdgeR normalized read counts. Read counts were normalized using the the trimmed mean of M-values (TMM) normalization method

growth_protocol: Prostate specimens were dissected and cultured as patient-derived explants in RPMI medium containing 10% fetal calf serum

extract_protocol:
Enzalutamide or vehicle treated patient derived explants preserved in RNAlater were homogenized with the Precellys24 Tissue Homogenizer (Bertin Technologies, France) using 0.5 mL Precellys24 tubes containing 1.4 mm ceramic beads and 500 mL Tri Reagent (Sigma). RNA was then extracted using a Qiagen RNeasy mini kit adapted for Tri Reagent using the manufacturer instructions.
Libraries were generated using Illumina TruSeq RNA kits; Illumina NextSeq 500 (High Output v2) single-end 100 bp reads.

treatment_protocol: Explants were treated with enzalutamide (Selleckchem; 10μM) or vehicle control (DMSO) for 48 hours

value: prostate

tag: disease state

value: prostate cancer

value: RNA (rRNA depleted)


title: 32840L_DMSO_S23_R1_001.fastq

source_name: Primary prostate tumour_DMSO


title: 32804L_DMSO_S21_R1_001.fastq


title: Control macrophages, biological replicate 2


title: Acute MAS macrophages, biological replicate 2


title: 32840L_10uM_MDV_S24_R1_001.fastq


title: 32800R_DMSO_S17_R1_001.fastq


title: 32802L_DMSO_S19_R1_001.fastq


title: CHEQ-seq Enhancer tiling A MM099 cDNA rep 1


title: 32802L_10uM_MDV_S20_R1_001.fastq


title: 32771R_DMSO_S15_R1_001.fastq


title: 32800R_10uM_MDV_S18_R1_001.fastq


title: 32771R_10uM_MDV_S16_R1_001.fastq


title: 32760L_10uM_MDV_S12_R1_001.fastq


title: 32764R_DMSO_S13_R1_001.fastq


title: 32764R_10uM_MDV_S14_R1_001.fastq


title: 32760L_DMSO_S11_R1_001.fastq


title: Control macrophages, biological replicate 1


title: 32755R_DMSO_S9_R1_001.fastq


title: 32743L_DMSO_S5_R1_001.fastq


title: 32747R_10uM_MDV_S8_R1_001.fastq


title: 32747R_DMSO_S7_R1_001.fastq


title: 32743L_10uM_MDV_S6_R1_001.fastq


title: 32732R_DMSO_S3_R1_001.fastq


title: 32755R_10uM_MDV_S10_R1_001.fastq


title: 32717R_10uM_MDV_S2_R1_001.fastq


title: 32732R_10uM_MDV_S4_R1_001.fastq


title: 32717R_DMSO_S1_R1_001.fastq


title: replicative senescent hVSMC-Exo-01

city: Semenyih

first: Yuh-Fen

last: Pung

address: Jalan Broga

country: Malaysia

institute: University of Nottingham Malaysia

description:
hVSMC-Exo-01
15H-18M-01-P7X_S2_L001

data_processing:
Basecalls performed using CASAVA 1.8
Rawreads were QC and trimmed using Cutadapt
Trimmed reads were aligned to Homo sapiens reference genome (GRCh38) using miRDeep2
Mapped transcripts were aligned with miRBase version 22
Known mature miRNAs were analyzed for differential expression using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: One MS Excel files containing normalized reads of mature miRNAs in all samples. Two MS Excel files containing differentially expressed miRNAs (normalized count, fold change, p values and FDR values) in cells and exosomes

source_name: human vascular smooth muscle cell-derived exosomes

growth_protocol: HVSMCs were first maintained in Smooth Muscle Basal Medium (SmBM) (Lonza, Switzerland) then underwent gradual SmBM replacement with Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 2% L-glutamine, 1% penicillin-streptomycin and 10% FBS. Media was changed every 48 hr.

extract_protocol:
RNA extraction was carried out using miRNeasy Micro Kit (QIAGEN, Germany).
Libraries for sequencing were prepared according to the manufacturer’s protocol TruSeq Small RNA Library Prep (Illumina, San Diego CA).
RNA sequencing was carried out using NextSeq 500 Mid v2 Kit, 150 cycles (Illumina, San Diego CA).

treatment_protocol: Cells were continuousely passaged until replicative senescence was achieved. No treatment was performed.

tag: source

value: exosomes

tag: condition

value: replicative senescent