title: striatum, DF-1059

city: Shenzhen

first: Jun

last: Ju

state: China

address: No. 628, Zhenyuan Road, Guangming District,  Shenzhen518107, China

institute: Tomas Lindahl Nobel Laureate Laboratory

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 file include total FPKM value for each sample
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts and FPKM for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text file with gene difference analysis for every gene

source_name: striatum

extract_protocol:
RNA extraction and RNAseq analysis were performed by Applied Protein Technology (Shanghai, China). Briefly, total RNA was isolated using TRIzol (Thermo Fisher Scientific, Shanghai) and 2µg RNA per sample was used as input material to prepare a cDNA library (paired end 250bp) for high-throughput sequencing with the HiSeq 2000 sequencing system (Illumina, Shanghai).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post natal day 60

value: striatum


title: striatum, DF-1062

status: Public on Jun 29 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype

tag: age

tag: tissue


title: JR65A_NNR1_RNA-Seq

city: Norwich

first: Daniel

last: Zilberman

address: Norwich Research Park

country: United Kingdom

institute: John Innes Centre

data_processing:
Reference genomes used for alignments: Using SNPs identified by alignment of resequencing data to the MSU Nipponbare genome, we generated Nipponbare-based pseudogenomes for Kitaake, IR64 and 93-11. Endosperm and embryo of self-fertilized seed was sligned to the corresponding genome or pseudogenome while those of F1 seed were aligned to both parental ones.
Alignment of BS-seq reads: After merging together sequencing runs from the same sample, we used Perl scripts to convert all the Cs in the reads (and in the genome scaffolds) to Ts, and aligned the converted reads to converted scaffolds using the aligner Bowtie, allowing up to two mismatches per read. For data from F1 seed, reads were assigned to parental genomes based on differences in the number of mismatches or failure to align.
Alignment of small RNA-seq reads: We used Perl and Python scripts to trim adapter sequences in the reads, sorted reads according to size, and aligned 24 nt reads to genome scaffolds using the aligner Bowtie, allowing up to one mismatch per read. For data from F1 seed, reads were assigned to parental genomes based on differences in the number of mismatches or failure to align.
Alignment of strand-specific RNA-seq reads: After merging together sequencing runs from the same sample, we aligned reads both to chromosome scaffolds using the aligners Bowtie or TopHat and also to cDNA models using the aligner Bowtie. We allowed up to two mismatches per read. As results using chromosome scaffolds and cDNA models were similar, we only used cDNA models for further analysis. For data from F1 seed, reads were assigned to parental genomes based on differences in the number of mismatches or failure to align. Custom Perl and Python scripts were used to calculate parental biases and assess imprinting.
Single_C calculation of BS-seq data: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
Calculation of 50 bp window data (w50 gff file): For BS-seq data, we used a Perl script to calculate fractional methylation (#C/(#C+#T)) within 50 bp windows of the genome for each sequence context (CG, CHG, CHH). For small RNA-seq, we used a Perl script to calculate the number of reads mapping within 50 bp windows of the genome. Data for self-fertilized seed include alll mapped reads while those for F1 seed consist only of those reads that could be sorted to one of the two parental genomes.
Calculation of transcript abundance (win-anno gff file): For RNA-seq data, we used a Perl script to calculate the number of reads mapping to the first listed isoforn of all annotated genes. Data for self-fertilized seed include alll mapped reads while those for F1 seed consist only of those reads that could be sorted to one of the two parental genomes.
Genome_build: Oryza sativa L. cv Nipponbare rice reference genome (MSU 7.0)
Supplementary_files_format_and_content: All files are in GFF format. BS-seq files contain fractional methylation data over 50 bp windows of the genome. Small RNA-seq and strand-specific RNA-seq files have sequencing read abundance calculated in 50 bp windows across the genome or per annotated gene. Note that only 24 nt small RNA reads were processed. GFF columns of .7.win-anno and .0.win-anno files for RNA-seq: Column 1 is the transcript id; column 2 indicates this file was generated by our in-house windowing script; column 3 indicates that the feature being analyzed is a window that corresponds to the whole mRNA length plus extra 5' and 3' sequence either 300 bp away from each of the annotated transcription termini or till the next genic feature (whichever is shorter); column 4 and 5 are the stop and start coordinates, respectively, of the window being analyzed; column 6 is a count of the number of RNA-seq reads that fall within the window (.0 files sum all mapped reads, while .7 files sum only the sorted reads that aligned to one particular parental genome better than the other); column 7 indicates the strand of the transcript with respect to the genome; column 8 indicates that the frame of the CDS is not relevant to the analysis; column 9 lists the parent gene to which the transcript belongs. GFF columns of .7.w50 and .0.w50 files for sRNA-seq: Column 1 is the name of the chromosome sequence being analysized; column 2 is kept null to decrease file size; column 3 is either null to decrease file size or indicates that the score in column 6 corresponds to read abundance; column 4 and 5 are the stop and start coordinates, respectively, of the 50 bp window being analyzed from the chromosome; column 6 is a count of the number of 24nt small RNA-seq reads that fall within the window (.0 files sum all mapped reads, while .7 files sum only the sorted reads that aligned to one particular parental genome better than the other); column 7 indicates that strand information was ignored and small RNA from both strands were summed together; column 8 indicates that the frame of the CDS is not relevant to the analysis; column 9 is kept null to decrease file size. GFF columns of w50 files for BS-seq: Column 1 is the name of the chromosome sequence being analysized; column 2 is kept null to decrease file size; column 3 indicates the methylation context (i.e. CG, CHG or CHH) that the score in column 6 corresponds to; column 4 and 5 are the stop and start coordinates, respectively, of the 50 bp window being analyzed from the chromosome; column 6 is the fractional methylation of cytosines within the window (files for parent cultivars calculate this from all mapped reads, while files for F1 crosses use only the sorted reads that aligned to one particular parental genome better than the other); column 7 indicates that strand information was ignored and reads from both strands were used for the calculation; column 8 indicates that the frame of the CDS is not relevant to the analysis; column 9 contains information on how the fractional methylation was calculated from BS-seq reads (c=total number of cytosines not converted by bisulfite treatment, t=total number of cytosines converted by bisulfite treatment, n=number of informative cytosine sites within the 50 bp window).

organism: Oryza sativa

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar Nipponbare

growth_protocol: Endosperm and embryo samples were obtained by dissection of 7 to 8 DAF seeds from rice plants germinated in petri dishes at 28° with light for 1 week before transplantation to field soil in an environment-controlled green house at the UC Davis Core facility. Green house conditions during the period of growth included a temperature between 27-30°C, humidity at 50%, and natural sunlight.

extract_protocol:
DNA and total RNA was extracted from snap-frozen tissues using CTAB and TRIzol reagent (Invitrogen), respectively.
For bisulfite sequencing, about 1µg of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec.
For small RNA libraries, 10 µg of total RNA was loaded on a 15% polyacrylamide, 7M urea gel, and small RNA in the 17-30 nt size range were excised. The 3' miRNA cloning linker 1 (IDT) was ligated to the gel-excised small RNA using truncated T4 RNA ligase 2 (NEB), and ligation products were purified on a 15% polyacrylamide, 7M urea gel. The 5' Illumina RNA linker (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3') was added using T4 RNA ligase (NEB) and ligation products were again purified on a 15% polyacrylamide, 7M urea gel. Purified ligated small RNAs were reverse transcribed using SuperScriptIII (Invitrogen) and PCR-amplified with Phusion High-Fidelity DNA Polymerase (NEB) for 25 cycles (Forward primer: 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3', Reverse primer: 5'-CAAGCAGAAGACGGCATACGATTGATGGTGCCTACAG-3').
Strand-specific RNA-seq libraries were constructed as described in Wang et al. (2011), beginning with ribosomal RNA-depleted total RNA. TRIzol-extracted total RNA treated with DNase I (Qiagen) was purified using the RNeasy Mini kit (Qiagen) as per manufacturer’s instructions. After verifying RNA integrity on a denaturing agarose gel, 5 μg of purified total RNA was depleted for ribosomal RNA using the Ribo-Zero rRNA removal kit for plant seed and root (Epicentre) as per manufacturer’s instructions. Ribosomal-depleted total RNA was purified using AM-Pure beads (Beckman Coulter) and fragmented using the Ambion RNA fragmentation kit (Ambion). After overnight precipitation in 75% ethanol, the resuspended pellet was reverse transcribed using Random Hexamer primers (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). After AM-Pure bead purification. second-strand synthesis proceeded with DNA polymerase I (Invitrogen) and a dUTP mix of 10 mM dA, 10 mM dC, 10 mM dG, and 20 mM dU. After purification of second-strand synthesis products with AM-Pure beads, cDNA was end-repaired using the End Repair Mix LC (Enzymatics) while still attached to AM-Pure beads. Using XP buffer (Wang et al., 2011) for intermediate size selection and washing steps, dA-tailing with Klenow exo minus (NEB) was also performed while cDNA still remained attached to the beads. cDNA was eluted off beads for Y-shape adapter ligation with DNA quick ligase (NEB) and adapters (adapter 1: 5'A*C*ACTCTTTCCCTACACGACGCTCTTCCGAT*C*T 3'; adapter 2: 5'P-G*A*TCGGAAGAGCACACGT*C*T 3'). After purifying adapter-ligated cDNA with AM-Pure beads, dUTP excision was performed with Uracil DNA glycosylase (NEB), and products were directly amplified using Phusion Hot Start 2 DNA polymerase (NEB) and indexed pair-end primers for multiplexing. After dUTP excision and PCR, products were purified and concentrated using AM-Pure beads. Where indicated, duplex-specific nuclease treatment was performed as described by Matvienko et al. (2013). In short, 200 to 300 ng of library product was denatured and hybridized in TMAC buffer (3 M TMAC, 50 mM HEPES, pH 7.5) for 5 hours at 68°C. At the end of 5 hours, duplex-specific nuclease (DSN; Evrogen) was added along with DSN buffer as instructed by the manufacturer. Resulting DSN-treated products were amplified a second time using Phusion Hot Start 2 DNA polymerase (NEB) and indexed pair-end primers for multiplexing. Final DSN-treated library products were gel-purified on 2% agarose to obtain fragments between 300 to 400 bp in length for sequencing.
library strategy: Bisulfite sequencing, strand-specific total RNA (with or without duplex-specific nuclease treatment), and small RNA sequencing with Illumina technology.
sequencing platform: Illumina HiSeq 2000 (run by the Vincent J. Coates Genomic Sequencing Laboratory at UC Berkeley)

treatment_protocol: No specific treatments were applied, other than controlled growth conditions. Emasculation by heat treatment and dissection was followed by artificial pollination of rice flowers to obtain F1 seeds. The palea and lemma were separated from the seed coat and a razor blade was used to slice open the seed coat. Milky stage endosperm was pipetted out from inside the seed coat and stored either in 2% CTAB (Hexadecyltrimethylammonium bromide) for extraction of genomic DNA or TRIzol reagent (Ambion) for extraction of total RNA. Embryos were isolated after the endosperm had been collected and were washed individually through vigorous agitation in 0.5 ml of 1x Phosphate Buffered Saline solution. Individually isolated F1 seeds were verified for heterozygosity with a PCR-based assay using microsatellite marker RM1 for crosses of Nipponbare with any other cultivar and RM72 for crosses between 93-11 and IR64 cultivars (McCouch et al., 2002; http://archive.gramene.org/).

tag: cultivar

value: O. Sativa L Endosperm, Cultivar Nipponbare

value: endosperm

tag: library type

value: Strand-specific total RNA-Seq

tag: duplex-specific nuclease treatment

value: No duplex-specific nuclease treatment

tag: molecule subtype

value: fragmented total RNA, 150 to 300 nt


title: JR65C_6NR1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar IR64

value: O. Sativa L Endosperm, Cultivar IR64


title: Liver_NASH-HCC_Tumor_20

type: RNA

city: Barcelona

first: Marta

last: Piqué

state: Barcelona

address: Rosselló, 153

country: Spain

institute: IDIBAPS

hyb_protocol: Total mRNA was prepared for hybridization using the GeneChip 3’ IVT Pico Kit assay (Thermo Fisher) following the manufacturer’s protocols. Samples were hybridized to the Human Genome U219 Array (Affymetrix) also following the manufacturer protocols.

scan_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: Gene expression profiles that passed the quality control were submitted to the GenePattern ExpressionFileCreator Module20 to generate the final dataset. In this last step, the background was corrected with the Robust Multi-array Average (RMA) algorithm and data were normalized using quantiles.

label: biotin

organism: Homo sapiens

label_protocol: Double-stranded cDNAs were synthesized from total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: 50ng of total mRNA was isolated from FFPE samples using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.  DNA FFPE kits (Qiagen).

value: NASH-HCC tumor


title: JR65B_KNR1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar Kitaake

value: O. Sativa L Endosperm, Cultivar Kitaake


title: Liver_NASH-HCC_Tumor_17


title: Subject_HCAF002_Day0

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

hyb_protocol: Samples were hybridized on  HG-133 plus 2.0 PM  chips

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish

label: Biotin

source_name: Subject HCAF002, Day0 post vaccination

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject

tag: day post vacciantion

tag: vaccine


title: smooth muscle cells with H2O2 treatment

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

country: Japan

institute: Kanazawa Medical University

description: Gene expression data from H2O2-treated human aortic smooth muscle cells

hyb_protocol: Fragmented and labeled cDNAs were then hybridized onto Affymetrix GeneChip Human Gene 1.0 ST arrays in a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Arrays were then washed and stained using a GeneChip Fluidics Station 450 and detected using a 3000 7G GeneChip Scanner (Affymetrix).

data_processing: All arrays passed quality control criteria of Expression Console (Affymetrix). Raw data CEL files were then normalized using the RMA algorithm, and data were exported using Expression Console or Gene Spring (Agilent Technologies, Santa Clara, CA, USA). DNA microarray analysis of untreated SMCs, H2O2-treated SMCs, and H2O2- and CTP-treated SMCs was performed identical to HAECs cultured in HuMedia-SG2 medium containing 2.5% (v/v) FBS

source_name: SMC

label_protocol: Subsequently, 300 ng of total RNA was labeled using a GeneChip WT Sense Target Labeling Kit (Affymetrix, Santa Clara, CA, USA) according to manufacturer’s instructions.

growth_protocol: HAECs were cultured at 37°C at 5% CO2 and maintained in HuMedia-EG2 medium containing 2% (v/v) FBS, 10 ng/mL hEGF, 1.34 µg/mL hydrocortisone hemisuccinate, and 10 µg/mL heparin (growth medium) according to the manufacturer’s instructions (Kurabo Corp.). SMCs were cultured at 37°C at 5% CO2 and maintained in HuMedia-SG2 medium containing 5% (v/v) FBS, 5 ng/mL hEGF, 5 ng/mL hFGF-B, and 5 µg/mL insulin according to the manufacturer’s instructions (Kurabo Corp.).

extract_protocol: After CTP treatment, total RNA was extracted from untreated HAECs, H2O2-treated HAECs, and H2O2- and CTP-treated HAECs using a RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA quality was determined by the ratio of 28S to 18S ribosomal RNA band intensities on electrophoretic gels under denaturing conditions.

treatment_protocol: HAECs were seeded at 5,000 cells/cm2 and cultured in growth medium. At 60% cell density, cells were preincubated in HuMedia-EG2 medium containing 1% (v/v) FBS, 5 ng/mL hFGF-B, and 10 µg/mL heparin (assay medium) at 37°C for 2 h. After a 2-h preincubation, H2O2 (200 µM) was added, and cells were then incubated at 37°C for 10 min. Next, CTP (CTP-50) was added to the culture at 100 µg/mL and incubated at 37°C for 24 h.

value: aortic smooth muscle cells (SMCs)

tag: treatment


title: striatum, DF-1037


title: smooth muscle cells with H2O2 and CTP treatment

description: Gene expression data from H2O2 and CTP-treated human aortic smooth muscle cells

value: H2O2 + Collagen tripeptide


title: endothelial cells with H2O2 treatment

description: Gene expression data from H2O2-treated human aortic endothelial cells

source_name: HAEC

value: aortic endothelial cells (HAEC)


title: endothelial cells with H2O2 and CTP treatment

description: Gene expression data from H2O2 and CTP-treated human aortic endothelial cells


title: si_5-6 days – 2

city: Moscow

first: Evgeniya

last: Shcherbinina

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
For mapping samples, genome annotations were obtained from Ensembl, release 93.
Reads were mapped using STAR v2.5.3a with default settings except for the following one: –quantMode GeneCounts.
The resulting gene counts were further processed with R package DESeq2, where it was further normalized using RLE method.
To take into account unwanted variation in the data, we obtained by sva package additional variables and introduced them into design matrix to capture unwanted variations.
DESeq2 package were used for performing differential expression analysis based on Wald test. We defined genes as differentially expressed if they passed the thresholds: FDR < 0.05.
Genome_build: Ensembl, release 93.
Supplementary_files_format_and_content: FC and p-value for knockdown samples versus control

source_name: Liver

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum and 1% pen/strep

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Neb indexes prior to 12 cycles of PCR.
Library was prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB 7760, New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and treated with 10 nM siRNA#5 and siRNA#7 for 4 days.   1 mg/kg siRNA#5 and siRNA#7 were formulated in lipid nanoparticles and injected in murine tail vein for 6 and 13 days.

value: liver

value: Balb/c

value: treated with LNP-siRNA 5 for DDX3 knockdown, 6 days after injection


title: Liver_NASH-HCC_Tumor_18


title: Control endothelial cells

description: Gene expression data from non-treated human aortic endothelial cells

value: control


title: Liver_NASH-HCC_Tumor_19


title: Subject_HCAF002_Day21

source_name: Subject HCAF002, Day21 post vaccination


title: Liver_NASH-HCC_Tumor_16


title: Subject_HCAF004_Day22

source_name: Subject HCAF004, Day22 post vaccination


title: Subject_HCAF002_Day1

source_name: Subject HCAF002, Day1 post vaccination


title: JR65D_9NR1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar 93-11

value: O. Sativa L Endosperm, Cultivar 93-11


title: Liver_NASH-HCC_Tumor_14


title: si_5-6 days – 1


title: JR67G_NKNR3N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar Kitaake

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar Kitaake

value: Duplex-specific nuclease treatment performed


title: JR65L_NKNR3S_RNA-Seq

value: endosperm


title: striatum, WT-1063

value: wild type

value: post natal day 60

value: striatum


title: striatum, WT-1061


title: si_luc-6 days – 3

value: treated with control (luciferase) LNP-siRNA, 6 days after injection


title: si_luc-6 days – 1


title: Liver_NASH-HCC_Tumor_15

value: NASH-HCC tumor


title: JR67A_N6NR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar IR64

value: Strand-specific total RNA-Seq

value: fragmented total RNA, 150 to 300 nt


title: Liver_NASH-HCC_Tumor_13


title: Liver_NASH-HCC_Tumor_12


title: JR65E_N6NR1S_RNA-Seq

value: No duplex-specific nuclease treatment


title: K7M2

city: Columbus

first: Timothy

middle: P

last: Cripe

state: OH

address: 700 Childrens Drive

department: Center for Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

description: Paired-end 2 x 150bp reads, Illumina HiSeq 4000.

data_processing:
bcl to fastq was performed using Illumina bcl2fastq conversion software version 2.20.0.422.
Paired-end FASTQ files were used as input for salmon version 0.9.1 (https://combine-lab.github.io/salmon/getting_started/).
The salmon transcriptome index was prepared using the following command: "salmon index -t GCF_000001635.24_GRCm38.p4_rna.fna -i GRCh38_latest_rna.fna_transcripts_index -k 31"; the GRCm38.p4_rna.fna was obtained from NCBI via ftp.ncbi.nlm.nih.gov.
The following parameters were used for salmon processing:
libType: A
numBootstraps: 100
mates1: Read1.fastq
mates2: Read2.fastq
index: GRCh38_latest_rna.fna_transcripts_index
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf"; salmon TPM output.

source_name: murine osteosarcoma

growth_protocol: All murine osteosarcoma cell lines were maintained in RPMI 1640 supplemented with 15% heat-inactivated fetal bovine serum (FBS), 1% L-glutamine, 1% nonessential amino acids, 50 mM 2-metacaptoethanol, 100 IU/mL penicillin, and 100 mg/mL streptomycin. Vero cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in DMEM supplemented with 10% FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin. All cell lines used in this study were verified to be free of mycoplasma contamination by the MycoAlert Mycoplasma Detection Kit (LT07-318; Lonza, Allendale, NJ, USA).

extract_protocol:
Total RNA was extracted from tumor tissue without treatment and treated with DNase and RiboZero capture beads (Illumina, San Diego, CA) to deplete DNA and ribosomal contaminants, respectively.
RNA was used as input for Illumina TruSeq Stranded Total RNA library preparation kit and sequenced on HiSeq 4000.

treatment_protocol: F420 osteosarcoma tumors were established by subcutaneously injecting 5 x 10^6 osteosarcoma cells into the flanks of 6-week-old C57BL/6 mice (Envigo, Frederick, MD). K7M2 tumors were established by transplanting small pieces of sectioned tumor (~2mm3) into the flanks of 6-week-old Balb/C mice (Envigo).

tag: mouse background

value: Balb/C

tag: cell line

tag: Sex

value: female

value: osteosarcoma

value: treatment-naive


title: striatum, WT-1015


title: striatum, DF-1018


title: F420


title: JR67C_N9NR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar 93-11


title: JR65G_N9NR1S_RNA-Seq


title: NNB_HS2_BS-Seq

library_source: genomic

molecule: genomic DNA

value: O. Sativa L Endosperm Cultivar Nipponbare

value: embryo

value: BS-Seq


title: si_luc-6 days – 2

value: liver

value: Balb/c


title: JR67H_KNNR2Z4.2N, DZYK14J_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Kitaake x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare

value: endosperm

value: Duplex-specific nuclease treatment performed


title: JR65K_KNNR2Z4.2S, DZYK14I_RNA-Seq


title: NEB_HS2_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF Cultivar Nipponbare

value: O. Sativa L Embryo Cultivar Nipponbare


title: F27 DUSP1 KO

city: Madrid

first: Jose M

middle: Bermúdez

last: Muñoz

state: Madrid

address: ARTURO DUPERIER 4

institute: INSTITUTO DE INVESTIGACIONES BIOMÉDICAS "ALBERTO SOLS"

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software.
Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG). Unaligned single read sequences are provided in BAM files. BAM is the binary version of a SAM file, which stands for Sequence Alignment/Map format. The SAM/BAM format contains among other elements the sequencing Read Sequence and the corresponding Read Quality. Read qualities are provided in the standard Qscore Sanger encoding (Illumina 1.9, ASCII offset of 33).
50bp single-end sequenced reads were analyzed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/), 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(1) using Bowtie 1.0.0(2) and Samtools 0.1.19(3), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1(1), using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
REFERENCES: 1)Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012); 2)Langmead, B. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009); 3)Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples
Supplementary_files_format_and_content: tab-delimited text files include pearson correlations among samples
Supplementary_files_format_and_content: tab-delimited text files include differential expressed genes in 5-months-old Dusp1-/- (DN 5months) compared to 5-months-old wild type (DP 5months)
Supplementary_files_format_and_content: tab-delimited text files include differential expressed genes in 8-months-old Dusp1-/- (DN 8months) compared to 5-months-old Dusp1-/- (DN 5months)
Supplementary_files_format_and_content: tab-delimited text files include differential expressed genes in 8-months-old Dusp1-/- (DN 8months) compared to 8-months-old wild type (DP 8months)
Supplementary_files_format_and_content: tab-delimited text files include differential expressed genes in 8-months-old wild type (DP 8months) compared to 5-months-old wild type (DP 5months)
Supplementary_files_format_and_content: tab-delimited text files include GSEA for postive and negative enrichment gene sets from BioCarta, Reactome and KEGG databases in  5-months-old Dusp1-/- (DN 5months) compared to 5-months-old wild type (DP 5months)
Supplementary_files_format_and_content: tab-delimited text files include GSEA for postive and negative enrichment gene sets from BioCarta, Reactome and KEGG databases in  8-months-old Dusp1-/- (DN 8months) compared to 5-months-old Dusp1-/- (DN 5months)
Supplementary_files_format_and_content: tab-delimited text files include GSEA for postive and negative enrichment gene sets from BioCarta, Reactome and KEGG databases in  8-months-old Dusp1-/- (DN 8months) compared to 8-months-old wild type (DP 8months)
Supplementary_files_format_and_content: tab-delimited text files include GSEA for postive and negative enrichment gene sets from BioCarta, Reactome and KEGG databases in 8-months-old wild type (DP 8months) compared to 5-months-old wild type (DP 5months)

source_name: Cochlea

extract_protocol:
Inner ears were dissected after mice euthanasia with a sodium pentobarbital overdose (Vetoquinol, Spain) and immediately immersed in RNAlater® solution (Sigma-Aldrich, St. Louis, MO, USA). Adjacent tissues were carefully detached from the inner ear to avoid contamination. Finally, cochleae were isolated from vestibules and frozen in RNAlater® solution
1 µg of total RNA samples was used as provided by the user. Sample RNA Integrity Numbers were in the range 9.2 to 9.7 when assayed on an Agilent 2100 Bioanalyzer. 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 on an Illumina instrument (see below) by following manufacturer's protocols.

value: Cochlea


title: F6 DUSP1 KO


title: Liver_NASH-HCC_Tumor_11

value: NASH-HCC tumor


title: JR67B_6NNR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar Nipponbare

value: Strand-specific total RNA-Seq

value: fragmented total RNA, 150 to 300 nt


title: striatum, WT-1041

source_name: striatum

value: wild type

value: post natal day 60

value: striatum


title: F5 DUSP1 KO


title: F12 DUSP1 WT


title: JR65F_6NNR1S_RNA-Seq

value: No duplex-specific nuclease treatment


title: A375 shTFAP2A scRNA-seq Replicate 4

city: Iowa City

first: Jeffrey

last: White

state: Iowa

address: 285 Newton Road 5269 CBRB

institute: University of Iowa

description:
scRNA-seq of A375 transduced with shTFAP2A
A375_shTFAP2A_filtered_feature_bc_matrix.tar
Cuffdiff_on_A375_shNT_vs_shTFAP2A_gene_differential_expression_testing.tabular.txt

data_processing:
For bulk RNA-seq, RNA was isolated from the four TFAP2A knockout clones using the RNeasy Plus kit (Qiagen) and sequenced with 75 base pair, single end reads. Reads from parental A375, A375 shNT, and A375 shTFAP2A scRNA-seq had the 28 base 10X Genomics UMIs/barcodes removed from the start of R1 and the first low-quality base removed from the start of R2 using the HEADCROP operation of Trimmomatic. All reads were aligned using RNA STAR with parameters for Cufflinks compatibility. Differential expression was then calculated using Cufflinks/Cuffdiff.
For the parental A375 versus TFAP2AKO scRNA-seq, A375 was obtained from ATCC, thawed, and allowed to recover without passaging. Sub-confluent (~40% confluent) A375 (passage 0) or sub-confluent (~40% confluent) TFAP2AKO4 were trypsinized, prepared according to 10X Genomics sample preparation guidelines, and counted by hemocytometer. For shNT versus shTFAP2A scRNA-seq, minimally passaged A375 was transduced as described above with no chemical selection, and likewise prepared according to 10X Genomics sample preparation protocol and counted by hemocytometer. Cells were suspended in 0.04% BSA/PBS and libraries were prepared using 10X Genomics v3 Chemistry targeting 5000 cells per condition and sequenced on an Illumina HiSeq 4000 with 150 base pair, paired end reads. Libraries yielded between 1,611 and 5,160 cells. All libraries were above the 10X Genomics recommended minimum of 20,000 average reads per cell. A custom reference genome accounting for polymorphisms within the A375 genome was generated by aligning publicly available A375 whole genome sequencing reads (NCBI SRA: SRR8639175) to the GRCh38 reference genome using BWA-MEM, converted to a BAM file (Samtools v1.3.1), duplicates removed (GATK v4.0.5.2), and sorted (GATK v4.0.5.2). This alignment was then used to create an A375-specific genome assembly with RGAAT v2. 10X Genomics scRNA-seq reads were then processed and aligned to this assembly with Cell Ranger v3.1.0 (Cell Ranger Count function).
Bulk RNA-seq was aligned to GRCh38. scRNA-seq was aligned to an A375-specific GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tabular.txt: Cuffdiff results.
Supplementary_files_format_and_content: *.tar: Tar archive includes barcodes.tsv, features.tsv, matrix.mtx.

source_name: A375 Human Melanoma Cell Line

growth_protocol: All cells were grown at 37 degrees Celsius with 5% CO2.

extract_protocol: scRNA-seq was performed with 10X Genomics 3' Gene Expression v3 Chemistry.

treatment_protocol: Cells were transduced with TRCN0000004926 (Sigma Aldrich) lentiviruses 96-hours prior to sample preparation.

tag: cell type

value: Melanoma cell line

value: shRNA Lentivirus Targeting TFAP2A


title: Liver_NASH-HCC_Tumor_8


title: A375 shTFAP2A scRNA-seq Replicate 3


title: Liver_NASH-HCC_Tumor_10


title: Liver_NASH-HCC_Tumor_9


title: Liver_NASH-HCC_Tumor_7


title: A375 shTFAP2A scRNA-seq Replicate 2


title: F10 DUSP1 WT


title: F1 DUSP1 WT


title: Liver_NASH-HCC_Tumor_6


title: JR67E_69NR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar 93-11


title: JR65I_69NR1S_RNA-Seq


title: A375 shTFAP2A scRNA-seq Replicate 1


title: A375 shNT scRNA-seq Replicate 4

description:
scRNA-seq of A375 transduced with shNT
A375_shNT_filtered_feature_bc_matrix.tar
Cuffdiff_on_A375_shNT_vs_shTFAP2A_gene_differential_expression_testing.tabular.txt

treatment_protocol: Cells were transduced with SHC002 (Sigma Aldrich) lentiviruses 96-hours prior to sample preparation.

value: Non-Targeting shRNA Lentivirus


title: JR67D_9NNR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar Nipponbare


title: JR65H_9NNR1S_RNA-Seq

value: endosperm


title: A375 shNT scRNA-seq Replicate 3


title: F18 DUSP1 KO


title: Liver_NASH-HCC_Tumor_5


title: Liver_NASH-HCC_Tumor_2


title: Liver_NASH-HCC_Tumor_3


title: JR67F_96NR1N_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar IR64

value: Duplex-specific nuclease treatment performed


title: A375 shNT scRNA-seq Replicate 1


title: F19 DUSP1 KO

value: Cochlea


title: Parental A375 scRNA-seq Replicate 4

description:
scRNA-seq of A375
Parental_A375_filtered_feature_bc_matrix.tar

treatment_protocol: Cells were obtained from ATCC, thawed, and prepared for scRNA-seq after allowing time to recover in culture without passaging.

value: Unmanipulated Cell Line


title: Liver_NASH-HCC_Tumor_4

value: NASH-HCC tumor


title: Liver_NASH-HCC_NonTumoral_Adjacent_28

value: Non-tumoral NASH liver adjacent to HCC


title: E1 DUSP1 WT


title: E7 DUSP1 KO


title: Parental A375 scRNA-seq Replicate 2


title: JR66B_KER1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar Kitaake

value: O. Sativa L Embryo, Cultivar Kitaake

value: embryo

value: Strand-specific total RNA-Seq

value: fragmented total RNA, 150 to 300 nt


title: JR66C_6ER1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar IR64

value: O. Sativa L Embryo, Cultivar IR64

value: No duplex-specific nuclease treatment


title: JR66D_9ER1_RNA-Seq

value: O. Sativa L Embryo, Cultivar 93-11


title: Liver_NASH-HCC_NonTumoral_Adjacent_26


title: Liver_NASH-HCC_NonTumoral_Adjacent_29


title: Liver_NASH-HCC_NonTumoral_Adjacent_27


title: SH9051-treated sample_2

city: Murfreesboro

first: Fatmah

last: Alqahtani

state: TN

address: 1301 East Main Street

department: Biology

institute: Middle Tennessee State University

description:
SH9051_2
Diploid Pathogenic Fungi

data_processing:
An average of ~ 26873797 paired-end reads per sample (150 bp) was received as Fastq file.
Pre-processing quality control was preformed using FastQC  and Trimmomatic tools by trimming the low quality reads (Qscore < 20), adaptor sequences, and sequence containing N.
The  sequence reads were aligned to reference C. albicans genome SC5314_A21 using HISAT2.
The alignments for each sample was assembled using C_albicansSC5314__A21_features.gff annotation file with StringTie. Assembled transcripts  were merged together by StringTie-merge
The merged transcripts were used as input file to quantify the transcripts in each sample using featureCounts.  Then, Limma-voom tool compared the transcripts level of SH1009-treated and SH9051-treated samples to the transcripts level of untreated samples. The count data were normalized with trimmed mean of M value (TMM) method after filtering out the genes (unexpressed genes) with < 1 count per million reads.
Genome_build: GCF_000182965.3_ASM18296v3_genomic.fna
Supplementary_files_format_and_content: Normalized_GeneExpression_Counts_file

organism: Candida albicans

source_name: Microorganism Cells

growth_protocol: After growing C. albicans SC5314 cells at 30°C in YPD broth for 12 h, the culture was diluted 1:200 and allowed to grow with agitation at 30°C until reaching early exponential phase (OD530 = ~ 0.154).

extract_protocol:
The total RNA were extracted according to TRIzol™ reagent protocol
All samples were sent to Novogene Corporation Inc. (Sacramento, CA. US) for library preparation and RNA sequencing. Breifly, mRNA were enriched using oligo(dT) beads; Then, fragmented randomly by adding fragmentation buffer, then the cDNA were synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library were completed through size selection and PCR enrichment.

treatment_protocol: The treated samples were treated with aurones SH1009 and SH9051 separately at the concentration that caused 30% inhibition for one hour.

tag: agent

value: aurones SH9051


title: SH9051-treated sample_3

description:
SH9051_3
Diploid Pathogenic Fungi

tag: strain


title: Liver_NASH-HCC_NonTumoral_Adjacent_25


title: Parental A375 scRNA-seq Replicate 1

value: Melanoma cell line


title: JR65J_96NR1S_RNA-Seq


title: SH9051-treated sample_1

description:
SH9051_1
Diploid Pathogenic Fungi


title: E3 DUSP1 WT

tag: genotype

value: wild type


title: JR66A_NER1_RNA-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar Nipponbare

value: O. Sativa L Embryo, Cultivar Nipponbare


title: Liver_NASH-HCC_Tumor_1


title: JR68G_NKER2N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar Kitaake

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar Kitaake


title: TFAP2A KO4 scRNA-seq Replicate 4

description:
scRNA-seq of A375 TFAP2A KO4
A375_TFAP2A_KO4_filtered_feature_bc_matrix.tar

treatment_protocol: A complete genetic knockout of TFAP2A was generated by using CRISPR/Cas9 to disrupt exon 3.

value: CRISPR Knockout of TFAP2A


title: Liver_NASH-HCC_NonTumoral_Adjacent_24


title: Parental A375 scRNA-seq Replicate 3


title: SH1009-treated sample_3

description:
SH1009_3
Diploid Pathogenic Fungi

value: aurones SH1009


title: JR66L_NKER2S_RNA-Seq


title: Liver_NASH-HCC_NonTumoral_Adjacent_23


title: TFAP2A KO4 scRNA-seq Replicate 3


title: SH1009-treated sample_2

description:
SH1009_2
Diploid Pathogenic Fungi


title: Liver_NASH-HCC_NonTumoral_Adjacent_22


title: JR68A_N6ER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar IR64

value: Duplex-specific nuclease treatment performed


title: Liver_NASH-HCC_NonTumoral_Adjacent_21

value: Non-tumoral NASH liver adjacent to HCC


title: TFAP2A KO4 scRNA-seq Replicate 2


title: untreated sample_3

description:
Untreated_3
Diploid Pathogenic Fungi

value: Control


title: TFAP2A KO4 scRNA-seq Replicate 1


title: TFAP2A KO4 Bulk RNA-seq Replicate 4

description:
Bulk RNA-seq of A375 TFAP2A KO4
Cuffdiff_on_parental_A375_vs_TFAP2A_KO4_gene_differential_expression_testing.tabular.txt

extract_protocol: RNA was isolated with the RNeasy Plus Mini Kit (Qiagen).


title: JR66E_N6ER1S_RNA-Seq

value: embryo


title: untreated sample_2

description:
Untreated_2
Diploid Pathogenic Fungi


title: TFAP2A KO4 Bulk RNA-seq Replicate 3


title: JR68C_N9ER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar 93-11

value: Strand-specific total RNA-Seq


title: untreated sample_1

description:
Untreated_1
Diploid Pathogenic Fungi


title: JR66G_N9ER1S_RNA-Seq

value: fragmented total RNA, 150 to 300 nt


title: TFAP2A KO4 Bulk RNA-seq Replicate 2


title: E4 DUSP1 WT

value: Cochlea

tag: age


title: miR_iab_8_rep2

city: New York

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
RNA-seq data were aligned to the Drosophila melanogaster reference genome (Version r6.21) using HISAT2 software with standard parameters. We used featureCounts in the Rsubread package to compute features and read numbers for each bam file. The read counts per gene were then normalized to obtain RPKM values using edgeR package from R Bioconductor and extracting transcript length from biomaRt. Fold changes between samples were calculated using edgeR applying no filter. Genes targeted by miR-iab-8-5p were identified using conserved TargetScanFly predictions.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig

organism: Drosophila melanogaster

source_name: dissected VNC

extract_protocol:
Larvae were dissected on ice for a maximum of 30s minutes (30-40 larvae). The posterior third of larvae was removed with forceps, the remaining was turned inside down. Using 2mm curved blade spring scissors (Fine Science Tools #15000-04), VNC were severed at the level of the A7 pair of nerves, and immediately placed into TRIzol (Thermo Fisher Scientific #15596018). After dissections, samples in TRIzol were stored at −80° C. Each biological replicate pooled severed VNCs of 120-150 larvae, dissected in 4-5 periods of 30 min.
500 ng of total RNA per dissected VNC sample was used for TruSeq stranded mRNA library preparation (Illumina)

tag: protocol


title: JR68H_KNER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Kitaake x Cultivar Nipponbare

tag: cultivar

value: O. Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare

tag: tissue


title: TFAP2A KO3 Bulk RNA-seq Replicate 4

description:
Bulk RNA-seq of A375 TFAP2A KO3
Cuffdiff_on_parental_A375_vs_TFAP2A_KO3_gene_differential_expression_testing.tabular.txt


title: TFAP2A KO4 Bulk RNA-seq Replicate 1


title: Liver_NASH-HCC_NonTumoral_Adjacent_20


title: JR66K_KNER1S_RNA-Seq

tag: library type

tag: duplex-specific nuclease treatment

value: No duplex-specific nuclease treatment


title: SH1009-treated sample_1

description:
SH1009_1
Diploid Pathogenic Fungi


title: Liver_NASH-HCC_NonTumoral_Adjacent_19


title: JR68B_6NER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar Nipponbare

tag: molecule subtype


title: JR66F_6NER1S_RNA-Seq


title: Liver_NASH-HCC_NonTumoral_Adjacent_16


title: hthBS_iab_8_rep3


title: TFAP2A KO3 Bulk RNA-seq Replicate 3

value: Melanoma cell line


title: TFAP2A KO3 Bulk RNA-seq Replicate 2


title: Liver_NASH-HCC_NonTumoral_Adjacent_15


title: miR_iab_8_rep3


title: hthBS_iab_8_rep2


title: Liver_NASH-HCC_NonTumoral_Adjacent_14


title: TFAP2A KO3 Bulk RNA-seq Replicate 1


title: JR68E_69ER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar 93-11


title: Liver_NASH-HCC_NonTumoral_Adjacent_18


title: Liver_NASH-HCC_NonTumoral_Adjacent_17


title: JR68D_9NER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar Nipponbare


title: CS_iab_8_rep3


title: hthBS_iab_8_rep1


title: TFAP2A KO2 Bulk RNA-seq Replicate 4

description:
Bulk RNA-seq of A375 TFAP2A KO2
Cuffdiff_on_parental_A375_vs_TFAP2A_KO2_gene_differential_expression_testing.tabular.txt

value: CRISPR Knockout of TFAP2A


title: miR_iab_8_rep1


title: TFAP2A KO2 Bulk RNA-seq Replicate 3


title: JR66H_9NER1S_RNA-Seq


title: Liver_NASH-HCC_NonTumoral_Adjacent_12


title: CS_iab_8_rep2


title: JR68F_96ER1N_RNA-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar IR64


title: TFAP2A KO2 Bulk RNA-seq Replicate 2

source_name: A375 Human Melanoma Cell Line


title: JR66I_69ER1S_RNA-Seq


title: JR66J_96ER1S_RNA-Seq


title: TFAP2A KO1 Bulk RNA-seq Replicate 4

description:
Bulk RNA-seq of A375 TFAP2A KO1
Cuffdiff_on_parental_A375_vs_TFAP2A_KO1_gene_differential_expression_testing.tabular.txt


title: TFAP2A KO2 Bulk RNA-seq Replicate 1


title: JR054_N6NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar IR64

value: endosperm

value: small RNA-seq

value: total RNA, 17 to 30 nt


title: RNA GAS strain 854∆csrR B

city: Boston

first: Michael

last: Wessels

state: MA

address: 330 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

data_processing:
Sequencing reads from each pooled sample were demulitplexed based on their associated barcod sequence using custom scripts; allowing up to 1 mismatch in the barcode, provided this did not make assignemtn of the read to a different barcode possible. Barcode sequencese were subsequently trimmed from the first read as were terminal G's from the second read that may have been added by SMARTScirbe during template switching.
Reads were aligned to the S. pyogenes MGAS5005 genome (NCBI RefSeq NC_007297) using bowtie2 version 2.3.1
Read counts were assigned to annotated genes using HTSeq version 0.10.0
Differential expression analysis was conducted with DESeq2 version 1.20.0
Genome_build: NC_007297
Supplementary_files_format_and_content: tab-delimited text file includes read counts assigned to each feature for each sample

organism: Streptococcus pyogenes

source_name: Bacterial cells grown to OD ∼0.4

growth_protocol: Cultures were grown to mid-log-phase (OD600 of ~0.4)

extract_protocol:
Cell pellets were mechanically disrupted by bead beating in Trizol reagent. Chloroform was added and RNA was extracted from the aqueous phase via Direct-Zol RNA Miniprep Kit (Zymo Research)
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol. 500 ng - 1 µg total RNA was fragmented, depleted of genomic DNA, dephosphorylated and ligated to DNA adapters carrying 5'-AN8-3' barcodes of known sequence with a 5' phosphate and a 3' blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (EpiCentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcode adaptor with addition of an adapter to the 3' end of the cDNA by template switching using SMARTScribe (Clonetech); (ii) PCR amplification using primers whose 5' ends target the constant region of the 3' or 5' adaptors and whose 3' ends contain the full Illumina P5 or P7 sequences.


title: RNA GAS strain 854∆csrR C


title: JR050_N9NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar 93-11


title: TFAP2A KO1 Bulk RNA-seq Replicate 3


title: TFAP2A KO1 Bulk RNA-seq Replicate 2


title: RNA GAS strain 854 C

value: 854 wild-type


title: RNA GAS strain 854∆csrR A


title: RNA GAS strain 854 B


title: Liver_NASH-HCC_NonTumoral_Adjacent_10

value: Non-tumoral NASH liver adjacent to HCC


title: CS_iab_8_rep1


title: TFAP2A KO1 Bulk RNA-seq Replicate 1


title: JR056_6NNS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar Nipponbare


title: Liver_NASH-HCC_NonTumoral_Adjacent_13


title: JR058_69NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar 93-11


title: Liver_NASH-HCC_NonTumoral_Adjacent_11


title: Liver_NASH-HCC_NonTumoral_Adjacent_9


title: Liver_NASH-HCC_NonTumoral_Adjacent_8


title: RNA-seq_AJJN3.1

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

data_processing:
RNA-seq. Read cleaning and filtering: Paired-end RNA-seq reads were adapter trimmed by the DNA sequencing facility at Centre for Haematology, Division of Experimental Medicine Faculty of Medicine, Imperial College London were quality controlled with FastQC version 0.11.3.
RNA-seq Quantification. Expression estimates for each sample were obtained using Salmon version 0.11.4(Patro et al., 2017), using the complete Ensembl 85 transcriptome. Salmon was used with fragment GC bias correction, 100 bootstrap samples and using an auxiliary k-mer hash over k-mers of length 31. Counts over different transcripts were summed to get gene level counts.
Genome_build: Ensembl 85 human transcriptome
Supplementary_files_format_and_content: Matrix of estiamated read counts per gene

source_name: JJN3 multiple myeloma cell line t(14;16) MAF

growth_protocol: The human multiple myeloma cell line(MMCLs) MM.1S (ATCC, Manassas, VA, USA) was cultured in RPMI1640 media (Sigma, UK) and 20% FBS (Life Technologies). JJN3 cells(DSMZ, Germany) were cultured in 40/40% DMEM/IMEM medium (Sigma, UK), and 20% FBS

extract_protocol:
Total RNA was isolated using the Nucleospin RNA kit (Macherey-Nagel) and quantified using the Qubit RNA Assay kit (Life Technologies) and RNA quality was assessed on the Bioanalyser  using  the  RNA  pico  kit  (Agilent).
Total  RNA  libraries  were  prepared  by removing the ribosomal RNA with NEBNext rRNA depletion kit (New England Biolabs) and  NEBNext  Ultra  II  Directional  RNA  Library  Prep  kit  for  Illumina  (New  England Biolabs), following manufacturer’s instructions. Library quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent).

value: multiple myeloma cell line

tag: condition

value: MM

tag: cytogenetics

tag: selected surface markers

tag: sequencing batch


title: Liver_NASH-HCC_NonTumoral_Adjacent_6


title: Liver_NASH-HCC_NonTumoral_Adjacent_4


title: JR052_9NNS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar Nipponbare

value: No duplex-specific nuclease treatment


title: Liver_NASH-HCC_NonTumoral_Adjacent_3


title: Liver_NASH-HCC_NonTumoral_Adjacent_5


title: RNA GAS strain 854 A


title: Liver_NASH-HCC_NonTumoral_Adjacent_7


title: JR046_6NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar IR64

value: O. Sativa L Endosperm Cultivar IR64


title: JR060_96NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar IR64


title: RNA-seq_A28c.6

source_name: U266 multiple myeloma cell line - t(11;14) CCND1

tag: cell line


title: RNA-seq_A28c.3

source_name: MM1S multiple myeloma cell line t(14;16) MAF


title: JR048_9NS1_small RNA-seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar 93-11

value: O. Sativa L Endosperm Cultivar 93-11


title: RNA-seq_A28.15

source_name: Primary plasma cell multiple myeloma

extract_protocol:
Patient BM aspirates were subjected to red cell lysis. Multiple myeloma plasma cells were purified by two rounds of CD138 immunomagnetic selection (MiltenyiBiotech) following the manufacturer’s instructions. Pre and post selection purity was assessed by FACs analysis (BD LSR-Fortessa) using CD138, CD45, CD19, CD56 and CD38 panel antibodies
Total RNA was isolated using the Nucleospin RNA kit (Macherey-Nagel) and quantified using the Qubit RNA Assay kit (Life Technologies) and RNA quality was assessed on the Bioanalyser  using  the  RNA  pico  kit  (Agilent).
Total  RNA  libraries  were  prepared  by removing the ribosomal RNA with NEBNext rRNA depletion kit (New England Biolabs) and  NEBNext  Ultra  II  Directional  RNA  Library  Prep  kit  for  Illumina  (New  England Biolabs), following manufacturer’s instructions. Library quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent).

value: Bone marrow

tag: primary subgroup


title: JR053_N6ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar IR64

value: embryo


title: JR049_N9ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar 93-11

value: small RNA-seq


title: RNA-seq_A28.7

source_name: OPM2 multiple myeloma cell line t(4;14) MMSET

value: OPM2 t(4;14) MMSET


title: JR055_6NES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar Nipponbare

value: total RNA, 17 to 30 nt


title: RNA-seq_A27.19

value: MMSET


title: Liver_NASH-HCC_NonTumoral_Adjacent_2

value: Non-tumoral NASH liver adjacent to HCC


title: RNA-seq_A26.11

value: t(14;16) - MAF, pseudohyperdiploid, cMAF, +1q

value: MAF


title: RNA-seq_A26.14

value: MM

value: t(11;14) - CCND1, gain of 1q and partial deletion of TP53


title: JR057_69ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar 93-11

value: No duplex-specific nuclease treatment


title: RNA-seq_A28c.5

source_name: KMS12BM multiple myeloma cell line t(11;14) CCND1

value: multiple myeloma cell line

value: KMS12BM t(11;14) CCND1


title: Liver_NASH-HCC_NonTumoral_Adjacent_1


title: Liver_NASH_73

value: NASH liver


title: JR051_9NES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar Nipponbare

value: embryo


title: Liver_NASH_74


title: Liver_NASH_70


title: RNA-seq_A24.11

value: Bone marrow

value: hyperdiploid, +1q

value: HD


title: JR059_96ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar IR64

value: small RNA-seq

value: total RNA, 17 to 30 nt


title: Liver_NASH_72


title: JR045_6ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF Cultivar IR64

value: O. Sativa L Embryo Cultivar IR64


title: JR047_9ES1_small RNA-seq

source_name: O. Sativa L. Embryo 7 to 8 DAF Cultivar 93-11

value: O. Sativa L Embryo Cultivar 93-11


title: TKLP-AP2A

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: bedGraph files

source_name: Mouse Melanoma

extract_protocol: ChIP using TFAP2A monoclonal antibody.

value: TKLP

tag: cell type

value: Melanoma cell line

tag: chip antibody

value: TFAP2A monoclonal antibody


title: JR028_N6NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar IR64

value: Endosperm

value: BS-Seq

value: No duplex-specific nuclease treatment


title: RNA-seq_A24.10

value: MM


title: A375 shNT scRNA-seq Replicate 2

source_name: A375 Human Melanoma Cell Line

tag: treatment

value: Non-Targeting shRNA Lentivirus


title: JR038_N9NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar Nipponbare x Cultivar 93-11


title: RNA-seq_A27.22

source_name: Plasma cell CD19 minus, donor 271017

extract_protocol:
BM-MNCs from BM aspirates were isolated by ficoll (Histopaque, Sigma). The MNCs were pre-cleared of T cells and Monocytes by consecutive immunomagnetic negative selection (CD3 and CD14-EasySep StemCell Technologies) following manufacturer’s instructions. The sample was stained and sorted for positive CD138, CD319, CD27, CD45 and CD38, and negative for CD2, CD3, CD14, CD16, GPA and 7AAD. (FACSAriaII, BD Biosciences) and CD19+or CD19-
Total RNA was isolated using the Nucleospin RNA kit (Macherey-Nagel) and quantified using the Qubit RNA Assay kit (Life Technologies) and RNA quality was assessed on the Bioanalyser  using  the  RNA  pico  kit  (Agilent).
Total  RNA  libraries  were  prepared  by removing the ribosomal RNA with NEBNext rRNA depletion kit (New England Biolabs) and  NEBNext  Ultra  II  Directional  RNA  Library  Prep  kit  for  Illumina  (New  England Biolabs), following manufacturer’s instructions. Library quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent).

value: Bone marrow

value: PC

value: ND

tag: pc cd19 status

value: minus

tag: pc donor id


title: RNA-seq_A17.5


title: JR030_6NNB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar Nipponbare


title: RNA-seq_A24.8

source_name: Primary plasma cell multiple myeloma

value: hyperdiploid, +1q

value: HD


title: JR042_69NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Endosperm F1 Cultivar IR64 x Cultivar 93-11


title: B10_IP

city: KunMing

first: Zhou

last: yiran

state: YunNan

address: B: No. 245 East Renmin Road

department: general surgery department

institute: Yan 'an Hospital Affiliated to Kunming Medical University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
hen sequence quality was verified using FastQC. We used HISAT2 to map reads to the genome of Homo sapiens (Version: v96) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software.
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house. Called peaks were annotated by intersection with gene architecture using ChIPseeker.
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: peak text files

source_name: para-carcinoma tissue

extract_protocol:
 we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.
Me-RIP-seq

value: para-carcinoma


title: B9_IP


title: B8_IP


title: RNA-seq_A26.19

source_name: Plasma cell CD19 minus, donor 160617


title: B7_IP


title: RNA-seq_A26.18

description: Note: This is the matching RNA file for the both A26.20 and A26.18 ATAC samples.

source_name: Primary plasma cell CD19 plus 160617

value: plus


title: B6_IP


title: Liver_NASH_67

value: NASH liver


title: Liver_NASH_66


title: Liver_NASH_68


title: B5_IP


title: Liver_NASH_71


title: Liver_NASH_69


title: JR040_9NNB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

extract_protocol:
DNA and total RNA was extracted from snap-frozen tissues using CTAB and TRIzol reagent (Invitrogen), respectively.
For bisulfite sequencing, about 1µg of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec.
For small RNA libraries, 10 µg of total RNA was loaded on a 15% polyacrylamide, 7M urea gel, and small RNA in the 17-30 nt size range were excised. The 3' miRNA cloning linker 1 (IDT) was ligated to the gel-excised small RNA using truncated T4 RNA ligase 2 (NEB), and ligation products were purified on a 15% polyacrylamide, 7M urea gel. The 5' Illumina RNA linker (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3') was added using T4 RNA ligase (NEB) and ligation products were again purified on a 15% polyacrylamide, 7M urea gel. Purified ligated small RNAs were reverse transcribed using SuperScriptIII (Invitrogen) and PCR-amplified with Phusion High-Fidelity DNA Polymerase (NEB) for 25 cycles (Forward primer: 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3', Reverse primer: 5'-CAAGCAGAAGACGGCATACGATTGATGGTGCCTACAG-3').
Strand-specific RNA-seq libraries were constructed as described in Wang et al. (2011), beginning with ribosomal RNA-depleted total RNA. TRIzol-extracted total RNA treated with DNase I (Qiagen) was purified using the RNeasy Mini kit (Qiagen) as per manufacturer’s instructions. After verifying RNA integrity on a denaturing agarose gel, 5 μg of purified total RNA was depleted for ribosomal RNA using the Ribo-Zero rRNA removal kit for plant seed and root (Epicentre) as per manufacturer’s instructions. Ribosomal-depleted total RNA was purified using AM-Pure beads (Beckman Coulter) and fragmented using the Ambion RNA fragmentation kit (Ambion). After overnight precipitation in 75% ethanol, the resuspended pellet was reverse transcribed using Random Hexamer primers (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). After AM-Pure bead purification. second-strand synthesis proceeded with DNA polymerase I (Invitrogen) and a dUTP mix of 10 mM dA, 10 mM dC, 10 mM dG, and 20 mM dU. After purification of second-strand synthesis products with AM-Pure beads, cDNA was end-repaired using the End Repair Mix LC (Enzymatics) while still attached to AM-Pure beads. Using XP buffer (Wang et al., 2011) for intermediate size selection and washing steps, dA-tailing with Klenow exo minus (NEB) was also performed while cDNA still remained attached to the beads. cDNA was eluted off beads for Y-shape adapter ligation with DNA quick ligase (NEB) and adapters (adapter 1: 5'A*C*ACTCTTTCCCTACACGACGCTCTTCCGAT*C*T 3'; adapter 2: 5'P-G*A*TCGGAAGAGCACACGT*C*T 3'). After purifying adapter-ligated cDNA with AM-Pure beads, dUTP excision was performed with Uracil DNA glycosylase (NEB), and products were directly amplified using Phusion Hot Start 2 DNA polymerase (NEB) and indexed pair-end primers for multiplexing. After dUTP excision and PCR, products were purified and concentrated using AM-Pure beads. Where indicated, duplex-specific nuclease treatment was performed as described by Matvienko et al. (2013). In short, 200 to 300 ng of library product was denatured and hybridized in TMAC buffer (3 M TMAC, 50 mM HEPES, pH 7.5) for 5 hours at 68°C. At the end of 5 hours, duplex-specific nuclease (DSN; Evrogen) was added along with DSN buffer as instructed by the manufacturer. Resulting DSN-treated products were amplified a second time using Phusion Hot Start 2 DNA polymerase (NEB) and indexed pair-end primers for multiplexing. Final DSN-treated library products were gel-purified on 2% agarose to obtain fragments between 300 to 400 bp in length for sequencing.
library strategy: Bisulfite sequencing, strand-specific total RNA (with or without duplex-specific nuclease treatment), and small RNA sequencing with Illumina technology.
sequencing platform: Illumina HiSeq 2000 (run by the Vincent J. Coates Genomic Sequencing Laboratory at UC Berkeley)

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar Nipponbare

value: Endosperm


title: RNA-seq_A27.21

source_name: Plasma cell CD19 plus, donor 271017


title: JR044_96NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Endosperm F1 Cultivar 93-11 x Cultivar IR64

value: BS-Seq

value: No duplex-specific nuclease treatment


title: Liver_NASH_60

extract_protocol: 50ng of total mRNA was isolated from FFPE samples using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.  DNA FFPE kits (Qiagen).


title: Liver_NASH_64


title: Liver_NASH_65


title: Liver_NASH_63


title: Liver_NASH_61


title: Liver_NASH_62


title: RNA-seq_A27.18

value: MM


title: B4_IP


title: Liver_NASH_59


title: Liver_NASH_58


title: B3_IP


title: JR034_6NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar IR64

value: O. Sativa L Endosperm Cultivar IR64


title: RNA-seq_A26.13

value: Bone marrow

value: hyperdiploid


title: JR036_9NB1_BS-Seq

source_name: O. Sativa L. Endosperm 7 to 8 DAF Cultivar 93-11

value: O. Sativa L Endosperm Cultivar 93-11


title: B2_IP


title: RNA-seq_A26.1


title: JR027_N6EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar IR64

value: embryo


title: JR037_N9EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar Nipponbare x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar Nipponbare x Cultivar 93-11


title: RNA-seq_A26.12

value: MAF


title: RNA-seq_A26.10B

value: MMSET


title: B1_IP

value: para-carcinoma


title: Liver_NASH_56

value: NASH liver


title: Liver_NASH_57


title: RNA-seq_A26.9B

value: hyperdiploid, TP53 del, +1q

value: HD


title: JR041_69EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar 93-11

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar 93-11


title: A9_IP

source_name: Colon cancer tissue

value: Colon cancer


title: Liver_NASH_55


title: A8_IP


title: JR039_9NEB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar Nipponbare

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar Nipponbare

value: BS-Seq

value: No duplex-specific nuclease treatment


title: RNA-seq_A26.8

value: Bone marrow

value: MM


title: Liver_NASH_54


title: JR043_96EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar 93-11 x Cultivar IR64

value: O. Sativa L Embryo F1 Cultivar 93-11 x Cultivar IR64


title: A7_IP


title: RNA-seq_A27.20

value: TP53 deletion


title: RNA-seq_A26.15B

value: hyperdiploid (+17, +9, +15)


title: Liver_NASH_53


title: JR035_9EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF Cultivar 93-11

value: O. Sativa L Embryo Cultivar 93-11

value: embryo


title: A6_IP


title: RNA-seq_A26.6B

source_name: Primary plasma cell multiple myeloma

value: hyperdiploid, subclonal +1q (30%)


title: Liver_NASH_52


title: A10_IP


title: A5_IP


title: Liver_NASH_51


title: Liver_NASH_50


title: HeLa_pM

city: Hefei

first: Fazhi

last: Yu

address: huangshan road 443

institute: USTC

data_processing:
Sequence reads were aligned to the human reference genome with GRCh38.p11(hg38) or hg19.
Genome_build: GRCh38.p11(hg38) for Notch2-KD, and hg19 for Ribosome profiling.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
For ribosome profiling, HeLa cells were synchronized by double thymidine (2 mM, Sigma). Cells were lysed in lysis buffer (20 mM Tris pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol, 8% glycerol) supplemented with 0.5% Triton X-100, 30 U/ml Turbo DNase (Ambion, Life Technologies, CA, United States) and 100 μg/ml cycloheximide (Sigma Aldrich, MO, United States); ribosomeprotected fragments were then isolated and sequenced as previously described (Nat Protoc. 2012 Jul 26;7(8):1534-50.). Total RNA was isolated from cells using Trizol Reagent (Ambion). Polyadenylated RNA was purified from total RNA using magnetic oligo(dT) beads. The resulting mRNA was modestly fragmented by partial hydrolysis in bicarbonate buffer so that the average size of fragments was ∼80 bp. The fragmented mRNA was separated by denaturing PAGE and fragments 50–80 nt were selected. The sequencing libraries were prepared and sequenced as previously described (Nat Protoc. 2012 Jul 26;7(8):1534-50.).  For transcriptomes of OVCAR8 cells, mRNA was extracted from OVCAR8 cells using Trizol Reagent according to the manufacturer’s protocol. RNA samples were quantified using Nanodrop (Life Technologies, Carlsbad, CA, USA) and send to The Beijing Genomics Institute (BGI, Shenzhen, China) for RNA integrity checking, library preparation and sequencing. RNA quality was confirmed using an Agilent 2100 Bioanalyzer by BGI again.
For ribosome profiling mRNA, RNA libraries were prepared for sequencing using standard Illumina protocols.  For Notch2 knockdown mRNA, Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: HeLa

tag: tissue source

value: cervical cancer

value: 5nM Taxol

tag: time point

value: HeLa cells in prolonged mitosis were collected.


title: JR029_6NEB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF F1 Cultivar IR64 x Cultivar Nipponbare

tag: cultivar

value: O. Sativa L Embryo F1 Cultivar IR64 x Cultivar Nipponbare

tag: tissue


title: RNA-seq_A28c.14

source_name: Plasma cell CD19 plus, donor 230218

value: PC

value: ND

value: plus


title: HeLa_M

value: DMSO

value: HeLa cells in mitosis were collected.


title: A3_IP

value: Colon cancer


title: RNA-seq_A28.13

value: Bone marrow

value: MM

value: MMSET


title: A4_IP


title: RNA-seq_A27.12

value: hyperdiploid

value: HD


title: Liver_NASH_49

value: NASH liver


title: A1_IP


title: RNA-seq_A19.6


title: RNA-seq_A24.4

value: hyperdiploid, +1q


title: A2_IP


title: RIP10 Input

first: Oscar

last: Reina Garcia

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

description: Input

data_processing:
BAM to FastQ conversion was done with bedtools v2.17.0
FastQ files were aligned against the human reference genome h19 with Bowtie2 v2.2.2 in local mode, allowing for one mismatch and reporting the best possible alignment per read
Alignments were sorted and indexed with sambamba v0.5.1. Putative over-amplification artifacts (duplicated reads) were assessed and removed with the same software
Afterwards, significantly enriched regions between IP CPEB1 and IP CPEB4 against matched Input samples were detected using the enrichedRegions function of the htSeqTools package using default settings and a Benjamini-Hochberg adjusted p-value of 0.05.
The identified peaks (enriched regions) were annotated against all genes and exons in the human reference genome release hg19 (UCSC March 2015) using the ChIPpeakAnno package version 2.16.1.
Genome_build: h19
Supplementary_files_format_and_content: Processed data files include htSeqTools output with enriched regions in IP vs Input including counts and RPKM quantification for each sample and BH p-value.

source_name: Hela S3

growth_protocol: HeLa S3 cells  were grown in DMEM 10% FBS

extract_protocol:
RNP-complexes were crosslinked with 0.5% PFA for 5 min, then CPEB1/4 were immunoprecipitated with anti-CPEB1/4 specific antibodies and associated-mRNAs were extracted with phenol-chlorophorm.
Inputs and IPs samples from a RIP experiment were quantified by Qubit RNA HS (Life Technologies) when it was possible, and fragment size distribution was checked by Bioanalyzer Pico Chip (Agilent). Library generation was done with the kit NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following manufacturer´s instructions and 14-15 cycles of library amplification. Previous Poly A purification was only performance on Input samples in only one step of purification. Size selection of the libraries and purification were done by magnetic beads (Agencourt AMPure XP, Beckman Coulter). Finally, library quantification was performance with Qubit DNA HS (Life Technologies) and fragment size distribution with Bioanalyzer DNA HS (Agilent)

treatment_protocol: Cells were treated with the Cdk1 inhibitor (RO-330, 9 uM) for 21 hours. For CPEB1-RIP cells remained arrested while for CPEB4 cells were released for 1 hour.

value: Hela S3

tag: rip antibody


title: RIP10 IP CPEB4

description: RIP mRNA

value: anti-CPEB4 (ab83009)


title: RIP9 IP CPEB4

description: RIP mRNA


title: B10_input

source_name: para-carcinoma tissue

value: para-carcinoma


title: RNA-seq_A24.7

value: hyperdiploid with subclonal gain of 1q


title: RNA-seq_A19.8


title: RIP9 Input CPEB1

description: Input


title: B9_input


title: B8_input


title: RNA-seq_A19.2

value: t(11;14) - CCND1, pending in house FISH


title: RIP8 IP CPEB1

description: RIP mRNA


title: RIP 8 Input CPEB1

description: Input


title: B7_input


title: RNA-seq_A19.5

value: hyperdiploid, +9q subclonal


title: Liver_NASH_46


title: Liver_NASH_48


title: Liver_NASH_43


title: Liver_NASH_47


title: Liver_NASH_45


title: Liver_NASH_44


title: JR033_6EB1_BS-Seq

source_name: O. Sativa L. Embryo 7 to 8 DAF Cultivar IR64

value: O. Sativa L Embryo Cultivar IR64

value: embryo

tag: library type

value: BS-Seq

tag: duplex-specific nuclease treatment

value: No duplex-specific nuclease treatment


title: Primed Exosome_2

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

institute: Rutgers NJ Medical School

description: Primed Exosome treatment

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Lognormal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: Normalized read file  includes RPKM values for each sample

source_name: Breast Cancer Cell line MDA-MB-231

growth_protocol: The cells were cultured up to 7 days in DMEM supplemented with 2% exosome depleted FCS and glutamine.

extract_protocol:
Total heterogeneous population was harvested and taken to Genomics Core Facility for sequencing. Using a microfluidic system, single cell droplets were encapsulated with a micoparticle coated with unique moleuclar identifier (UMI), PCR handler, cell-specific barcode and a terminal oligo-dT in lysis buffer.
Libraries were prepared using Nextera Library construction reagents (Illumina NextSeq550).

treatment_protocol: Mesenchymal Stem Cells (MSCs) were cultured in a transwell system (0.4 µm insert; BD Falcon, ThermoFisher) with or without MDA-MB-231 cells (1:1 ratio, upper chamber) for 24 h. After 24 h the transwells were discarded and media was replaced with fresh DMEM supplemented with 2% exosome depleted FBS for 48 h. After 48 h media was harvested and exosomes were purified.  MSC derived exosomes isolated following co-cultured with MDA-MB-231 cells were termed primed exosomes, and those not in co-culture were termed naïve exosomes. Fresh MDA-MB-231 cells were then treated with 10^8 primed or naïve exosomes every 48 h for 7 daysMesenchymal Stem Cells were either co-cultured at 1:1 ratio in a transwell system with MDA-MB-231 for 24 h using 0.4 µm insert (BD Falcon, ThermoFisher) containing MDA-MB-231 in the upper chamber and MSC in the lower chamber. Transwell insert was discarded after 24 h. and media was replaced with fresh DMEM supplemented with 2% exosome depleted FCS for 48h. After 48h co-culture conditioned media  MSCs that were exposed to MDA-MB-231 were characterized as primed MSC and MSC that were not in contact with MDA-MB-231 were characterized as naive MSC. The conditioned media was harvested and exosomes were purified. Naive MDA-MB-231 was treated with 10^8 exosomes every 48 h. for 7 days.  .

tag: transfected with

tag: exosome source

value: Exosome source 2

tag: exosome status

value: primed


title: B6_input


title: Liver_NASH_41


title: RNA-seq_A17.9

value: Bone marrow

tag: condition

value: MM

tag: cytogenetics

value: hyperdiploid, TP53 deletion, IgH rearranged

tag: selected surface markers

tag: sequencing batch


title: RNA-seq_A19.1

tag: primary subgroup

value: HD


title: B5_input


title: B4_input


title: Naïve Exosome_2

description: Naïve Exosome treatment

tag: cell line

value: naive


title: Primed Exosome_3

description: Primed Exosome treatment

value: Exosome source 3


title: AJJN3.1

data_processing:
Read cleaning and filtering: Raw paired-end ATAC-seq reads were quality controlled using FastQC version 0.11.3. ATAC-seq adapters were removed, uncalled bases (N's) on ends of reads were trimmed using Cutadapt version 1.9.1(Martin, 2011). Only read pairs with both single end fragments remaining were kept. A second quality pass was performed using Sickle version 1.33 (https://github.com/najoshi/sickle), trimming was performed with a sliding window average Phred quality threshold of 30 (without five prime trimming). Only pairs with a minimum of 20 bases in each read were retained.
Mapping: Reads were mapped using Bowtie2 version 2.3.0 in paired-end mode  reporting up to 4 alignments per read, with maximum fragment length 2000bp.
Calling chromatin accessible peaks: Processing was performed using pipeline_atac_consensus_balanced_peaks (https://doi.org/10.15131/shef.data.12280904). Correctly mapped reads were filtered using Samtools version 1.3.1 (samtools view -F 524 -f 2 flags). Read pairs non-overlapping reads in RF orientation were removed with Samtools and Bedtools.  Multimapped reads and duplicates were removed.  Read pairs were converted into two single end tags and Tags. Soft clipped bases re-added and the TN5 added base pairs on the 5' sites of each read were trimmed.   Two consensus peak sets were created: the pan myeloma set and the subgroup set. For the pan myeloma set, the tags in each sample were down-sampled so that each sample had the same number of tags. Samples were then pooled into two categories – MM and NPC.   Broad and narrow peaks were called on each pool using MACS2 version 2.1.1.20160309 (https://github.com/taoliu/MACS)(Zhang, Liu et al. 2008) with the following options for narrow peaks:  -g hs -q 0.01 --nomodel --shift -100 --extsize 200 -B --SPMR --keep-dup all --call-summits  And for broad peaks:  -g hs -q 0.01 --nomodel --shift -100 --extsize 200 --broad --broad-cutoff 0.01 --keep-dup all  Narrow and broad peaks were filtered to remove areas of low mappability and those in ENCODE blacklist reagions,  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz and  https://www.encodeproject.org/files/ENCFF419RSJ/@@download/ENCFF419RSJ.bed.gz).
MM and PC consensus peak set: for the pan myeloma set, the tags in each sample were down-sampled so that each sample had the same number of tags. Samples were then pooled into two categories – MM and NPC.
MM and PC consensus peak set: for subgroup peak set, samples without a cytogenetic classification were excluded, and the remaining samples downsampled to the new minimum. Tags from samples in the same cytogenetic group (MAF, MMSET, CCND1, HD or ND PC) were pooled and peaks called on each poolSamples were then pooled into two categories – MM and NPC.
Reads in peaks quantification: shifted tags from each sample were transformed to obtain only the initial 1bp reflecting the 5' and filtered to remove tags overlapping with areas of low and high mappability defined previously. The number tags overlapping each peak in the peak set is reported using Bedtools intersect version 2.22.1(Quinlan and Hall, 2010).
Genome_build: hg38 analysis ready
Supplementary_files_format_and_content: Narrowpeak and broadpeak files from each sample. Suppplementary files contain the coordinates for consensus peak sets and the read count in them for each sample.

source_name: JJN3 multiple myeloma cell line t(14;16) MAF

extract_protocol:
ATAC-seq was performed as described(Buenrostro et al., 2013). Briefly, 50,000 purified plasma cells, myeloma plasma cells or cell lines, were washed with cold PBS (Sigma, UK) at 500g at 40C for 5 min. The cells were resuspended in 50 μL of cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and washed at 500g at 40C for 10 min. The libraries were sequenced at the Genomics Facility at ICL using the Illumina HiSeq 4000 platform to obtain paired-end 75bp reads.
The nuclei were subjected to transposase reaction for 30 min at 370C; termination of the reaction and DNA purification was performed using a MiniElute Kit (Qiagen) and eluted twice with 10 μL. The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). The PCR amplified product was cleaned twice with (0.9X) AMPure beads (Beckman). The quality of the libraries was assessed with the Bioanalyzer High Sensitivity DNA kit (Agilent). The libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs) on a StepOne Plus Real-Time PCR (Applied Biosystems).

value: myeloma cell line


title: Primed Exosome_1

description: Primed Exosome treatment

value: Exosome source 1


title: A28c.6

source_name: U266 multiple myeloma cell line - t(11;14) CCND1


title: Liver_NASH_42

data_processing: Gene expression profiles that passed the quality control were submitted to the GenePattern ExpressionFileCreator Module20 to generate the final dataset. In this last step, the background was corrected with the Robust Multi-array Average (RMA) algorithm and data were normalized using quantiles.

value: NASH liver


title: B3_input

value: para-carcinoma


title: Liver_NASH_40


title: Liver_NASH_37


title: Liver_NASH_39


title: B2_input


title: No Exosome_2

description: No Exosome treatment


title: Naïve Exosome_3

description: Naïve Exosome treatment


title: B1_input


title: No Exosome_1

description: No Exosome treatment


title: Liver_NASH_38


title: Naïve Exosome_1

description: Naïve Exosome treatment


title: A10_input

value: Colon cancer


title: A28c.3

source_name: MM1S multiple myeloma cell line t(14;16) MAF


title: A28c.5

source_name: KMS12BM multiple myeloma cell line t(11;14) CCND1

value: KMS12BM t(11;14) CCND1


title: A28.15

extract_protocol:
Patient BM aspirates were subjected to red cell lysis. Multiple myeloma plasma cells were purified by two rounds of CD138 immunomagnetic selection (MiltenyiBiotech) following the manufacturer’s instructions. Pre and post selection purity was assessed by FACs analysis (BD LSR-Fortessa) using CD138, CD45, CD19, CD56 and CD38 panel antibodies
ATAC-seq was performed as described(Buenrostro et al., 2013). Briefly, 50,000 purified plasma cells, myeloma plasma cells or cell lines, were washed with cold PBS (Sigma, UK) at 500g at 40C for 5 min. The cells were resuspended in 50 μL of cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and washed at 500g at 40C for 10 min. The libraries were sequenced at the Genomics Facility at ICL using the Illumina HiSeq 4000 platform to obtain paired-end 75bp reads.
The nuclei were subjected to transposase reaction for 30 min at 370C; termination of the reaction and DNA purification was performed using a MiniElute Kit (Qiagen) and eluted twice with 10 μL. The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). The PCR amplified product was cleaned twice with (0.9X) AMPure beads (Beckman). The quality of the libraries was assessed with the Bioanalyzer High Sensitivity DNA kit (Agilent). The libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs) on a StepOne Plus Real-Time PCR (Applied Biosystems).

value: singleton


title: A8_input


title: No Exosome_3

description: No Exosome treatment


title: A27.19

value: MMSET


title: A7_input


title: A26.11

value: t(14;16) - MAF, pseudohyperdiploid, cMAF, +1q

value: MAF


title: KO_10X_RNA

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Bulk RNAseq samples were processed and aligned to the mm10 genome using Illumina BaseSpace RNAseq protocol v1.1.0 with default parameters.
10X Genomics 3’ single-cell data were processed with Cell Ranger v3.0.2 using default settings
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: CSV files contain non-normalized gene level read counts for each bulk RNAseq sample.  H5 files contain non-normalized gene X cell UMI counts from 10X single-cell RNAseq data.

molecule: polyA RNA

source_name: Bone marrow cells positively selected for B220+ CD11c+ cells with negative selection of Ter119, CD11b, CD8 and Gr1 by flow cytometry

extract_protocol:
Bulk RNAseq samples were extracted using TRIzol and mRNA was enriched using NEBNext polyA mRNA  magnetic isolate module. Single cell RNAseq libraries were constructed using the 10X Genomics Single Cell 3’ v2 kit.
Bulk RNAseq samples were prepared for sequencing using the NEBNext Ultra RNA library prep kit for Illumina. Single cell RNAseq libraries were constructed using the 10X Genomics Single Cell 3’ v2 kit.

tag: strain

tag: genotype

value: St3gal1 flox/flox Pf4/cre

tag: cell type

value: Bone marrow cells


title: Liver_NASH_35


title: Liver_NASH_34


title: SPL-WT4

source_name: Splenic CD4 cells sorted by flow cytometry

value: St3gal1 flox/flox

value: Splenic CD4 cells


title: A28.7

source_name: OPM2 multiple myeloma cell line t(4;14) MMSET

value: MM

value: OPM2 t(4;14) MMSET


title: Liver_NASH_36


title: A9_input

source_name: Colon cancer tissue


title: Liver_NASH_31


title: A26.14

value: Bone marrow

value: t(11;14) - CCND1, gain of 1q and partial deletion of TP53


title: SPL-WT3


title: A6_input


title: A4_input


title: A5_input


title: A17.5


title: Liver_NASH_32


title: A24.8

value: hyperdiploid, +1q

value: HD

value: B+C


title: A3_input

value: Colon cancer


title: SPL-KO6


title: A2_input


title: BM-WT9

source_name: Bone Marrow CD4 cells sorted by flow cytometry

value: Bone Marrow CD4 cells


title: A24.10

value: singleton


title: Liver_NASH_33

value: NASH liver


title: A24.11


title: SPL-KO8


title: A1_input


title: BM-WT4


title: A27.22

source_name: Plasma cell CD19 minus, donor 271017

extract_protocol:
BM-MNCs from BM aspirates were isolated by ficoll (Histopaque, Sigma). The MNCs were pre-cleared of T cells and Monocytes by consecutive immunomagnetic negative selection (CD3 and CD14-EasySep StemCell Technologies) following manufacturer’s instructions. The sample was stained and sorted for positive CD138, CD319, CD27, CD45 and CD38, and negative for CD2, CD3, CD14, CD16, GPA and 7AAD. (FACSAriaII, BD Biosciences) and CD19+or CD19-
ATAC-seq was performed as described(Buenrostro et al., 2013). Briefly, 50,000 purified plasma cells, myeloma plasma cells or cell lines, were washed with cold PBS (Sigma, UK) at 500g at 40C for 5 min. The cells were resuspended in 50 μL of cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and washed at 500g at 40C for 10 min. The libraries were sequenced at the Genomics Facility at ICL using the Illumina HiSeq 4000 platform to obtain paired-end 75bp reads.
The nuclei were subjected to transposase reaction for 30 min at 370C; termination of the reaction and DNA purification was performed using a MiniElute Kit (Qiagen) and eluted twice with 10 μL. The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). The PCR amplified product was cleaned twice with (0.9X) AMPure beads (Beckman). The quality of the libraries was assessed with the Bioanalyzer High Sensitivity DNA kit (Agilent). The libraries were quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs) on a StepOne Plus Real-Time PCR (Applied Biosystems).

value: PC

value: ND

tag: pc cd19 status

value: minus

tag: pc donor id

value: D


title: Liver_NASH_30

tag: tissue


title: SPL-KO10

value: St3gal1 flox/flox Pf4/cre


title: S-S3

city: Changsha

first: Zekai

last: Cui

state: Hunan

address: 18th floor, the New Century Building, #198, Furong Middle Road

institute: Aier Eye Institute

description:
S-S3_S176
processed data file: S_count.txt

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: GRCg6A, hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human corneal stromal cells

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

tag: treatment

value: CSCs in the S model

tag: culture time

value: 7 days


title: Liver_NASH_29

first: Marta

last: Piqué

address: Rosselló, 153

institute: IDIBAPS


title: Liver_NASH_28


title: BM-WT1

value: St3gal1 flox/flox


title: Liver_NASH_27


title: BM-KO10


title: Liver_NASH_26


title: Liver_NASH_25


title: Liver_NASH_24


title: A26.19

source_name: Plasma cell CD19 minus, donor 160617

value: Bone marrow

value: C


title: BM-KO6


title: A26.20

source_name: Plasma cell CD19 plus, donor 160617

value: plus


title: S-S1

description:
S-S1_S174
processed data file: S_count.txt


title: DS-S2

description:
DS-S2_S181
processed data file: S_count.txt

value: CSCs in the DS model


title: A26.18

source_name: Primary plasma cell CD19 plus 160617


title: A26.1

source_name: Primary plasma cell multiple myeloma

value: MM

value: hyperdiploid, +1q

value: HD


title: BM-KO5

value: Bone Marrow CD4 cells


title: H3K9ac pooled input

city: Baltimore

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description: H3K9ac pooled input for calculating ChIP enrichment

data_processing:
Library construction and base calling were performed according to Active Motif company protocol .
ChIP-seq single-end 75nt sequencing reads were mapped to mm10 genome using the BWA algorthim with “bwaln/samse” default settings.
Uniqely mapped reads were further processed to remove those with mapq score < 25, mitochondria reads, PCR duplicates, and reads with more than 2 mismatches.
To normalize, tag numbers of all samples (within a comparison group) were reduced by random sampling to the number of usable tags present in the smallest sample.
Peaks were identified using the MACS2 (2.1.0) algorithm with default cutoff values. Pooled input samples were used to determine ChIP enrichment over background. ENCODE blacklist regions were removed.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak calling output provided as ENCODE narrowPeak format (BED 6+4)
Supplementary_files_format_and_content: bigWig files were generated using a 32nt bin with a 200bp in silico tag extension
Supplementary_files_format_and_content: Consensus peakset as well as intervals for individual samples are provided in BED format

source_name: Liver

growth_protocol: Mice were housed in a facility with ventilated racks on a 14h light/10h dark cycle with ad libitum access to a standard rodent chow.

extract_protocol:
Genomic DNA was isolated from flash-frozen mouse liver tissue accordng to Active Motif company protocol
Library construction was performed according to Active Motif company protocol.

treatment_protocol: 24 hour fast (3pm-3pm).

value: Liver

value: 24 hour fast


title: A27.21

source_name: Plasma cell CD19 plus, donor 271017

value: PC

value: ND


title: Liver_NASH_23

city: Barcelona

value: NASH liver


title: A27.18

value: D


title: DS-S1

description:
DS-S1_S180
processed data file: S_count.txt


title: H3K4me1+H3K27ac pooled input

description: H3K4me1+H3K27ac pooled input for calculating ChIP enrichment


title: S-S2

description:
S-S2_S175
processed data file: S_count.txt

value: CSCs in the S model


title: A27.12

value: hyperdiploid